diff --git a/AUTHORS.md b/AUTHORS.md new file mode 100644 index 0000000..fb8c80a --- /dev/null +++ b/AUTHORS.md @@ -0,0 +1,4 @@ +**NUCLEUS** is developed by + +* Stephan Costabel (since 2020), stephan.costabel@bgr.de +* Thomas Hiller (since 2018), thomas.hiller@bgr.de \ No newline at end of file diff --git a/CHANGELOG.md b/CHANGELOG.md index b9fb491..2274cc9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,14 @@ # Changelog +## [0.1.14] - 2023-09-27 + +### Added +- New optional sub GUI *FixedTimeView* in **NUCLEUSinv** that allows to fix relaxation times (up to five) if the *N free exp. (2-5)* option for inversion is chosen and thus only the corresponding amplitudes are fitted +- New import routine in **NUCLEUSinv** for the LIAG core scanner (several NMR measurements along a core) + +### Changed +- Changed the import routines in **NUCLEUSinv** for *BGR* devices (*Mouse* and *Helios*) due to device software updates + ## [0.1.13] - 2022-08-11 ### Changed @@ -65,7 +74,7 @@ ### Added - A *last export* entry added to the export menu. It always shows the last chosen export routine (speeds up exporting when handling a lot of data). **NUCLEUSinv** -- Session files from an older *NUCLEUSinv* version can now be imported (starting from v.0.1.8). **NUCLEUSinv** +- Session files from an older **NUCLEUSinv** version can now be imported (starting from v.0.1.8). **NUCLEUSinv** ### Changed - Within the context menu of the signal list the entry *all* was renamed to *batch*. Now it indicates what it is actually doing - batch processing of multiple files. **NUCLEUSinv** @@ -181,6 +190,7 @@ Initial Version +[0.1.14]: https://github.com/ThoHiller/nmr-nucleus/compare/v.0.1.13...v.0.1.14 [0.1.13]: https://github.com/ThoHiller/nmr-nucleus/compare/v.0.1.12...v.0.1.13 [0.1.12]: https://github.com/ThoHiller/nmr-nucleus/compare/v.0.1.11...v.0.1.12 [0.1.11]: https://github.com/ThoHiller/nmr-nucleus/compare/v.0.1.10...v.0.1.11 diff --git a/NUCLEUSinv/NUCLEUSinv.m b/NUCLEUSinv/NUCLEUSinv.m index edc8bdd..0a0df4d 100644 --- a/NUCLEUSinv/NUCLEUSinv.m +++ b/NUCLEUSinv/NUCLEUSinv.m @@ -38,8 +38,8 @@ if ~isempty(h0); close(h0); end %% GUI 'header' info and defaults -myui.version = '0.1.13'; -myui.date = '11.08.2022'; +myui.version = '0.1.14'; +myui.date = '27.09.2023'; myui.author = {'Stephan Costabel','Thomas Hiller'}; myui.email = 'thomas.hiller[at]bgr.de'; myui.fontsize = 10; diff --git a/NUCLEUSinv/NUCLEUSinv_createMenus.m b/NUCLEUSinv/NUCLEUSinv_createMenus.m index b1c535a..e132cee 100644 --- a/NUCLEUSinv/NUCLEUSinv_createMenus.m +++ b/NUCLEUSinv/NUCLEUSinv_createMenus.m @@ -67,17 +67,17 @@ % 1.1.1.2.3 Mouse CPMG data, single data subfolders from CPMG gui.menu.file_import_lab_bgr_mouse_cpmg = uimenu(gui.menu.file_import_lab_bgr,... 'Label','MouseCPMG','Tag','Lab','Callback',@onMenuImport); -% 1.1.1.2.4 Mouse plus Lift, single data subfolder from t1test,... -% ...cpmgfastautotest, or (old Prospa Versions) cpmgfastauto -gui.menu.file_import_lab_bgr_mouse_liftsingle = uimenu(gui.menu.file_import_lab_bgr,... - 'Label','MouseLiftSingle','Tag','Lab','Callback',@onMenuImport); -% 1.1.1.2.5 Mouse plus Lift, all data subfolders from t1test,... +% 1.1.1.2.4 Mouse plus Lift, all data subfolders from t1test,... % cpmgfastautotest, or (old Prospa Versions) cpmgfastauto -gui.menu.file_import_lab_bgr_mouse_liftall = uimenu(gui.menu.file_import_lab_bgr,... - 'Label','MouseLiftAll','Tag','Lab','Callback',@onMenuImport); -% 1.1.1.2.6 Helios -gui.menu.file_import_lab_bgr_helios = uimenu(gui.menu.file_import_lab_bgr,... - 'Label','Helios','Tag','Lab','Callback',@onMenuImport); +gui.menu.file_import_lab_bgr_mouse_lift = uimenu(gui.menu.file_import_lab_bgr,... + 'Label','MouseLift','Tag','Lab','Callback',@onMenuImport); +% 1.1.1.2.5 Helios CPMG standard data, single subfolders with individual data files +gui.menu.file_import_lab_bgr_helios_cpmg = uimenu(gui.menu.file_import_lab_bgr,... + 'Label','HeliosCPMG','Tag','Lab','Callback',@onMenuImport); +% 1.1.1.2.6 Helios series of CPMG data, several files of a series in the target +% folder, as used e.g. for T1 measurements +gui.menu.file_import_lab_bgr_helios_series = uimenu(gui.menu.file_import_lab_bgr,... + 'Label','HeliosSeries','Tag','Lab','Callback',@onMenuImport); % 1.1.1.3 LIAG gui.menu.file_import_lab_liag = uimenu(gui.menu.file_import_lab,... @@ -88,6 +88,9 @@ % 1.1.1.3.2 LIAG gui.menu.file_import_lab_liag_project = uimenu(gui.menu.file_import_lab_liag,... 'Label','LIAG from project','Tag','Lab','Callback',@onMenuImport); +% 1.1.1.3.3 LIAG +gui.menu.file_import_lab_liag_core = uimenu(gui.menu.file_import_lab_liag,... + 'Label','LIAG core','Tag','Lab','Callback',@onMenuImport); % 1.1.1.4 RWTH gui.menu.file_import_lab_rwth = uimenu(gui.menu.file_import_lab,... @@ -203,6 +206,9 @@ % 1.2.1.9 LIAG CSV T2 gui.menu.file_export_data_liag_csvT2 = uimenu(gui.menu.file_export_data,... 'Label','LIAG CSV T2','Callback',@onMenuExportData); +% 1.2.1.10 BGR data repository ascii +gui.menu.file_export_data_bgr_repo = uimenu(gui.menu.file_export_data,... + 'Label','BGR repository','Callback',@onMenuExportData); % 1.2.2 Graphics gui.menu.file_export_graphics = uimenu(gui.menu.file_export,... @@ -306,6 +312,9 @@ % 2.7 ConductVIEW -> hydraulic conductivity gui.menu.extra_conduct = uimenu(gui.menu.view,... 'Label','ConductView GUI','Enable','off','Callback',@onMenuViewFigures); +% 2.8 FixedTime VIEW +gui.menu.extra_fixedtime = uimenu(gui.menu.view,... + 'Label','FixedTimeView GUI','Enable','off','Callback',@FixedTimeView); %% 3. Extras gui.menu.extra = uimenu(gui.figh,... diff --git a/NUCLEUSinv/NUCLEUSinv_loadDefaults.m b/NUCLEUSinv/NUCLEUSinv_loadDefaults.m index 5e3985b..38b8a15 100644 --- a/NUCLEUSinv/NUCLEUSinv_loadDefaults.m +++ b/NUCLEUSinv/NUCLEUSinv_loadDefaults.m @@ -103,6 +103,9 @@ out.invstd.invtype = 'NNLS'; % when inversion method is 'free' choose No. of free relaxation times out.invstd.freeDT = 2; +% option to fix some of the 'free' relaxation times to a certain value +out.invstd.Tfixed_bool = [0 0 0 0 0]; +out.invstd.Tfixed_val = [0 0 0 0 0]; % regularization options for multi-exponential fitting routines % 'NNLS' and 'LU' out.invstd.regtype = 'manual'; diff --git a/NUCLEUSinv/NUCLEUSinv_updateInterface.m b/NUCLEUSinv/NUCLEUSinv_updateInterface.m index 9141613..b47f550 100644 --- a/NUCLEUSinv/NUCLEUSinv_updateInterface.m +++ b/NUCLEUSinv/NUCLEUSinv_updateInterface.m @@ -102,7 +102,7 @@ 'Value',data.invstd.freeDT,... 'String',{'1','2','3','4','5'}); set(gui.text_handles.invstd_InvTypeOpt,... - 'String','No. of free decay times T'); + 'String','No. of free relaxation times T'); % lambda, smoothness constraint and RTD limits gui = updateLambda(gui,data.invstd.regtype,0,0,0); @@ -586,7 +586,7 @@ 'Value',data.invstd.freeDT,... 'String',{'1','2','3','4','5'}); set(gui.text_handles.invstd_InvTypeOpt,... - 'String','No. of free decay times T'); + 'String','No. of relaxation decay times T'); % lambda, smoothness constraint and RTD limits gui = updateLambda(gui,data.invstd.regtype,0,0,0); @@ -675,22 +675,19 @@ switch gatetype - case 'log' - + case 'log' set(gui.radio_handles.process_gates_log,'Value',1); set(gui.radio_handles.process_gates_lin,'Value',0); set(gui.radio_handles.process_gates_none,'Value',0); set(gui.edit_handles.process_Nechoes,'Enable','on'); - case 'lin' - + case 'lin' set(gui.radio_handles.process_gates_log,'Value',0); set(gui.radio_handles.process_gates_lin,'Value',1); set(gui.radio_handles.process_gates_none,'Value',0); set(gui.edit_handles.process_Nechoes,'Enable','on'); - case 'raw' - + case 'raw' set(gui.radio_handles.process_gates_log,'Value',0); set(gui.radio_handles.process_gates_lin,'Value',0); set(gui.radio_handles.process_gates_none,'Value',1); diff --git a/NUCLEUSmod/NUCLEUSmod.m b/NUCLEUSmod/NUCLEUSmod.m index 9ed5920..1b1d52a 100644 --- a/NUCLEUSmod/NUCLEUSmod.m +++ b/NUCLEUSmod/NUCLEUSmod.m @@ -41,8 +41,8 @@ if ~isempty(h0); close(h0); end %% GUI 'header' info and defaults -myui.version = '0.1.13'; -myui.date = '11.08.2022'; +myui.version = '0.1.14'; +myui.date = '27.09.2023'; myui.author = {'Stephan Costabel','Thomas Hiller'}; myui.email = 'thomas.hiller[at]bgr.de'; myui.fontsize = 10; diff --git a/README.md b/README.md index ec75e0e..4c0cd75 100644 --- a/README.md +++ b/README.md @@ -108,7 +108,7 @@ In no particular order and without guarantee that it will ever happen :-) : ### Cite as If you use NUCLEUS for your research, please cite it as: -Thomas Hiller. (2022, Aug 11). ThoHiller/nmr-nucleus: v0.1.13 (Version v0.1.13). Zenodo. [https://doi.org/10.5281/zenodo.4022195] +Thomas Hiller. (2023, Sep 27). ThoHiller/nmr-nucleus: v0.1.14 (Version v0.1.14). Zenodo. [https://doi.org/10.5281/zenodo.4022195] Note: Even though the version number might change due to updates, this DOI is permanent (represents all versions) and always links to the latest version. diff --git a/callbacks/listboxes/onListboxData.m b/callbacks/listboxes/onListboxData.m index 07706f7..1adc6b3 100644 --- a/callbacks/listboxes/onListboxData.m +++ b/callbacks/listboxes/onListboxData.m @@ -69,6 +69,13 @@ function onListboxData(src,~) data_upd.calib = data.calib; data_upd.pressure = data.pressure; data = data_upd; + + % if "mono" or "free" inversion is chossen update the internal + % fixed relaxation times field + if strcmp(data.invstd.invtype,'mono') ||... + strcmp(data.invstd.invtype,'free') + data.invstd.Tfixed_val = [data.results.invstd.T zeros(1,5-data.invstd.freeDT)]; + end setappdata(fig,'data',data); % update interface and plot axes @@ -190,6 +197,10 @@ function onListboxData(src,~) if ~isempty(findobj('Tag','PHASEVIEW')) PhaseView(gui.menu.extra_phaseview); end + % if the FixedTimeView window is open update it + if ~isempty(findobj('Tag','FIXEDTIMEVIEW')) + FixedTimeView(gui.menu.extra_fixedtime); + end else helpdlg({'onListboxData:','Only choose one data set at a time.'},... 'too many data'); diff --git a/callbacks/menus/onMenuExpert.m b/callbacks/menus/onMenuExpert.m index f566e50..f7505cf 100644 --- a/callbacks/menus/onMenuExpert.m +++ b/callbacks/menus/onMenuExpert.m @@ -55,6 +55,17 @@ function onMenuExpert(src,~) % update GUI data setappdata(fig,'data',data); setappdata(fig,'gui',gui); + + % dectivate FixedTime View GUI + data.invstd.Tfixed_bool = zeros(1,5); + data.invstd.Tfixed_val = zeros(1,5); + setappdata(fig,'data',data); + % check if the figure is already open + fig_fixedtime = findobj('Tag','FIXEDTIMEVIEW'); + if ~isempty(fig_fixedtime) + delete(fig_fixedtime); + end + set(gui.menu.extra_fixedtime,'Enable','off'); % deactivate solver menu and set to default onMenuSolver(gui.menu.extra_solver_lsqnonneg); @@ -87,7 +98,10 @@ function onMenuExpert(src,~) data.info.ExpertMode = 'on'; % menu entry set(gui.menu.extra_expert,'Checked','on'); - + + % activate FixedTime View GUI + set(gui.menu.extra_fixedtime,'Enable','on'); + % activate solver menu if optimization toolbox is available switch data.info.has_optim case 'on' diff --git a/callbacks/menus/onMenuExportData.m b/callbacks/menus/onMenuExportData.m index 9765c05..7d562b0 100644 --- a/callbacks/menus/onMenuExportData.m +++ b/callbacks/menus/onMenuExportData.m @@ -58,7 +58,9 @@ function onMenuExportData(src,~) case 'LIAG archive' exportData(fig_tag,'LIAG'); case 'LIAG CSV T2' - exportData(fig_tag,'LIAGcsvT2'); + exportData(fig_tag,'LIAGcsvT2'); + case 'BGR repository' + exportData(fig_tag,'BGR_repos'); end % update the "last export" value within the ini-file gui = getappdata(fig,'gui'); diff --git a/callbacks/menus/onMenuExtraColor.m b/callbacks/menus/onMenuExtraColor.m index 2c0860a..0fcb813 100644 --- a/callbacks/menus/onMenuExtraColor.m +++ b/callbacks/menus/onMenuExtraColor.m @@ -33,7 +33,6 @@ function onMenuExtraColor(src,~) fig = ancestor(src,'figure','toplevel'); fig_tag = get(fig,'Tag'); gui = getappdata(fig,'gui'); -data = getappdata(fig,'data'); % get the menu label label = get(src,'Label'); @@ -65,6 +64,11 @@ function onMenuExtraColor(src,~) % adjust the colors changeColorTheme(fig_tag,label); +% check the sub GUIs +if ~isempty(findobj('Tag','FIXEDTIMEVIEW')) + changeColorTheme('FIXEDTIMEVIEW',label); +end + end %------------- END OF CODE -------------- diff --git a/callbacks/popup/onPopupInvstdType.m b/callbacks/popup/onPopupInvstdType.m index fe4c6ee..f646451 100644 --- a/callbacks/popup/onPopupInvstdType.m +++ b/callbacks/popup/onPopupInvstdType.m @@ -47,12 +47,32 @@ function onPopupInvstdType(src,~) data.invstd.invtype = 'mono'; data.invstd.regtype = 'none'; data.invstd.lambda = 1; + data.invstd.freeDT = 1; + +% % if the FixedTimeView window is open update it +% if ~isempty(findobj('Tag','FIXEDTIMEVIEW')) +% data.invstd.Tfixed_bool = zeros(1,5); +% % update GUI data +% setappdata(fig,'data',data); +% FixedTimeView(gui.menu.extra_fixedtime); +% data = getappdata(fig,'data'); +% end case 2 data.invstd.invtype = 'free'; data.invstd.regtype = 'none'; data.invstd.lambda = 1; - + data.invstd.freeDT = 2; + +% % if the FixedTimeView window is open update it +% if ~isempty(findobj('Tag','FIXEDTIMEVIEW')) +% data.invstd.Tfixed_bool = zeros(1,5); +% % update GUI data +% setappdata(fig,'data',data); +% FixedTimeView(gui.menu.extra_fixedtime); +% data = getappdata(fig,'data'); +% end + case 3 data.invstd.invtype = 'NNLS'; data.invstd.regtype = 'manual'; @@ -75,11 +95,13 @@ function onPopupInvstdType(src,~) data.invstd.invtype = 'mono'; data.invstd.regtype = 'none'; data.invstd.lambda = 1; + data.invstd.freeDT = 1; case 2 data.invstd.invtype = 'free'; data.invstd.regtype = 'none'; data.invstd.lambda = 1; + data.invstd.freeDT = 2; case 3 data.invstd.invtype = 'NNLS'; @@ -107,6 +129,16 @@ function onPopupInvstdType(src,~) data.invstd.lambda = 1; end end + +% if the FixedTimeView window is open update it +if ~isempty(findobj('Tag','FIXEDTIMEVIEW')) + data.invstd.Tfixed_bool = zeros(1,5); + % update GUI data + setappdata(fig,'data',data); + FixedTimeView(gui.menu.extra_fixedtime); + data = getappdata(fig,'data'); +end + % update GUI data setappdata(fig,'data',data); % update interface diff --git a/callbacks/popup/onPopupInvstdTypeOptional.m b/callbacks/popup/onPopupInvstdTypeOptional.m index e9b6278..39371ca 100644 --- a/callbacks/popup/onPopupInvstdTypeOptional.m +++ b/callbacks/popup/onPopupInvstdTypeOptional.m @@ -46,8 +46,16 @@ function onPopupInvstdTypeOptional(src,~) % change settings accordingly switch invtype case 'free' - % # free decay times = value (1 to 5) + % # free relaxation times = value (1 to 5) data.invstd.freeDT = value; + + % if the FixedTimeView window is open update it + if ~isempty(findobj('Tag','FIXEDTIMEVIEW')) + % update GUI data + setappdata(fig,'data',data); + FixedTimeView(gui.menu.extra_fixedtime); + data = getappdata(fig,'data'); + end case 'NNLS' switch data.info.ExpertMode diff --git a/doc/menu.html b/doc/menu.html index 1cd7e85..2a650a4 100644 --- a/doc/menu.html +++ b/doc/menu.html @@ -16,7 +16,7 @@

Matlab Index

Matlab Directories

- +
Generated by m2html © 2005
diff --git a/doc/nucleus/NUCLEUSinv/NUCLEUSinv.html b/doc/nucleus/NUCLEUSinv/NUCLEUSinv.html index 38415d7..84214d8 100644 --- a/doc/nucleus/NUCLEUSinv/NUCLEUSinv.html +++ b/doc/nucleus/NUCLEUSinv/NUCLEUSinv.html @@ -111,8 +111,8 @@

SOURCE CODE ^if ~isempty(h0); close(h0); end 0039 0040 %% GUI 'header' info and defaults -0041 myui.version = '0.1.13'; -0042 myui.date = '11.08.2022'; +0041 myui.version = '0.1.14'; +0042 myui.date = '27.09.2023'; 0043 myui.author = {'Stephan Costabel','Thomas Hiller'}; 0044 myui.email = 'thomas.hiller[at]bgr.de'; 0045 myui.fontsize = 10; diff --git a/doc/nucleus/NUCLEUSinv/NUCLEUSinv_createMenus.html b/doc/nucleus/NUCLEUSinv/NUCLEUSinv_createMenus.html index 5cd56ee..fd8a866 100644 --- a/doc/nucleus/NUCLEUSinv/NUCLEUSinv_createMenus.html +++ b/doc/nucleus/NUCLEUSinv/NUCLEUSinv_createMenus.html @@ -59,7 +59,7 @@

DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

This function calls: +
  • onMenuExpert handles the call from the menu that activates / deactivates
  • onMenuExportData handles the calls from the export menu
  • onMenuExportGraphics handles the graphics export menu and calls the export
  • onMenuExtraColor handles the color theme menu of both GUIs
  • onMenuExtraRhoBounds sets inversion bounds for the surface relaxivity
  • onMenuHelp shows the Help Information for both GUIs
  • onMenuImport handles the import menu entries
  • onMenuJointInversion handles the call from the menu that activates / deactivates
  • onMenuRestartQuit restarts or closes the GUIs
  • onMenuSolver handles the call from the menu that allows to choose the LSQ
  • onMenuView handles the view menu entries
  • onMenuViewFigures handles the extra menu entries to show additional
  • FixedTimeView is an extra subGUI to fix certain relaxation times during
  • PhaseView is an extra subGUI to visualize the phase of a T2 signal
    • This function is called by: @@ -137,17 +137,17 @@

    SOURCE CODE ^% 1.1.1.2.3 Mouse CPMG data, single data subfolders from CPMG 0068 gui.menu.file_import_lab_bgr_mouse_cpmg = uimenu(gui.menu.file_import_lab_bgr,... 0069 'Label','MouseCPMG','Tag','Lab','Callback',@onMenuImport); -0070 % 1.1.1.2.4 Mouse plus Lift, single data subfolder from t1test,... -0071 % ...cpmgfastautotest, or (old Prospa Versions) cpmgfastauto -0072 gui.menu.file_import_lab_bgr_mouse_liftsingle = uimenu(gui.menu.file_import_lab_bgr,... -0073 'Label','MouseLiftSingle','Tag','Lab','Callback',@onMenuImport); -0074 % 1.1.1.2.5 Mouse plus Lift, all data subfolders from t1test,... -0075 % cpmgfastautotest, or (old Prospa Versions) cpmgfastauto -0076 gui.menu.file_import_lab_bgr_mouse_liftall = uimenu(gui.menu.file_import_lab_bgr,... -0077 'Label','MouseLiftAll','Tag','Lab','Callback',@onMenuImport); -0078 % 1.1.1.2.6 Helios -0079 gui.menu.file_import_lab_bgr_helios = uimenu(gui.menu.file_import_lab_bgr,... -0080 'Label','Helios','Tag','Lab','Callback',@onMenuImport); +0070 % 1.1.1.2.4 Mouse plus Lift, all data subfolders from t1test,... +0071 % cpmgfastautotest, or (old Prospa Versions) cpmgfastauto +0072 gui.menu.file_import_lab_bgr_mouse_lift = uimenu(gui.menu.file_import_lab_bgr,... +0073 'Label','MouseLift','Tag','Lab','Callback',@onMenuImport); +0074 % 1.1.1.2.5 Helios CPMG standard data, single subfolders with individual data files +0075 gui.menu.file_import_lab_bgr_helios_cpmg = uimenu(gui.menu.file_import_lab_bgr,... +0076 'Label','HeliosCPMG','Tag','Lab','Callback',@onMenuImport); +0077 % 1.1.1.2.6 Helios series of CPMG data, several files of a series in the target +0078 % folder, as used e.g. for T1 measurements +0079 gui.menu.file_import_lab_bgr_helios_series = uimenu(gui.menu.file_import_lab_bgr,... +0080 'Label','HeliosSeries','Tag','Lab','Callback',@onMenuImport); 0081 0082 % 1.1.1.3 LIAG 0083 gui.menu.file_import_lab_liag = uimenu(gui.menu.file_import_lab,... @@ -158,337 +158,346 @@

    SOURCE CODE ^% 1.1.1.3.2 LIAG 0089 gui.menu.file_import_lab_liag_project = uimenu(gui.menu.file_import_lab_liag,... 0090 'Label','LIAG from project','Tag','Lab','Callback',@onMenuImport); -0091 -0092 % 1.1.1.4 RWTH -0093 gui.menu.file_import_lab_rwth = uimenu(gui.menu.file_import_lab,... -0094 'Label','RWTH'); -0095 % 1.1.1.4.1 IBAC -0096 gui.menu.file_import_lab_ibac = uimenu(gui.menu.file_import_lab_rwth,... -0097 'Label','IBAC'); -0098 % 1.1.1.4.1.1 IBAC -0099 gui.menu.file_import_lab_ibac_pm5 = uimenu(gui.menu.file_import_lab_ibac,... -0100 'Label','PM5','Tag','Lab','Callback',@onMenuImport); -0101 % 1.1.1.4.1.2 IBAC -0102 gui.menu.file_import_lab_ibac_pm25 = uimenu(gui.menu.file_import_lab_ibac,... -0103 'Label','PM25','Tag','Lab','Callback',@onMenuImport); -0104 -0105 % 1.1.1.4.2 GGE -0106 gui.menu.file_import_lab_gge = uimenu(gui.menu.file_import_lab_rwth,... -0107 'Label','GGE'); -0108 % 1.1.1.4.2.1 GGE ascii -0109 gui.menu.file_import_lab_gge_ascii = uimenu(gui.menu.file_import_lab_gge,... -0110 'Label','GGE ascii','Tag','Lab','Callback',@onMenuImport); -0111 % 1.1.1.4.2.2 GGE field -0112 gui.menu.file_import_lab_gge_field = uimenu(gui.menu.file_import_lab_gge,... -0113 'Label','GGE field','Tag','Lab','Callback',@onMenuImport); -0114 % 1.1.1.4.2.3 GGE Dart -0115 gui.menu.file_import_lab_gge_dart = uimenu(gui.menu.file_import_lab_gge,... -0116 'Label','GGE Dart','Tag','Lab','Callback',@onMenuImport); -0117 -0118 % 1.1.1.5 OTHER -0119 gui.menu.file_import_lab_other = uimenu(gui.menu.file_import_lab,... -0120 'Label','OTHER'); -0121 % 1.1.1.5.1 CoreLab ascii -0122 gui.menu.file_import_lab_corelab = uimenu(gui.menu.file_import_lab_other,... -0123 'Label','CoreLab ascii','Tag','Lab','Callback',@onMenuImport); -0124 % 1.1.1.5.2 MOUSE -0125 gui.menu.file_import_lab_mouse = uimenu(gui.menu.file_import_lab_other,... -0126 'Label','MOUSE','Tag','Lab','Callback',@onMenuImport); -0127 % 1.1.1.5.3 DART (University of Vienna) -0128 gui.menu.file_import_lab_dart = uimenu(gui.menu.file_import_lab_other,... -0129 'Label','DART','Tag','Lab','Callback',@onMenuImport); -0130 -0131 % 1.1.2 Ascii -0132 gui.menu.file_import_ascii = uimenu(gui.menu.file_import,... -0133 'Label','Ascii'); -0134 % 1.1.2.1 T1 -0135 gui.menu.file_import_lab_ascii_T1 = uimenu(gui.menu.file_import_ascii,... -0136 'Label','T1','Tag','Ascii','Callback',@onMenuImport); -0137 % 1.1.2.2 T2 -0138 gui.menu.file_import_lab_ascii_T2 = uimenu(gui.menu.file_import_ascii,... -0139 'Label','T2','Tag','Ascii','Callback',@onMenuImport); -0140 -0141 % 1.1.3 Excel -0142 gui.menu.file_import_excel = uimenu(gui.menu.file_import,... -0143 'Label','Excel'); -0144 % 1.1.3.1 T1 -0145 gui.menu.file_import_lab_excel_T1 = uimenu(gui.menu.file_import_excel,... -0146 'Label','T1','Tag','Excel','Callback',@onMenuImport); -0147 % 1.1.3.2 T2 -0148 gui.menu.file_import_lab_excel_T2 = uimenu(gui.menu.file_import_excel,... -0149 'Label','T2','Tag','Excel','Callback',@onMenuImport); -0150 -0151 % 1.1.4 NUCLEUSinv -0152 gui.menu.file_import_nmrinv = uimenu(gui.menu.file_import,... -0153 'Label','NUCLEUSinv','Separator','on'); -0154 % 1.1.4.1 NUCLEUSinv session file -0155 gui.menu.file_import_nmrinv_file = uimenu(gui.menu.file_import_nmrinv,... -0156 'Label','Session','Tag','NUCLEUSinv','Callback',@onMenuImport); -0157 -0158 % 1.1.5 NUCLEUSmod -0159 gui.menu.file_import_nmrmod = uimenu(gui.menu.file_import,... -0160 'Label','NUCLEUSmod'); -0161 % 1.1.5.1 NUCLEUSmod from file -0162 gui.menu.file_import_nmrmod_file = uimenu(gui.menu.file_import_nmrmod,... -0163 'Label','File','Tag','NUCLEUSmod','Callback',@onMenuImport); -0164 % 1.1.5.2 NUCLEUSmod from GUI -0165 gui.menu.file_import_nmrmod_gui = uimenu(gui.menu.file_import_nmrmod,.... -0166 'Label','GUI','Tag','NUCLEUSmod','Callback',@onMenuImport); -0167 -0168 % 1.2 Export -0169 gui.menu.file_export = uimenu(gui.menu.file,... -0170 'Label','Export'); -0171 % 1.2.0 Last export -0172 lastexport = gui.myui.inidata.lastexport; -0173 gui.menu.file_export_lastexport = uimenu(gui.menu.file_export,... -0174 'Label',lastexport,'Callback',@onMenuExportData); -0175 % 1.2.1 Data -0176 gui.menu.file_export_data = uimenu(gui.menu.file_export,... -0177 'Label','Data'); -0178 % 1.2.1.1 GUI raw data mat-file -0179 gui.menu.file_export_data_GUImat = uimenu(gui.menu.file_export_data,... -0180 'Label','NUCLEUSinv (raw)','Callback',@onMenuExportData); -0181 % 1.2.1.2 GUI session mat-file +0091 % 1.1.1.3.3 LIAG +0092 gui.menu.file_import_lab_liag_core = uimenu(gui.menu.file_import_lab_liag,... +0093 'Label','LIAG core','Tag','Lab','Callback',@onMenuImport); +0094 +0095 % 1.1.1.4 RWTH +0096 gui.menu.file_import_lab_rwth = uimenu(gui.menu.file_import_lab,... +0097 'Label','RWTH'); +0098 % 1.1.1.4.1 IBAC +0099 gui.menu.file_import_lab_ibac = uimenu(gui.menu.file_import_lab_rwth,... +0100 'Label','IBAC'); +0101 % 1.1.1.4.1.1 IBAC +0102 gui.menu.file_import_lab_ibac_pm5 = uimenu(gui.menu.file_import_lab_ibac,... +0103 'Label','PM5','Tag','Lab','Callback',@onMenuImport); +0104 % 1.1.1.4.1.2 IBAC +0105 gui.menu.file_import_lab_ibac_pm25 = uimenu(gui.menu.file_import_lab_ibac,... +0106 'Label','PM25','Tag','Lab','Callback',@onMenuImport); +0107 +0108 % 1.1.1.4.2 GGE +0109 gui.menu.file_import_lab_gge = uimenu(gui.menu.file_import_lab_rwth,... +0110 'Label','GGE'); +0111 % 1.1.1.4.2.1 GGE ascii +0112 gui.menu.file_import_lab_gge_ascii = uimenu(gui.menu.file_import_lab_gge,... +0113 'Label','GGE ascii','Tag','Lab','Callback',@onMenuImport); +0114 % 1.1.1.4.2.2 GGE field +0115 gui.menu.file_import_lab_gge_field = uimenu(gui.menu.file_import_lab_gge,... +0116 'Label','GGE field','Tag','Lab','Callback',@onMenuImport); +0117 % 1.1.1.4.2.3 GGE Dart +0118 gui.menu.file_import_lab_gge_dart = uimenu(gui.menu.file_import_lab_gge,... +0119 'Label','GGE Dart','Tag','Lab','Callback',@onMenuImport); +0120 +0121 % 1.1.1.5 OTHER +0122 gui.menu.file_import_lab_other = uimenu(gui.menu.file_import_lab,... +0123 'Label','OTHER'); +0124 % 1.1.1.5.1 CoreLab ascii +0125 gui.menu.file_import_lab_corelab = uimenu(gui.menu.file_import_lab_other,... +0126 'Label','CoreLab ascii','Tag','Lab','Callback',@onMenuImport); +0127 % 1.1.1.5.2 MOUSE +0128 gui.menu.file_import_lab_mouse = uimenu(gui.menu.file_import_lab_other,... +0129 'Label','MOUSE','Tag','Lab','Callback',@onMenuImport); +0130 % 1.1.1.5.3 DART (University of Vienna) +0131 gui.menu.file_import_lab_dart = uimenu(gui.menu.file_import_lab_other,... +0132 'Label','DART','Tag','Lab','Callback',@onMenuImport); +0133 +0134 % 1.1.2 Ascii +0135 gui.menu.file_import_ascii = uimenu(gui.menu.file_import,... +0136 'Label','Ascii'); +0137 % 1.1.2.1 T1 +0138 gui.menu.file_import_lab_ascii_T1 = uimenu(gui.menu.file_import_ascii,... +0139 'Label','T1','Tag','Ascii','Callback',@onMenuImport); +0140 % 1.1.2.2 T2 +0141 gui.menu.file_import_lab_ascii_T2 = uimenu(gui.menu.file_import_ascii,... +0142 'Label','T2','Tag','Ascii','Callback',@onMenuImport); +0143 +0144 % 1.1.3 Excel +0145 gui.menu.file_import_excel = uimenu(gui.menu.file_import,... +0146 'Label','Excel'); +0147 % 1.1.3.1 T1 +0148 gui.menu.file_import_lab_excel_T1 = uimenu(gui.menu.file_import_excel,... +0149 'Label','T1','Tag','Excel','Callback',@onMenuImport); +0150 % 1.1.3.2 T2 +0151 gui.menu.file_import_lab_excel_T2 = uimenu(gui.menu.file_import_excel,... +0152 'Label','T2','Tag','Excel','Callback',@onMenuImport); +0153 +0154 % 1.1.4 NUCLEUSinv +0155 gui.menu.file_import_nmrinv = uimenu(gui.menu.file_import,... +0156 'Label','NUCLEUSinv','Separator','on'); +0157 % 1.1.4.1 NUCLEUSinv session file +0158 gui.menu.file_import_nmrinv_file = uimenu(gui.menu.file_import_nmrinv,... +0159 'Label','Session','Tag','NUCLEUSinv','Callback',@onMenuImport); +0160 +0161 % 1.1.5 NUCLEUSmod +0162 gui.menu.file_import_nmrmod = uimenu(gui.menu.file_import,... +0163 'Label','NUCLEUSmod'); +0164 % 1.1.5.1 NUCLEUSmod from file +0165 gui.menu.file_import_nmrmod_file = uimenu(gui.menu.file_import_nmrmod,... +0166 'Label','File','Tag','NUCLEUSmod','Callback',@onMenuImport); +0167 % 1.1.5.2 NUCLEUSmod from GUI +0168 gui.menu.file_import_nmrmod_gui = uimenu(gui.menu.file_import_nmrmod,.... +0169 'Label','GUI','Tag','NUCLEUSmod','Callback',@onMenuImport); +0170 +0171 % 1.2 Export +0172 gui.menu.file_export = uimenu(gui.menu.file,... +0173 'Label','Export'); +0174 % 1.2.0 Last export +0175 lastexport = gui.myui.inidata.lastexport; +0176 gui.menu.file_export_lastexport = uimenu(gui.menu.file_export,... +0177 'Label',lastexport,'Callback',@onMenuExportData); +0178 % 1.2.1 Data +0179 gui.menu.file_export_data = uimenu(gui.menu.file_export,... +0180 'Label','Data'); +0181 % 1.2.1.1 GUI raw data mat-file 0182 gui.menu.file_export_data_GUImat = uimenu(gui.menu.file_export_data,... -0183 'Label','NUCLEUSinv (session)','Callback',@onMenuExportData); -0184 % 1.2.1.3 Inversion results single xls -0185 gui.menu.file_export_data_invstd_excel = uimenu(gui.menu.file_export_data,... -0186 'Label','EXCEL single (std)','Separator','on','Callback',@onMenuExportData); -0187 % 1.2.1.4 Inversion results single mat-file -0188 gui.menu.file_export_data_invstd_mat_single = uimenu(gui.menu.file_export_data,... -0189 'Label','MAT single (std)','Callback',@onMenuExportData); -0190 % 1.2.1.5 Inversion results all mat-file -0191 gui.menu.file_export_data_invstd_mat_all = uimenu(gui.menu.file_export_data,... -0192 'Label','MAT all (std)','Callback',@onMenuExportData); -0193 % 1.2.1.6 Joint Inversion results xls -0194 gui.menu.file_export_data_invjoint_excel = uimenu(gui.menu.file_export_data,... -0195 'Label','EXCEL all (joint)','Separator','on','Enable','off',... -0196 'Callback',@onMenuExportData); -0197 % 1.2.1.7 Joint Inversion results mat-file -0198 gui.menu.file_export_data_invjoint_mat = uimenu(gui.menu.file_export_data,... -0199 'Label','MAT all (joint)','Enable','off','Callback',@onMenuExportData); -0200 % 1.2.1.8 LIAG archive -0201 gui.menu.file_export_data_liag_archive = uimenu(gui.menu.file_export_data,... -0202 'Label','LIAG archive','Separator','on','Callback',@onMenuExportData); -0203 % 1.2.1.9 LIAG CSV T2 -0204 gui.menu.file_export_data_liag_csvT2 = uimenu(gui.menu.file_export_data,... -0205 'Label','LIAG CSV T2','Callback',@onMenuExportData); -0206 -0207 % 1.2.2 Graphics -0208 gui.menu.file_export_graphics = uimenu(gui.menu.file_export,... -0209 'Label','Graphics'); -0210 % 1.2.2.1 Layout -0211 gui.menu.file_export_graphics_layout = uimenu(gui.menu.file_export_graphics,... -0212 'Label','Layout'); -0213 % 1.2.2.1.1 Layout vertical -0214 gui.menu.file_export_graphics_layout_vert = uimenu(gui.menu.file_export_graphics_layout,... -0215 'Label','vert','Checked','on','Callback',@onMenuExportGraphics); -0216 % 1.2.2.1.2 Layout horizontal -0217 gui.menu.file_export_graphics_layout_horz = uimenu(gui.menu.file_export_graphics_layout,... -0218 'Label','horz','Callback',@onMenuExportGraphics); -0219 % 1.2.2.2 fig -0220 gui.menu.file_export_graphics_fig = uimenu(gui.menu.file_export_graphics,... -0221 'Label','FIG','Callback',@onMenuExportGraphics); -0222 % 1.2.2.3 png -0223 gui.menu.file_export_graphicspng = uimenu(gui.menu.file_export_graphics,... -0224 'Label','PNG','Callback',@onMenuExportGraphics); -0225 % 1.2.2.4 tiff -0226 gui.menu.file_export_graphicstiff = uimenu(gui.menu.file_export_graphics,... -0227 'Label','TIFF','Callback',@onMenuExportGraphics); -0228 % 1.2.2.5 eps -0229 gui.menu.file_export_graphicseps = uimenu(gui.menu.file_export_graphics,... -0230 'Label','EPS','Callback',@onMenuExportGraphics); -0231 -0232 % 1.3 Restart -0233 gui.menu.file_restart = uimenu(gui.menu.file,... -0234 'Label','Restart','Separator','on','Callback',@onMenuRestartQuit); -0235 -0236 % 1.4 Quit -0237 gui.menu.file_quit = uimenu(gui.menu.file,... -0238 'Label','Quit','Callback',@onMenuRestartQuit); -0239 -0240 %% 2. View -0241 gui.menu.view = uimenu(gui.figh,... -0242 'Label','View','Enable','off'); -0243 -0244 % 2.1 tooltips (on/off) -0245 gui.menu.view_tooltips = uimenu(gui.menu.view,... -0246 'Label','Tooltips','Checked','off','Callback',@onMenuView); -0247 switch gui.myui.inidata.tooltips -0248 case 'on' -0249 set(gui.menu.view_tooltips,'Checked','on'); -0250 case 'off' -0251 set(gui.menu.view_tooltips,'Checked','off'); -0252 end -0253 % 2.2 Figure Toolbar -0254 gui.menu.view_toolbar = uimenu(gui.menu.view,... -0255 'Label','Figure Toolbar','Callback',@onMenuView); -0256 -0257 % 2.3 INFO fields in plot panels (on/off) -0258 gui.menu.view_infofields = uimenu(gui.menu.view,... -0259 'Label','INFO fields','Separator','on','Callback',@onMenuView); -0260 -0261 % 2.4 inversion info on command line (on/off) -0262 gui.menu.view_invinfo = uimenu(gui.menu.view,... -0263 'Label','CLI Inv. Info','Callback',@onMenuView); -0264 switch gui.myui.inidata.invinfo -0265 case 'on' -0266 set(gui.menu.view_invinfo,'Checked','on'); -0267 case 'off' -0268 set(gui.menu.view_invinfo,'Checked','off'); -0269 end -0270 -0271 % 2.5 figures -0272 gui.menu.extra_graphics = uimenu(gui.menu.view,... -0273 'Label','Figures','Separator','on'); -0274 % 2.5.1 parameter file info -0275 gui.menu.extra_graphics_parinfo = uimenu(gui.menu.extra_graphics,... -0276 'Label','Parameter Info','Callback',@onMenuViewFigures); -0277 % 2.5.2 fit statistics -0278 gui.menu.extra_graphics_stats = uimenu(gui.menu.extra_graphics,... -0279 'Label','Fit statistics','Callback',@onMenuViewFigures); -0280 switch gui.myui.inidata.expertmode -0281 case 'on' -0282 % 2.5.3 amplitude over time -0283 gui.menu.extra_graphics_amp = uimenu(gui.menu.extra_graphics,... -0284 'Label','AMP-TLGM-SNR','Callback',@onMenuViewFigures); -0285 % 2.5.4 amplitude vs tlgm -0286 gui.menu.extra_graphics_amp2 = uimenu(gui.menu.extra_graphics,... -0287 'Label','AMP vs TLGM','Callback',@onMenuViewFigures); -0288 % 2.5.5 relaxation time distribution over time -0289 gui.menu.extra_graphics_rtd = uimenu(gui.menu.extra_graphics,... -0290 'Label','RTD','Callback',@onMenuViewFigures); -0291 case 'off' -0292 % 2.5.3 amplitude over time -0293 gui.menu.extra_graphics_amp = uimenu(gui.menu.extra_graphics,... -0294 'Label','AMP-TLGM-SNR','Enable','off','Callback',@onMenuViewFigures); -0295 % 2.5.4 amplitude vs tlgm -0296 gui.menu.extra_graphics_amp2 = uimenu(gui.menu.extra_graphics,... -0297 'Label','AMP vs TLGM','Enable','off','Callback',@onMenuViewFigures); -0298 % 2.5.5 relaxation time distribution over time -0299 gui.menu.extra_graphics_rtd = uimenu(gui.menu.extra_graphics,... -0300 'Label','RTD','Enable','off','Callback',@onMenuViewFigures); -0301 end -0302 -0303 % 2.6 PhaseView -0304 gui.menu.extra_phaseview = uimenu(gui.menu.view,... -0305 'Label','PhaseView GUI','Enable','off','Callback',@PhaseView); -0306 % 2.7 ConductVIEW -> hydraulic conductivity -0307 gui.menu.extra_conduct = uimenu(gui.menu.view,... -0308 'Label','ConductView GUI','Enable','off','Callback',@onMenuViewFigures); -0309 -0310 %% 3. Extras -0311 gui.menu.extra = uimenu(gui.figh,... -0312 'Label','Extra','Enable','off'); -0313 -0314 % 3.1 expert mode (on/off) -0315 gui.menu.extra_expert = uimenu(gui.menu.extra,... -0316 'Label','Expert Mode','Callback',@onMenuExpert); -0317 switch gui.myui.inidata.expertmode -0318 case 'on' -0319 set(gui.menu.extra_expert,'Checked','on'); -0320 case 'off' -0321 set(gui.menu.extra_expert,'Checked','of'); -0322 end -0323 -0324 % 3.2 optimization toolbox (on/off) -0325 switch gui.myui.inidata.expertmode -0326 case 'on' -0327 switch data.info.has_optim -0328 case 'on' -0329 gui.menu.extra_solver = uimenu(gui.menu.extra,... -0330 'Label','LSQ Solver','Enable','on'); -0331 case 'off' -0332 gui.menu.extra_solver = uimenu(gui.menu.extra,... -0333 'Label','LSQ Solver','Enable','off'); -0334 end -0335 case 'off' -0336 gui.menu.extra_solver = uimenu(gui.menu.extra,... -0337 'Label','LSQ Solver','Enable','off'); -0338 end -0339 gui.menu.extra_solver_lsqlin = uimenu(gui.menu.extra_solver,... -0340 'Label','LSQLIN (Optim. TB)','Callback',@onMenuSolver); -0341 gui.menu.extra_solver_lsqnonneg = uimenu(gui.menu.extra_solver,... -0342 'Label','LSQNONNEG (default)','Checked','on','Callback',@onMenuSolver); -0343 -0344 % 3.3 joint inversion (on/off) -0345 gui.menu.extra_joint = uimenu(gui.menu.extra,... -0346 'Label','Joint Inversion','Checked','off','Separator','on',... -0347 'Callback',@onMenuJointInversion); -0348 switch gui.myui.inidata.expertmode -0349 case 'on' -0350 set(gui.menu.extra_joint,'Enable','on'); -0351 case 'off' -0352 set(gui.menu.extra_joint,'Enable','off'); -0353 end -0354 -0355 % 3.4 set inversion bounds for surface relaxivity rho -0356 gui.menu.extra_joint_rhobounds = uimenu(gui.menu.extra,... -0357 'Label','Surface relaxivity bounds','Enable','off',... -0358 'Callback',@onMenuExtraRhoBounds); -0359 -0360 -0361 %% 4. Color theme -0362 gui.menu.color_theme = uimenu(gui.figh,... -0363 'Label','Color Theme','Enable','off'); -0364 -0365 % 4.1 default color theme -0366 gui.menu.color_theme_standard = uimenu(gui.menu.color_theme,... -0367 'Label','standard','Callback',@onMenuExtraColor); -0368 % 4.2 basic color theme -0369 gui.menu.color_theme_basic = uimenu(gui.menu.color_theme,... -0370 'Label','basic','Callback',@onMenuExtraColor); -0371 % 4.3 dark color theme -0372 gui.menu.color_theme_dark = uimenu(gui.menu.color_theme,... -0373 'Label','dark','Callback',@onMenuExtraColor); -0374 % 4.4 black color theme -0375 gui.menu.color_theme_black = uimenu(gui.menu.color_theme,... -0376 'Label','black','Callback',@onMenuExtraColor); -0377 switch gui.myui.inidata.colortheme -0378 case 'standard' -0379 set(gui.menu.color_theme_standard,'Checked','on'); -0380 case 'basic' -0381 set(gui.menu.color_theme_basic,'Checked','on'); -0382 case 'dark' -0383 set(gui.menu.color_theme_dark,'Checked','on'); -0384 case 'black' -0385 set(gui.menu.color_theme_black,'Checked','on'); -0386 end -0387 -0388 %% 5. Help -0389 gui.menu.help = uimenu(gui.figh,... -0390 'Label','Help','Enable','off'); -0391 -0392 % 5.1 About -0393 gui.menu.help_about = uimenu(gui.menu.help,... -0394 'Label','About','Callback',@onMenuHelp); -0395 -0396 return -0397 -0398 %------------- END OF CODE -------------- -0399 -0400 %% License: -0401 % MIT License -0402 % -0403 % Copyright (c) 2018 Thomas Hiller -0404 % -0405 % Permission is hereby granted, free of charge, to any person obtaining a copy -0406 % of this software and associated documentation files (the "Software"), to deal -0407 % in the Software without restriction, including without limitation the rights -0408 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0409 % copies of the Software, and to permit persons to whom the Software is -0410 % furnished to do so, subject to the following conditions: +0183 'Label','NUCLEUSinv (raw)','Callback',@onMenuExportData); +0184 % 1.2.1.2 GUI session mat-file +0185 gui.menu.file_export_data_GUImat = uimenu(gui.menu.file_export_data,... +0186 'Label','NUCLEUSinv (session)','Callback',@onMenuExportData); +0187 % 1.2.1.3 Inversion results single xls +0188 gui.menu.file_export_data_invstd_excel = uimenu(gui.menu.file_export_data,... +0189 'Label','EXCEL single (std)','Separator','on','Callback',@onMenuExportData); +0190 % 1.2.1.4 Inversion results single mat-file +0191 gui.menu.file_export_data_invstd_mat_single = uimenu(gui.menu.file_export_data,... +0192 'Label','MAT single (std)','Callback',@onMenuExportData); +0193 % 1.2.1.5 Inversion results all mat-file +0194 gui.menu.file_export_data_invstd_mat_all = uimenu(gui.menu.file_export_data,... +0195 'Label','MAT all (std)','Callback',@onMenuExportData); +0196 % 1.2.1.6 Joint Inversion results xls +0197 gui.menu.file_export_data_invjoint_excel = uimenu(gui.menu.file_export_data,... +0198 'Label','EXCEL all (joint)','Separator','on','Enable','off',... +0199 'Callback',@onMenuExportData); +0200 % 1.2.1.7 Joint Inversion results mat-file +0201 gui.menu.file_export_data_invjoint_mat = uimenu(gui.menu.file_export_data,... +0202 'Label','MAT all (joint)','Enable','off','Callback',@onMenuExportData); +0203 % 1.2.1.8 LIAG archive +0204 gui.menu.file_export_data_liag_archive = uimenu(gui.menu.file_export_data,... +0205 'Label','LIAG archive','Separator','on','Callback',@onMenuExportData); +0206 % 1.2.1.9 LIAG CSV T2 +0207 gui.menu.file_export_data_liag_csvT2 = uimenu(gui.menu.file_export_data,... +0208 'Label','LIAG CSV T2','Callback',@onMenuExportData); +0209 % 1.2.1.10 BGR data repository ascii +0210 gui.menu.file_export_data_bgr_repo = uimenu(gui.menu.file_export_data,... +0211 'Label','BGR repository','Callback',@onMenuExportData); +0212 +0213 % 1.2.2 Graphics +0214 gui.menu.file_export_graphics = uimenu(gui.menu.file_export,... +0215 'Label','Graphics'); +0216 % 1.2.2.1 Layout +0217 gui.menu.file_export_graphics_layout = uimenu(gui.menu.file_export_graphics,... +0218 'Label','Layout'); +0219 % 1.2.2.1.1 Layout vertical +0220 gui.menu.file_export_graphics_layout_vert = uimenu(gui.menu.file_export_graphics_layout,... +0221 'Label','vert','Checked','on','Callback',@onMenuExportGraphics); +0222 % 1.2.2.1.2 Layout horizontal +0223 gui.menu.file_export_graphics_layout_horz = uimenu(gui.menu.file_export_graphics_layout,... +0224 'Label','horz','Callback',@onMenuExportGraphics); +0225 % 1.2.2.2 fig +0226 gui.menu.file_export_graphics_fig = uimenu(gui.menu.file_export_graphics,... +0227 'Label','FIG','Callback',@onMenuExportGraphics); +0228 % 1.2.2.3 png +0229 gui.menu.file_export_graphicspng = uimenu(gui.menu.file_export_graphics,... +0230 'Label','PNG','Callback',@onMenuExportGraphics); +0231 % 1.2.2.4 tiff +0232 gui.menu.file_export_graphicstiff = uimenu(gui.menu.file_export_graphics,... +0233 'Label','TIFF','Callback',@onMenuExportGraphics); +0234 % 1.2.2.5 eps +0235 gui.menu.file_export_graphicseps = uimenu(gui.menu.file_export_graphics,... +0236 'Label','EPS','Callback',@onMenuExportGraphics); +0237 +0238 % 1.3 Restart +0239 gui.menu.file_restart = uimenu(gui.menu.file,... +0240 'Label','Restart','Separator','on','Callback',@onMenuRestartQuit); +0241 +0242 % 1.4 Quit +0243 gui.menu.file_quit = uimenu(gui.menu.file,... +0244 'Label','Quit','Callback',@onMenuRestartQuit); +0245 +0246 %% 2. View +0247 gui.menu.view = uimenu(gui.figh,... +0248 'Label','View','Enable','off'); +0249 +0250 % 2.1 tooltips (on/off) +0251 gui.menu.view_tooltips = uimenu(gui.menu.view,... +0252 'Label','Tooltips','Checked','off','Callback',@onMenuView); +0253 switch gui.myui.inidata.tooltips +0254 case 'on' +0255 set(gui.menu.view_tooltips,'Checked','on'); +0256 case 'off' +0257 set(gui.menu.view_tooltips,'Checked','off'); +0258 end +0259 % 2.2 Figure Toolbar +0260 gui.menu.view_toolbar = uimenu(gui.menu.view,... +0261 'Label','Figure Toolbar','Callback',@onMenuView); +0262 +0263 % 2.3 INFO fields in plot panels (on/off) +0264 gui.menu.view_infofields = uimenu(gui.menu.view,... +0265 'Label','INFO fields','Separator','on','Callback',@onMenuView); +0266 +0267 % 2.4 inversion info on command line (on/off) +0268 gui.menu.view_invinfo = uimenu(gui.menu.view,... +0269 'Label','CLI Inv. Info','Callback',@onMenuView); +0270 switch gui.myui.inidata.invinfo +0271 case 'on' +0272 set(gui.menu.view_invinfo,'Checked','on'); +0273 case 'off' +0274 set(gui.menu.view_invinfo,'Checked','off'); +0275 end +0276 +0277 % 2.5 figures +0278 gui.menu.extra_graphics = uimenu(gui.menu.view,... +0279 'Label','Figures','Separator','on'); +0280 % 2.5.1 parameter file info +0281 gui.menu.extra_graphics_parinfo = uimenu(gui.menu.extra_graphics,... +0282 'Label','Parameter Info','Callback',@onMenuViewFigures); +0283 % 2.5.2 fit statistics +0284 gui.menu.extra_graphics_stats = uimenu(gui.menu.extra_graphics,... +0285 'Label','Fit statistics','Callback',@onMenuViewFigures); +0286 switch gui.myui.inidata.expertmode +0287 case 'on' +0288 % 2.5.3 amplitude over time +0289 gui.menu.extra_graphics_amp = uimenu(gui.menu.extra_graphics,... +0290 'Label','AMP-TLGM-SNR','Callback',@onMenuViewFigures); +0291 % 2.5.4 amplitude vs tlgm +0292 gui.menu.extra_graphics_amp2 = uimenu(gui.menu.extra_graphics,... +0293 'Label','AMP vs TLGM','Callback',@onMenuViewFigures); +0294 % 2.5.5 relaxation time distribution over time +0295 gui.menu.extra_graphics_rtd = uimenu(gui.menu.extra_graphics,... +0296 'Label','RTD','Callback',@onMenuViewFigures); +0297 case 'off' +0298 % 2.5.3 amplitude over time +0299 gui.menu.extra_graphics_amp = uimenu(gui.menu.extra_graphics,... +0300 'Label','AMP-TLGM-SNR','Enable','off','Callback',@onMenuViewFigures); +0301 % 2.5.4 amplitude vs tlgm +0302 gui.menu.extra_graphics_amp2 = uimenu(gui.menu.extra_graphics,... +0303 'Label','AMP vs TLGM','Enable','off','Callback',@onMenuViewFigures); +0304 % 2.5.5 relaxation time distribution over time +0305 gui.menu.extra_graphics_rtd = uimenu(gui.menu.extra_graphics,... +0306 'Label','RTD','Enable','off','Callback',@onMenuViewFigures); +0307 end +0308 +0309 % 2.6 PhaseView +0310 gui.menu.extra_phaseview = uimenu(gui.menu.view,... +0311 'Label','PhaseView GUI','Enable','off','Callback',@PhaseView); +0312 % 2.7 ConductVIEW -> hydraulic conductivity +0313 gui.menu.extra_conduct = uimenu(gui.menu.view,... +0314 'Label','ConductView GUI','Enable','off','Callback',@onMenuViewFigures); +0315 % 2.8 FixedTime VIEW +0316 gui.menu.extra_fixedtime = uimenu(gui.menu.view,... +0317 'Label','FixedTimeView GUI','Enable','off','Callback',@FixedTimeView); +0318 +0319 %% 3. Extras +0320 gui.menu.extra = uimenu(gui.figh,... +0321 'Label','Extra','Enable','off'); +0322 +0323 % 3.1 expert mode (on/off) +0324 gui.menu.extra_expert = uimenu(gui.menu.extra,... +0325 'Label','Expert Mode','Callback',@onMenuExpert); +0326 switch gui.myui.inidata.expertmode +0327 case 'on' +0328 set(gui.menu.extra_expert,'Checked','on'); +0329 case 'off' +0330 set(gui.menu.extra_expert,'Checked','of'); +0331 end +0332 +0333 % 3.2 optimization toolbox (on/off) +0334 switch gui.myui.inidata.expertmode +0335 case 'on' +0336 switch data.info.has_optim +0337 case 'on' +0338 gui.menu.extra_solver = uimenu(gui.menu.extra,... +0339 'Label','LSQ Solver','Enable','on'); +0340 case 'off' +0341 gui.menu.extra_solver = uimenu(gui.menu.extra,... +0342 'Label','LSQ Solver','Enable','off'); +0343 end +0344 case 'off' +0345 gui.menu.extra_solver = uimenu(gui.menu.extra,... +0346 'Label','LSQ Solver','Enable','off'); +0347 end +0348 gui.menu.extra_solver_lsqlin = uimenu(gui.menu.extra_solver,... +0349 'Label','LSQLIN (Optim. TB)','Callback',@onMenuSolver); +0350 gui.menu.extra_solver_lsqnonneg = uimenu(gui.menu.extra_solver,... +0351 'Label','LSQNONNEG (default)','Checked','on','Callback',@onMenuSolver); +0352 +0353 % 3.3 joint inversion (on/off) +0354 gui.menu.extra_joint = uimenu(gui.menu.extra,... +0355 'Label','Joint Inversion','Checked','off','Separator','on',... +0356 'Callback',@onMenuJointInversion); +0357 switch gui.myui.inidata.expertmode +0358 case 'on' +0359 set(gui.menu.extra_joint,'Enable','on'); +0360 case 'off' +0361 set(gui.menu.extra_joint,'Enable','off'); +0362 end +0363 +0364 % 3.4 set inversion bounds for surface relaxivity rho +0365 gui.menu.extra_joint_rhobounds = uimenu(gui.menu.extra,... +0366 'Label','Surface relaxivity bounds','Enable','off',... +0367 'Callback',@onMenuExtraRhoBounds); +0368 +0369 +0370 %% 4. Color theme +0371 gui.menu.color_theme = uimenu(gui.figh,... +0372 'Label','Color Theme','Enable','off'); +0373 +0374 % 4.1 default color theme +0375 gui.menu.color_theme_standard = uimenu(gui.menu.color_theme,... +0376 'Label','standard','Callback',@onMenuExtraColor); +0377 % 4.2 basic color theme +0378 gui.menu.color_theme_basic = uimenu(gui.menu.color_theme,... +0379 'Label','basic','Callback',@onMenuExtraColor); +0380 % 4.3 dark color theme +0381 gui.menu.color_theme_dark = uimenu(gui.menu.color_theme,... +0382 'Label','dark','Callback',@onMenuExtraColor); +0383 % 4.4 black color theme +0384 gui.menu.color_theme_black = uimenu(gui.menu.color_theme,... +0385 'Label','black','Callback',@onMenuExtraColor); +0386 switch gui.myui.inidata.colortheme +0387 case 'standard' +0388 set(gui.menu.color_theme_standard,'Checked','on'); +0389 case 'basic' +0390 set(gui.menu.color_theme_basic,'Checked','on'); +0391 case 'dark' +0392 set(gui.menu.color_theme_dark,'Checked','on'); +0393 case 'black' +0394 set(gui.menu.color_theme_black,'Checked','on'); +0395 end +0396 +0397 %% 5. Help +0398 gui.menu.help = uimenu(gui.figh,... +0399 'Label','Help','Enable','off'); +0400 +0401 % 5.1 About +0402 gui.menu.help_about = uimenu(gui.menu.help,... +0403 'Label','About','Callback',@onMenuHelp); +0404 +0405 return +0406 +0407 %------------- END OF CODE -------------- +0408 +0409 %% License: +0410 % MIT License 0411 % -0412 % The above copyright notice and this permission notice shall be included in all -0413 % copies or substantial portions of the Software. -0414 % -0415 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0416 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0417 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0418 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0419 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0420 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0421 % SOFTWARE. +0412 % Copyright (c) 2018 Thomas Hiller +0413 % +0414 % Permission is hereby granted, free of charge, to any person obtaining a copy +0415 % of this software and associated documentation files (the "Software"), to deal +0416 % in the Software without restriction, including without limitation the rights +0417 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0418 % copies of the Software, and to permit persons to whom the Software is +0419 % furnished to do so, subject to the following conditions: +0420 % +0421 % The above copyright notice and this permission notice shall be included in all +0422 % copies or substantial portions of the Software. +0423 % +0424 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0425 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0426 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0427 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0428 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0429 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0430 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/NUCLEUSinv/NUCLEUSinv_loadDefaults.html b/doc/nucleus/NUCLEUSinv/NUCLEUSinv_loadDefaults.html index 0a433a9..8edb209 100644 --- a/doc/nucleus/NUCLEUSinv/NUCLEUSinv_loadDefaults.html +++ b/doc/nucleus/NUCLEUSinv/NUCLEUSinv_loadDefaults.html @@ -172,111 +172,114 @@

    SOURCE CODE ^'NNLS'; 0104 % when inversion method is 'free' choose No. of free relaxation times 0105 out.invstd.freeDT = 2; -0106 % regularization options for multi-exponential fitting routines -0107 % 'NNLS' and 'LU' -0108 out.invstd.regtype = 'manual'; -0109 % smoothness constraint (order) for multi-exponential fitting routines +0106 % option to fix some of the 'free' relaxation times to a certain value +0107 out.invstd.Tfixed_bool = [0 0 0 0 0]; +0108 out.invstd.Tfixed_val = [0 0 0 0 0]; +0109 % regularization options for multi-exponential fitting routines 0110 % 'NNLS' and 'LU' -0111 out.invstd.Lorder = 1; -0112 % regularization parameter for multi-exponential fitting routines +0111 out.invstd.regtype = 'manual'; +0112 % smoothness constraint (order) for multi-exponential fitting routines 0113 % 'NNLS' and 'LU' -0114 out.invstd.lambda = 1; -0115 % L-curve range (lambda) for multi-exponential fitting routine 'NNLS' -0116 out.invstd.lambdaR = [1e-3 1e2]; -0117 % initial L-curve range (lambda) for multi-exponential fitting routine -0118 % 'NNLS' -0119 out.invstd.lambdaRinit = [1e-3 1e2]; -0120 % number of lambda values in L-curve -0121 out.invstd.NlambdaR = 20; -0122 % range for RTD [min max] in [s] -0123 out.invstd.time = [1e-4 1e2]; -0124 % number of points per decade in RTD -0125 out.invstd.Ntime = 30; -0126 % noise level (taken from data if available) -0127 out.invstd.noise = 0; -0128 % water bulk relaxation time [s] -0129 out.invstd.Tbulk = 1e6; -0130 % diffusion relaxation time [s] -0131 out.invstd.Tdiff = 1e6; -0132 % porosity value between 0 and 1 [-] -0133 out.invstd.porosity = 1; -0134 -0135 out.invstd.useUncert = 1; -0136 out.invstd.uncertMethod = 'thresh'; -0137 out.invstd.uncertThresh = 0.05; -0138 out.invstd.uncertChi2 = 0.005; -0139 out.invstd.uncertN = 100; -0140 out.invstd.uncertMax = 1e4; -0141 -0142 %% joint inversion panel defaults -0143 % joint inversion methods to choose 'free' | 'fixed' | 'shape' -0144 out.invjoint.invtype = 'free'; -0145 % pore size distribution in [m] -0146 out.invjoint.radii = [1e-8 1e-2]; -0147 % No. of steps per decade in pore size distribution -0148 out.invjoint.Nradii = 25; -0149 % regularization options for joint inversion 'free' -0150 out.invjoint.regtype = 'manual'; -0151 % smoothness constraint (order) for joint inversion 'free' -0152 out.invjoint.Lorder = 1; -0153 % regularization parameter for joint inversion 'free' -0154 out.invjoint.lambda = 1; -0155 % L-curve range (lambda) for joint inversion 'free' -0156 out.invjoint.lambdaR = [1e-3 1e2]; -0157 % initial L-curve range (lambda) for joint inversion 'free' -0158 out.invjoint.lambdaRinit = [1e-3 1e2]; -0159 out.invjoint.NlambdaR = 20; -0160 % available pore geometries 'cyl' | 'ang' | 'poly' -0161 out.invjoint.geometry_type = 'cyl'; -0162 % number of polygon sides for geometry 'poly' (3 to 12) -0163 out.invjoint.polyN = 3; -0164 % angle alpha [deg] - fixed to 90° -0165 out.invjoint.alpha = 90; -0166 % angle beta [deg] - changed by user -0167 out.invjoint.beta = 60; -0168 % gamma [deg] - alpha-beta -0169 out.invjoint.gamma = 30; -0170 % start value rho [µm/s] -0171 out.invjoint.rhostart = 20; -0172 % lower and upper boundary for rho [µm/s] -0173 out.invjoint.rhobounds = [0.01 1000]; -0174 % sart value beta [deg] -0175 out.invjoint.anglestart = 25; -0176 -0177 % pressure settings -0178 % CPS table initial values (use,p,S,drain/imb) -0179 out.pressure.table = {true,0,1,'D'}; -0180 % pressure units 'Pa' | 'kPa' | 'MPa' | 'bar' -0181 out.pressure.unit = 'Pa'; -0182 % corresponding scale factors - 1 | 1e-3 | 1e-6 | 1e-5 -0183 out.pressure.unitfac = 1; -0184 -0185 return -0186 -0187 %------------- END OF CODE -------------- -0188 -0189 %% License: -0190 % MIT License -0191 % -0192 % Copyright (c) 2018 Thomas Hiller -0193 % -0194 % Permission is hereby granted, free of charge, to any person obtaining a copy -0195 % of this software and associated documentation files (the "Software"), to deal -0196 % in the Software without restriction, including without limitation the rights -0197 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0198 % copies of the Software, and to permit persons to whom the Software is -0199 % furnished to do so, subject to the following conditions: -0200 % -0201 % The above copyright notice and this permission notice shall be included in all -0202 % copies or substantial portions of the Software. +0114 out.invstd.Lorder = 1; +0115 % regularization parameter for multi-exponential fitting routines +0116 % 'NNLS' and 'LU' +0117 out.invstd.lambda = 1; +0118 % L-curve range (lambda) for multi-exponential fitting routine 'NNLS' +0119 out.invstd.lambdaR = [1e-3 1e2]; +0120 % initial L-curve range (lambda) for multi-exponential fitting routine +0121 % 'NNLS' +0122 out.invstd.lambdaRinit = [1e-3 1e2]; +0123 % number of lambda values in L-curve +0124 out.invstd.NlambdaR = 20; +0125 % range for RTD [min max] in [s] +0126 out.invstd.time = [1e-4 1e2]; +0127 % number of points per decade in RTD +0128 out.invstd.Ntime = 30; +0129 % noise level (taken from data if available) +0130 out.invstd.noise = 0; +0131 % water bulk relaxation time [s] +0132 out.invstd.Tbulk = 1e6; +0133 % diffusion relaxation time [s] +0134 out.invstd.Tdiff = 1e6; +0135 % porosity value between 0 and 1 [-] +0136 out.invstd.porosity = 1; +0137 +0138 out.invstd.useUncert = 1; +0139 out.invstd.uncertMethod = 'thresh'; +0140 out.invstd.uncertThresh = 0.05; +0141 out.invstd.uncertChi2 = 0.005; +0142 out.invstd.uncertN = 100; +0143 out.invstd.uncertMax = 1e4; +0144 +0145 %% joint inversion panel defaults +0146 % joint inversion methods to choose 'free' | 'fixed' | 'shape' +0147 out.invjoint.invtype = 'free'; +0148 % pore size distribution in [m] +0149 out.invjoint.radii = [1e-8 1e-2]; +0150 % No. of steps per decade in pore size distribution +0151 out.invjoint.Nradii = 25; +0152 % regularization options for joint inversion 'free' +0153 out.invjoint.regtype = 'manual'; +0154 % smoothness constraint (order) for joint inversion 'free' +0155 out.invjoint.Lorder = 1; +0156 % regularization parameter for joint inversion 'free' +0157 out.invjoint.lambda = 1; +0158 % L-curve range (lambda) for joint inversion 'free' +0159 out.invjoint.lambdaR = [1e-3 1e2]; +0160 % initial L-curve range (lambda) for joint inversion 'free' +0161 out.invjoint.lambdaRinit = [1e-3 1e2]; +0162 out.invjoint.NlambdaR = 20; +0163 % available pore geometries 'cyl' | 'ang' | 'poly' +0164 out.invjoint.geometry_type = 'cyl'; +0165 % number of polygon sides for geometry 'poly' (3 to 12) +0166 out.invjoint.polyN = 3; +0167 % angle alpha [deg] - fixed to 90° +0168 out.invjoint.alpha = 90; +0169 % angle beta [deg] - changed by user +0170 out.invjoint.beta = 60; +0171 % gamma [deg] - alpha-beta +0172 out.invjoint.gamma = 30; +0173 % start value rho [µm/s] +0174 out.invjoint.rhostart = 20; +0175 % lower and upper boundary for rho [µm/s] +0176 out.invjoint.rhobounds = [0.01 1000]; +0177 % sart value beta [deg] +0178 out.invjoint.anglestart = 25; +0179 +0180 % pressure settings +0181 % CPS table initial values (use,p,S,drain/imb) +0182 out.pressure.table = {true,0,1,'D'}; +0183 % pressure units 'Pa' | 'kPa' | 'MPa' | 'bar' +0184 out.pressure.unit = 'Pa'; +0185 % corresponding scale factors - 1 | 1e-3 | 1e-6 | 1e-5 +0186 out.pressure.unitfac = 1; +0187 +0188 return +0189 +0190 %------------- END OF CODE -------------- +0191 +0192 %% License: +0193 % MIT License +0194 % +0195 % Copyright (c) 2018 Thomas Hiller +0196 % +0197 % Permission is hereby granted, free of charge, to any person obtaining a copy +0198 % of this software and associated documentation files (the "Software"), to deal +0199 % in the Software without restriction, including without limitation the rights +0200 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0201 % copies of the Software, and to permit persons to whom the Software is +0202 % furnished to do so, subject to the following conditions: 0203 % -0204 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0205 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0206 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0207 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0208 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0209 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0210 % SOFTWARE. +0204 % The above copyright notice and this permission notice shall be included in all +0205 % copies or substantial portions of the Software. +0206 % +0207 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0208 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0209 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0210 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0211 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0212 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0213 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/NUCLEUSinv/NUCLEUSinv_updateInterface.html b/doc/nucleus/NUCLEUSinv/NUCLEUSinv_updateInterface.html index 2b0bc55..d1d526e 100644 --- a/doc/nucleus/NUCLEUSinv/NUCLEUSinv_updateInterface.html +++ b/doc/nucleus/NUCLEUSinv/NUCLEUSinv_updateInterface.html @@ -182,7 +182,7 @@

    SOURCE CODE ^'Value',data.invstd.freeDT,... 0103 'String',{'1','2','3','4','5'}); 0104 set(gui.text_handles.invstd_InvTypeOpt,... -0105 'String','No. of free decay times T'); +0105 'String','No. of free relaxation times T'); 0106 0107 % lambda, smoothness constraint and RTD limits 0108 gui = updateLambda(gui,data.invstd.regtype,0,0,0); @@ -666,7 +666,7 @@

    SOURCE CODE ^'Value',data.invstd.freeDT,... 0587 'String',{'1','2','3','4','5'}); 0588 set(gui.text_handles.invstd_InvTypeOpt,... -0589 'String','No. of free decay times T'); +0589 'String','No. of relaxation decay times T'); 0590 0591 % lambda, smoothness constraint and RTD limits 0592 gui = updateLambda(gui,data.invstd.regtype,0,0,0); @@ -755,291 +755,288 @@

    SOURCE CODE ^switch gatetype 0677 -0678 case 'log' -0679 -0680 set(gui.radio_handles.process_gates_log,'Value',1); -0681 set(gui.radio_handles.process_gates_lin,'Value',0); -0682 set(gui.radio_handles.process_gates_none,'Value',0); -0683 set(gui.edit_handles.process_Nechoes,'Enable','on'); -0684 -0685 case 'lin' -0686 -0687 set(gui.radio_handles.process_gates_log,'Value',0); -0688 set(gui.radio_handles.process_gates_lin,'Value',1); -0689 set(gui.radio_handles.process_gates_none,'Value',0); -0690 set(gui.edit_handles.process_Nechoes,'Enable','on'); -0691 -0692 case 'raw' -0693 -0694 set(gui.radio_handles.process_gates_log,'Value',0); -0695 set(gui.radio_handles.process_gates_lin,'Value',0); -0696 set(gui.radio_handles.process_gates_none,'Value',1); -0697 set(gui.edit_handles.process_Nechoes,'Enable','off'); -0698 -0699 end -0700 -0701 end -0702 -0703 function gui = updateNormalize(gui,norm) -0704 -0705 switch norm -0706 case 0 -0707 set(gui.radio_handles.process_normalize_on,'Enable','on','Value',0); -0708 set(gui.radio_handles.process_normalize_off,'Enable','on','Value',1); -0709 -0710 case 1 -0711 set(gui.radio_handles.process_normalize_on,'Enable','on','Value',1); -0712 set(gui.radio_handles.process_normalize_off,'Enable','on','Value',0); -0713 end -0714 -0715 end -0716 -0717 function gui = updateTimescale(gui,timescale) -0718 -0719 switch timescale -0720 -0721 case 's' -0722 set(gui.radio_handles.process_timescale_s,'Enable','on','Value',1); -0723 set(gui.radio_handles.process_timescale_ms,'Enable','on','Value',0); -0724 set(gui.text_handles.invstd_RTDtimes,'String','RTD - min [s] | max [s] | # / dec',... -0725 'FontSize',10); -0726 set(gui.text_handles.petro_Tbulk,'String','Tbulk [s] | Tdiff [s]'); -0727 set(gui.text_handles.petro_rho,'String',[char(hex2dec('03C1')),' [µm/s] | geom ']); -0728 -0729 case 'ms' -0730 set(gui.radio_handles.process_timescale_s,'Enable','on','Value',0); -0731 set(gui.radio_handles.process_timescale_ms,'Enable','on','Value',1); -0732 set(gui.text_handles.invstd_RTDtimes,'String','RTD - min [ms] | max [ms] | # / dec',... -0733 'FontSize',9); -0734 set(gui.text_handles.petro_Tbulk,'String','Tbulk [ms] | Tdiff [ms]'); -0735 set(gui.text_handles.petro_rho,'String',[char(hex2dec('03C1')),' [µm/s] | geom ']); -0736 end -0737 -0738 end -0739 -0740 function gui = updateInvstdTime(gui,invtype,time,Ntime) -0741 -0742 switch invtype -0743 -0744 case {'mono','free'} -0745 set(gui.edit_handles.invstd_time_min,'Enable','off'); -0746 set(gui.edit_handles.invstd_time_max,'Enable','off'); -0747 set(gui.edit_handles.invstd_Ntime,'Enable','off'); -0748 -0749 case {'LU','NNLS','MUMO'} -0750 set(gui.edit_handles.invstd_time_min,'Enable','on','String',num2str(time(1))); -0751 set(gui.edit_handles.invstd_time_max,'Enable','on','String',num2str(time(2))); -0752 set(gui.edit_handles.invstd_Ntime,'Enable','on','String',num2str(Ntime)); -0753 end -0754 -0755 end -0756 -0757 function gui = updateInvjointRadii(gui,invtype,radii,Nradii) -0758 -0759 switch invtype -0760 case {'fixed','shape','off'} -0761 set(gui.edit_handles.invjoint_radii_min,'Enable','off'); -0762 set(gui.edit_handles.invjoint_radii_max,'Enable','off'); -0763 set(gui.edit_handles.invjoint_Nradii,'Enable','off'); -0764 -0765 case {'free'} -0766 set(gui.edit_handles.invjoint_radii_min,'Enable','on','String',num2str(radii(1))); -0767 set(gui.edit_handles.invjoint_radii_max,'Enable','on','String',num2str(radii(2))); -0768 set(gui.edit_handles.invjoint_Nradii,'Enable','on','String',num2str(Nradii)); -0769 end -0770 -0771 end -0772 -0773 function gui = updateLambda(gui,regtype,lambda,lambdaR,NlambdaR) -0774 -0775 switch regtype -0776 case 'none' -0777 set(gui.edit_handles.invstd_lambda_min,'Enable','off'); -0778 set(gui.edit_handles.invstd_lambda_max,'Enable','off'); -0779 set(gui.edit_handles.invstd_NlambdaR,'Enable','off'); -0780 gui.plots.DistPanel.TabTitles = {'RTD','PSD','PSD (joint)'}; -0781 -0782 case 'manual' -0783 set(gui.edit_handles.invstd_lambda_min,'Enable','on','String',num2str(lambda)); -0784 set(gui.edit_handles.invstd_lambda_max,'Enable','off'); -0785 set(gui.edit_handles.invstd_NlambdaR,'Enable','off'); -0786 gui.plots.DistPanel.TabTitles = {'RTD','PSD','PSD (joint)'}; -0787 -0788 case 'auto' -0789 set(gui.edit_handles.invstd_lambda_min,'Enable','off','String',num2str(lambda)); -0790 set(gui.edit_handles.invstd_lambda_max,'Enable','off'); -0791 set(gui.edit_handles.invstd_NlambdaR,'Enable','off'); -0792 gui.plots.DistPanel.TabTitles = {'RTD','PSD','PSD (joint)'}; -0793 -0794 case 'lcurve' -0795 set(gui.edit_handles.invstd_lambda_min,'Enable','on','String',num2str(lambdaR(1))); -0796 set(gui.edit_handles.invstd_lambda_max,'Enable','on','String',num2str(lambdaR(2))); -0797 set(gui.edit_handles.invstd_NlambdaR,'Enable','on','String',num2str(NlambdaR)); -0798 gui.plots.DistPanel.TabTitles = {'L-CURVE','RMS','PSD (joint)'}; -0799 -0800 case {'gcv_tikh','gcv_trunc','gcv_damp','discrep'} -0801 set(gui.edit_handles.invstd_lambda_min,'Enable','off','String',num2str(lambda)); -0802 set(gui.edit_handles.invstd_lambda_max,'Enable','off'); -0803 set(gui.edit_handles.invstd_NlambdaR,'Enable','off'); -0804 gui.plots.DistPanel.TabTitles = {'RTD','PSD','PSD (joint)'}; -0805 end -0806 -0807 end -0808 -0809 function gui = updateLambdaJoint(gui,regtype,lambda,lambdaR,NlambdaR,regtypestd) -0810 -0811 switch regtype -0812 case 'none' -0813 switch regtypestd -0814 case 'lcurve' -0815 set(gui.edit_handles.invjoint_lambda_min,'Enable','off'); -0816 set(gui.edit_handles.invjoint_lambda_max,'Enable','off'); -0817 set(gui.edit_handles.invjoint_NlambdaR,'Enable','off'); -0818 gui.plots.DistPanel.TabTitles = {'L-CURVE','RMS','PSD (joint)'}; -0819 -0820 otherwise -0821 set(gui.edit_handles.invjoint_lambda_min,'Enable','off'); -0822 set(gui.edit_handles.invjoint_lambda_max,'Enable','off'); -0823 set(gui.edit_handles.invjoint_NlambdaR,'Enable','off'); -0824 gui.plots.DistPanel.TabTitles = {'RTD','PSD','PSD (joint)'}; -0825 end -0826 -0827 case 'manual' -0828 switch regtypestd -0829 case 'lcurve' -0830 set(gui.edit_handles.invjoint_lambda_min,'Enable','on','String',num2str(lambda)); -0831 set(gui.edit_handles.invjoint_lambda_max,'Enable','off'); -0832 set(gui.edit_handles.invjoint_NlambdaR,'Enable','off'); -0833 gui.plots.DistPanel.TabTitles = {'L-CURVE','RMS','PSD (joint)'}; -0834 -0835 otherwise -0836 set(gui.edit_handles.invjoint_lambda_min,'Enable','on','String',num2str(lambda)); -0837 set(gui.edit_handles.invjoint_lambda_max,'Enable','off'); -0838 set(gui.edit_handles.invjoint_NlambdaR,'Enable','off'); -0839 gui.plots.DistPanel.TabTitles = {'RTD','PSD','PSD (joint)'}; -0840 end -0841 -0842 case 'lcurve' -0843 set(gui.edit_handles.invjoint_lambda_min,'Enable','on','String',num2str(lambdaR(1))); -0844 set(gui.edit_handles.invjoint_lambda_max,'Enable','on','String',num2str(lambdaR(2))); -0845 set(gui.edit_handles.invjoint_NlambdaR,'Enable','on','String',num2str(NlambdaR)); -0846 gui.plots.DistPanel.TabTitles = {'L-CURVE','RMS','PSD (joint)'}; -0847 end -0848 -0849 end -0850 -0851 function gui = updateLorder(gui,invtype,Lorder) -0852 -0853 switch invtype -0854 case {'mono','free','MUMO'} -0855 set(gui.radio_handles.invstd_Lorder0,'Enable','off'); -0856 set(gui.radio_handles.invstd_Lorder1,'Enable','off'); -0857 set(gui.radio_handles.invstd_Lorder2,'Enable','off'); -0858 -0859 case {'LU','NNLS'} -0860 set(gui.radio_handles.invstd_Lorder0,'Enable','on'); -0861 set(gui.radio_handles.invstd_Lorder1,'Enable','on'); -0862 set(gui.radio_handles.invstd_Lorder2,'Enable','on'); -0863 -0864 switch Lorder -0865 case 0 -0866 set(gui.radio_handles.invstd_Lorder0,'Value',1); -0867 set(gui.radio_handles.invstd_Lorder1,'Value',0); -0868 set(gui.radio_handles.invstd_Lorder2,'Value',0); -0869 -0870 case 1 -0871 set(gui.radio_handles.invstd_Lorder0,'Value',0); -0872 set(gui.radio_handles.invstd_Lorder1,'Value',1); -0873 set(gui.radio_handles.invstd_Lorder2,'Value',0); -0874 -0875 case 2 -0876 set(gui.radio_handles.invstd_Lorder0,'Value',0); -0877 set(gui.radio_handles.invstd_Lorder1,'Value',0); -0878 set(gui.radio_handles.invstd_Lorder2,'Value',1); -0879 end -0880 end -0881 -0882 end -0883 -0884 function gui = updateLorderJoint(gui,invtype,Lorder) -0885 -0886 switch invtype -0887 case {'fixed','shape','off'} -0888 set(gui.radio_handles.invjoint_Lorder0,'Enable','off'); -0889 set(gui.radio_handles.invjoint_Lorder1,'Enable','off'); -0890 set(gui.radio_handles.invjoint_Lorder2,'Enable','off'); -0891 -0892 case 'free' -0893 set(gui.radio_handles.invjoint_Lorder0,'Enable','on'); -0894 set(gui.radio_handles.invjoint_Lorder1,'Enable','on'); -0895 set(gui.radio_handles.invjoint_Lorder2,'Enable','on'); -0896 -0897 switch Lorder -0898 case 0 -0899 set(gui.radio_handles.invjoint_Lorder0,'Value',1); -0900 set(gui.radio_handles.invjoint_Lorder1,'Value',0); -0901 set(gui.radio_handles.invjoint_Lorder2,'Value',0); -0902 -0903 case 1 -0904 set(gui.radio_handles.invjoint_Lorder0,'Value',0); -0905 set(gui.radio_handles.invjoint_Lorder1,'Value',1); -0906 set(gui.radio_handles.invjoint_Lorder2,'Value',0); -0907 -0908 case 2 -0909 set(gui.radio_handles.invjoint_Lorder0,'Value',0); -0910 set(gui.radio_handles.invjoint_Lorder1,'Value',0); -0911 set(gui.radio_handles.invjoint_Lorder2,'Value',1); -0912 end -0913 end -0914 -0915 end -0916 -0917 function gui = updateParams(gui,invtype,p) -0918 -0919 switch invtype -0920 case {'mono','free'} -0921 set(gui.edit_handles.param_CBW,'Enable','off','String',num2str(p.CBWcutoff)); -0922 set(gui.edit_handles.param_BVI,'Enable','off','String',num2str(p.BVIcutoff)); -0923 set(gui.edit_handles.param_rho,'Enable','on','String',num2str(p.rho)); -0924 set(gui.edit_handles.param_geom,'Enable','on','String',num2str(p.a)); -0925 -0926 case {'LU','NNLS','MUMO'} -0927 set(gui.edit_handles.param_CBW,'Enable','on','String',num2str(p.CBWcutoff)); -0928 set(gui.edit_handles.param_BVI,'Enable','on','String',num2str(p.BVIcutoff)); -0929 set(gui.edit_handles.param_rho,'Enable','on','String',num2str(p.rho)); -0930 set(gui.edit_handles.param_geom,'Enable','on','String',num2str(p.a)); -0931 -0932 end -0933 set(gui.edit_handles.param_calibVol,'Enable','on','String',num2str(p.calibVol)); -0934 set(gui.edit_handles.param_calibAmp,'Enable','on','String',num2str(p.calibAmp)); -0935 set(gui.edit_handles.param_sampVol,'Enable','on','String',num2str(p.sampVol)); -0936 -0937 end -0938 -0939 %------------- END OF CODE -------------- -0940 -0941 %% License: -0942 % MIT License -0943 % -0944 % Copyright (c) 2018 Thomas Hiller -0945 % -0946 % Permission is hereby granted, free of charge, to any person obtaining a copy -0947 % of this software and associated documentation files (the "Software"), to deal -0948 % in the Software without restriction, including without limitation the rights -0949 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0950 % copies of the Software, and to permit persons to whom the Software is -0951 % furnished to do so, subject to the following conditions: +0678 case 'log' +0679 set(gui.radio_handles.process_gates_log,'Value',1); +0680 set(gui.radio_handles.process_gates_lin,'Value',0); +0681 set(gui.radio_handles.process_gates_none,'Value',0); +0682 set(gui.edit_handles.process_Nechoes,'Enable','on'); +0683 +0684 case 'lin' +0685 set(gui.radio_handles.process_gates_log,'Value',0); +0686 set(gui.radio_handles.process_gates_lin,'Value',1); +0687 set(gui.radio_handles.process_gates_none,'Value',0); +0688 set(gui.edit_handles.process_Nechoes,'Enable','on'); +0689 +0690 case 'raw' +0691 set(gui.radio_handles.process_gates_log,'Value',0); +0692 set(gui.radio_handles.process_gates_lin,'Value',0); +0693 set(gui.radio_handles.process_gates_none,'Value',1); +0694 set(gui.edit_handles.process_Nechoes,'Enable','off'); +0695 +0696 end +0697 +0698 end +0699 +0700 function gui = updateNormalize(gui,norm) +0701 +0702 switch norm +0703 case 0 +0704 set(gui.radio_handles.process_normalize_on,'Enable','on','Value',0); +0705 set(gui.radio_handles.process_normalize_off,'Enable','on','Value',1); +0706 +0707 case 1 +0708 set(gui.radio_handles.process_normalize_on,'Enable','on','Value',1); +0709 set(gui.radio_handles.process_normalize_off,'Enable','on','Value',0); +0710 end +0711 +0712 end +0713 +0714 function gui = updateTimescale(gui,timescale) +0715 +0716 switch timescale +0717 +0718 case 's' +0719 set(gui.radio_handles.process_timescale_s,'Enable','on','Value',1); +0720 set(gui.radio_handles.process_timescale_ms,'Enable','on','Value',0); +0721 set(gui.text_handles.invstd_RTDtimes,'String','RTD - min [s] | max [s] | # / dec',... +0722 'FontSize',10); +0723 set(gui.text_handles.petro_Tbulk,'String','Tbulk [s] | Tdiff [s]'); +0724 set(gui.text_handles.petro_rho,'String',[char(hex2dec('03C1')),' [µm/s] | geom ']); +0725 +0726 case 'ms' +0727 set(gui.radio_handles.process_timescale_s,'Enable','on','Value',0); +0728 set(gui.radio_handles.process_timescale_ms,'Enable','on','Value',1); +0729 set(gui.text_handles.invstd_RTDtimes,'String','RTD - min [ms] | max [ms] | # / dec',... +0730 'FontSize',9); +0731 set(gui.text_handles.petro_Tbulk,'String','Tbulk [ms] | Tdiff [ms]'); +0732 set(gui.text_handles.petro_rho,'String',[char(hex2dec('03C1')),' [µm/s] | geom ']); +0733 end +0734 +0735 end +0736 +0737 function gui = updateInvstdTime(gui,invtype,time,Ntime) +0738 +0739 switch invtype +0740 +0741 case {'mono','free'} +0742 set(gui.edit_handles.invstd_time_min,'Enable','off'); +0743 set(gui.edit_handles.invstd_time_max,'Enable','off'); +0744 set(gui.edit_handles.invstd_Ntime,'Enable','off'); +0745 +0746 case {'LU','NNLS','MUMO'} +0747 set(gui.edit_handles.invstd_time_min,'Enable','on','String',num2str(time(1))); +0748 set(gui.edit_handles.invstd_time_max,'Enable','on','String',num2str(time(2))); +0749 set(gui.edit_handles.invstd_Ntime,'Enable','on','String',num2str(Ntime)); +0750 end +0751 +0752 end +0753 +0754 function gui = updateInvjointRadii(gui,invtype,radii,Nradii) +0755 +0756 switch invtype +0757 case {'fixed','shape','off'} +0758 set(gui.edit_handles.invjoint_radii_min,'Enable','off'); +0759 set(gui.edit_handles.invjoint_radii_max,'Enable','off'); +0760 set(gui.edit_handles.invjoint_Nradii,'Enable','off'); +0761 +0762 case {'free'} +0763 set(gui.edit_handles.invjoint_radii_min,'Enable','on','String',num2str(radii(1))); +0764 set(gui.edit_handles.invjoint_radii_max,'Enable','on','String',num2str(radii(2))); +0765 set(gui.edit_handles.invjoint_Nradii,'Enable','on','String',num2str(Nradii)); +0766 end +0767 +0768 end +0769 +0770 function gui = updateLambda(gui,regtype,lambda,lambdaR,NlambdaR) +0771 +0772 switch regtype +0773 case 'none' +0774 set(gui.edit_handles.invstd_lambda_min,'Enable','off'); +0775 set(gui.edit_handles.invstd_lambda_max,'Enable','off'); +0776 set(gui.edit_handles.invstd_NlambdaR,'Enable','off'); +0777 gui.plots.DistPanel.TabTitles = {'RTD','PSD','PSD (joint)'}; +0778 +0779 case 'manual' +0780 set(gui.edit_handles.invstd_lambda_min,'Enable','on','String',num2str(lambda)); +0781 set(gui.edit_handles.invstd_lambda_max,'Enable','off'); +0782 set(gui.edit_handles.invstd_NlambdaR,'Enable','off'); +0783 gui.plots.DistPanel.TabTitles = {'RTD','PSD','PSD (joint)'}; +0784 +0785 case 'auto' +0786 set(gui.edit_handles.invstd_lambda_min,'Enable','off','String',num2str(lambda)); +0787 set(gui.edit_handles.invstd_lambda_max,'Enable','off'); +0788 set(gui.edit_handles.invstd_NlambdaR,'Enable','off'); +0789 gui.plots.DistPanel.TabTitles = {'RTD','PSD','PSD (joint)'}; +0790 +0791 case 'lcurve' +0792 set(gui.edit_handles.invstd_lambda_min,'Enable','on','String',num2str(lambdaR(1))); +0793 set(gui.edit_handles.invstd_lambda_max,'Enable','on','String',num2str(lambdaR(2))); +0794 set(gui.edit_handles.invstd_NlambdaR,'Enable','on','String',num2str(NlambdaR)); +0795 gui.plots.DistPanel.TabTitles = {'L-CURVE','RMS','PSD (joint)'}; +0796 +0797 case {'gcv_tikh','gcv_trunc','gcv_damp','discrep'} +0798 set(gui.edit_handles.invstd_lambda_min,'Enable','off','String',num2str(lambda)); +0799 set(gui.edit_handles.invstd_lambda_max,'Enable','off'); +0800 set(gui.edit_handles.invstd_NlambdaR,'Enable','off'); +0801 gui.plots.DistPanel.TabTitles = {'RTD','PSD','PSD (joint)'}; +0802 end +0803 +0804 end +0805 +0806 function gui = updateLambdaJoint(gui,regtype,lambda,lambdaR,NlambdaR,regtypestd) +0807 +0808 switch regtype +0809 case 'none' +0810 switch regtypestd +0811 case 'lcurve' +0812 set(gui.edit_handles.invjoint_lambda_min,'Enable','off'); +0813 set(gui.edit_handles.invjoint_lambda_max,'Enable','off'); +0814 set(gui.edit_handles.invjoint_NlambdaR,'Enable','off'); +0815 gui.plots.DistPanel.TabTitles = {'L-CURVE','RMS','PSD (joint)'}; +0816 +0817 otherwise +0818 set(gui.edit_handles.invjoint_lambda_min,'Enable','off'); +0819 set(gui.edit_handles.invjoint_lambda_max,'Enable','off'); +0820 set(gui.edit_handles.invjoint_NlambdaR,'Enable','off'); +0821 gui.plots.DistPanel.TabTitles = {'RTD','PSD','PSD (joint)'}; +0822 end +0823 +0824 case 'manual' +0825 switch regtypestd +0826 case 'lcurve' +0827 set(gui.edit_handles.invjoint_lambda_min,'Enable','on','String',num2str(lambda)); +0828 set(gui.edit_handles.invjoint_lambda_max,'Enable','off'); +0829 set(gui.edit_handles.invjoint_NlambdaR,'Enable','off'); +0830 gui.plots.DistPanel.TabTitles = {'L-CURVE','RMS','PSD (joint)'}; +0831 +0832 otherwise +0833 set(gui.edit_handles.invjoint_lambda_min,'Enable','on','String',num2str(lambda)); +0834 set(gui.edit_handles.invjoint_lambda_max,'Enable','off'); +0835 set(gui.edit_handles.invjoint_NlambdaR,'Enable','off'); +0836 gui.plots.DistPanel.TabTitles = {'RTD','PSD','PSD (joint)'}; +0837 end +0838 +0839 case 'lcurve' +0840 set(gui.edit_handles.invjoint_lambda_min,'Enable','on','String',num2str(lambdaR(1))); +0841 set(gui.edit_handles.invjoint_lambda_max,'Enable','on','String',num2str(lambdaR(2))); +0842 set(gui.edit_handles.invjoint_NlambdaR,'Enable','on','String',num2str(NlambdaR)); +0843 gui.plots.DistPanel.TabTitles = {'L-CURVE','RMS','PSD (joint)'}; +0844 end +0845 +0846 end +0847 +0848 function gui = updateLorder(gui,invtype,Lorder) +0849 +0850 switch invtype +0851 case {'mono','free','MUMO'} +0852 set(gui.radio_handles.invstd_Lorder0,'Enable','off'); +0853 set(gui.radio_handles.invstd_Lorder1,'Enable','off'); +0854 set(gui.radio_handles.invstd_Lorder2,'Enable','off'); +0855 +0856 case {'LU','NNLS'} +0857 set(gui.radio_handles.invstd_Lorder0,'Enable','on'); +0858 set(gui.radio_handles.invstd_Lorder1,'Enable','on'); +0859 set(gui.radio_handles.invstd_Lorder2,'Enable','on'); +0860 +0861 switch Lorder +0862 case 0 +0863 set(gui.radio_handles.invstd_Lorder0,'Value',1); +0864 set(gui.radio_handles.invstd_Lorder1,'Value',0); +0865 set(gui.radio_handles.invstd_Lorder2,'Value',0); +0866 +0867 case 1 +0868 set(gui.radio_handles.invstd_Lorder0,'Value',0); +0869 set(gui.radio_handles.invstd_Lorder1,'Value',1); +0870 set(gui.radio_handles.invstd_Lorder2,'Value',0); +0871 +0872 case 2 +0873 set(gui.radio_handles.invstd_Lorder0,'Value',0); +0874 set(gui.radio_handles.invstd_Lorder1,'Value',0); +0875 set(gui.radio_handles.invstd_Lorder2,'Value',1); +0876 end +0877 end +0878 +0879 end +0880 +0881 function gui = updateLorderJoint(gui,invtype,Lorder) +0882 +0883 switch invtype +0884 case {'fixed','shape','off'} +0885 set(gui.radio_handles.invjoint_Lorder0,'Enable','off'); +0886 set(gui.radio_handles.invjoint_Lorder1,'Enable','off'); +0887 set(gui.radio_handles.invjoint_Lorder2,'Enable','off'); +0888 +0889 case 'free' +0890 set(gui.radio_handles.invjoint_Lorder0,'Enable','on'); +0891 set(gui.radio_handles.invjoint_Lorder1,'Enable','on'); +0892 set(gui.radio_handles.invjoint_Lorder2,'Enable','on'); +0893 +0894 switch Lorder +0895 case 0 +0896 set(gui.radio_handles.invjoint_Lorder0,'Value',1); +0897 set(gui.radio_handles.invjoint_Lorder1,'Value',0); +0898 set(gui.radio_handles.invjoint_Lorder2,'Value',0); +0899 +0900 case 1 +0901 set(gui.radio_handles.invjoint_Lorder0,'Value',0); +0902 set(gui.radio_handles.invjoint_Lorder1,'Value',1); +0903 set(gui.radio_handles.invjoint_Lorder2,'Value',0); +0904 +0905 case 2 +0906 set(gui.radio_handles.invjoint_Lorder0,'Value',0); +0907 set(gui.radio_handles.invjoint_Lorder1,'Value',0); +0908 set(gui.radio_handles.invjoint_Lorder2,'Value',1); +0909 end +0910 end +0911 +0912 end +0913 +0914 function gui = updateParams(gui,invtype,p) +0915 +0916 switch invtype +0917 case {'mono','free'} +0918 set(gui.edit_handles.param_CBW,'Enable','off','String',num2str(p.CBWcutoff)); +0919 set(gui.edit_handles.param_BVI,'Enable','off','String',num2str(p.BVIcutoff)); +0920 set(gui.edit_handles.param_rho,'Enable','on','String',num2str(p.rho)); +0921 set(gui.edit_handles.param_geom,'Enable','on','String',num2str(p.a)); +0922 +0923 case {'LU','NNLS','MUMO'} +0924 set(gui.edit_handles.param_CBW,'Enable','on','String',num2str(p.CBWcutoff)); +0925 set(gui.edit_handles.param_BVI,'Enable','on','String',num2str(p.BVIcutoff)); +0926 set(gui.edit_handles.param_rho,'Enable','on','String',num2str(p.rho)); +0927 set(gui.edit_handles.param_geom,'Enable','on','String',num2str(p.a)); +0928 +0929 end +0930 set(gui.edit_handles.param_calibVol,'Enable','on','String',num2str(p.calibVol)); +0931 set(gui.edit_handles.param_calibAmp,'Enable','on','String',num2str(p.calibAmp)); +0932 set(gui.edit_handles.param_sampVol,'Enable','on','String',num2str(p.sampVol)); +0933 +0934 end +0935 +0936 %------------- END OF CODE -------------- +0937 +0938 %% License: +0939 % MIT License +0940 % +0941 % Copyright (c) 2018 Thomas Hiller +0942 % +0943 % Permission is hereby granted, free of charge, to any person obtaining a copy +0944 % of this software and associated documentation files (the "Software"), to deal +0945 % in the Software without restriction, including without limitation the rights +0946 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0947 % copies of the Software, and to permit persons to whom the Software is +0948 % furnished to do so, subject to the following conditions: +0949 % +0950 % The above copyright notice and this permission notice shall be included in all +0951 % copies or substantial portions of the Software. 0952 % -0953 % The above copyright notice and this permission notice shall be included in all -0954 % copies or substantial portions of the Software. -0955 % -0956 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0957 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0958 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0959 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0960 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0961 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0962 % SOFTWARE. +0953 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0954 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0955 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0956 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0957 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0958 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0959 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/NUCLEUSmod/NUCLEUSmod.html b/doc/nucleus/NUCLEUSmod/NUCLEUSmod.html index 862a4be..aa903e2 100644 --- a/doc/nucleus/NUCLEUSmod/NUCLEUSmod.html +++ b/doc/nucleus/NUCLEUSmod/NUCLEUSmod.html @@ -117,8 +117,8 @@

    SOURCE CODE ^if ~isempty(h0); close(h0); end 0042 0043 %% GUI 'header' info and defaults -0044 myui.version = '0.1.13'; -0045 myui.date = '11.08.2022'; +0044 myui.version = '0.1.14'; +0045 myui.date = '27.09.2023'; 0046 myui.author = {'Stephan Costabel','Thomas Hiller'}; 0047 myui.email = 'thomas.hiller[at]bgr.de'; 0048 myui.fontsize = 10; diff --git a/doc/nucleus/callbacks/listboxes/onListboxData.html b/doc/nucleus/callbacks/listboxes/onListboxData.html index 35d90c8..42d9183 100644 --- a/doc/nucleus/callbacks/listboxes/onListboxData.html +++ b/doc/nucleus/callbacks/listboxes/onListboxData.html @@ -67,7 +67,7 @@

    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

    This function calls: +
  • NUCLEUSinv_updateInterface updates all GUI elements
  • onPopupInvstdType selects the inversion method for the standard inversion
  • onPushRun handles the callbacks to all RUN push buttons in both GUIs and
  • FixedTimeView is an extra subGUI to fix certain relaxation times during
  • PhaseView is an extra subGUI to visualize the phase of a T2 signal
  • clearSingleAxis clears an individual axis
  • processNMRDataControl prepares simple NMR raw data processing
  • removeInversionFields deletes all inversion result fields from NUCLEUSinv
  • showFitStatistics shows an extra fit statistics figure (for T2 data)
  • updateInfo updates the information shown in all information list boxes
  • updatePlotsDistribution plots the RTD and PSD curves into NUCLEUSinv
  • updatePlotsJointInversion plots the joint-inversion results in NUCLEUSinv
  • updatePlotsLcurve plots the results of the L-curve calculation
  • updatePlotsSignal plots the raw and processed NMR signals in NUCLEUSinv
    • This function is called by: @@ -147,165 +147,176 @@

    SOURCE CODE ^'data',data); -0073 -0074 % update interface and plot axes -0075 NUCLEUSinv_updateInterface; -0076 updatePlotsSignal; -0077 updateInfo(gui.plots.SignalPanel); -0078 gui = getappdata(fig,'gui'); -0079 if isfield(data,'results') -0080 if isfield(data.results,'invstd') -0081 updatePlotsDistribution; -0082 end -0083 if isfield(data.results,'invjoint') -0084 updatePlotsJointInversion; -0085 end -0086 if isfield(data.results,'lcurve') -0087 updatePlotsLcurve; -0088 end -0089 end -0090 else -0091 % remove temporary data fields -0092 data = removeInversionFields(data); -0093 -0094 % set format and T1/T2 dependent GUI elements -0095 switch data.import.NMR.data{id}.flag -0096 case 'T1' -0097 data.process.gatetype = 'raw'; -0098 data.process.start = 1; -0099 case 'T2' -0100 switch data.import.fileformat -0101 case {'dart','excel','field','helios','mouse','NMRMOD'} -0102 data.process.gatetype = 'raw'; -0103 data.process.start = 1; -0104 otherwise -0105 % standard T2 -0106 data.process.gatetype = 'log'; -0107 data.process.start = 1; -0108 end -0109 otherwise -0110 disp('onListboxData: Something is utterly wrong.') -0111 end -0112 -0113 % take all echoes -0114 data.process.end = length(data.import.NMR.data{id}.signal); -0115 -0116 % --- -0117 % special treatments -0118 % there is no volume or porosity -0119 data.param.sampVol = 1; -0120 if isfield(data.import,'BGR') -0121 data.invstd.porosity = data.import.BGR.porosity; -0122 else -0123 data.invstd.porosity = 1; -0124 end -0125 if isfield(data.import,'LIAG') -0126 data.param.sampVol = data.import.LIAG.sampleVol(id); -0127 if ~isempty(strfind(data.import.NMR.filesShort{id},' - calibration')) -0128 data.param.calibVol = data.import.LIAG.sampleVol(id); -0129 % update the GUI data -0130 setappdata(fig,'data',data); -0131 % set mono fit as default -0132 set(gui.popup_handles.invstd_InvType,'Value',1); -0133 onPopupInvstdType(gui.popup_handles.invstd_InvType); -0134 data = getappdata(fig,'data'); -0135 end -0136 if isempty(strfind(data.import.NMR.filesShort{id},' - calibration')) -0137 data.invstd.Tbulk = data.import.LIAG.Tbulk; -0138 % update the GUI data -0139 setappdata(fig,'data',data); -0140 % set mono fit as default -0141 set(gui.popup_handles.invstd_InvType,'Value',3); -0142 onPopupInvstdType(gui.popup_handles.invstd_InvType); -0143 data = getappdata(fig,'data'); -0144 end -0145 else -0146 data.param.sampVol = 1; -0147 end -0148 if isfield(data.import,'NMRMOD') -0149 data.param.rho = data.import.NMR.para{id}.rho*1e6; -0150 data.invstd.Tbulk = data.import.NMR.para{id}.Tbulk; -0151 data.invstd.Tdiff = data.import.NMR.para{id}.Tdiff; -0152 data.invstd.porosity = data.import.NMR.para{id}.porosity; -0153 end -0154 % --- -0155 -0156 % update the figure data -0157 setappdata(fig,'data',data); -0158 -0159 % process the NMR data -0160 processNMRDataControl(fig,id); -0161 % update interface -0162 NUCLEUSinv_updateInterface; -0163 -0164 % update the data plot axes -0165 updatePlotsSignal; -0166 % update the info fields -0167 updateInfo(gui.plots.SignalPanel); -0168 gui = getappdata(fig,'gui'); -0169 -0170 % clear inversion axes -0171 clearSingleAxis(gui.axes_handles.rtd); -0172 clearSingleAxis(gui.axes_handles.psd); -0173 end -0174 -0175 % set focus on data -0176 % set(gui.plots.SignalPanel,'Selection',1); -0177 % set(gui.plots.DistPanel,'Selection',1); -0178 -0179 % reset all RUN buttons -0180 set(gui.push_handles.invstd_run,'String','<HTML><u>R</u>UN',... -0181 'BackgroundColor','g','Enable','on','Callback',@onPushRun); -0182 set(gui.push_handles.invjoint_run,'String','<HTML><u>R</u>UN',... -0183 'BackgroundColor','g','Enable','on','Callback',@onPushRun); -0184 -0185 % if the Fit Statistics window is open update it -0186 if ~isempty(findobj('Tag','FITSTATS')) -0187 showFitStatistics; -0188 end -0189 % if the PhaseView window is open update it -0190 if ~isempty(findobj('Tag','PHASEVIEW')) -0191 PhaseView(gui.menu.extra_phaseview); -0192 end -0193 else -0194 helpdlg({'onListboxData:','Only choose one data set at a time.'},... -0195 'too many data'); -0196 end -0197 else -0198 helpdlg('Nothing to do because there is no data loaded!',... -0199 'onListboxData: Load NMR data first.'); -0200 end -0201 -0202 % update the figure data -0203 setappdata(fig,'gui',gui); -0204 -0205 end -0206 -0207 %------------- END OF CODE -------------- -0208 -0209 %% License: -0210 % MIT License -0211 % -0212 % Copyright (c) 2018 Thomas Hiller -0213 % -0214 % Permission is hereby granted, free of charge, to any person obtaining a copy -0215 % of this software and associated documentation files (the "Software"), to deal -0216 % in the Software without restriction, including without limitation the rights -0217 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0218 % copies of the Software, and to permit persons to whom the Software is -0219 % furnished to do so, subject to the following conditions: -0220 % -0221 % The above copyright notice and this permission notice shall be included in all -0222 % copies or substantial portions of the Software. -0223 % -0224 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0225 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0226 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0227 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0228 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0229 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0230 % SOFTWARE. +0072 +0073 % if "mono" or "free" inversion is chossen update the internal +0074 % fixed relaxation times field +0075 if strcmp(data.invstd.invtype,'mono') ||... +0076 strcmp(data.invstd.invtype,'free') +0077 data.invstd.Tfixed_val = [data.results.invstd.T zeros(1,5-data.invstd.freeDT)]; +0078 end +0079 setappdata(fig,'data',data); +0080 +0081 % update interface and plot axes +0082 NUCLEUSinv_updateInterface; +0083 updatePlotsSignal; +0084 updateInfo(gui.plots.SignalPanel); +0085 gui = getappdata(fig,'gui'); +0086 if isfield(data,'results') +0087 if isfield(data.results,'invstd') +0088 updatePlotsDistribution; +0089 end +0090 if isfield(data.results,'invjoint') +0091 updatePlotsJointInversion; +0092 end +0093 if isfield(data.results,'lcurve') +0094 updatePlotsLcurve; +0095 end +0096 end +0097 else +0098 % remove temporary data fields +0099 data = removeInversionFields(data); +0100 +0101 % set format and T1/T2 dependent GUI elements +0102 switch data.import.NMR.data{id}.flag +0103 case 'T1' +0104 data.process.gatetype = 'raw'; +0105 data.process.start = 1; +0106 case 'T2' +0107 switch data.import.fileformat +0108 case {'dart','excel','field','helios','mouse','NMRMOD'} +0109 data.process.gatetype = 'raw'; +0110 data.process.start = 1; +0111 otherwise +0112 % standard T2 +0113 data.process.gatetype = 'log'; +0114 data.process.start = 1; +0115 end +0116 otherwise +0117 disp('onListboxData: Something is utterly wrong.') +0118 end +0119 +0120 % take all echoes +0121 data.process.end = length(data.import.NMR.data{id}.signal); +0122 +0123 % --- +0124 % special treatments +0125 % there is no volume or porosity +0126 data.param.sampVol = 1; +0127 if isfield(data.import,'BGR') +0128 data.invstd.porosity = data.import.BGR.porosity; +0129 else +0130 data.invstd.porosity = 1; +0131 end +0132 if isfield(data.import,'LIAG') +0133 data.param.sampVol = data.import.LIAG.sampleVol(id); +0134 if ~isempty(strfind(data.import.NMR.filesShort{id},' - calibration')) +0135 data.param.calibVol = data.import.LIAG.sampleVol(id); +0136 % update the GUI data +0137 setappdata(fig,'data',data); +0138 % set mono fit as default +0139 set(gui.popup_handles.invstd_InvType,'Value',1); +0140 onPopupInvstdType(gui.popup_handles.invstd_InvType); +0141 data = getappdata(fig,'data'); +0142 end +0143 if isempty(strfind(data.import.NMR.filesShort{id},' - calibration')) +0144 data.invstd.Tbulk = data.import.LIAG.Tbulk; +0145 % update the GUI data +0146 setappdata(fig,'data',data); +0147 % set mono fit as default +0148 set(gui.popup_handles.invstd_InvType,'Value',3); +0149 onPopupInvstdType(gui.popup_handles.invstd_InvType); +0150 data = getappdata(fig,'data'); +0151 end +0152 else +0153 data.param.sampVol = 1; +0154 end +0155 if isfield(data.import,'NMRMOD') +0156 data.param.rho = data.import.NMR.para{id}.rho*1e6; +0157 data.invstd.Tbulk = data.import.NMR.para{id}.Tbulk; +0158 data.invstd.Tdiff = data.import.NMR.para{id}.Tdiff; +0159 data.invstd.porosity = data.import.NMR.para{id}.porosity; +0160 end +0161 % --- +0162 +0163 % update the figure data +0164 setappdata(fig,'data',data); +0165 +0166 % process the NMR data +0167 processNMRDataControl(fig,id); +0168 % update interface +0169 NUCLEUSinv_updateInterface; +0170 +0171 % update the data plot axes +0172 updatePlotsSignal; +0173 % update the info fields +0174 updateInfo(gui.plots.SignalPanel); +0175 gui = getappdata(fig,'gui'); +0176 +0177 % clear inversion axes +0178 clearSingleAxis(gui.axes_handles.rtd); +0179 clearSingleAxis(gui.axes_handles.psd); +0180 end +0181 +0182 % set focus on data +0183 % set(gui.plots.SignalPanel,'Selection',1); +0184 % set(gui.plots.DistPanel,'Selection',1); +0185 +0186 % reset all RUN buttons +0187 set(gui.push_handles.invstd_run,'String','<HTML><u>R</u>UN',... +0188 'BackgroundColor','g','Enable','on','Callback',@onPushRun); +0189 set(gui.push_handles.invjoint_run,'String','<HTML><u>R</u>UN',... +0190 'BackgroundColor','g','Enable','on','Callback',@onPushRun); +0191 +0192 % if the Fit Statistics window is open update it +0193 if ~isempty(findobj('Tag','FITSTATS')) +0194 showFitStatistics; +0195 end +0196 % if the PhaseView window is open update it +0197 if ~isempty(findobj('Tag','PHASEVIEW')) +0198 PhaseView(gui.menu.extra_phaseview); +0199 end +0200 % if the FixedTimeView window is open update it +0201 if ~isempty(findobj('Tag','FIXEDTIMEVIEW')) +0202 FixedTimeView(gui.menu.extra_fixedtime); +0203 end +0204 else +0205 helpdlg({'onListboxData:','Only choose one data set at a time.'},... +0206 'too many data'); +0207 end +0208 else +0209 helpdlg('Nothing to do because there is no data loaded!',... +0210 'onListboxData: Load NMR data first.'); +0211 end +0212 +0213 % update the figure data +0214 setappdata(fig,'gui',gui); +0215 +0216 end +0217 +0218 %------------- END OF CODE -------------- +0219 +0220 %% License: +0221 % MIT License +0222 % +0223 % Copyright (c) 2018 Thomas Hiller +0224 % +0225 % Permission is hereby granted, free of charge, to any person obtaining a copy +0226 % of this software and associated documentation files (the "Software"), to deal +0227 % in the Software without restriction, including without limitation the rights +0228 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0229 % copies of the Software, and to permit persons to whom the Software is +0230 % furnished to do so, subject to the following conditions: +0231 % +0232 % The above copyright notice and this permission notice shall be included in all +0233 % copies or substantial portions of the Software. +0234 % +0235 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0236 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0237 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0238 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0239 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0240 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0241 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/callbacks/menus/onMenuExpert.html b/doc/nucleus/callbacks/menus/onMenuExpert.html index 982a24b..3b2a2f2 100644 --- a/doc/nucleus/callbacks/menus/onMenuExpert.html +++ b/doc/nucleus/callbacks/menus/onMenuExpert.html @@ -132,94 +132,108 @@

    SOURCE CODE ^% update GUI data 0056 setappdata(fig,'data',data); 0057 setappdata(fig,'gui',gui); -0058 -0059 % deactivate solver menu and set to default -0060 onMenuSolver(gui.menu.extra_solver_lsqnonneg); -0061 % get changed GUI data -0062 data = getappdata(fig,'data'); -0063 set(gui.menu.extra_solver,'Enable','off'); -0064 -0065 % update GUI data -0066 setappdata(fig,'data',data); -0067 setappdata(fig,'gui',gui); -0068 -0069 % deactivate joint inversion panels -0070 set(gui.menu.extra_joint,'Checked','on'); -0071 onMenuJointInversion(gui.menu.extra_joint); +0058 +0059 % dectivate FixedTime View GUI +0060 data.invstd.Tfixed_bool = zeros(1,5); +0061 data.invstd.Tfixed_val = zeros(1,5); +0062 setappdata(fig,'data',data); +0063 % check if the figure is already open +0064 fig_fixedtime = findobj('Tag','FIXEDTIMEVIEW'); +0065 if ~isempty(fig_fixedtime) +0066 delete(fig_fixedtime); +0067 end +0068 set(gui.menu.extra_fixedtime,'Enable','off'); +0069 +0070 % deactivate solver menu and set to default +0071 onMenuSolver(gui.menu.extra_solver_lsqnonneg); 0072 % get changed GUI data 0073 data = getappdata(fig,'data'); -0074 INVdata = getappdata(fig,'INVdata'); -0075 % default std inversion settings -0076 data.invstd.invtype = 'NNLS'; -0077 data.invstd.regtype = 'manual'; -0078 data.invstd.lambda = 1; -0079 % deactivate joint inversion menu -0080 set(gui.menu.extra_joint,'Enable','off'); -0081 -0082 set(gui.menu.extra_graphics_amp,'Enable','off'); -0083 set(gui.menu.extra_graphics_amp2,'Enable','off'); -0084 set(gui.menu.extra_graphics_rtd,'Enable','off'); -0085 -0086 case 'off' % it it's off, switch it on -0087 data.info.ExpertMode = 'on'; -0088 % menu entry -0089 set(gui.menu.extra_expert,'Checked','on'); -0090 -0091 % activate solver menu if optimization toolbox is available -0092 switch data.info.has_optim -0093 case 'on' -0094 set(gui.menu.extra_solver,'Enable','on'); -0095 case 'off' -0096 set(gui.menu.extra_solver,'Enable','off'); -0097 end -0098 -0099 % activate joint inversion menu -0100 set(gui.menu.extra_joint,'Enable','on'); -0101 -0102 set(gui.menu.extra_graphics_amp,'Enable','on'); -0103 set(gui.menu.extra_graphics_amp2,'Enable','on'); -0104 set(gui.menu.extra_graphics_rtd,'Enable','on'); -0105 end -0106 -0107 % update GUI data -0108 setappdata(fig,'data',data); -0109 setappdata(fig,'gui',gui); -0110 % update ini-file -0111 gui.myui.inidata.expertmode = data.info.ExpertMode; -0112 gui = makeINIfile(gui,'update'); -0113 % update interface -0114 NUCLEUSinv_updateInterface; -0115 % update status information -0116 updateStatusInformation(fig); -0117 updateToolTips; -0118 onFigureSizeChange(fig); -0119 -0120 end -0121 -0122 %------------- END OF CODE -------------- -0123 -0124 %% License: -0125 % MIT License -0126 % -0127 % Copyright (c) 2018 Thomas Hiller -0128 % -0129 % Permission is hereby granted, free of charge, to any person obtaining a copy -0130 % of this software and associated documentation files (the "Software"), to deal -0131 % in the Software without restriction, including without limitation the rights -0132 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0133 % copies of the Software, and to permit persons to whom the Software is -0134 % furnished to do so, subject to the following conditions: -0135 % -0136 % The above copyright notice and this permission notice shall be included in all -0137 % copies or substantial portions of the Software. -0138 % -0139 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0140 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0141 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0142 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0143 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0144 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0145 % SOFTWARE. +0074 set(gui.menu.extra_solver,'Enable','off'); +0075 +0076 % update GUI data +0077 setappdata(fig,'data',data); +0078 setappdata(fig,'gui',gui); +0079 +0080 % deactivate joint inversion panels +0081 set(gui.menu.extra_joint,'Checked','on'); +0082 onMenuJointInversion(gui.menu.extra_joint); +0083 % get changed GUI data +0084 data = getappdata(fig,'data'); +0085 INVdata = getappdata(fig,'INVdata'); +0086 % default std inversion settings +0087 data.invstd.invtype = 'NNLS'; +0088 data.invstd.regtype = 'manual'; +0089 data.invstd.lambda = 1; +0090 % deactivate joint inversion menu +0091 set(gui.menu.extra_joint,'Enable','off'); +0092 +0093 set(gui.menu.extra_graphics_amp,'Enable','off'); +0094 set(gui.menu.extra_graphics_amp2,'Enable','off'); +0095 set(gui.menu.extra_graphics_rtd,'Enable','off'); +0096 +0097 case 'off' % it it's off, switch it on +0098 data.info.ExpertMode = 'on'; +0099 % menu entry +0100 set(gui.menu.extra_expert,'Checked','on'); +0101 +0102 % activate FixedTime View GUI +0103 set(gui.menu.extra_fixedtime,'Enable','on'); +0104 +0105 % activate solver menu if optimization toolbox is available +0106 switch data.info.has_optim +0107 case 'on' +0108 set(gui.menu.extra_solver,'Enable','on'); +0109 case 'off' +0110 set(gui.menu.extra_solver,'Enable','off'); +0111 end +0112 +0113 % activate joint inversion menu +0114 set(gui.menu.extra_joint,'Enable','on'); +0115 +0116 set(gui.menu.extra_graphics_amp,'Enable','on'); +0117 set(gui.menu.extra_graphics_amp2,'Enable','on'); +0118 set(gui.menu.extra_graphics_rtd,'Enable','on'); +0119 end +0120 +0121 % update GUI data +0122 setappdata(fig,'data',data); +0123 setappdata(fig,'gui',gui); +0124 % update ini-file +0125 gui.myui.inidata.expertmode = data.info.ExpertMode; +0126 gui = makeINIfile(gui,'update'); +0127 % update interface +0128 NUCLEUSinv_updateInterface; +0129 % update status information +0130 updateStatusInformation(fig); +0131 updateToolTips; +0132 onFigureSizeChange(fig); +0133 +0134 end +0135 +0136 %------------- END OF CODE -------------- +0137 +0138 %% License: +0139 % MIT License +0140 % +0141 % Copyright (c) 2018 Thomas Hiller +0142 % +0143 % Permission is hereby granted, free of charge, to any person obtaining a copy +0144 % of this software and associated documentation files (the "Software"), to deal +0145 % in the Software without restriction, including without limitation the rights +0146 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0147 % copies of the Software, and to permit persons to whom the Software is +0148 % furnished to do so, subject to the following conditions: +0149 % +0150 % The above copyright notice and this permission notice shall be included in all +0151 % copies or substantial portions of the Software. +0152 % +0153 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0154 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0155 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0156 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0157 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0158 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0159 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/callbacks/menus/onMenuExportData.html b/doc/nucleus/callbacks/menus/onMenuExportData.html index c1fb58a..6f73fec 100644 --- a/doc/nucleus/callbacks/menus/onMenuExportData.html +++ b/doc/nucleus/callbacks/menus/onMenuExportData.html @@ -128,57 +128,59 @@

    SOURCE CODE ^case 'LIAG archive' 0059 exportData(fig_tag,'LIAG'); 0060 case 'LIAG CSV T2' -0061 exportData(fig_tag,'LIAGcsvT2'); -0062 end -0063 % update the "last export" value within the ini-file -0064 gui = getappdata(fig,'gui'); -0065 gui.myui.inidata.lastexport = label; -0066 setappdata(fig,'gui',gui); -0067 gui = makeINIfile(gui,'update'); -0068 % and the menu entry itself -0069 set(gui.menu.file_export_lastexport,'Label',label,... -0070 'Callback',@onMenuExportData); -0071 setappdata(fig,'gui',gui); -0072 -0073 case 'MOD' -0074 switch label -0075 case 'NUCLEUSmod' -0076 exportData(fig_tag,'mat'); -0077 case 'XLS file' -0078 exportData(fig_tag,'xls'); -0079 case 'CSV file' -0080 exportData(fig_tag,'csv'); -0081 case 'DAT files' -0082 exportData(fig_tag,'dat'); -0083 end -0084 end -0085 +0061 exportData(fig_tag,'LIAGcsvT2'); +0062 case 'BGR repository' +0063 exportData(fig_tag,'BGR_repos'); +0064 end +0065 % update the "last export" value within the ini-file +0066 gui = getappdata(fig,'gui'); +0067 gui.myui.inidata.lastexport = label; +0068 setappdata(fig,'gui',gui); +0069 gui = makeINIfile(gui,'update'); +0070 % and the menu entry itself +0071 set(gui.menu.file_export_lastexport,'Label',label,... +0072 'Callback',@onMenuExportData); +0073 setappdata(fig,'gui',gui); +0074 +0075 case 'MOD' +0076 switch label +0077 case 'NUCLEUSmod' +0078 exportData(fig_tag,'mat'); +0079 case 'XLS file' +0080 exportData(fig_tag,'xls'); +0081 case 'CSV file' +0082 exportData(fig_tag,'csv'); +0083 case 'DAT files' +0084 exportData(fig_tag,'dat'); +0085 end 0086 end 0087 -0088 %------------- END OF CODE -------------- +0088 end 0089 -0090 %% License: -0091 % MIT License -0092 % -0093 % Copyright (c) 2018 Thomas Hiller +0090 %------------- END OF CODE -------------- +0091 +0092 %% License: +0093 % MIT License 0094 % -0095 % Permission is hereby granted, free of charge, to any person obtaining a copy -0096 % of this software and associated documentation files (the "Software"), to deal -0097 % in the Software without restriction, including without limitation the rights -0098 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0099 % copies of the Software, and to permit persons to whom the Software is -0100 % furnished to do so, subject to the following conditions: -0101 % -0102 % The above copyright notice and this permission notice shall be included in all -0103 % copies or substantial portions of the Software. -0104 % -0105 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0106 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0107 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0108 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0109 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0110 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0111 % SOFTWARE. +0095 % Copyright (c) 2018 Thomas Hiller +0096 % +0097 % Permission is hereby granted, free of charge, to any person obtaining a copy +0098 % of this software and associated documentation files (the "Software"), to deal +0099 % in the Software without restriction, including without limitation the rights +0100 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0101 % copies of the Software, and to permit persons to whom the Software is +0102 % furnished to do so, subject to the following conditions: +0103 % +0104 % The above copyright notice and this permission notice shall be included in all +0105 % copies or substantial portions of the Software. +0106 % +0107 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0108 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0109 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0110 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0111 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0112 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0113 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/callbacks/menus/onMenuExtraColor.html b/doc/nucleus/callbacks/menus/onMenuExtraColor.html index bdad2b5..96e5cb8 100644 --- a/doc/nucleus/callbacks/menus/onMenuExtraColor.html +++ b/doc/nucleus/callbacks/menus/onMenuExtraColor.html @@ -102,64 +102,68 @@

    SOURCE CODE ^'figure','toplevel'); 0034 fig_tag = get(fig,'Tag'); 0035 gui = getappdata(fig,'gui'); -0036 data = getappdata(fig,'data'); -0037 -0038 % get the menu label -0039 label = get(src,'Label'); -0040 -0041 % mark the selected menu entry -0042 switch label -0043 case 'standard' -0044 set(gui.menu.color_theme_standard,'Checked','on'); -0045 set(gui.menu.color_theme_basic,'Checked','off'); -0046 set(gui.menu.color_theme_dark,'Checked','off'); -0047 set(gui.menu.color_theme_black,'Checked','off'); -0048 case 'basic' -0049 set(gui.menu.color_theme_standard,'Checked','off'); -0050 set(gui.menu.color_theme_basic,'Checked','on'); -0051 set(gui.menu.color_theme_dark,'Checked','off'); -0052 set(gui.menu.color_theme_black,'Checked','off'); -0053 case 'dark' -0054 set(gui.menu.color_theme_standard,'Checked','off'); -0055 set(gui.menu.color_theme_basic,'Checked','off'); -0056 set(gui.menu.color_theme_dark,'Checked','on'); -0057 set(gui.menu.color_theme_black,'Checked','off'); -0058 case 'black' -0059 set(gui.menu.color_theme_standard,'Checked','off'); -0060 set(gui.menu.color_theme_basic,'Checked','off'); -0061 set(gui.menu.color_theme_dark,'Checked','off'); -0062 set(gui.menu.color_theme_black,'Checked','on'); -0063 end -0064 -0065 % adjust the colors -0066 changeColorTheme(fig_tag,label); -0067 -0068 end -0069 -0070 %------------- END OF CODE -------------- +0036 +0037 % get the menu label +0038 label = get(src,'Label'); +0039 +0040 % mark the selected menu entry +0041 switch label +0042 case 'standard' +0043 set(gui.menu.color_theme_standard,'Checked','on'); +0044 set(gui.menu.color_theme_basic,'Checked','off'); +0045 set(gui.menu.color_theme_dark,'Checked','off'); +0046 set(gui.menu.color_theme_black,'Checked','off'); +0047 case 'basic' +0048 set(gui.menu.color_theme_standard,'Checked','off'); +0049 set(gui.menu.color_theme_basic,'Checked','on'); +0050 set(gui.menu.color_theme_dark,'Checked','off'); +0051 set(gui.menu.color_theme_black,'Checked','off'); +0052 case 'dark' +0053 set(gui.menu.color_theme_standard,'Checked','off'); +0054 set(gui.menu.color_theme_basic,'Checked','off'); +0055 set(gui.menu.color_theme_dark,'Checked','on'); +0056 set(gui.menu.color_theme_black,'Checked','off'); +0057 case 'black' +0058 set(gui.menu.color_theme_standard,'Checked','off'); +0059 set(gui.menu.color_theme_basic,'Checked','off'); +0060 set(gui.menu.color_theme_dark,'Checked','off'); +0061 set(gui.menu.color_theme_black,'Checked','on'); +0062 end +0063 +0064 % adjust the colors +0065 changeColorTheme(fig_tag,label); +0066 +0067 % check the sub GUIs +0068 if ~isempty(findobj('Tag','FIXEDTIMEVIEW')) +0069 changeColorTheme('FIXEDTIMEVIEW',label); +0070 end 0071 -0072 %% License: -0073 % MIT License -0074 % -0075 % Copyright (c) 2018 Thomas Hiller -0076 % -0077 % Permission is hereby granted, free of charge, to any person obtaining a copy -0078 % of this software and associated documentation files (the "Software"), to deal -0079 % in the Software without restriction, including without limitation the rights -0080 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0081 % copies of the Software, and to permit persons to whom the Software is -0082 % furnished to do so, subject to the following conditions: -0083 % -0084 % The above copyright notice and this permission notice shall be included in all -0085 % copies or substantial portions of the Software. -0086 % -0087 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0088 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0089 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0090 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0091 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0092 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0093 % SOFTWARE. +0072 end +0073 +0074 %------------- END OF CODE -------------- +0075 +0076 %% License: +0077 % MIT License +0078 % +0079 % Copyright (c) 2018 Thomas Hiller +0080 % +0081 % Permission is hereby granted, free of charge, to any person obtaining a copy +0082 % of this software and associated documentation files (the "Software"), to deal +0083 % in the Software without restriction, including without limitation the rights +0084 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0085 % copies of the Software, and to permit persons to whom the Software is +0086 % furnished to do so, subject to the following conditions: +0087 % +0088 % The above copyright notice and this permission notice shall be included in all +0089 % copies or substantial portions of the Software. +0090 % +0091 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0092 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0093 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0094 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0095 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0096 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0097 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/callbacks/popup/onPopupInvstdType.html b/doc/nucleus/callbacks/popup/onPopupInvstdType.html index 37a51e5..61c72aa 100644 --- a/doc/nucleus/callbacks/popup/onPopupInvstdType.html +++ b/doc/nucleus/callbacks/popup/onPopupInvstdType.html @@ -60,7 +60,7 @@

    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

    This function calls: +
  • NUCLEUSinv_updateInterface updates all GUI elements
  • onRadioGates selects the re-sampling / gating method ("log", "lin" or "none")
  • FixedTimeView is an extra subGUI to fix certain relaxation times during
    • This function is called by: @@ -118,97 +118,129 @@

    SOURCE CODE ^'mono'; 0048 data.invstd.regtype = 'none'; 0049 data.invstd.lambda = 1; -0050 -0051 case 2 -0052 data.invstd.invtype = 'free'; -0053 data.invstd.regtype = 'none'; -0054 data.invstd.lambda = 1; -0055 -0056 case 3 -0057 data.invstd.invtype = 'NNLS'; -0058 data.invstd.regtype = 'manual'; -0059 data.invstd.lambda = 1; +0050 data.invstd.freeDT = 1; +0051 +0052 % % if the FixedTimeView window is open update it +0053 % if ~isempty(findobj('Tag','FIXEDTIMEVIEW')) +0054 % data.invstd.Tfixed_bool = zeros(1,5); +0055 % % update GUI data +0056 % setappdata(fig,'data',data); +0057 % FixedTimeView(gui.menu.extra_fixedtime); +0058 % data = getappdata(fig,'data'); +0059 % end 0060 -0061 case 4 -0062 data.invstd.invtype = 'LU'; -0063 data.invstd.regtype = 'auto'; -0064 data.invstd.lambda = -1; -0065 -0066 case 5 -0067 data.invstd.invtype = 'MUMO'; -0068 data.invstd.regtype = 'none'; -0069 data.invstd.lambda = 1; -0070 end -0071 -0072 case 'off' -0073 switch value -0074 case 1 -0075 data.invstd.invtype = 'mono'; -0076 data.invstd.regtype = 'none'; -0077 data.invstd.lambda = 1; -0078 -0079 case 2 -0080 data.invstd.invtype = 'free'; -0081 data.invstd.regtype = 'none'; -0082 data.invstd.lambda = 1; -0083 -0084 case 3 -0085 data.invstd.invtype = 'NNLS'; -0086 % for multi-exponential inversion log-gating is default -0087 data.process.gatetype = 'log'; -0088 -0089 % set LIAG defaults -0090 if isfield(data.import,'LIAG') -0091 data.invstd.regtype = 'lcurve'; -0092 data.invstd.lambda = 1; -0093 data.invstd.lambdaR = [1e-5 1]; -0094 else -0095 data.invstd.regtype = 'manual'; -0096 data.invstd.lambda = 1e-2; -0097 end -0098 % update GUI data -0099 setappdata(fig,'data',data); -0100 % because the gate type could have changed update data -0101 onRadioGates(gui.radio_handles.process_gates_log); -0102 data = getappdata(fig,'data'); -0103 -0104 case 4 -0105 data.invstd.invtype = 'MUMO'; -0106 data.invstd.regtype = 'none'; -0107 data.invstd.lambda = 1; -0108 end -0109 end -0110 % update GUI data -0111 setappdata(fig,'data',data); -0112 % update interface -0113 NUCLEUSinv_updateInterface; -0114 -0115 end -0116 -0117 %------------- END OF CODE -------------- -0118 -0119 %% License: -0120 % MIT License -0121 % -0122 % Copyright (c) 2018 Thomas Hiller -0123 % -0124 % Permission is hereby granted, free of charge, to any person obtaining a copy -0125 % of this software and associated documentation files (the "Software"), to deal -0126 % in the Software without restriction, including without limitation the rights -0127 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0128 % copies of the Software, and to permit persons to whom the Software is -0129 % furnished to do so, subject to the following conditions: -0130 % -0131 % The above copyright notice and this permission notice shall be included in all -0132 % copies or substantial portions of the Software. -0133 % -0134 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0135 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0136 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0137 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0138 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0139 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0140 % SOFTWARE. +0061 case 2 +0062 data.invstd.invtype = 'free'; +0063 data.invstd.regtype = 'none'; +0064 data.invstd.lambda = 1; +0065 data.invstd.freeDT = 2; +0066 +0067 % % if the FixedTimeView window is open update it +0068 % if ~isempty(findobj('Tag','FIXEDTIMEVIEW')) +0069 % data.invstd.Tfixed_bool = zeros(1,5); +0070 % % update GUI data +0071 % setappdata(fig,'data',data); +0072 % FixedTimeView(gui.menu.extra_fixedtime); +0073 % data = getappdata(fig,'data'); +0074 % end +0075 +0076 case 3 +0077 data.invstd.invtype = 'NNLS'; +0078 data.invstd.regtype = 'manual'; +0079 data.invstd.lambda = 1; +0080 +0081 case 4 +0082 data.invstd.invtype = 'LU'; +0083 data.invstd.regtype = 'auto'; +0084 data.invstd.lambda = -1; +0085 +0086 case 5 +0087 data.invstd.invtype = 'MUMO'; +0088 data.invstd.regtype = 'none'; +0089 data.invstd.lambda = 1; +0090 end +0091 +0092 case 'off' +0093 switch value +0094 case 1 +0095 data.invstd.invtype = 'mono'; +0096 data.invstd.regtype = 'none'; +0097 data.invstd.lambda = 1; +0098 data.invstd.freeDT = 1; +0099 +0100 case 2 +0101 data.invstd.invtype = 'free'; +0102 data.invstd.regtype = 'none'; +0103 data.invstd.lambda = 1; +0104 data.invstd.freeDT = 2; +0105 +0106 case 3 +0107 data.invstd.invtype = 'NNLS'; +0108 % for multi-exponential inversion log-gating is default +0109 data.process.gatetype = 'log'; +0110 +0111 % set LIAG defaults +0112 if isfield(data.import,'LIAG') +0113 data.invstd.regtype = 'lcurve'; +0114 data.invstd.lambda = 1; +0115 data.invstd.lambdaR = [1e-5 1]; +0116 else +0117 data.invstd.regtype = 'manual'; +0118 data.invstd.lambda = 1e-2; +0119 end +0120 % update GUI data +0121 setappdata(fig,'data',data); +0122 % because the gate type could have changed update data +0123 onRadioGates(gui.radio_handles.process_gates_log); +0124 data = getappdata(fig,'data'); +0125 +0126 case 4 +0127 data.invstd.invtype = 'MUMO'; +0128 data.invstd.regtype = 'none'; +0129 data.invstd.lambda = 1; +0130 end +0131 end +0132 +0133 % if the FixedTimeView window is open update it +0134 if ~isempty(findobj('Tag','FIXEDTIMEVIEW')) +0135 data.invstd.Tfixed_bool = zeros(1,5); +0136 % update GUI data +0137 setappdata(fig,'data',data); +0138 FixedTimeView(gui.menu.extra_fixedtime); +0139 data = getappdata(fig,'data'); +0140 end +0141 +0142 % update GUI data +0143 setappdata(fig,'data',data); +0144 % update interface +0145 NUCLEUSinv_updateInterface; +0146 +0147 end +0148 +0149 %------------- END OF CODE -------------- +0150 +0151 %% License: +0152 % MIT License +0153 % +0154 % Copyright (c) 2018 Thomas Hiller +0155 % +0156 % Permission is hereby granted, free of charge, to any person obtaining a copy +0157 % of this software and associated documentation files (the "Software"), to deal +0158 % in the Software without restriction, including without limitation the rights +0159 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0160 % copies of the Software, and to permit persons to whom the Software is +0161 % furnished to do so, subject to the following conditions: +0162 % +0163 % The above copyright notice and this permission notice shall be included in all +0164 % copies or substantial portions of the Software. +0165 % +0166 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0167 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0168 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0169 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0170 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0171 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0172 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/callbacks/popup/onPopupInvstdTypeOptional.html b/doc/nucleus/callbacks/popup/onPopupInvstdTypeOptional.html index b4741b1..819b096 100644 --- a/doc/nucleus/callbacks/popup/onPopupInvstdTypeOptional.html +++ b/doc/nucleus/callbacks/popup/onPopupInvstdTypeOptional.html @@ -62,7 +62,7 @@

    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

    This function calls: +
  • NUCLEUSinv_updateInterface updates all GUI elements
  • FixedTimeView is an extra subGUI to fix certain relaxation times during
  • clearSingleAxis clears an individual axis
    • This function is called by: @@ -119,132 +119,140 @@

    SOURCE CODE ^% change settings accordingly 0047 switch invtype 0048 case 'free' -0049 % # free decay times = value (1 to 5) +0049 % # free relaxation times = value (1 to 5) 0050 data.invstd.freeDT = value; -0051 -0052 case 'NNLS' -0053 switch data.info.ExpertMode -0054 case 'on' -0055 switch value % different regularization options/methods -0056 case 1 % manual -0057 data.invstd.regtype = 'manual'; -0058 data.invstd.lambda = 1; -0059 % if there is an optimal lambda from the L-curve -0060 % use it -0061 if isfield(data,'results') && ... -0062 isfield(data.results,'lcurve') -0063 index = data.results.lcurve.index; -0064 data.invstd.lambda = data.results.lcurve.lambda(index); -0065 end -0066 -0067 case 2 % gcv_tikh -0068 data.invstd.regtype = 'gcv_tikh'; -0069 data.invstd.lambda = 1; -0070 -0071 case 3 % gcv_trunc -0072 data.invstd.regtype = 'gcv_trunc'; -0073 data.invstd.lambda = 1; +0051 +0052 % if the FixedTimeView window is open update it +0053 if ~isempty(findobj('Tag','FIXEDTIMEVIEW')) +0054 % update GUI data +0055 setappdata(fig,'data',data); +0056 FixedTimeView(gui.menu.extra_fixedtime); +0057 data = getappdata(fig,'data'); +0058 end +0059 +0060 case 'NNLS' +0061 switch data.info.ExpertMode +0062 case 'on' +0063 switch value % different regularization options/methods +0064 case 1 % manual +0065 data.invstd.regtype = 'manual'; +0066 data.invstd.lambda = 1; +0067 % if there is an optimal lambda from the L-curve +0068 % use it +0069 if isfield(data,'results') && ... +0070 isfield(data.results,'lcurve') +0071 index = data.results.lcurve.index; +0072 data.invstd.lambda = data.results.lcurve.lambda(index); +0073 end 0074 -0075 case 4 % gcv_damp -0076 data.invstd.regtype = 'gcv_damp'; +0075 case 2 % gcv_tikh +0076 data.invstd.regtype = 'gcv_tikh'; 0077 data.invstd.lambda = 1; 0078 -0079 case 5 % discrep. principle -0080 if data.results.nmrproc.noise == 0 -0081 helpdlg('Discrepancy Principle does not work with noise = 0','Change Regularization Method'); -0082 data.invstd.regtype = 'manual'; -0083 data.invstd.lambda = 1; -0084 else -0085 data.invstd.regtype = 'discrep'; -0086 data.invstd.lambda = 1; -0087 end -0088 -0089 case 6 % l-curve -0090 data.invstd.regtype = 'lcurve'; -0091 lambdaFAK = 1; -0092 if strcmp(data.process.gatetype,'log') || strcmp(data.process.gatetype,'lin') -0093 lambdaFAK = 100; -0094 end -0095 data.invstd.lambdaR = data.invstd.lambdaRinit./lambdaFAK; -0096 clearSingleAxis(gui.axes_handles.rtd); -0097 clearSingleAxis(gui.axes_handles.psd); -0098 end -0099 -0100 case 'off' -0101 switch value % different regularization options/methods -0102 case 1 % manual -0103 data.invstd.regtype = 'manual'; -0104 lambdaFAK = 1; -0105 if strcmp(data.process.gatetype,'log') || strcmp(data.process.gatetype,'lin') -0106 lambdaFAK = 100; -0107 end -0108 data.invstd.lambda = 1/lambdaFAK; -0109 % if there is an optimal lambda from the L-curve -0110 % use it -0111 if isfield(data,'results') && ... -0112 isfield(data.results,'lcurve') -0113 index = data.results.lcurve.index; -0114 data.invstd.lambda = data.results.lcurve.lambda(index); -0115 end -0116 case 2 % l-curve -0117 data.invstd.regtype = 'lcurve'; -0118 lambdaFAK = 1; -0119 if strcmp(data.process.gatetype,'log') || strcmp(data.process.gatetype,'lin') -0120 lambdaFAK = 100; -0121 end -0122 data.invstd.lambdaR = data.invstd.lambdaRinit./lambdaFAK; -0123 clearSingleAxis(gui.axes_handles.rtd); -0124 clearSingleAxis(gui.axes_handles.psd); -0125 end -0126 end -0127 -0128 case 'LU' -0129 switch value % different regularization options/methods -0130 case 1 % manual -0131 data.invstd.regtype = 'manual'; -0132 data.invstd.lambda = 1; -0133 -0134 case 2 % automatic -0135 data.invstd.regtype = 'auto'; -0136 data.invstd.lambda = -1; -0137 end -0138 -0139 case 'MUMO' -0140 % # free distributions = value (1 to 4) -0141 data.invstd.freeDT = value; -0142 end -0143 -0144 % update GUI data -0145 setappdata(fig,'data',data); -0146 % update interface -0147 NUCLEUSinv_updateInterface; -0148 -0149 end -0150 -0151 %------------- END OF CODE -------------- -0152 -0153 %% License: -0154 % MIT License -0155 % -0156 % Copyright (c) 2018 Thomas Hiller -0157 % -0158 % Permission is hereby granted, free of charge, to any person obtaining a copy -0159 % of this software and associated documentation files (the "Software"), to deal -0160 % in the Software without restriction, including without limitation the rights -0161 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0162 % copies of the Software, and to permit persons to whom the Software is -0163 % furnished to do so, subject to the following conditions: -0164 % -0165 % The above copyright notice and this permission notice shall be included in all -0166 % copies or substantial portions of the Software. -0167 % -0168 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0169 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0170 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0171 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0172 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0173 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0174 % SOFTWARE. +0079 case 3 % gcv_trunc +0080 data.invstd.regtype = 'gcv_trunc'; +0081 data.invstd.lambda = 1; +0082 +0083 case 4 % gcv_damp +0084 data.invstd.regtype = 'gcv_damp'; +0085 data.invstd.lambda = 1; +0086 +0087 case 5 % discrep. principle +0088 if data.results.nmrproc.noise == 0 +0089 helpdlg('Discrepancy Principle does not work with noise = 0','Change Regularization Method'); +0090 data.invstd.regtype = 'manual'; +0091 data.invstd.lambda = 1; +0092 else +0093 data.invstd.regtype = 'discrep'; +0094 data.invstd.lambda = 1; +0095 end +0096 +0097 case 6 % l-curve +0098 data.invstd.regtype = 'lcurve'; +0099 lambdaFAK = 1; +0100 if strcmp(data.process.gatetype,'log') || strcmp(data.process.gatetype,'lin') +0101 lambdaFAK = 100; +0102 end +0103 data.invstd.lambdaR = data.invstd.lambdaRinit./lambdaFAK; +0104 clearSingleAxis(gui.axes_handles.rtd); +0105 clearSingleAxis(gui.axes_handles.psd); +0106 end +0107 +0108 case 'off' +0109 switch value % different regularization options/methods +0110 case 1 % manual +0111 data.invstd.regtype = 'manual'; +0112 lambdaFAK = 1; +0113 if strcmp(data.process.gatetype,'log') || strcmp(data.process.gatetype,'lin') +0114 lambdaFAK = 100; +0115 end +0116 data.invstd.lambda = 1/lambdaFAK; +0117 % if there is an optimal lambda from the L-curve +0118 % use it +0119 if isfield(data,'results') && ... +0120 isfield(data.results,'lcurve') +0121 index = data.results.lcurve.index; +0122 data.invstd.lambda = data.results.lcurve.lambda(index); +0123 end +0124 case 2 % l-curve +0125 data.invstd.regtype = 'lcurve'; +0126 lambdaFAK = 1; +0127 if strcmp(data.process.gatetype,'log') || strcmp(data.process.gatetype,'lin') +0128 lambdaFAK = 100; +0129 end +0130 data.invstd.lambdaR = data.invstd.lambdaRinit./lambdaFAK; +0131 clearSingleAxis(gui.axes_handles.rtd); +0132 clearSingleAxis(gui.axes_handles.psd); +0133 end +0134 end +0135 +0136 case 'LU' +0137 switch value % different regularization options/methods +0138 case 1 % manual +0139 data.invstd.regtype = 'manual'; +0140 data.invstd.lambda = 1; +0141 +0142 case 2 % automatic +0143 data.invstd.regtype = 'auto'; +0144 data.invstd.lambda = -1; +0145 end +0146 +0147 case 'MUMO' +0148 % # free distributions = value (1 to 4) +0149 data.invstd.freeDT = value; +0150 end +0151 +0152 % update GUI data +0153 setappdata(fig,'data',data); +0154 % update interface +0155 NUCLEUSinv_updateInterface; +0156 +0157 end +0158 +0159 %------------- END OF CODE -------------- +0160 +0161 %% License: +0162 % MIT License +0163 % +0164 % Copyright (c) 2018 Thomas Hiller +0165 % +0166 % Permission is hereby granted, free of charge, to any person obtaining a copy +0167 % of this software and associated documentation files (the "Software"), to deal +0168 % in the Software without restriction, including without limitation the rights +0169 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0170 % copies of the Software, and to permit persons to whom the Software is +0171 % furnished to do so, subject to the following conditions: +0172 % +0173 % The above copyright notice and this permission notice shall be included in all +0174 % copies or substantial portions of the Software. +0175 % +0176 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0177 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0178 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0179 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0180 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0181 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0182 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/functions/import/LoadNMRData_driver.html b/doc/nucleus/functions/import/LoadNMRData_driver.html index c36ee62..6656f6c 100644 --- a/doc/nucleus/functions/import/LoadNMRData_driver.html +++ b/doc/nucleus/functions/import/LoadNMRData_driver.html @@ -74,7 +74,7 @@

    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

    This function calls: +
  • LoadNMRData_bamtom loads BAM TOM data
  • LoadNMRData_bgr loads standard BGR NMR data
  • LoadNMRData_bgrmat loads already preprocessed BGR NMR data; check the
  • LoadNMRData_corelab loads NMR data as provided by Corelab
  • LoadNMRData_dart loads RWTH NMR data (recorded with the Dart device); the
  • LoadNMRData_field loads RWTH field NMR data (Blümich group bore-hole tool)
  • LoadNMRData_helios loads BGR NMR data from a typical folder structure
  • LoadNMRData_ibac imports NMR data from the PM5 and PM25
  • LoadNMRData_liag loads LIAG NMR data
  • LoadNMRData_mouse loads NMR data saved by the MOUSE
  • LoadNMRData_mousecpmg
  • LoadNMRData_mouselift loads NMR Mouse data from an original folder structure as
  • LoadNMRData_rwth loads RWTH NMR data (saved by the old Prospa version)
  • fitDataFree is a control routine that uses 'lsqcurvefit' to fit NMR data
    • This function is called by: @@ -136,24 +136,24 @@

    SOURCE CODE ^LoadNMRData_bamtom(in); 0052 case 'bgr' 0053 out = LoadNMRData_bgr(in); -0054 case 'MouseCPMG' -0055 out = LoadNMRData_mousecpmg(in); -0056 case 'bgrmat' -0057 out = LoadNMRData_bgrmat(in); -0058 case {'MouseLiftSingle','MouseLiftAll'} -0059 out = LoadNMRData_mouselift(in); -0060 case 'helios' -0061 out = LoadNMRData_helios(in); -0062 case 'corelab' -0063 out = LoadNMRData_corelab(in); -0064 case 'dart' -0065 out = LoadNMRData_dart(in); -0066 case 'field' -0067 out = LoadNMRData_field(in); -0068 case 'liag' -0069 out = LoadNMRData_liag(in); -0070 case 'mouse' -0071 out = LoadNMRData_mouse(in); +0054 case 'bgrmat' +0055 out = LoadNMRData_bgrmat(in); +0056 case 'corelab' +0057 out = LoadNMRData_corelab(in); +0058 case 'dart' +0059 out = LoadNMRData_dart(in); +0060 case 'field' +0061 out = LoadNMRData_field(in); +0062 case {'heliosCPMG','heliosSeries'} +0063 out = LoadNMRData_helios(in); +0064 case 'liag' +0065 out = LoadNMRData_liag(in); +0066 case 'mouse' +0067 out = LoadNMRData_mouse(in); +0068 case 'MouseCPMG' +0069 out = LoadNMRData_mousecpmg(in); +0070 case 'MouseLift' +0071 out = LoadNMRData_mouselift(in); 0072 case 'rwth' 0073 out = LoadNMRData_rwth(in); 0074 case 'pm5' @@ -164,47 +164,50 @@

    SOURCE CODE ^% if an imported T2 signal has no imaginary part, the noise is estimated 0081 % from an exponential fit -0082 if ~strcmp(in.fileformat,'helios') -0083 for i = 1:numel(out.nmrData) -0084 if isreal(out.nmrData{i}.signal) -0085 disp('NUCLUESinv import: Estimating noise from exponential fit ...'); -0086 param.T1IRfac = out.nmrData{i}.T1IRfac; -0087 param.noise = 0; -0088 param.optim = 'off'; -0089 invstd = fitDataFree(out.nmrData{i}.time,out.nmrData{i}.signal,... -0090 out.nmrData{i}.flag,param,5); -0091 out.nmrData{i}.noise = invstd.rms; -0092 disp('NUCLUESinv import: done.') -0093 end -0094 end -0095 end -0096 -0097 return -0098 -0099 %------------- END OF CODE -------------- -0100 -0101 %% License: -0102 % MIT License -0103 % -0104 % Copyright (c) 2018 Thomas Hiller -0105 % -0106 % Permission is hereby granted, free of charge, to any person obtaining a copy -0107 % of this software and associated documentation files (the "Software"), to deal -0108 % in the Software without restriction, including without limitation the rights -0109 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0110 % copies of the Software, and to permit persons to whom the Software is -0111 % furnished to do so, subject to the following conditions: -0112 % -0113 % The above copyright notice and this permission notice shall be included in all -0114 % copies or substantial portions of the Software. +0082 if ~strcmp(in.fileformat,'heliosCPMG') && ~strcmp(in.fileformat,'heliosSeries')... +0083 && (isfield(in,'T1T2') && ~strcmp(in.T1T2,'T1')) +0084 for i = 1:numel(out.nmrData) +0085 if isreal(out.nmrData{i}.signal) +0086 disp('NUCLUESinv import: Estimating noise from exponential fit ...'); +0087 param.T1IRfac = out.nmrData{i}.T1IRfac; +0088 param.noise = 0; +0089 param.optim = 'off'; +0090 param.Tfixed_bool = [0 0 0 0 0]; +0091 param.Tfixed_val = [0 0 0 0 0]; +0092 invstd = fitDataFree(out.nmrData{i}.time,out.nmrData{i}.signal,... +0093 out.nmrData{i}.flag,param,5); +0094 out.nmrData{i}.noise = invstd.rms; +0095 disp('NUCLUESinv import: done.') +0096 end +0097 end +0098 end +0099 +0100 return +0101 +0102 %------------- END OF CODE -------------- +0103 +0104 %% License: +0105 % MIT License +0106 % +0107 % Copyright (c) 2018 Thomas Hiller +0108 % +0109 % Permission is hereby granted, free of charge, to any person obtaining a copy +0110 % of this software and associated documentation files (the "Software"), to deal +0111 % in the Software without restriction, including without limitation the rights +0112 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0113 % copies of the Software, and to permit persons to whom the Software is +0114 % furnished to do so, subject to the following conditions: 0115 % -0116 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0117 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0118 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0119 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0120 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0121 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0122 % SOFTWARE. +0116 % The above copyright notice and this permission notice shall be included in all +0117 % copies or substantial portions of the Software. +0118 % +0119 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0120 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0121 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0122 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0123 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0124 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0125 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/functions/import/LoadNMRData_helios.html b/doc/nucleus/functions/import/LoadNMRData_helios.html index 42ebcea..0fedea1 100644 --- a/doc/nucleus/functions/import/LoadNMRData_helios.html +++ b/doc/nucleus/functions/import/LoadNMRData_helios.html @@ -26,8 +26,8 @@

    SYNOPSIS ^function out = LoadNMRData_helios(in)

    DESCRIPTION ^

    -
    LoadNMRData_helios loads BGR NMR data from a typical folder structure 
-produced by the Helios NMR Scanner 
+
    LoadNMRData_helios loads BGR NMR data from a typical folder structure
+produced by the Helios NMR Scanner
 
  Syntax:
        out = LoadNMRData_helios(in)
@@ -143,53 +143,76 @@ 
    SOURCE CODE ^%% load NMR data file
 0067 function [data,pardata] = LoadDataFile(datapath,fname,flag)
 0068 
-0069 A = importdata(fullfile(datapath,fname),'\t');
-0070 t_echo = A(1,2);
-0071 n_echo = A(1,3);
-0072 
-0073 time = t_echo:t_echo:t_echo*n_echo;
-0074 time = time(:);
-0075 re = -A(2,1:length(time));
-0076 im = -A(3,1:length(time));
-0077 re = re(:);
-0078 im = im(:);
-0079 
-0080 data.flag = flag;
-0081 data.time = time;
-0082 data.signal = complex(re,im);
-0083 [data.signal,data.phase] = rotateT2phase(data.signal);
+0069 % importdata is rather slow for row data
+0070 % A = importdata(fullfile(datapath,fname),'\t');
+0071 
+0072 % first read the file to get the number of echos
+0073 fid = fopen(fullfile(datapath,fname));
+0074 A0 = textscan(fid,'%f','Delimiter','\n');
+0075 fclose(fid);
+0076 % now read all three lines
+0077 fid = fopen(fullfile(datapath,fname));
+0078 A1 = textscan(fid,'%f',A0{1}(3));
+0079 A2 = textscan(fid,'%f',A0{1}(3));
+0080 A3 = textscan(fid,'%f',A0{1}(3));
+0081 fclose(fid);
+0082 % and stitch them together
+0083 A = [A1{1}';A2{1}';A3{1}'];
 0084 
-0085 data.raw.time = data.time;
-0086 data.raw.signal = data.signal;
-0087 
-0088 pardata.t_echo = t_echo; 
-0089 pardata.n_echo = n_echo; 
-0090 
-0091 end
-0092 %------------- END OF CODE --------------
-0093 
-0094 %% License:
-0095 % MIT License
-0096 %
-0097 % Copyright (c) 2021 Stephan Costabel
-0098 %
-0099 % Permission is hereby granted, free of charge, to any person obtaining a copy
-0100 % of this software and associated documentation files (the "Software"), to deal
-0101 % in the Software without restriction, including without limitation the rights
-0102 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-0103 % copies of the Software, and to permit persons to whom the Software is
-0104 % furnished to do so, subject to the following conditions:
-0105 %
-0106 % The above copyright notice and this permission notice shall be included in all
-0107 % copies or substantial portions of the Software.
-0108 %
-0109 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-0110 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-0111 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-0112 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-0113 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-0114 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-0115 % SOFTWARE.
    
+0085 t_echo = A(1,2);
+0086 n_echo = A(1,3);
+0087 freq = A(1,4);
+0088 Nscans = A(1,5);
+0089 
+0090 time = t_echo:t_echo:t_echo*n_echo;
+0091 time = time(:);
+0092 re = A(2,1:length(time));
+0093 im = A(3,1:length(time));
+0094 re = re(:);
+0095 im = im(:);
+0096 
+0097 data.flag = flag;
+0098 data.raw.time = time;
+0099 data.raw.signal = complex(re,im);
+0100 [data.signal,data.phase] = rotateT2phase(data.raw.signal);
+0101 
+0102 data.time = data.raw.time;
+0103 
+0104 pardata.t_echo = t_echo;
+0105 pardata.n_echo = n_echo;
+0106 pardata.freq = freq;
+0107 pardata.Nscans = Nscans;
+0108 d{1}{1,1} = ['t_echo = ',num2str(t_echo)];
+0109 d{1}{2,1} = ['n_echo = ',num2str(n_echo)];
+0110 d{1}{3,1} = ['freq = ',num2str(freq)];
+0111 d{1}{4,1} = ['Nscans = ',num2str(Nscans)];
+0112 pardata.all = d;
+0113 
+0114 end
+0115 %------------- END OF CODE --------------
+0116 
+0117 %% License:
+0118 % MIT License
+0119 %
+0120 % Copyright (c) 2021 Stephan Costabel
+0121 %
+0122 % Permission is hereby granted, free of charge, to any person obtaining a copy
+0123 % of this software and associated documentation files (the "Software"), to deal
+0124 % in the Software without restriction, including without limitation the rights
+0125 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+0126 % copies of the Software, and to permit persons to whom the Software is
+0127 % furnished to do so, subject to the following conditions:
+0128 %
+0129 % The above copyright notice and this permission notice shall be included in all
+0130 % copies or substantial portions of the Software.
+0131 %
+0132 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+0133 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+0134 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+0135 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+0136 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+0137 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+0138 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/functions/import/LoadNMRData_liag.html b/doc/nucleus/functions/import/LoadNMRData_liag.html index 6b3f19d..e7182f1 100644 --- a/doc/nucleus/functions/import/LoadNMRData_liag.html +++ b/doc/nucleus/functions/import/LoadNMRData_liag.html @@ -195,7 +195,7 @@

    SOURCE CODE ^for i = 1:size(d{1},1) 0120 str = char(d{1}(i)); 0121 str = fixParameterString(str); -0122 eval(['data.',str,';']); +0122 eval(['data.',str,';']); %#ok<EVLDOT> 0123 end 0124 data.all = d; 0125 diff --git a/doc/nucleus/functions/import/LoadNMRData_mousecpmg.html b/doc/nucleus/functions/import/LoadNMRData_mousecpmg.html new file mode 100644 index 0000000..54addb5 --- /dev/null +++ b/doc/nucleus/functions/import/LoadNMRData_mousecpmg.html @@ -0,0 +1,227 @@ + + + + Description of LoadNMRData_mousecpmg + + + + + + + + + + + +

    LoadNMRData_mousecpmg +

    + +

    PURPOSE ^

    +
    + +

    SYNOPSIS ^

    +
    function out = LoadNMRData_mousecpmg(in)
    + +

    DESCRIPTION ^

    +
    LoadNMRData_bgr2 loads BGR NMR data from an original folder structure as
+generated by the NMR MOUSE (the routines are also similar to
+"LoadNMRData_mouse" the only difference is the in.T1T2 input flag)
+
+ Syntax:
+       out = LoadNMRData_mousecpmg(in)
+
+ Inputs:
+       in - input structure
+       in.path - data path
+       in.T1T2 - T1 / T2 flag
+       in.fileformat - 'mouse'
+
+ Outputs:
+       out - output structure
+       out.parData - parameter file data
+       out.nmrData - NMR data
+
+ Example:
+       out = LoadNMRData_mousecpmg(in)
+
+ Other m-files required:
+       fixParameterString
+
+ Subfunctions:
+       LoadDataFile
+       LoadParameterFile
+
+ MAT-files required:
+       none
+
+ See also: NUCLEUSinv
+ Author: Stephan Costabel
+ email: stephan.costabel[at]bgr.de
+ License: MIT License (at end)
    + + +

    CROSS-REFERENCE INFORMATION ^

    +This function calls: + +This function is called by: + + + +

    SUBFUNCTIONS ^

    + + +

    SOURCE CODE ^

    +
    0001 function out = LoadNMRData_mousecpmg(in)
+0002 %LoadNMRData_bgr2 loads BGR NMR data from an original folder structure as
+0003 %generated by the NMR MOUSE (the routines are also similar to
+0004 %"LoadNMRData_mouse" the only difference is the in.T1T2 input flag)
+0005 %
+0006 % Syntax:
+0007 %       out = LoadNMRData_mousecpmg(in)
+0008 %
+0009 % Inputs:
+0010 %       in - input structure
+0011 %       in.path - data path
+0012 %       in.T1T2 - T1 / T2 flag
+0013 %       in.fileformat - 'mouse'
+0014 %
+0015 % Outputs:
+0016 %       out - output structure
+0017 %       out.parData - parameter file data
+0018 %       out.nmrData - NMR data
+0019 %
+0020 % Example:
+0021 %       out = LoadNMRData_mousecpmg(in)
+0022 %
+0023 % Other m-files required:
+0024 %       fixParameterString
+0025 %
+0026 % Subfunctions:
+0027 %       LoadDataFile
+0028 %       LoadParameterFile
+0029 %
+0030 % MAT-files required:
+0031 %       none
+0032 %
+0033 % See also: NUCLEUSinv
+0034 % Author: Stephan Costabel
+0035 % email: stephan.costabel[at]bgr.de
+0036 % License: MIT License (at end)
+0037 
+0038 %------------- BEGIN CODE --------------
+0039 
+0040 %% start processing the files
+0041 % load Parameter file
+0042 [parData] = LoadParameterFile(in.path,'acqu.par');
+0043 
+0044 % find all data files
+0045 files = dir(fullfile(in.path,'*.csv'));
+0046 
+0047 % remove not needed csv-files
+0048 files = files(~ismember({files.name},'data2.csv'));
+0049 
+0050 nmrData = cell(1,size(files,1));
+0051 for i = 1:size(files,1)
+0052     % read the data file
+0053     data  = Load_csvDataFile(in.path,files(i).name,in.T1T2);
+0054     
+0055     % get file statistics
+0056     nmrData{i}.datfile = files(i).name;
+0057     nmrData{i}.date = files(i).date;
+0058     nmrData{i}.datenum = files(i).datenum;
+0059     nmrData{i}.bytes = files(i).bytes;
+0060     
+0061     % save the NMR data
+0062     nmrData{i}.flag = data.flag;
+0063     nmrData{i}.T1IRfac = 1;
+0064     nmrData{i}.time = data.time;
+0065     nmrData{i}.signal = data.signal;
+0066     nmrData{i}.raw = data.raw;
+0067     if strcmp(in.T1T2,'T2')
+0068         %nmrData{i}.phase = data.phase;
+0069         nmrData{i}.phase = 0;
+0070     end
+0071     clear data
+0072 end
+0073 
+0074 % save data to output struct
+0075 out.parData = parData;
+0076 out.nmrData = nmrData;
+0077 
+0078 end
+0079 
+0080 %% load NMR data file
+0081 function [data] = Load_csvDataFile(datapath,fname,flag)
+0082 
+0083 d = csvread(fullfile(datapath,fname));
+0084 
+0085 if size(d,2) == 2
+0086     data.flag = flag;
+0087     data.time = d(:,1)/1000000;
+0088     data.signal = d(:,2);
+0089 
+0090 else
+0091     data.flag = '0';
+0092     data.time = 0;
+0093     data.signal = 0;
+0094     data.phase = 0;
+0095 end
+0096 
+0097 data.raw.time = data.time;
+0098 data.raw.signal = data.signal;
+0099 
+0100 end
+0101 
+0102 %% load parameter file
+0103 function [data] = LoadParameterFile(datapath,fname)
+0104 
+0105 fid = fopen(fullfile(datapath,fname));
+0106 d = textscan(fid,'%s','Delimiter','\n');
+0107 fclose(fid);
+0108 
+0109 for i = 1:size(d{1},1)
+0110     str = char(d{1}(i));
+0111     str = fixParameterString(str);
+0112     if strcmp(str(end),'d')
+0113         str = str(1:end-1);
+0114         %frag nich...
+0115     end
+0116     eval(['data.',str,';']);
+0117 end
+0118 data.all = d;
+0119 
+0120 end
+0121 
+0122 %------------- END OF CODE --------------
+0123 
+0124 %% License:
+0125 % MIT License
+0126 %
+0127 % Copyright (c) 2018 Thomas Hiller
+0128 %
+0129 % Permission is hereby granted, free of charge, to any person obtaining a copy
+0130 % of this software and associated documentation files (the "Software"), to deal
+0131 % in the Software without restriction, including without limitation the rights
+0132 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+0133 % copies of the Software, and to permit persons to whom the Software is
+0134 % furnished to do so, subject to the following conditions:
+0135 %
+0136 % The above copyright notice and this permission notice shall be included in all
+0137 % copies or substantial portions of the Software.
+0138 %
+0139 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+0140 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+0141 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+0142 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+0143 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+0144 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+0145 % SOFTWARE.
    +
    Generated by m2html © 2005
    + + \ No newline at end of file diff --git a/doc/nucleus/functions/import/LoadNMRData_mouselift.html b/doc/nucleus/functions/import/LoadNMRData_mouselift.html index 5fe5694..3736f33 100644 --- a/doc/nucleus/functions/import/LoadNMRData_mouselift.html +++ b/doc/nucleus/functions/import/LoadNMRData_mouselift.html @@ -197,7 +197,7 @@

    SOURCE CODE ^for i = 1:size(d{1},1) 0120 str = char(d{1}(i)); 0121 str = fixParameterString(str); -0122 eval(['data.',str,';']); +0122 eval(['data.',str,';']); %#ok<EVLDOT> 0123 end 0124 data.all = d; 0125 diff --git a/doc/nucleus/functions/import/fixParameterString.html b/doc/nucleus/functions/import/fixParameterString.html index c89dc8e..6f3ebad 100644 --- a/doc/nucleus/functions/import/fixParameterString.html +++ b/doc/nucleus/functions/import/fixParameterString.html @@ -62,7 +62,7 @@

    CROSS-REFERENCE INFORMATION ^ </ul> This function is called by: <ul style= -
  • LoadNMRData_bamtom loads BAM TOM data
  • LoadNMRData_bgr loads standard BGR NMR data
  • LoadNMRData_bgr2 loads BGR NMR data from an original folder structure as
  • LoadNMRData_field loads RWTH field NMR data (Blümich group bore-hole tool)
  • LoadNMRData_ibac imports NMR data from the PM5 and PM25
  • LoadNMRData_liag loads LIAG NMR data
  • LoadNMRData_mouse loads NMR data saved by the MOUSE
  • LoadNMRData_mouselift loads NMR Mouse data from an original folder structure as
  • LoadNMRData_rwth loads RWTH NMR data (saved by the old Prospa version)
  • importNMRdata is the general import routine for NMR data
    • +
  • LoadNMRData_bamtom loads BAM TOM data
  • LoadNMRData_bgr loads standard BGR NMR data
  • LoadNMRData_bgr2 loads BGR NMR data from an original folder structure as
  • LoadNMRData_field loads RWTH field NMR data (Blümich group bore-hole tool)
  • LoadNMRData_ibac imports NMR data from the PM5 and PM25
  • LoadNMRData_liag loads LIAG NMR data
  • LoadNMRData_mouse loads NMR data saved by the MOUSE
  • LoadNMRData_mousecpmg
  • LoadNMRData_mouselift loads NMR Mouse data from an original folder structure as
  • LoadNMRData_rwth loads RWTH NMR data (saved by the old Prospa version)
  • importNMRdata is the general import routine for NMR data
    • @@ -115,32 +115,37 @@

    SOURCE CODE ^%% check for " and make it '' 0046 str = strrep(str,'"',''''); 0047 -0048 return -0049 -0050 %------------- END OF CODE -------------- -0051 -0052 %% License: -0053 % MIT License -0054 % -0055 % Copyright (c) 2018 Thomas Hiller -0056 % -0057 % Permission is hereby granted, free of charge, to any person obtaining a copy -0058 % of this software and associated documentation files (the "Software"), to deal -0059 % in the Software without restriction, including without limitation the rights -0060 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0061 % copies of the Software, and to permit persons to whom the Software is -0062 % furnished to do so, subject to the following conditions: -0063 % -0064 % The above copyright notice and this permission notice shall be included in all -0065 % copies or substantial portions of the Software. -0066 % -0067 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0068 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0069 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0070 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0071 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0072 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0073 % SOFTWARE. +0048 %% check for "d" at the end of a number and delete it +0049 if strncmpi(str,'b1Freq',6) +0050 str = strrep(str,'d',''); +0051 end +0052 +0053 return +0054 +0055 %------------- END OF CODE -------------- +0056 +0057 %% License: +0058 % MIT License +0059 % +0060 % Copyright (c) 2018 Thomas Hiller +0061 % +0062 % Permission is hereby granted, free of charge, to any person obtaining a copy +0063 % of this software and associated documentation files (the "Software"), to deal +0064 % in the Software without restriction, including without limitation the rights +0065 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0066 % copies of the Software, and to permit persons to whom the Software is +0067 % furnished to do so, subject to the following conditions: +0068 % +0069 % The above copyright notice and this permission notice shall be included in all +0070 % copies or substantial portions of the Software. +0071 % +0072 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0073 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0074 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0075 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0076 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0077 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0078 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/functions/import/menu.html b/doc/nucleus/functions/import/menu.html index 11c11c6..9b2cf27 100644 --- a/doc/nucleus/functions/import/menu.html +++ b/doc/nucleus/functions/import/menu.html @@ -18,7 +18,7 @@

    Index for nucleus\functions\import

    Matlab files in this directory:

    +
  • LoadNMRData_bamtom
  • LoadNMRData_bgr
  • LoadNMRData_bgr2
  • LoadNMRData_bgrmat
  • LoadNMRData_corelab
  • LoadNMRData_dart
  • LoadNMRData_driver
  • LoadNMRData_field
  • LoadNMRData_helios
  • LoadNMRData_ibac
  • LoadNMRData_liag
  • LoadNMRData_mouse
  • LoadNMRData_mousecpmg
  • LoadNMRData_mouselift
  • LoadNMRData_rwth
  • fixParameterString
  • rotateT2phase
    • diff --git a/doc/nucleus/functions/interface/FixedTimeView.html b/doc/nucleus/functions/interface/FixedTimeView.html new file mode 100644 index 0000000..6efb83e --- /dev/null +++ b/doc/nucleus/functions/interface/FixedTimeView.html @@ -0,0 +1,297 @@ + + + + Description of FixedTimeView + + + + + + + + + + + +

    FixedTimeView +

    + +

    PURPOSE ^

    +
    is an extra subGUI to fix certain relaxation times during
    + +

    SYNOPSIS ^

    +
    function FixedTimeView(src,~)
    + +

    DESCRIPTION ^

    +
    FixedTimeView is an extra subGUI to fix certain relaxation times during
+the free inversion with #1-5 free relaxation times; thus only the
+amplitude gets fitted
+
+ Syntax:
+       FixedTimeView
+
+ Inputs:
+       src - handle of the calling object
+
+ Outputs:
+       none
+
+ Example:
+       FixedTimeView(src,~)
+
+ Other m-files required:
+       none
+
+ Subfunctions:
+       ft_closeme
+       ft_updateChecked
+       ft_updateEdit
+
+ MAT-files required:
+       none
+
+ See also: NUCLEUSinv
+ Author: see AUTHORS.md
+ email: see AUTHORS.md
+ License: MIT License (at end)
    + + +

    CROSS-REFERENCE INFORMATION ^

    +This function calls: + +This function is called by: + + + +

    SUBFUNCTIONS ^

    + + +

    SOURCE CODE ^

    +
    0001 function FixedTimeView(src,~)
+0002 %FixedTimeView is an extra subGUI to fix certain relaxation times during
+0003 %the free inversion with #1-5 free relaxation times; thus only the
+0004 %amplitude gets fitted
+0005 %
+0006 % Syntax:
+0007 %       FixedTimeView
+0008 %
+0009 % Inputs:
+0010 %       src - handle of the calling object
+0011 %
+0012 % Outputs:
+0013 %       none
+0014 %
+0015 % Example:
+0016 %       FixedTimeView(src,~)
+0017 %
+0018 % Other m-files required:
+0019 %       none
+0020 %
+0021 % Subfunctions:
+0022 %       ft_closeme
+0023 %       ft_updateChecked
+0024 %       ft_updateEdit
+0025 %
+0026 % MAT-files required:
+0027 %       none
+0028 %
+0029 % See also: NUCLEUSinv
+0030 % Author: see AUTHORS.md
+0031 % email: see AUTHORS.md
+0032 % License: MIT License (at end)
+0033 
+0034 %------------- BEGIN CODE --------------
+0035 
+0036 %% get GUI handle and data
+0037 figh_nucleus = ancestor(src,'figure','toplevel');
+0038 nucleus.data = getappdata(figh_nucleus,'data');
+0039 nucleus.gui = getappdata(figh_nucleus,'gui');
+0040 colors = nucleus.gui.myui.colors;
+0041 
+0042 %% proceed if the correct inversion type is chosen
+0043 if strcmp(nucleus.data.invstd.invtype,'mono') || strcmp(nucleus.data.invstd.invtype,'free')
+0044 
+0045     % check if the figure is already open
+0046     fig_fixedtime = findobj('Tag','FIXEDTIMEVIEW');
+0047     % if not, create it
+0048     if isempty(fig_fixedtime)
+0049         % draw the figure on top of NUCLEUSinv
+0050         fig_fixedtime = figure('Name','NUCLEUSinv - Fix Relaxation Time',...
+0051             'NumberTitle','off','Resize','on','ToolBar','none',...
+0052             'CloseRequestFcn',@ft_closeme,...
+0053             'MenuBar','none','Tag','FIXEDTIMEVIEW');
+0054         pos0 = get(figh_nucleus,'Position');
+0055         cent(1) = (pos0(1)+pos0(3)/2);
+0056         cent(2) = (pos0(2)+pos0(4)/2);
+0057         posf = [cent(1)-pos0(3)/6 pos0(2)+pos0(4)-pos0(4)/5 pos0(3)/3 pos0(4)/5];
+0058 %         posf = [cent(1)-pos0(3)/6 pos0(2)+pos0(4)-140 350 145];
+0059         set(fig_fixedtime,'Position',posf);
+0060 
+0061         % create the main layout
+0062         gui.main = uix.VBox('Parent',fig_fixedtime,'BackGroundColor',colors.panelBG,'Spacing',5,'Padding',5);
+0063         gui.row1 = uicontainer('Parent',gui.main,'BackGroundColor',colors.panelBG); % check boxes
+0064         gui.row2 = uicontainer('Parent',gui.main,'BackGroundColor',colors.panelBG); % edit fields
+0065         gui.row3 = uicontainer('Parent',gui.main,'BackGroundColor',colors.panelBG); % text fields
+0066         set(gui.main,'Heights',[-1 -1 -1]);
+0067 
+0068         % horizontal boxes
+0069         gui.hbox1 = uix.HBox('Parent',gui.row1,'BackGroundColor',colors.panelBG,'Spacing',5,'Padding',5); % control elements
+0070         gui.hbox2 = uix.HBox('Parent',gui.row2,'BackGroundColor',colors.panelBG,'Spacing',5,'Padding',5); % control elements
+0071         gui.hbox3 = uix.HBox('Parent',gui.row3,'BackGroundColor',colors.panelBG,'Spacing',5,'Padding',5); % text
+0072 
+0073         % create the ui elements inside the horizontal boxes
+0074         for i = 1:5
+0075             % check boxes
+0076             gui.check(i).fixed = uicontrol('Parent',gui.hbox1,...
+0077                 'Style','checkbox','FontSize',nucleus.gui.myui.fontsize,'Tag',num2str(i),...
+0078                 'Value',nucleus.data.invstd.Tfixed_bool(i),'String','fix it',...
+0079                 'BackGroundColor',colors.panelBG,'ForeGroundColor',colors.panelFG,...
+0080                 'Callback',@ft_updateChecked);
+0081             jh = findjobj(gui.check(i).fixed);
+0082             jh.setHorizontalAlignment(javax.swing.JLabel.CENTER);
+0083 
+0084             % edit fields
+0085             gui.edit(i).fixed = uicontrol('Parent',gui.hbox2,...
+0086                 'Style','edit','FontSize',nucleus.gui.myui.fontsize,'Tag',num2str(i),...
+0087                 'String',sprintf('%6.4f',nucleus.data.invstd.Tfixed_val(i)),...
+0088                 'BackGroundColor',colors.editBG,'ForeGroundColor',colors.panelFG,...
+0089                 'Callback',@ft_updateEdit);
+0090 
+0091             % text fields
+0092             gui.text(i).fixed = uicontrol('Parent',gui.hbox3,...
+0093                 'Style','text','FontSize',nucleus.gui.myui.fontsize,'Tag',['text',num2str(i)],...
+0094                 'HorizontalAlignment','center',...
+0095                 'BackGroundColor',colors.panelBG,'ForeGroundColor',colors.panelFG,...
+0096                 'String',['#',num2str(i)]);
+0097         end
+0098 
+0099         % store main GUI settings
+0100         gui.myui = nucleus.gui.myui;
+0101         gui.figh_nucleus = figh_nucleus;
+0102 
+0103         % save to GUI
+0104         setappdata(fig_fixedtime,'gui',gui);
+0105     end
+0106 
+0107     % if the figure is already open load the GUI data
+0108     gui = getappdata(fig_fixedtime,'gui');
+0109     
+0110     % update all edit fields and check boxes
+0111     for i = 1:5
+0112         set(gui.edit(i).fixed,'String',sprintf('%6.4f',nucleus.data.invstd.Tfixed_val(i)));
+0113         set(gui.check(i).fixed,'Value',nucleus.data.invstd.Tfixed_bool(i))
+0114 
+0115         % enable only the needed ones
+0116         if i <=nucleus.data.invstd.freeDT
+0117             set(gui.check(i).fixed,'Enable','on');
+0118             set(gui.edit(i).fixed,'Enable','on');
+0119         else
+0120             set(gui.check(i).fixed,'Enable','off');
+0121             set(gui.edit(i).fixed,'Enable','off');
+0122         end
+0123     end
+0124 else
+0125     % check if the figure is already open
+0126     fig_fixedtime = findobj('Tag','FIXEDTIMEVIEW');
+0127     if ~isempty(fig_fixedtime)
+0128         ft_closeme(fig_fixedtime)
+0129     else
+0130         helpdlg({'function: FixedTimeView',...
+0131             'Cannot continue because wrong inversion method!'},...
+0132             'Wrong inversion method.');
+0133     end
+0134 end
+0135 
+0136 end
+0137 
+0138 % subfunction to update the check boxes
+0139 function ft_updateChecked(src,~)
+0140 fig_fixedtime = ancestor(src,'figure','toplevel');
+0141 gui = getappdata(fig_fixedtime,'gui');
+0142 data = getappdata(gui.figh_nucleus,'data');
+0143 
+0144 id = str2double(get(src,'Tag'));
+0145 value = get(src,'Value');
+0146 
+0147 data.invstd.Tfixed_bool(id) = value;
+0148 
+0149 % update local GUI
+0150 setappdata(fig_fixedtime,'gui',gui);
+0151 
+0152 % update NUCLEUSinv
+0153 setappdata(gui.figh_nucleus,'data',data);
+0154 end
+0155 
+0156 % subfunction to update the edit fields
+0157 function ft_updateEdit(src,~)
+0158 fig_fixedtime = ancestor(src,'figure','toplevel');
+0159 gui = getappdata(fig_fixedtime,'gui');
+0160 data = getappdata(gui.figh_nucleus,'data');
+0161 
+0162 id = str2double(get(src,'Tag'));
+0163 value = str2double(get(src,'String'));
+0164 
+0165 data.invstd.Tfixed_val(id) = value;
+0166 
+0167 % update local GUI
+0168 setappdata(fig_fixedtime,'gui',gui);
+0169 
+0170 % update NUCLEUSinv
+0171 setappdata(gui.figh_nucleus,'data',data);
+0172 end
+0173 
+0174 % subfunction to update the edit fields
+0175 function ft_closeme(src,~)
+0176 fig_fixedtime = ancestor(src,'figure','toplevel');
+0177 % try to close the sub GUI in a clean manner
+0178 try
+0179     gui = getappdata(fig_fixedtime,'gui');
+0180     data = getappdata(gui.figh_nucleus,'data');
+0181     % reset ui controls
+0182     data.invstd.Tfixed_bool = zeros(1,5);
+0183     data.invstd.Tfixed_val = zeros(1,5);
+0184 
+0185     % update NUCLEUSinv
+0186     setappdata(gui.figh_nucleus,'data',data);
+0187     delete(fig_fixedtime);
+0188 catch
+0189     % if this is not working: just close it
+0190     delete(fig_fixedtime);
+0191 end
+0192 
+0193 
+0194 end
+0195 
+0196 %------------- END OF CODE --------------
+0197 
+0198 %% License:
+0199 % MIT License
+0200 %
+0201 % Copyright (c) 2023 Thomas Hiller
+0202 %
+0203 % Permission is hereby granted, free of charge, to any person obtaining a copy
+0204 % of this software and associated documentation files (the "Software"), to deal
+0205 % in the Software without restriction, including without limitation the rights
+0206 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+0207 % copies of the Software, and to permit persons to whom the Software is
+0208 % furnished to do so, subject to the following conditions:
+0209 %
+0210 % The above copyright notice and this permission notice shall be included in all
+0211 % copies or substantial portions of the Software.
+0212 %
+0213 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+0214 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+0215 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+0216 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+0217 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+0218 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+0219 % SOFTWARE.
    +
    Generated by m2html © 2005
    + + \ No newline at end of file diff --git a/doc/nucleus/functions/interface/changeColorTheme.html b/doc/nucleus/functions/interface/changeColorTheme.html index e25643e..289a155 100644 --- a/doc/nucleus/functions/interface/changeColorTheme.html +++ b/doc/nucleus/functions/interface/changeColorTheme.html @@ -262,34 +262,51 @@

    SOURCE CODE ^updatePlotsPSD; 0186 updatePlotsCPS; 0187 updatePlotsNMR; -0188 end -0189 -0190 end -0191 -0192 %------------- END OF CODE -------------- -0193 -0194 %% License: -0195 % MIT License -0196 % -0197 % Copyright (c) 2018 Thomas Hiller -0198 % -0199 % Permission is hereby granted, free of charge, to any person obtaining a copy -0200 % of this software and associated documentation files (the "Software"), to deal -0201 % in the Software without restriction, including without limitation the rights -0202 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0203 % copies of the Software, and to permit persons to whom the Software is -0204 % furnished to do so, subject to the following conditions: -0205 % -0206 % The above copyright notice and this permission notice shall be included in all -0207 % copies or substantial portions of the Software. -0208 % -0209 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0210 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0211 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0212 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0213 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0214 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0215 % SOFTWARE. +0188 +0189 case 'FIXEDTIMEVIEW' +0190 % set the background color for all uicontainer (HBox, VBox, etc.) +0191 h = findall(fig,'-depth',inf,'Type','uicontainer'); +0192 set(h,'BackGroundColor',myui.colors.panelBG); +0193 +0194 % chekcbox controls +0195 h = findobj(fig,'Type','uicontrol','-and','Style','checkbox'); +0196 set(h,'BackGroundColor',myui.colors.panelBG,'ForeGroundColor',myui.colors.panelFG); +0197 +0198 % edit field +0199 h = findall(fig,'Type','uicontrol','-and','Style','edit'); +0200 set(h,'BackGroundColor',myui.colors.editBG,'ForeGroundColor',myui.colors.panelFG); +0201 +0202 % text field +0203 h = findobj(fig,'Type','uicontrol','-and','Style','text'); +0204 set(h,'BackGroundColor',myui.colors.panelBG,'ForeGroundColor',myui.colors.panelFG); +0205 end +0206 +0207 end +0208 +0209 %------------- END OF CODE -------------- +0210 +0211 %% License: +0212 % MIT License +0213 % +0214 % Copyright (c) 2018 Thomas Hiller +0215 % +0216 % Permission is hereby granted, free of charge, to any person obtaining a copy +0217 % of this software and associated documentation files (the "Software"), to deal +0218 % in the Software without restriction, including without limitation the rights +0219 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0220 % copies of the Software, and to permit persons to whom the Software is +0221 % furnished to do so, subject to the following conditions: +0222 % +0223 % The above copyright notice and this permission notice shall be included in all +0224 % copies or substantial portions of the Software. +0225 % +0226 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0227 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0228 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0229 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0230 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0231 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0232 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/functions/interface/exportData.html b/doc/nucleus/functions/interface/exportData.html index 96e5aae..24ec3cd 100644 --- a/doc/nucleus/functions/interface/exportData.html +++ b/doc/nucleus/functions/interface/exportData.html @@ -33,7 +33,7 @@

    DESCRIPTION ^DESCRIPTION ^CROSS-REFERENCE INFORMATION ^ <h2><a name=SUBFUNCTIONS ^

    +
  • function exportINV_EXCEL(gui,INVdata,id,sfile,spath)
  • function exportINV_CSV(INVdata,sfile)
  • function exportINV_BGR_repos(INVdata,sfile)
  • function exportMOD_EXCEL()
  • function doexport = checkINV(INVdata,id)
  • function doexport = checkMOD(data)
  • function amp = findApproxTlgmAmplitude(t,f,TLGM)

    • SOURCE CODE ^

    0001 function exportData(fig_tag,format)
@@ -83,7 +84,7 @@ 
    SOURCE CODE ^%
 0007 % Inputs:
 0008 %       fig_tag - 'MOD' or 'INV'
-0009 %       format - 'matS', 'matA', 'excelS' or 'LIAG'
+0009 %       format - 'matS', 'matA', 'excelS', 'LIAG', or 'bgr_repo'
 0010 %
 0011 % Outputs:
 0012 %       none
@@ -99,115 +100,115 @@ 
    SOURCE CODE ^%       checkMOD
 0023 %       exportINV_EXCEL
 0024 %       exportINV_CSV
-0025 %       exportMOD_EXCEL
-0026 %       findApproxTlgmAmplitude
-0027 %
-0028 % MAT-files required:
-0029 %       none
-0030 %
-0031 % See also: NUCLEUSinv, NUCLEUSmod
-0032 % Author: see AUTHORS.md
-0033 % email: see AUTHORS.md
-0034 % License: MIT License (at end)
-0035 
-0036 %------------- BEGIN CODE --------------
-0037 
-0038 %% get GUI handle and data
-0039 fig = findobj('Tag',fig_tag);
-0040 gui = getappdata(fig,'gui');
-0041 data = getappdata(fig,'data');
-0042 
-0043 switch fig_tag
-0044     case 'INV'
-0045         % get inversion data
-0046         INVdata = getappdata(fig,'INVdata');
-0047         
-0048         % which NMR signal
-0049         id = get(gui.listbox_handles.signal,'Value');
-0050         
-0051         % different export formats
-0052         switch format
-0053             
-0054             case 'LIAGcsvT2' % raw data
-0055                 % check if there is any data at all
-0056                 if isfield(data.import,'NMR')
-0057                     
-0058                     % display info text
-0059                     displayStatusText(gui,...
-0060                         'Exporting LIAG csv T2 raw data ...');
-0061                     % which NMR signal
-0062                     id = get(gui.listbox_handles.signal,'Value');
-0063                     % export path
-0064                     spath = data.import.path;
-0065                     % export file names
-0066                     fname = data.import.NMR.data{id}.datfile;
-0067                     fname_org = [fname,'.org'];
-0068                     % ask the user if the imag part should be set to zero
-0069                     quest = 'Set imaginary part to ZERO?';
-0070                     title = 'Saving T2 data';
-0071                     answer = questdlg(quest,title,'Yes');
-0072                     
-0073                     switch answer
-0074                         case {'Yes','No'}
-0075                             % first copy original file to backup file
-0076                             sourcef = fullfile(spath,fname);
-0077                             destf = fullfile(spath,fname_org);
-0078                             [status,~,~] = copyfile(sourcef,destf);
-0079                             % if the backup was successful save the data
-0080                             if status == 1
-0081                                 t = data.import.NMR.data{id}.time;
-0082                                 s = data.import.NMR.data{id}.signal;
-0083                                 
-0084                                 switch answer
-0085                                     case 'Yes'
-0086                                         out = [t real(s) zeros(size(t))];
-0087                                     case 'No'
-0088                                         out = [t real(s) imag(s)];
-0089                                 end
-0090                                 dlmwrite(sourcef,out,'precision','%.6f');
-0091                                 
-0092                                 % display info text
-0093                                 displayStatusText(gui,...
-0094                                     'Exporting LIAG csv T2 raw data ... done');
-0095                             else
-0096                                 % display info text
-0097                                 displayStatusText(gui,...
-0098                                     'Exporting LIAG csv T2 raw data ... canceled');
-0099                             end
-0100                         otherwise
-0101                             % display info text
-0102                             displayStatusText(gui,...
-0103                                 'Exporting LIAG csv T2 raw data ... canceled');
-0104                     end
-0105                 end
-0106                 
-0107             otherwise % inv data
-0108                 % check if data can be exported
-0109                 doexport_inv = checkINV(INVdata,id);
-0110                 
-0111                 if doexport_inv
-0112                     % get the new file name
-0113                     sfilename = data.import.NMR.filesShort{id};
-0114                     ind1 = strfind(sfilename,'.');
-0115                     if isempty(ind1)
-0116                         sfilename = [sfilename,'_INV'];
-0117                     else
-0118                         sfilename = [sfilename(1:ind1-1),'_INV'];
-0119                     end
-0120                     
-0121                     % different export formats
-0122                     switch format
-0123                         case 'excelS'
-0124                             % get the file name
-0125                             [sfile,spath] = uiputfile('*.xlsx',...
-0126                                 'Save inversion to Excel-file',...
-0127                                 fullfile(data.import.path,[sfilename,'.xlsx']));
-0128                             
-0129                             % if user didn't cancel
-0130                             if sum([sfile spath]) > 0
-0131                                 exportINV_EXCEL(gui,INVdata,id,sfile,spath);
-0132                             end
-0133                             
+0025 %       exportINV_BGR_repos
+0026 %       exportMOD_EXCEL
+0027 %       findApproxTlgmAmplitude
+0028 %
+0029 % MAT-files required:
+0030 %       none
+0031 %
+0032 % See also: NUCLEUSinv, NUCLEUSmod
+0033 % Author: see AUTHORS.md
+0034 % email: see AUTHORS.md
+0035 % License: MIT License (at end)
+0036 
+0037 %------------- BEGIN CODE --------------
+0038 
+0039 %% get GUI handle and data
+0040 fig = findobj('Tag',fig_tag);
+0041 gui = getappdata(fig,'gui');
+0042 data = getappdata(fig,'data');
+0043 
+0044 switch fig_tag
+0045     case 'INV'
+0046         % get inversion data
+0047         INVdata = getappdata(fig,'INVdata');
+0048         
+0049         % which NMR signal
+0050         id = get(gui.listbox_handles.signal,'Value');
+0051         
+0052         % different export formats
+0053         switch format
+0054             
+0055             case 'LIAGcsvT2' % raw data
+0056                 % check if there is any data at all
+0057                 if isfield(data.import,'NMR')
+0058                     
+0059                     % display info text
+0060                     displayStatusText(gui,...
+0061                         'Exporting LIAG csv T2 raw data ...');
+0062                     % which NMR signal
+0063                     id = get(gui.listbox_handles.signal,'Value');
+0064                     % export path
+0065                     spath = data.import.path;
+0066                     % export file names
+0067                     fname = data.import.NMR.data{id}.datfile;
+0068                     fname_org = [fname,'.org'];
+0069                     % ask the user if the imag part should be set to zero
+0070                     quest = 'Set imaginary part to ZERO?';
+0071                     title = 'Saving T2 data';
+0072                     answer = questdlg(quest,title,'Yes');
+0073                     
+0074                     switch answer
+0075                         case {'Yes','No'}
+0076                             % first copy original file to backup file
+0077                             sourcef = fullfile(spath,fname);
+0078                             destf = fullfile(spath,fname_org);
+0079                             [status,~,~] = copyfile(sourcef,destf);
+0080                             % if the backup was successful save the data
+0081                             if status == 1
+0082                                 t = data.import.NMR.data{id}.time;
+0083                                 s = data.import.NMR.data{id}.signal;
+0084                                 
+0085                                 switch answer
+0086                                     case 'Yes'
+0087                                         out = [t real(s) zeros(size(t))];
+0088                                     case 'No'
+0089                                         out = [t real(s) imag(s)];
+0090                                 end
+0091                                 dlmwrite(sourcef,out,'precision','%.6f');
+0092                                 
+0093                                 % display info text
+0094                                 displayStatusText(gui,...
+0095                                     'Exporting LIAG csv T2 raw data ... done');
+0096                             else
+0097                                 % display info text
+0098                                 displayStatusText(gui,...
+0099                                     'Exporting LIAG csv T2 raw data ... canceled');
+0100                             end
+0101                         otherwise
+0102                             % display info text
+0103                             displayStatusText(gui,...
+0104                                 'Exporting LIAG csv T2 raw data ... canceled');
+0105                     end
+0106                 end
+0107                 
+0108             otherwise % inv data
+0109                 % check if data can be exported
+0110                 doexport_inv = checkINV(INVdata,id);
+0111                 
+0112                 if doexport_inv
+0113                     % get the new file name
+0114                     sfilename = data.import.NMR.filesShort{id};
+0115                     ind1 = strfind(sfilename,'.');
+0116                     if isempty(ind1)
+0117                         sfilename = [sfilename,'_INV'];
+0118                     else
+0119                         sfilename = [sfilename(1:ind1-1),'_INV'];
+0120                     end
+0121                     
+0122                     % different export formats
+0123                     switch format
+0124                         case 'excelS'
+0125                             % get the file name
+0126                             [sfile,spath] = uiputfile('*.xlsx',...
+0127                                 'Save inversion to Excel-file',...
+0128                                 fullfile(data.import.path,[sfilename,'.xlsx']));
+0129                             
+0130                             % if user didn't cancel
+0131                             if sum([sfile spath]) > 0
+0132                                 exportINV_EXCEL(gui,INVdata,id,sfile,spath);
+0133                             end
 0134                         case 'matS'
 0135                             % get the file name
 0136                             [sfile,spath] = uiputfile('*.mat',...
@@ -318,7 +319,7 @@ 
    SOURCE CODE ^findApproxTlgmAmplitude(T,F,TLGM);
+0244                                         amp = findApproxTlgmAmplitude(T,F,TLGM);
 0245                                         stem(TLGM,amp,...
 0246                                             'x-','Color',[0.3 0.3 0.3],'LineWidth',2,...
 0247                                             'Tag','TLGM','Parent',ax(2));
@@ -378,381 +379,504 @@ 
    SOURCE CODE ^'This routine works only on LIAG specific project data.'},...
 0302                                     'No LIAG data');
 0303                             end
-0304                     end
-0305                 end
-0306         end
-0307     case 'MOD'
-0308         % check if data can be exported
-0309         doexport_mod = checkMOD(data);
-0310         if doexport_mod
-0311             % different export formats
-0312             switch format
-0313                 case 'mat'
-0314                     % gather all relevant data
-0315                     out = data.results;
-0316                     if isfield(out.NMR.raw,'Tb')
-0317                         out.NMR.raw = rmfield(out.NMR.raw,'Tb');
-0318                     end
-0319                     if isfield(out.NMR.raw,'rho')
-0320                         out.NMR.raw = rmfield(out.NMR.raw,'rho');
-0321                     end
-0322                     out.NMRMOD_GUI.geometry = data.geometry;
-0323                     out.NMRMOD_GUI.pressure = data.pressure;
-0324                     out.NMRMOD_GUI.nmr = data.nmr;
-0325                     out.NMRMOD_GUI.myui = gui.myui;
-0326                     
-0327                     displayStatusText(gui,'Saving to MAT-file ...');
-0328                     [FileName,PathName,~] = uiputfile({'*.mat','Matlab file'},'NUCLEUSmod: Save Data',fullfile(pwd,'NUCLEUSmod_forward.mat'));
-0329                     
-0330                     if ~isequal(FileName,0) || ~isequal(PathName,0)
-0331                         clear data
-0332                         data = out; %#ok<NASGU>
-0333                         save(fullfile(PathName,FileName),'data','-v7.3');
-0334                         displayStatusText(gui,'Saving to MAT-file ... done.');
-0335                     else
-0336                         displayStatusText(gui,'Saving to MAT-file ... canceled.');
-0337                     end
-0338                     
-0339                 case 'xls'
-0340                     indd = data.pressure.DrainLevels;
-0341                     indi = data.pressure.ImbLevels;
-0342                     results = data.results;
-0343                     
-0344                     displayStatusText(gui,'Saving to XLS-file ...');
-0345                     [FileName,PathName,~] = uiputfile({'*.xls','XLS file'},'NUCLEUSmod: Save Data',fullfile(pwd,'NUCLEUSmod_forward.xls'));
-0346                     
-0347                     if ~isequal(FileName,0) || ~isequal(PathName,0)
-0348                         exportMOD_EXCEL;
-0349                         displayStatusText(gui,'Saving to XLS-file ... done.');
-0350                     else
-0351                         displayStatusText(gui,'Saving to XLS-file ... canceled.');
-0352                     end
-0353                     
-0354                 otherwise
-0355                     helpdlg({'exportData:','Not yet implemented.'},'NUCLEUSmod info:');
+0304                         case 'BGR_repos'
+0305                             
+0306                             % get the file name
+0307                             [sfile,spath] = uiputfile('*.csv',...
+0308                                 'Save measurement and inversion data and parameters csv-file',...
+0309                                 fullfile(data.import.path,[sfilename,'.csv']));
+0310                             % if user didn't cancel
+0311                             if sum([sfile spath]) > 0
+0312                                 csvname = fullfile(spath,sfile);
+0313                                 exportINV_BGR_repos(INVdata{id},csvname);
+0314                             end
+0315                             
+0316                                 
+0317                     end
+0318                 end
+0319         end
+0320     case 'MOD'
+0321         % check if data can be exported
+0322         doexport_mod = checkMOD(data);
+0323         if doexport_mod
+0324             % different export formats
+0325             switch format
+0326                 case 'mat'
+0327                     % gather all relevant data
+0328                     out = data.results;
+0329                     if isfield(out.NMR.raw,'Tb')
+0330                         out.NMR.raw = rmfield(out.NMR.raw,'Tb');
+0331                     end
+0332                     if isfield(out.NMR.raw,'rho')
+0333                         out.NMR.raw = rmfield(out.NMR.raw,'rho');
+0334                     end
+0335                     out.NMRMOD_GUI.geometry = data.geometry;
+0336                     out.NMRMOD_GUI.pressure = data.pressure;
+0337                     out.NMRMOD_GUI.nmr = data.nmr;
+0338                     out.NMRMOD_GUI.myui = gui.myui;
+0339                     
+0340                     displayStatusText(gui,'Saving to MAT-file ...');
+0341                     [FileName,PathName,~] = uiputfile({'*.mat','Matlab file'},'NUCLEUSmod: Save Data',fullfile(pwd,'NUCLEUSmod_forward.mat'));
+0342                     
+0343                     if ~isequal(FileName,0) || ~isequal(PathName,0)
+0344                         clear data
+0345                         data = out; %#ok<NASGU>
+0346                         save(fullfile(PathName,FileName),'data','-v7.3');
+0347                         displayStatusText(gui,'Saving to MAT-file ... done.');
+0348                     else
+0349                         displayStatusText(gui,'Saving to MAT-file ... canceled.');
+0350                     end
+0351                     
+0352                 case 'xls'
+0353                     indd = data.pressure.DrainLevels;
+0354                     indi = data.pressure.ImbLevels;
+0355                     results = data.results;
 0356                     
-0357             end
-0358         end
-0359 end
-0360 
-0361 end
-0362 
-0363 %%
-0364 function exportINV_EXCEL(gui,INVdata,id,sfile,spath)
-0365 unit = INVdata{id}.process.timescale;
-0366 
-0367 % gather all data
-0368 % raw data
-0369 tmp1(:,1) = INVdata{id}.results.nmrraw.t(:);
-0370 header1{1} = ['time [',unit,']'];
-0371 if isreal(INVdata{id}.results.nmrraw.s(:))
-0372     header1{2} = 'amplitude [a.u.]';
-0373     tmp1(:,2) = INVdata{id}.results.nmrraw.s(:);
-0374     
-0375     b1 = {'raw data',''};
-0376     b1(2,:) = header1;
-0377     b1(3:2+size(tmp1,1),:) = [num2cell(tmp1(:,1)),num2cell(tmp1(:,2))];
-0378 else
-0379     header1{2} = 'real [a.u.]';
-0380     header1{3} = 'imag [a.u.]';
-0381     tmp1(:,2) = real(INVdata{id}.results.nmrraw.s(:));
-0382     tmp1(:,3) = imag(INVdata{id}.results.nmrraw.s(:));
-0383     
-0384     b1 = {'raw data','',''};
-0385     b1(2,:) = header1;
-0386     b1(3:2+size(tmp1,1),:) = [num2cell(tmp1(:,1)),num2cell(tmp1(:,2)),...
-0387         num2cell(tmp1(:,3))];
-0388 end
-0389 
-0390 % proc data
-0391 tmp2(:,1) = INVdata{id}.results.nmrproc.t(:);
-0392 tmp2(:,2) = INVdata{id}.results.nmrproc.s(:);
-0393 header2{1} = ['time [',unit,']'];
-0394 header2{2} = 'amplitude [a.u.]';
-0395 
-0396 b2 = {'proc data',''};
-0397 b2(2,:) = header2;
-0398 b2(3:2+size(tmp2,1),:) = [num2cell(tmp2(:,1)),num2cell(tmp2(:,2))];
-0399 
-0400 % fit data (incl. residuals)
-0401 tmp3(:,1) = INVdata{id}.results.invstd.fit_t(:);
-0402 tmp3(:,2) = INVdata{id}.results.invstd.fit_s(:);
-0403 tmp3(:,3) = INVdata{id}.results.invstd.residual(:);
-0404 header3{1} = ['time [',unit,']'];
-0405 header3{2} = 'amplitude [a.u.]';
-0406 header3{3} = 'residual [-]';
-0407 
-0408 b3 = {'fit data','',''};
-0409 b3(2,:) = header3;
-0410 b3(3:2+size(tmp3,1),:) = [num2cell(tmp3(:,1)),num2cell(tmp3(:,2)),...
-0411     num2cell(tmp3(:,3))];
+0357                     displayStatusText(gui,'Saving to XLS-file ...');
+0358                     [FileName,PathName,~] = uiputfile({'*.xls','XLS file'},'NUCLEUSmod: Save Data',fullfile(pwd,'NUCLEUSmod_forward.xls'));
+0359                     
+0360                     if ~isequal(FileName,0) || ~isequal(PathName,0)
+0361                         exportMOD_EXCEL;
+0362                         displayStatusText(gui,'Saving to XLS-file ... done.');
+0363                     else
+0364                         displayStatusText(gui,'Saving to XLS-file ... canceled.');
+0365                     end
+0366                     
+0367                 otherwise
+0368                     helpdlg({'exportData:','Not yet implemented.'},'NUCLEUSmod info:');
+0369                     
+0370             end
+0371         end
+0372 end
+0373 
+0374 end
+0375 
+0376 %%
+0377 function exportINV_EXCEL(gui,INVdata,id,sfile,spath)
+0378 unit = INVdata{id}.process.timescale;
+0379 
+0380 % gather all data
+0381 % raw data
+0382 tmp1(:,1) = INVdata{id}.results.nmrraw.t(:);
+0383 header1{1} = ['time [',unit,']'];
+0384 if isreal(INVdata{id}.results.nmrraw.s(:))
+0385     header1{2} = 'amplitude [a.u.]';
+0386     tmp1(:,2) = INVdata{id}.results.nmrraw.s(:);
+0387     
+0388     b1 = {'raw data',''};
+0389     b1(2,:) = header1;
+0390     b1(3:2+size(tmp1,1),:) = [num2cell(tmp1(:,1)),num2cell(tmp1(:,2))];
+0391 else
+0392     header1{2} = 'real [a.u.]';
+0393     header1{3} = 'imag [a.u.]';
+0394     tmp1(:,2) = real(INVdata{id}.results.nmrraw.s(:));
+0395     tmp1(:,3) = imag(INVdata{id}.results.nmrraw.s(:));
+0396     
+0397     b1 = {'raw data','',''};
+0398     b1(2,:) = header1;
+0399     b1(3:2+size(tmp1,1),:) = [num2cell(tmp1(:,1)),num2cell(tmp1(:,2)),...
+0400         num2cell(tmp1(:,3))];
+0401 end
+0402 
+0403 % proc data
+0404 tmp2(:,1) = INVdata{id}.results.nmrproc.t(:);
+0405 tmp2(:,2) = INVdata{id}.results.nmrproc.s(:);
+0406 header2{1} = ['time [',unit,']'];
+0407 header2{2} = 'amplitude [a.u.]';
+0408 
+0409 b2 = {'proc data',''};
+0410 b2(2,:) = header2;
+0411 b2(3:2+size(tmp2,1),:) = [num2cell(tmp2(:,1)),num2cell(tmp2(:,2))];
 0412 
-0413 % relaxation times
-0414 switch INVdata{id}.invstd.invtype
-0415     case {'mono','free'}
-0416         switch INVdata{id}.results.nmrproc.T1T2
-0417             case 'T1'
-0418                 tmp4 = [INVdata{id}.results.invstd.T1(:)...
-0419                     INVdata{id}.results.invstd.E0(:)];
-0420                 header4 = {['T1 [',unit,']'],'amplitude [a.u.]'};
-0421             case 'T2'
-0422                 tmp4 = [INVdata{id}.results.invstd.T2(:)...
-0423                     INVdata{id}.results.invstd.E0(:)];
-0424                 header4 = {['T2 [',unit,']'],'amplitude [a.u.]'};
-0425         end
-0426         
-0427     case {'LU','NNLS','MUMO'}
-0428         tmp4 = [INVdata{id}.results.invstd.T1T2me(:)...
-0429             INVdata{id}.results.invstd.T1T2f(:)];
-0430         header4 = {['relaxation times [',unit,']'],'amplitudes [a.u.]'};
-0431         
-0432     otherwise
-0433         disp('Something is utterly wrong.')
-0434 end
-0435 
-0436 b4 = {'relaxation times',''};
-0437 b4(2,:) = header4;
-0438 b4(3:2+size(tmp4,1),:) = [num2cell(tmp4(:,1)),num2cell(tmp4(:,2))];
-0439 
-0440 % glue together the output matrix
-0441 out(1:size(b1,1),1:size(b1,2)) = b1;
-0442 yi = size(b1,2)+2;
-0443 out(1:size(b2,1),yi:yi-1+size(b2,2)) = b2;
-0444 yi = yi + size(b2,2)+1;
-0445 out(1:size(b3,1),yi:yi-1+size(b3,2)) = b3;
-0446 yi = yi + size(b3,2)+1;
-0447 out(1:size(b4,1),yi:yi-1+size(b4,2)) = b4;
+0413 % fit data (incl. residuals)
+0414 tmp3(:,1) = INVdata{id}.results.invstd.fit_t(:);
+0415 tmp3(:,2) = INVdata{id}.results.invstd.fit_s(:);
+0416 tmp3(:,3) = INVdata{id}.results.invstd.residual(:);
+0417 header3{1} = ['time [',unit,']'];
+0418 header3{2} = 'amplitude [a.u.]';
+0419 header3{3} = 'residual [-]';
+0420 
+0421 b3 = {'fit data','',''};
+0422 b3(2,:) = header3;
+0423 b3(3:2+size(tmp3,1),:) = [num2cell(tmp3(:,1)),num2cell(tmp3(:,2)),...
+0424     num2cell(tmp3(:,3))];
+0425 
+0426 % relaxation times
+0427 switch INVdata{id}.invstd.invtype
+0428     case {'mono','free'}
+0429         switch INVdata{id}.results.nmrproc.T1T2
+0430             case 'T1'
+0431                 tmp4 = [INVdata{id}.results.invstd.T1(:)...
+0432                     INVdata{id}.results.invstd.E0(:)];
+0433                 header4 = {['T1 [',unit,']'],'amplitude [a.u.]'};
+0434             case 'T2'
+0435                 tmp4 = [INVdata{id}.results.invstd.T2(:)...
+0436                     INVdata{id}.results.invstd.E0(:)];
+0437                 header4 = {['T2 [',unit,']'],'amplitude [a.u.]'};
+0438         end
+0439         
+0440     case {'LU','NNLS','MUMO'}
+0441         tmp4 = [INVdata{id}.results.invstd.T1T2me(:)...
+0442             INVdata{id}.results.invstd.T1T2f(:)];
+0443         header4 = {['relaxation times [',unit,']'],'amplitudes [a.u.]'};
+0444         
+0445     otherwise
+0446         disp('Something is utterly wrong.')
+0447 end
 0448 
-0449 % display info text
-0450 displayStatusText(gui,...
-0451     'Exporting inversion data to Excel-file ...');
-0452 % save to file
-0453 xlswrite(fullfile(spath,sfile),out,'NMRdata','A1');
-0454 
-0455 % remove the first standard excel sheet
-0456 [~,sheets] = xlsfinfo(fullfile(spath,sfile));
-0457 objExcel = actxserver('Excel.Application');
-0458 objExcel.Workbooks.Open(fullfile(spath,sfile));
-0459 objExcel.ActiveWorkbook.Worksheets.Item(sheets{1}).Delete;
-0460 objExcel.ActiveWorkbook.Save;
-0461 objExcel.ActiveWorkbook.Close;
-0462 objExcel.Quit;
-0463 objExcel.delete;
-0464 % display info text
-0465 displayStatusText(gui,...
-0466     'Exporting inversion data to Excel-file ... done');
-0467 end
-0468 
-0469 %%
-0470 function exportINV_CSV(INVdata,sfile)
-0471 unit = INVdata.process.timescale;
-0472 
-0473 % gather all data
-0474 % proc data
-0475 tmp2(:,1) = INVdata.results.nmrproc.t(:);
-0476 tmp2(:,2) = INVdata.results.nmrproc.s(:);
-0477 header2{1} = ['time [',unit,']'];
-0478 header2{2} = 'signal [a.u.]';
-0479 
-0480 % fit data (incl. residuals)
-0481 tmp3(:,1) = INVdata.results.invstd.fit_t(:);
-0482 tmp3(:,2) = INVdata.results.invstd.fit_s(:);
-0483 tmp3(:,3) = INVdata.results.invstd.residual(:);
-0484 header3{1} = ['time [',unit,']'];
-0485 header3{2} = 'fit [a.u.]';
-0486 header3{3} = 'residual [-]';
-0487 
-0488 % relaxation times
-0489 switch INVdata.invstd.invtype
-0490     case {'LU','NNLS'}
-0491         por = INVdata.invstd.porosity;
-0492         F = INVdata.results.invstd.T1T2f(:);
-0493         F = 100*por.*F./sum(F);
-0494         tmp4 = [INVdata.results.invstd.T1T2me(:)...
-0495             INVdata.results.invstd.T1T2f(:) F];
-0496         header4 = {['relaxation times [',unit,']'],'frequency [-]',...
-0497             ' water content [vol. %]'};
-0498         
-0499     case {'mono','free'}
-0500         por = INVdata.invstd.porosity;
-0501         F = 100*por.*INVdata.results.invstd.E0./sum(INVdata.results.invstd.E0);
-0502         switch INVdata.results.nmrproc.T1T2
-0503             case 'T1'
-0504                 tmp4 = [INVdata.results.invstd.T1(:)...
-0505                     INVdata.results.invstd.E0(:) F(:)];
-0506                 header4 = {['relaxation time(s) T1 [',unit,']'],...
-0507                     'amplitude [a.u.]',' water content [vol. %]'};
-0508             case 'T2'
-0509                 tmp4 = [INVdata.results.invstd.T2(:)...
-0510                     INVdata.results.invstd.E0(:) F(:)];
-0511                 header4 = {['relaxation time(s) T2 [',unit,']'],...
-0512                     'amplitude [a.u.]',' water content [vol. %]'};
-0513         end
-0514         
-0515     otherwise
-0516         % Nothing to do
-0517 end
-0518 
-0519 % glue together headers
-0520 cHeader = [header2 header3 header4];
-0521 % insert commas
-0522 commaHeader = [cHeader;repmat({','},1,numel(cHeader))];
-0523 commaHeader = commaHeader(:)';
-0524 % cHeader as string with commas
-0525 textHeader = cell2mat(commaHeader(1:numel(commaHeader)-1));
-0526 
-0527 maxrows = max([size(tmp2,1) size(tmp3,1) size(tmp4,1)]);
-0528 % glue together data
-0529 if size(tmp2,1) < maxrows
-0530     tmp2(end+1:maxrows,:) = NaN;
-0531 end
-0532 if size(tmp3,1) < maxrows
-0533     tmp3(end+1:maxrows,:) = NaN;
-0534 end
-0535 if size(tmp4,1) < maxrows
-0536     tmp4(end+1:maxrows,:) = NaN;
-0537 end
-0538 out(1:maxrows,1:size(tmp2,2)) = tmp2;
-0539 yi = size(tmp2,2)+1;
-0540 out(1:maxrows,yi:yi-1+size(tmp3,2)) = tmp3;
-0541 yi = yi + size(tmp3,2);
-0542 out(1:maxrows,yi:yi-1+size(tmp4,2)) = tmp4;
-0543 
-0544 % save to file
-0545 %write header to file
-0546 fid = fopen(sfile,'w');
-0547 fprintf(fid,'%s\n',textHeader);
-0548 fclose(fid);
-0549 %write data to end of file
-0550 dlmwrite(sfile,out,'-append','precision','%.5f');
-0551 
-0552 end
-0553 
-0554 %%
-0555 function exportMOD_EXCEL()
-0556 xlswrite(fullfile(PathName,FileName),{'pressure [Pa]','saturation (drain)','saturation (imb)'},'CPS','A1');
-0557 xlswrite(fullfile(PathName,FileName),[results.SAT.pressure(:) results.SAT.Sdfull(:) results.SAT.Sifull(:)],'CPS','A2');
-0558 
-0559 out = zeros(numel(results.NMR.t),numel(indd)+1);
-0560 out(:,1) = results.NMR.t(:);
-0561 header = cell(1,1);
-0562 header{1} = 'time [s]';
-0563 for i = 1:numel(indd)
-0564     out(:,i+1) = results.NMR.EdT1(indd(i),:)';
-0565     header{i+1} = ['S',num2str(i)];
-0566 end
-0567 xlswrite(fullfile(PathName,FileName),header,'NMR_T1_drain','A1');
-0568 xlswrite(fullfile(PathName,FileName),out,'NMR_T1_drain','A2');
-0569 out = zeros(numel(results.NMR.t),numel(indd)+1);
-0570 out(:,1) = results.NMR.t(:);
-0571 header = cell(1,1);
-0572 header{1} = 'time [s]';
-0573 for i = 1:numel(indd)
-0574     out(:,i+1) = results.NMR.EdT2(indd(i),:)';
-0575     header{i+1} = ['S',num2str(i)];
-0576 end
-0577 xlswrite(fullfile(PathName,FileName),header,'NMR_T2_drain','A1');
-0578 xlswrite(fullfile(PathName,FileName),out,'NMR_T2_drain','A2');
-0579 
-0580 out = zeros(numel(results.NMR.t),numel(indi)+1);
-0581 out(:,1) = results.NMR.t(:);
-0582 header = cell(1,1);
-0583 header{1} = 'time [s]';
-0584 for i = 1:numel(indi)
-0585     out(:,i+1) = results.NMR.EiT1(indi(i),:)';
-0586     header{i+1} = ['S',num2str(i)];
-0587 end
-0588 xlswrite(fullfile(PathName,FileName),header,'NMR_T1_imb','A1');
-0589 xlswrite(fullfile(PathName,FileName),out,'NMR_T1_imb','A2');
-0590 
-0591 out = zeros(numel(results.NMR.t),numel(indi)+1);
-0592 out(:,1) = results.NMR.t(:);
-0593 header = cell(1,1);
-0594 header{1} = 'time [s]';
-0595 for i = 1:numel(indi)
-0596     out(:,i+1) = results.NMR.EiT2(indi(i),:)';
-0597     header{i+1} = ['S',num2str(i)];
-0598 end
-0599 xlswrite(fullfile(PathName,FileName),header,'NMR_T2_imb','A1');
-0600 xlswrite(fullfile(PathName,FileName),out,'NMR_T2_imb','A2');
-0601 
-0602 % remove the first standard excel sheet
-0603 [~,sheets] = xlsfinfo(fullfile(PathName,FileName));
-0604 objExcel = actxserver('Excel.Application');
-0605 objExcel.Workbooks.Open(fullfile(PathName,FileName));
-0606 objExcel.ActiveWorkbook.Worksheets.Item(sheets{1}).Delete;
-0607 objExcel.ActiveWorkbook.Save;
-0608 objExcel.ActiveWorkbook.Close;
-0609 objExcel.Quit;
-0610 objExcel.delete;
-0611 end
-0612 
-0613 %%
-0614 function doexport = checkINV(INVdata,id)
-0615 
-0616 doexport = false;
-0617 if ~isempty(INVdata) && ~isempty(id)
-0618     if isstruct(INVdata{id})
-0619         doexport = true;
-0620     else
-0621         helpdlg({'exportData:','No inversion data to save'},...
-0622             'Nothing to save');
-0623     end
-0624 else
-0625     helpdlg({'exportData:','No inversion data to save'},...
-0626         'Nothing to save');
-0627 end
-0628 
-0629 end
-0630 
-0631 %%
-0632 function doexport = checkMOD(data)
-0633 
-0634 doexport = false;
-0635 if isfield(data,'results')
-0636     if isfield(data.results,'NMR')
-0637         doexport = true;
-0638     else
-0639         helpdlg({'exportData:',...
-0640             'No data to save. Generate some data first.'},'NUCLEUSmod info:');
-0641     end
-0642 else
-0643     helpdlg({'exportData:',...
-0644         'No data to save. Generate some data first.'},'NUCLEUSmod info:');
-0645 end
-0646 
-0647 end
-0648 
-0649 %%
-0650 function amp = findApproxTlgmAmplitude(t,f,TLGM)
-0651 index = find(abs(t-TLGM)==min(abs(t-TLGM)));
-0652 amp = interp1(t(index-1:index+1),f(index-1:index+1),TLGM);
-0653 end
-0654 
-0655 %------------- END OF CODE --------------
-0656 
-0657 %% License:
-0658 % MIT License
-0659 %
-0660 % Copyright (c) 2018 Thomas Hiller
-0661 %
-0662 % Permission is hereby granted, free of charge, to any person obtaining a copy
-0663 % of this software and associated documentation files (the "Software"), to deal
-0664 % in the Software without restriction, including without limitation the rights
-0665 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-0666 % copies of the Software, and to permit persons to whom the Software is
-0667 % furnished to do so, subject to the following conditions:
-0668 %
-0669 % The above copyright notice and this permission notice shall be included in all
-0670 % copies or substantial portions of the Software.
-0671 %
-0672 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-0673 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-0674 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-0675 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-0676 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-0677 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-0678 % SOFTWARE.
    +0449 b4 = {'relaxation times',''}; +0450 b4(2,:) = header4; +0451 b4(3:2+size(tmp4,1),:) = [num2cell(tmp4(:,1)),num2cell(tmp4(:,2))]; +0452 +0453 % glue together the output matrix +0454 out(1:size(b1,1),1:size(b1,2)) = b1; +0455 yi = size(b1,2)+2; +0456 out(1:size(b2,1),yi:yi-1+size(b2,2)) = b2; +0457 yi = yi + size(b2,2)+1; +0458 out(1:size(b3,1),yi:yi-1+size(b3,2)) = b3; +0459 yi = yi + size(b3,2)+1; +0460 out(1:size(b4,1),yi:yi-1+size(b4,2)) = b4; +0461 +0462 % display info text +0463 displayStatusText(gui,... +0464 'Exporting inversion data to Excel-file ...'); +0465 % save to file +0466 xlswrite(fullfile(spath,sfile),out,'NMRdata','A1'); +0467 +0468 % remove the first standard excel sheet +0469 [~,sheets] = xlsfinfo(fullfile(spath,sfile)); +0470 objExcel = actxserver('Excel.Application'); +0471 objExcel.Workbooks.Open(fullfile(spath,sfile)); +0472 objExcel.ActiveWorkbook.Worksheets.Item(sheets{1}).Delete; +0473 objExcel.ActiveWorkbook.Save; +0474 objExcel.ActiveWorkbook.Close; +0475 objExcel.Quit; +0476 objExcel.delete; +0477 % display info text +0478 displayStatusText(gui,... +0479 'Exporting inversion data to Excel-file ... done'); +0480 end +0481 +0482 %% +0483 function exportINV_CSV(INVdata,sfile) +0484 unit = INVdata.process.timescale; +0485 +0486 % gather all data +0487 % proc data +0488 tmp2(:,1) = INVdata.results.nmrproc.t(:); +0489 tmp2(:,2) = INVdata.results.nmrproc.s(:); +0490 header2{1} = ['time [',unit,']']; +0491 header2{2} = 'signal [a.u.]'; +0492 +0493 % fit data (incl. residuals) +0494 tmp3(:,1) = INVdata.results.invstd.fit_t(:); +0495 tmp3(:,2) = INVdata.results.invstd.fit_s(:); +0496 tmp3(:,3) = INVdata.results.invstd.residual(:); +0497 header3{1} = ['time [',unit,']']; +0498 header3{2} = 'fit [a.u.]'; +0499 header3{3} = 'residual [-]'; +0500 +0501 % relaxation times +0502 switch INVdata.invstd.invtype +0503 case {'LU','NNLS'} +0504 por = INVdata.invstd.porosity; +0505 F = INVdata.results.invstd.T1T2f(:); +0506 F = 100*por.*F./sum(F); +0507 tmp4 = [INVdata.results.invstd.T1T2me(:)... +0508 INVdata.results.invstd.T1T2f(:) F]; +0509 header4 = {['relaxation times [',unit,']'],'frequency [-]',... +0510 ' water content [vol. %]'}; +0511 +0512 case {'mono','free'} +0513 por = INVdata.invstd.porosity; +0514 F = 100*por.*INVdata.results.invstd.E0./sum(INVdata.results.invstd.E0); +0515 switch INVdata.results.nmrproc.T1T2 +0516 case 'T1' +0517 tmp4 = [INVdata.results.invstd.T1(:)... +0518 INVdata.results.invstd.E0(:) F(:)]; +0519 header4 = {['relaxation time(s) T1 [',unit,']'],... +0520 'amplitude [a.u.]',' water content [vol. %]'}; +0521 case 'T2' +0522 tmp4 = [INVdata.results.invstd.T2(:)... +0523 INVdata.results.invstd.E0(:) F(:)]; +0524 header4 = {['relaxation time(s) T2 [',unit,']'],... +0525 'amplitude [a.u.]',' water content [vol. %]'}; +0526 end +0527 +0528 otherwise +0529 % Nothing to do +0530 end +0531 +0532 % glue together headers +0533 cHeader = [header2 header3 header4]; +0534 % insert commas +0535 commaHeader = [cHeader;repmat({','},1,numel(cHeader))]; +0536 commaHeader = commaHeader(:)'; +0537 % cHeader as string with commas +0538 textHeader = cell2mat(commaHeader(1:numel(commaHeader)-1)); +0539 +0540 maxrows = max([size(tmp2,1) size(tmp3,1) size(tmp4,1)]); +0541 % glue together data +0542 if size(tmp2,1) < maxrows +0543 tmp2(end+1:maxrows,:) = NaN; +0544 end +0545 if size(tmp3,1) < maxrows +0546 tmp3(end+1:maxrows,:) = NaN; +0547 end +0548 if size(tmp4,1) < maxrows +0549 tmp4(end+1:maxrows,:) = NaN; +0550 end +0551 out(1:maxrows,1:size(tmp2,2)) = tmp2; +0552 yi = size(tmp2,2)+1; +0553 out(1:maxrows,yi:yi-1+size(tmp3,2)) = tmp3; +0554 yi = yi + size(tmp3,2); +0555 out(1:maxrows,yi:yi-1+size(tmp4,2)) = tmp4; +0556 +0557 % save to file +0558 %write header to file +0559 fid = fopen(sfile,'w'); +0560 fprintf(fid,'%s\n',textHeader); +0561 fclose(fid); +0562 %write data to end of file +0563 dlmwrite(sfile,out,'-append','precision','%.5f'); +0564 +0565 end +0566 %% +0567 function exportINV_BGR_repos(INVdata,sfile) +0568 unit = INVdata.process.timescale; +0569 +0570 % gather all data +0571 % raw data +0572 tmp1(:,1) = INVdata.results.nmrraw.t(:); +0573 header1{1} = ['time [',unit,']']; +0574 if isreal(INVdata.results.nmrraw.s(:)) +0575 header1{2} = 'amplitude [a.u.]'; +0576 tmp1(:,2) = INVdata.results.nmrraw.s(:); +0577 +0578 b1 = {'raw data',''}; +0579 b1(2,:) = header1; +0580 b1(3:2+size(tmp1,1),:) = [num2cell(tmp1(:,1)),num2cell(tmp1(:,2))]; +0581 else +0582 header1{2} = 'real [a.u.]'; +0583 header1{3} = 'imag [a.u.]'; +0584 tmp1(:,2) = real(INVdata.results.nmrraw.s(:)); +0585 tmp1(:,3) = imag(INVdata.results.nmrraw.s(:)); +0586 +0587 b1 = {'raw data','',''}; +0588 b1(2,:) = header1; +0589 b1(3:2+size(tmp1,1),:) = [num2cell(tmp1(:,1)),num2cell(tmp1(:,2)),... +0590 num2cell(tmp1(:,3))]; +0591 end +0592 % proc data +0593 tmp2(:,1) = INVdata.results.nmrproc.t(:); +0594 tmp2(:,2) = INVdata.results.nmrproc.s(:); +0595 header2{1} = ['time [',unit,']']; +0596 header2{2} = 'signal [a.u.]'; +0597 +0598 % fit data (incl. residuals) +0599 tmp3(:,1) = INVdata.results.invstd.fit_t(:); +0600 tmp3(:,2) = INVdata.results.invstd.fit_s(:); +0601 tmp3(:,3) = INVdata.results.invstd.residual(:); +0602 header3{1} = ['time [',unit,']']; +0603 header3{2} = 'fit [a.u.]'; +0604 header3{3} = 'residual [-]'; +0605 +0606 % relaxation times +0607 switch INVdata.invstd.invtype +0608 case {'LU','NNLS'} +0609 por = INVdata.invstd.porosity; +0610 F = INVdata.results.invstd.T1T2f(:); +0611 F = 100*por.*F./sum(F); +0612 tmp4 = [INVdata.results.invstd.T1T2me(:)... +0613 INVdata.results.invstd.T1T2f(:) F]; +0614 header4 = {['relaxation times [',unit,']'],'amplitude [-]',... +0615 'partial water content [vol. %]'}; +0616 +0617 case {'mono','free'} +0618 por = INVdata.invstd.porosity; +0619 F = 100*por.*INVdata.results.invstd.E0./sum(INVdata.results.invstd.E0); +0620 switch INVdata.results.nmrproc.T1T2 +0621 case 'T1' +0622 tmp4 = [INVdata.results.invstd.T1(:)... +0623 INVdata.results.invstd.E0(:) F(:)]; +0624 header4 = {['relaxation time(s) T1 [',unit,']'],... +0625 'amplitude [a.u.]','partial water content [vol. %]'}; +0626 case 'T2' +0627 tmp4 = [INVdata.results.invstd.T2(:)... +0628 INVdata.results.invstd.E0(:) F(:)]; +0629 header4 = {['relaxation time(s) T2 [',unit,']'],... +0630 'amplitude [a.u.]','partial water content [vol. %]'}; +0631 end +0632 +0633 otherwise +0634 % Nothing to do +0635 end +0636 +0637 % glue together headers +0638 cHeader = [header1 header2 header3 header4]; +0639 % insert commas +0640 commaHeader = [cHeader;repmat({','},1,numel(cHeader))]; +0641 commaHeader = commaHeader(:)'; +0642 % cHeader as string with commas +0643 textHeader = cell2mat(commaHeader(1:numel(commaHeader)-1)); +0644 +0645 maxrows = max([size(tmp1,1) size(tmp2,1) size(tmp3,1) size(tmp4,1)]); +0646 % glue together data +0647 if size(tmp1,1) < maxrows +0648 tmp1(end+1:maxrows,:) = NaN; +0649 end +0650 if size(tmp2,1) < maxrows +0651 tmp2(end+1:maxrows,:) = NaN; +0652 end +0653 if size(tmp3,1) < maxrows +0654 tmp3(end+1:maxrows,:) = NaN; +0655 end +0656 if size(tmp4,1) < maxrows +0657 tmp4(end+1:maxrows,:) = NaN; +0658 end +0659 out(1:maxrows,1:size(tmp1,2)) = tmp1; +0660 yi = size(tmp1,2)+1; +0661 out(1:maxrows,yi:yi-1+size(tmp2,2)) = tmp2; +0662 yi = yi + size(tmp2,2); +0663 out(1:maxrows,yi:yi-1+size(tmp3,2)) = tmp3; +0664 yi = yi + size(tmp3,2); +0665 out(1:maxrows,yi:yi-1+size(tmp4,2)) = tmp4; +0666 +0667 % save data to file +0668 %write header to file +0669 fid = fopen(sfile,'w'); +0670 fprintf(fid,'%s\n',textHeader); +0671 fclose(fid); +0672 %write data to end of file +0673 dlmwrite(sfile,out,'-append','precision','%.5f'); +0674 +0675 end +0676 +0677 %% +0678 function exportMOD_EXCEL() +0679 xlswrite(fullfile(PathName,FileName),{'pressure [Pa]','saturation (drain)','saturation (imb)'},'CPS','A1'); +0680 xlswrite(fullfile(PathName,FileName),[results.SAT.pressure(:) results.SAT.Sdfull(:) results.SAT.Sifull(:)],'CPS','A2'); +0681 +0682 out = zeros(numel(results.NMR.t),numel(indd)+1); +0683 out(:,1) = results.NMR.t(:); +0684 header = cell(1,1); +0685 header{1} = 'time [s]'; +0686 for i = 1:numel(indd) +0687 out(:,i+1) = results.NMR.EdT1(indd(i),:)'; +0688 header{i+1} = ['S',num2str(i)]; +0689 end +0690 xlswrite(fullfile(PathName,FileName),header,'NMR_T1_drain','A1'); +0691 xlswrite(fullfile(PathName,FileName),out,'NMR_T1_drain','A2'); +0692 out = zeros(numel(results.NMR.t),numel(indd)+1); +0693 out(:,1) = results.NMR.t(:); +0694 header = cell(1,1); +0695 header{1} = 'time [s]'; +0696 for i = 1:numel(indd) +0697 out(:,i+1) = results.NMR.EdT2(indd(i),:)'; +0698 header{i+1} = ['S',num2str(i)]; +0699 end +0700 xlswrite(fullfile(PathName,FileName),header,'NMR_T2_drain','A1'); +0701 xlswrite(fullfile(PathName,FileName),out,'NMR_T2_drain','A2'); +0702 +0703 out = zeros(numel(results.NMR.t),numel(indi)+1); +0704 out(:,1) = results.NMR.t(:); +0705 header = cell(1,1); +0706 header{1} = 'time [s]'; +0707 for i = 1:numel(indi) +0708 out(:,i+1) = results.NMR.EiT1(indi(i),:)'; +0709 header{i+1} = ['S',num2str(i)]; +0710 end +0711 xlswrite(fullfile(PathName,FileName),header,'NMR_T1_imb','A1'); +0712 xlswrite(fullfile(PathName,FileName),out,'NMR_T1_imb','A2'); +0713 +0714 out = zeros(numel(results.NMR.t),numel(indi)+1); +0715 out(:,1) = results.NMR.t(:); +0716 header = cell(1,1); +0717 header{1} = 'time [s]'; +0718 for i = 1:numel(indi) +0719 out(:,i+1) = results.NMR.EiT2(indi(i),:)'; +0720 header{i+1} = ['S',num2str(i)]; +0721 end +0722 xlswrite(fullfile(PathName,FileName),header,'NMR_T2_imb','A1'); +0723 xlswrite(fullfile(PathName,FileName),out,'NMR_T2_imb','A2'); +0724 +0725 % remove the first standard excel sheet +0726 [~,sheets] = xlsfinfo(fullfile(PathName,FileName)); +0727 objExcel = actxserver('Excel.Application'); +0728 objExcel.Workbooks.Open(fullfile(PathName,FileName)); +0729 objExcel.ActiveWorkbook.Worksheets.Item(sheets{1}).Delete; +0730 objExcel.ActiveWorkbook.Save; +0731 objExcel.ActiveWorkbook.Close; +0732 objExcel.Quit; +0733 objExcel.delete; +0734 end +0735 +0736 %% +0737 function doexport = checkINV(INVdata,id) +0738 +0739 doexport = false; +0740 if ~isempty(INVdata) && ~isempty(id) +0741 if isstruct(INVdata{id}) +0742 doexport = true; +0743 else +0744 helpdlg({'exportData:','No inversion data to save'},... +0745 'Nothing to save'); +0746 end +0747 else +0748 helpdlg({'exportData:','No inversion data to save'},... +0749 'Nothing to save'); +0750 end +0751 +0752 end +0753 +0754 %% +0755 function doexport = checkMOD(data) +0756 +0757 doexport = false; +0758 if isfield(data,'results') +0759 if isfield(data.results,'NMR') +0760 doexport = true; +0761 else +0762 helpdlg({'exportData:',... +0763 'No data to save. Generate some data first.'},'NUCLEUSmod info:'); +0764 end +0765 else +0766 helpdlg({'exportData:',... +0767 'No data to save. Generate some data first.'},'NUCLEUSmod info:'); +0768 end +0769 +0770 end +0771 +0772 %% +0773 function amp = findApproxTlgmAmplitude(t,f,TLGM) +0774 index = find(abs(t-TLGM)==min(abs(t-TLGM))); +0775 amp = interp1(t(index-1:index+1),f(index-1:index+1),TLGM); +0776 end +0777 +0778 %------------- END OF CODE -------------- +0779 +0780 %% License: +0781 % MIT License +0782 % +0783 % Copyright (c) 2018 Thomas Hiller +0784 % +0785 % Permission is hereby granted, free of charge, to any person obtaining a copy +0786 % of this software and associated documentation files (the "Software"), to deal +0787 % in the Software without restriction, including without limitation the rights +0788 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0789 % copies of the Software, and to permit persons to whom the Software is +0790 % furnished to do so, subject to the following conditions: +0791 % +0792 % The above copyright notice and this permission notice shall be included in all +0793 % copies or substantial portions of the Software. +0794 % +0795 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0796 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0797 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0798 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0799 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0800 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0801 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/functions/interface/getColorTheme.html b/doc/nucleus/functions/interface/getColorTheme.html index d230002..96fd6e4 100644 --- a/doc/nucleus/functions/interface/getColorTheme.html +++ b/doc/nucleus/functions/interface/getColorTheme.html @@ -103,7 +103,7 @@

    SOURCE CODE ^%% switch depending on the calling figure 0035 switch fig_tag -0036 case 'INV' +0036 case {'INV','FIXEDTIMEVIEW'} 0037 % chose selected theme 0038 switch th 0039 case 'standard' diff --git a/doc/nucleus/functions/interface/importASCIIdata.html b/doc/nucleus/functions/interface/importASCIIdata.html index f7b750c..40207fd 100644 --- a/doc/nucleus/functions/interface/importASCIIdata.html +++ b/doc/nucleus/functions/interface/importASCIIdata.html @@ -213,67 +213,68 @@

    SOURCE CODE ^% dummy parameter data -0146 data.import.NMR.para{c} = 0; -0147 end -0148 end -0149 -0150 % save file names -0151 data.import.NMR.files = fnames; -0152 data.import.NMR.filesShort = shownames; -0153 -0154 % update the ini-file -0155 gui.myui.inidata.importpath = data.import.path; -0156 gui = makeINIfile(gui,'update'); -0157 -0158 % update the list of file names -0159 set(gui.listbox_handles.signal,'String',data.import.NMR.filesShort); -0160 set(gui.listbox_handles.signal,'Value',[],'Max',2,'Min',0); -0161 -0162 % create a global INVdata struct for every file in the list -0163 if isstruct(getappdata(fig,'INVdata')) -0164 setappdata(fig,'INVdata',[]); -0165 end -0166 INVdata = cell(length(data.import.NMR.filesShort),1); -0167 setappdata(fig,'INVdata',INVdata); -0168 -0169 % clear all axes -0170 clearAllAxes(gui.figh); -0171 -0172 % update GUI data and interface -0173 setappdata(fig,'data',data); -0174 setappdata(fig,'gui',gui); -0175 enableGUIelements('ASCII'); -0176 NUCLEUSinv_updateInterface; -0177 end -0178 -0179 end -0180 -0181 %------------- END OF CODE -------------- -0182 -0183 %% License: -0184 % MIT License -0185 % -0186 % Copyright (c) 2018 Thomas Hiller -0187 % -0188 % Permission is hereby granted, free of charge, to any person obtaining a copy -0189 % of this software and associated documentation files (the "Software"), to deal -0190 % in the Software without restriction, including without limitation the rights -0191 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0192 % copies of the Software, and to permit persons to whom the Software is -0193 % furnished to do so, subject to the following conditions: -0194 % -0195 % The above copyright notice and this permission notice shall be included in all -0196 % copies or substantial portions of the Software. -0197 % -0198 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0199 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0200 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0201 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0202 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0203 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0204 % SOFTWARE. +0144 data.import.NMR.data{c}.phase = 0; +0145 +0146 % dummy parameter data +0147 data.import.NMR.para{c} = 0; +0148 end +0149 end +0150 +0151 % save file names +0152 data.import.NMR.files = fnames; +0153 data.import.NMR.filesShort = shownames; +0154 +0155 % update the ini-file +0156 gui.myui.inidata.importpath = data.import.path; +0157 gui = makeINIfile(gui,'update'); +0158 +0159 % update the list of file names +0160 set(gui.listbox_handles.signal,'String',data.import.NMR.filesShort); +0161 set(gui.listbox_handles.signal,'Value',[],'Max',2,'Min',0); +0162 +0163 % create a global INVdata struct for every file in the list +0164 if isstruct(getappdata(fig,'INVdata')) +0165 setappdata(fig,'INVdata',[]); +0166 end +0167 INVdata = cell(length(data.import.NMR.filesShort),1); +0168 setappdata(fig,'INVdata',INVdata); +0169 +0170 % clear all axes +0171 clearAllAxes(gui.figh); +0172 +0173 % update GUI data and interface +0174 setappdata(fig,'data',data); +0175 setappdata(fig,'gui',gui); +0176 enableGUIelements('ASCII'); +0177 NUCLEUSinv_updateInterface; +0178 end +0179 +0180 end +0181 +0182 %------------- END OF CODE -------------- +0183 +0184 %% License: +0185 % MIT License +0186 % +0187 % Copyright (c) 2018 Thomas Hiller +0188 % +0189 % Permission is hereby granted, free of charge, to any person obtaining a copy +0190 % of this software and associated documentation files (the "Software"), to deal +0191 % in the Software without restriction, including without limitation the rights +0192 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0193 % copies of the Software, and to permit persons to whom the Software is +0194 % furnished to do so, subject to the following conditions: +0195 % +0196 % The above copyright notice and this permission notice shall be included in all +0197 % copies or substantial portions of the Software. +0198 % +0199 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0200 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0201 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0202 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0203 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0204 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0205 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/functions/interface/importINV2INV.html b/doc/nucleus/functions/interface/importINV2INV.html index 734b1de..cf148f6 100644 --- a/doc/nucleus/functions/interface/importINV2INV.html +++ b/doc/nucleus/functions/interface/importINV2INV.html @@ -170,149 +170,160 @@

    SOURCE CODE ^end 0098 end 0099 end -0100 end -0101 -0102 % update GUI data from session mat-file -0103 data = savedata.data; -0104 INVdata = savedata.INVdata; -0105 -0106 % display info text -0107 displayStatusText(gui,'Importing GUI session from mat-file ... update GUI data.'); -0108 % check if the import path exists on this machine -0109 isdir_import = dir(data.import.path); -0110 % if not replace it with the path the session-file was loaded from -0111 if isempty(isdir_import) -0112 data.import.path = Sessionpath; -0113 end -0114 % update the path info field with "path" ("file") -0115 if data.import.file > 0 -0116 tmpstr = fullfile(data.import.path,data.import.file); -0117 else -0118 tmpstr = data.import.path; -0119 end -0120 % update GUI data -0121 setappdata(fig,'data',data); -0122 setappdata(fig,'gui',gui); -0123 setappdata(fig,'INVdata',INVdata); -0124 -0125 % update the ini-file -0126 gui.myui.inidata.importpath = data.import.path; -0127 gui = makeINIfile(gui,'update'); -0128 setappdata(fig,'gui',gui); -0129 -0130 if length(tmpstr)>50 -0131 set(gui.text_handles.data_path,'String',['...',tmpstr(end-50:end)],... -0132 'HorizontalAlignment','left'); -0133 else -0134 set(gui.text_handles.data_path,'String',tmpstr,... -0135 'HorizontalAlignment','left'); -0136 end -0137 set(gui.text_handles.data_path,'TooltipString',tmpstr); -0138 -0139 % update the list of file names -0140 set(gui.listbox_handles.signal,'String',data.import.NMR.filesShort); -0141 set(gui.listbox_handles.signal,'Value',[],'Max',2,'Min',0); -0142 -0143 % display info text -0144 displayStatusText(gui,'Importing GUI session from mat-file ... update GUI interface.'); -0145 % update GUI interface -0146 NUCLEUSinv_updateInterface; -0147 -0148 % color the file names where there is an inversion set -0149 for id = 1:size(INVdata,1) -0150 if isstruct(INVdata{id}) -0151 strL = get(gui.listbox_handles.signal,'String'); -0152 str1 = strL{id}; -0153 str2 = ['<HTML><BODY bgcolor="rgb(',... -0154 sprintf('%d,%d,%d',gui.myui.colors.listINV.*255),')">',... -0155 str1,'</BODY></HTML>']; -0156 strL{id} = str2; -0157 set(gui.listbox_handles.signal,'String',strL); -0158 end -0159 end -0160 -0161 % display info text -0162 displayStatusText(gui,'Importing GUI session from mat-file ... update GUI menus.'); -0163 % adjust menu entry for expert mode -0164 switch savedata.data.info.ExpertMode -0165 case 'on' -0166 set(gui.menu.extra_expert,'Checked','off'); -0167 case 'off' -0168 set(gui.menu.extra_expert,'Checked','on'); -0169 end -0170 onMenuExpert(gui.menu.extra_expert); +0100 if version_in < 114 % changes introduced with v.0.1.14 +0101 % add 'Tfixed_bool' & 'Tfixed_val' field to savedata +0102 savedata.data.invstd.Tfixed_bool = data.invstd.Tfixed_bool; +0103 savedata.data.invstd.Tfixed_val = data.invstd.Tfixed_val; +0104 for i = 1:numel(savedata.INVdata) +0105 if isstruct(savedata.INVdata{i}) +0106 savedata.INVdata{i}.invstd.Tfixed_bool = data.invstd.Tfixed_bool; +0107 savedata.INVdata{i}.invstd.Tfixed_val = data.invstd.Tfixed_val; +0108 end +0109 end +0110 end +0111 end +0112 +0113 % update GUI data from session mat-file +0114 data = savedata.data; +0115 INVdata = savedata.INVdata; +0116 +0117 % display info text +0118 displayStatusText(gui,'Importing GUI session from mat-file ... update GUI data.'); +0119 % check if the import path exists on this machine +0120 isdir_import = dir(data.import.path); +0121 % if not replace it with the path the session-file was loaded from +0122 if isempty(isdir_import) +0123 data.import.path = Sessionpath; +0124 end +0125 % update the path info field with "path" ("file") +0126 if data.import.file > 0 +0127 tmpstr = fullfile(data.import.path,data.import.file); +0128 else +0129 tmpstr = data.import.path; +0130 end +0131 % update GUI data +0132 setappdata(fig,'data',data); +0133 setappdata(fig,'gui',gui); +0134 setappdata(fig,'INVdata',INVdata); +0135 +0136 % update the ini-file +0137 gui.myui.inidata.importpath = data.import.path; +0138 gui = makeINIfile(gui,'update'); +0139 setappdata(fig,'gui',gui); +0140 +0141 if length(tmpstr)>50 +0142 set(gui.text_handles.data_path,'String',['...',tmpstr(end-50:end)],... +0143 'HorizontalAlignment','left'); +0144 else +0145 set(gui.text_handles.data_path,'String',tmpstr,... +0146 'HorizontalAlignment','left'); +0147 end +0148 set(gui.text_handles.data_path,'TooltipString',tmpstr); +0149 +0150 % update the list of file names +0151 set(gui.listbox_handles.signal,'String',data.import.NMR.filesShort); +0152 set(gui.listbox_handles.signal,'Value',[],'Max',2,'Min',0); +0153 +0154 % display info text +0155 displayStatusText(gui,'Importing GUI session from mat-file ... update GUI interface.'); +0156 % update GUI interface +0157 NUCLEUSinv_updateInterface; +0158 +0159 % color the file names where there is an inversion set +0160 for id = 1:size(INVdata,1) +0161 if isstruct(INVdata{id}) +0162 strL = get(gui.listbox_handles.signal,'String'); +0163 str1 = strL{id}; +0164 str2 = ['<HTML><BODY bgcolor="rgb(',... +0165 sprintf('%d,%d,%d',gui.myui.colors.listINV.*255),')">',... +0166 str1,'</BODY></HTML>']; +0167 strL{id} = str2; +0168 set(gui.listbox_handles.signal,'String',strL); +0169 end +0170 end 0171 -0172 % adjust menu entry for joint inversion -0173 switch savedata.data.info.JointInv -0174 case 'on' -0175 set(gui.menu.extra_joint,'Checked','off'); -0176 case 'off' -0177 set(gui.menu.extra_joint,'Checked','on'); -0178 end -0179 onMenuJointInversion(gui.menu.extra_joint); -0180 enableGUIelements('NMR'); -0181 -0182 % adjust menu entry for comand line inversion info -0183 switch savedata.data.info.InvInfo -0184 case 'on' -0185 set(gui.menu.view_invinfo,'Checked','off'); -0186 case 'off' -0187 set(gui.menu.view_invinfo,'Checked','on'); -0188 end -0189 onMenuView(gui.menu.view_invinfo); -0190 -0191 % adjust menu entry for tool tips -0192 switch savedata.data.info.ToolTips -0193 case 'on' -0194 set(gui.menu.view_tooltips,'Checked','off'); -0195 case 'off' -0196 set(gui.menu.view_tooltips,'Checked','on'); -0197 end -0198 onMenuView(gui.menu.view_tooltips); -0199 -0200 % display info text -0201 displayStatusText(gui,'Importing GUI session from mat-file ... show last file.'); -0202 % set focus on last file used in previous session -0203 set(gui.listbox_handles.signal,'Value',savedata.id); -0204 % and simulate click to update all relevant GUI elements -0205 onListboxData(gui.listbox_handles.signal); -0206 -0207 % display info text -0208 displayStatusText(gui,'Importing GUI session from mat-file ... done.'); -0209 else -0210 % display info text -0211 displayStatusText(gui,'Importing GUI session from mat-file ... cancelled.'); -0212 -0213 helpdlg({'importINV2INV:';... -0214 'This seems to be not a valid NUCLEUSinv session file'},... -0215 'No session data found'); -0216 end -0217 end -0218 -0219 %------------- END OF CODE -------------- -0220 -0221 %% License: -0222 % MIT License -0223 % -0224 % Copyright (c) 2018 Thomas Hiller -0225 % -0226 % Permission is hereby granted, free of charge, to any person obtaining a copy -0227 % of this software and associated documentation files (the "Software"), to deal -0228 % in the Software without restriction, including without limitation the rights -0229 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0230 % copies of the Software, and to permit persons to whom the Software is -0231 % furnished to do so, subject to the following conditions: -0232 % -0233 % The above copyright notice and this permission notice shall be included in all -0234 % copies or substantial portions of the Software. -0235 % -0236 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0237 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0238 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0239 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0240 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0241 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0242 % SOFTWARE. +0172 % display info text +0173 displayStatusText(gui,'Importing GUI session from mat-file ... update GUI menus.'); +0174 % adjust menu entry for expert mode +0175 switch savedata.data.info.ExpertMode +0176 case 'on' +0177 set(gui.menu.extra_expert,'Checked','off'); +0178 case 'off' +0179 set(gui.menu.extra_expert,'Checked','on'); +0180 end +0181 onMenuExpert(gui.menu.extra_expert); +0182 +0183 % adjust menu entry for joint inversion +0184 switch savedata.data.info.JointInv +0185 case 'on' +0186 set(gui.menu.extra_joint,'Checked','off'); +0187 case 'off' +0188 set(gui.menu.extra_joint,'Checked','on'); +0189 end +0190 onMenuJointInversion(gui.menu.extra_joint); +0191 enableGUIelements('NMR'); +0192 +0193 % adjust menu entry for comand line inversion info +0194 switch savedata.data.info.InvInfo +0195 case 'on' +0196 set(gui.menu.view_invinfo,'Checked','off'); +0197 case 'off' +0198 set(gui.menu.view_invinfo,'Checked','on'); +0199 end +0200 onMenuView(gui.menu.view_invinfo); +0201 +0202 % adjust menu entry for tool tips +0203 switch savedata.data.info.ToolTips +0204 case 'on' +0205 set(gui.menu.view_tooltips,'Checked','off'); +0206 case 'off' +0207 set(gui.menu.view_tooltips,'Checked','on'); +0208 end +0209 onMenuView(gui.menu.view_tooltips); +0210 +0211 % display info text +0212 displayStatusText(gui,'Importing GUI session from mat-file ... show last file.'); +0213 % set focus on last file used in previous session +0214 set(gui.listbox_handles.signal,'Value',savedata.id); +0215 % and simulate click to update all relevant GUI elements +0216 onListboxData(gui.listbox_handles.signal); +0217 +0218 % display info text +0219 displayStatusText(gui,'Importing GUI session from mat-file ... done.'); +0220 else +0221 % display info text +0222 displayStatusText(gui,'Importing GUI session from mat-file ... cancelled.'); +0223 +0224 helpdlg({'importINV2INV:';... +0225 'This seems to be not a valid NUCLEUSinv session file'},... +0226 'No session data found'); +0227 end +0228 end +0229 +0230 %------------- END OF CODE -------------- +0231 +0232 %% License: +0233 % MIT License +0234 % +0235 % Copyright (c) 2018 Thomas Hiller +0236 % +0237 % Permission is hereby granted, free of charge, to any person obtaining a copy +0238 % of this software and associated documentation files (the "Software"), to deal +0239 % in the Software without restriction, including without limitation the rights +0240 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0241 % copies of the Software, and to permit persons to whom the Software is +0242 % furnished to do so, subject to the following conditions: +0243 % +0244 % The above copyright notice and this permission notice shall be included in all +0245 % copies or substantial portions of the Software. +0246 % +0247 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0248 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0249 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0250 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0251 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0252 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0253 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/functions/interface/importNMRdata.html b/doc/nucleus/functions/interface/importNMRdata.html index ed8da92..386697e 100644 --- a/doc/nucleus/functions/interface/importNMRdata.html +++ b/doc/nucleus/functions/interface/importNMRdata.html @@ -81,7 +81,7 @@

    CROSS-REFERENCE INFORMATION ^ <h2><a name=SUBFUNCTIONS ^

    +
  • function [NMRpath,NMRfile] = getNMRPathFile(label,import)
  • function [data,gui] = importDataMouseCPMG(data,gui)
  • function [data,gui] = importDataBGRmat(data,gui)
  • function [data,gui] = importDataBGRliftSingle(data,gui)
  • function [data,gui] = importDataBGRlift(data,gui)
  • function [data,gui] = importDataHeliosCPMG(data,gui)
  • function [data,gui] = importDataHeliosSeries(data,gui)
  • function [data,gui] = importDataDart(data,gui)
  • function [data,gui] = importDataGeneral(data,gui)
  • function [data,gui] = importDataLIAG(data,gui)
  • function [data,gui] = importDataLIAGcore(data,gui)
  • function [data,gui] = importDataLIAGproject(data,gui)
  • function [data,gui] = importDataMouse(data,gui)
  • function [data,gui] = importDataIBAC(data,gui)
  • function data = loadGUIParameters(datapath,fname)
  • function data = loadGUIrawdata(data,NMRpath,NMRfile)

    • SOURCE CODE ^

    0001 function importNMRdata(src)
@@ -142,1186 +142,1473 @@ 
    SOURCE CODE ^'Label');
 0057     
 0058     % set file format for later use
-0059     if strcmp(label,'GGE ascii')
-0060         data.import.fileformat = 'rwth';
-0061     elseif strcmp(label,'GGE field')
-0062         data.import.fileformat = 'field';
-0063     elseif strcmp(label,'GGE Dart')
-0064         data.import.fileformat = 'dart';
+0059     if strcmp(label,'BAM TOM')
+0060         data.import.fileformat = 'bamtom';
+0061     elseif strcmp(label,'BGR mat')
+0062         data.import.fileformat = 'bgrmat';
+0063     elseif strcmp(label,'BGR std')
+0064         data.import.fileformat = 'bgr';
 0065     elseif strcmp(label,'CoreLab ascii')
 0066         data.import.fileformat = 'corelab';
 0067     elseif strcmp(label,'DART')
 0068         data.import.fileformat = 'dart';    
-0069     elseif strcmp(label,'MOUSE')
-0070         data.import.fileformat = 'mouse';
-0071     elseif strcmp(label,'LIAG single')
-0072         data.import.fileformat = 'liag';
-0073     elseif strcmp(label,'LIAG from project')
-0074         data.import.fileformat = 'liag';
-0075     elseif strcmp(label,'LIAG last project')
-0076         data.import.fileformat = 'liag';
-0077     elseif strcmp(label,'BGR std')
-0078         data.import.fileformat = 'bgr';
-0079     elseif strcmp(label,'MouseCPMG')
-0080         data.import.fileformat = 'MouseCPMG';
-0081     elseif strcmp(label,'BGR mat')
-0082         data.import.fileformat = 'bgrmat';
-0083     elseif strcmp(label,'MouseLiftSingle')
-0084         data.import.fileformat = 'MouseLiftSingle';
-0085     elseif strcmp(label,'MouseLiftAll')
-0086         data.import.fileformat = 'MouseLiftAll';
-0087     elseif strcmp(label,'Helios')
-0088         data.import.fileformat = 'helios';
-0089     elseif strcmp(label,'BAM TOM')
-0090         data.import.fileformat = 'bamtom';
-0091     elseif strcmp(label,'PM5')
-0092         data.import.fileformat = 'pm5';
-0093     elseif strcmp(label,'PM25')
-0094         data.import.fileformat = 'pm25';
-0095     else
-0096         helpdlg('Something is utterly wrong.','onMenuImport: Choose again.');
-0097     end
-0098     
-0099     % remove info field if any
-0100     ih = findobj('Tag','inv_info');
-0101     if ~isempty(ih); delete(ih); end
-0102     
-0103     % depending on the import format get the corresponding path / file
-0104     [NMRpath,NMRfile] = getNMRPathFile(label,data.import);
-0105     
-0106     % only continue if user didn't cancel
-0107     if sum([NMRpath NMRfile]) > 0
-0108         %  remove old fields and data
-0109         data = cleanupGUIData(data);
-0110         
-0111         % check for mat-file with GUI rawdata and import data
-0112         isfile = dir(fullfile(NMRpath,'NUCLEUSinv_raw.mat'));
-0113         
-0114         % if there is no raw-file import from folder/file
-0115         if isempty(isfile)
-0116             % import data
-0117             data.import.path = NMRpath;
-0118             data.import.file = -1;
-0119             displayStatusText(gui,'Reading NMR Data ...');
-0120             % call the corresponding subroutines
-0121             switch label
-0122                 case {'GGE ascii','GGE field','CoreLab ascii','BGR std',...
-0123                         'BAM TOM'}
-0124                     [data,gui] = importDataGeneral(data,gui);
-0125                 case 'GGE Dart'
-0126                     data.import.file = NMRfile;
-0127                     % the data in the example folder is an older type
-0128                     if contains(NMRpath,'nucleus\example_data\dart')
-0129                         data.import.version = 1;
-0130                     else
-0131                         data.import.version = 2;
-0132                     end
-0133                     [data,gui] = importDataDart(data,gui);
-0134                 case 'DART'
-0135                     data.import.file = NMRfile;
-0136                     data.import.version = 3;
-0137                     [data,gui] = importDataDart(data,gui);    
-0138                 case 'MOUSE'
-0139                     [data,gui] = importDataMouse(data,gui);
-0140                 case 'LIAG single'
-0141                     [data,gui] = importDataLIAG(data,gui);
-0142                 case {'LIAG from project','LIAG last project'}
-0143                     [data,gui] = importDataLIAGproject(data,gui);
-0144                     % make the Petro Panel visible as default
-0145                     tmp_h = gui.myui.heights(2,:);
-0146                     tmp_h(3) = gui.myui.heights(2,3);
-0147                     % but the CPS panel stays minimized
-0148                     tmp_h(5) = gui.myui.heights(1,3);
-0149                     set(gui.panels.main,'Heights',tmp_h);
-0150                     set(gui.panels.petro.main,'Minimized',false);
-0151                 case 'BGR mat'
-0152                     data.import.file = NMRfile;
-0153                     [data,gui] = importDataBGRmat(data,gui);
-0154                 case 'MouseCPMG'
-0155                     [data,gui] = importDataMouseCPMG(data,gui);
-0156                 case 'MouseLiftSingle'
-0157                     [data,gui] = importDataBGRliftSingle(data,gui);
-0158                 case 'MouseLiftAll'
-0159                     [data,gui] = importDataBGRliftAll(data,gui);
-0160                 case 'Helios'
-0161                     data.import.file = NMRfile;
-0162                     [data,gui] = importDataHelios(data,gui);
-0163                 case {'PM5','PM25'}
-0164                     data.import.file = NMRfile;
-0165                     [data,gui] = importDataIBAC(data,gui);
-0166             end
-0167             displayStatusText(gui,'Reading NMR Data ... done');
-0168         else
-0169             % import from mat-file
-0170             displayStatusText(gui,'Importing NMR raw data from mat-file ...');
-0171             data = loadGUIrawdata(data,NMRpath,NMRfile);
-0172             displayStatusText(gui,'Importing NMR raw data from mat-file ... done');
-0173         end
-0174         
-0175         % update the path info field with "NMRpath" ("NMRfile")
-0176         if NMRfile > 0
-0177             tmpstr = fullfile(NMRpath,NMRfile);
-0178         else
-0179             tmpstr = NMRpath;
-0180         end
-0181         if length(tmpstr)>50
-0182             set(gui.text_handles.data_path,'String',['...',tmpstr(end-50:end)],...
-0183                 'HorizontalAlignment','left');
-0184         else
-0185             set(gui.text_handles.data_path,'String',tmpstr,...
-0186                 'HorizontalAlignment','left');
-0187         end
-0188         set(gui.text_handles.data_path,'TooltipString',tmpstr);
-0189         
-0190         % update the ini-file
-0191         gui.myui.inidata.importpath = data.import.path;
-0192         gui = makeINIfile(gui,'update');
-0193         
-0194         % update the list of file names
-0195         set(gui.listbox_handles.signal,'String',data.import.NMR.filesShort);
-0196         set(gui.listbox_handles.signal,'Value',[],'Max',2,'Min',0);
-0197         
-0198         % create a global INVdata struct for every file in the list
-0199         if isstruct(getappdata(fig,'INVdata'))
-0200             setappdata(fig,'INVdata',[]);
-0201         end
-0202         INVdata = cell(length(data.import.NMR.filesShort),1);
-0203         setappdata(fig,'INVdata',INVdata);
-0204         
-0205         % clear all axes
-0206         clearAllAxes(gui.figh);
-0207         
-0208         % update GUI data and interface
-0209         setappdata(fig,'data',data);
-0210         setappdata(fig,'gui',gui);
-0211         enableGUIelements('NMR');
+0069     elseif strcmp(label,'GGE ascii')
+0070         data.import.fileformat = 'rwth';
+0071     elseif strcmp(label,'GGE field')
+0072         data.import.fileformat = 'field';
+0073     elseif strcmp(label,'GGE Dart')
+0074         data.import.fileformat = 'dart';
+0075     elseif strcmp(label,'HeliosCPMG')
+0076         data.import.fileformat = 'heliosCPMG';
+0077     elseif strcmp(label,'HeliosSeries')
+0078         data.import.fileformat = 'heliosSeries';    
+0079     elseif strcmp(label,'LIAG core')
+0080         data.import.fileformat = 'liag';
+0081     elseif strcmp(label,'LIAG from project')
+0082         data.import.fileformat = 'liag';
+0083     elseif strcmp(label,'LIAG last project')
+0084         data.import.fileformat = 'liag';
+0085     elseif strcmp(label,'LIAG single')
+0086         data.import.fileformat = 'liag';
+0087     elseif strcmp(label,'MOUSE')
+0088         data.import.fileformat = 'mouse';
+0089     elseif strcmp(label,'MouseCPMG')
+0090         data.import.fileformat = 'MouseCPMG';
+0091     elseif strcmp(label,'MouseLift')
+0092         data.import.fileformat = 'MouseLift';
+0093     elseif strcmp(label,'PM5')
+0094         data.import.fileformat = 'pm5';
+0095     elseif strcmp(label,'PM25')
+0096         data.import.fileformat = 'pm25';
+0097     else
+0098         helpdlg('Something is utterly wrong.','onMenuImport: Choose again.');
+0099     end
+0100     
+0101     % remove info field if any
+0102     ih = findobj('Tag','inv_info');
+0103     if ~isempty(ih); delete(ih); end
+0104     
+0105     % depending on the import format get the corresponding path / file
+0106     [NMRpath,NMRfile] = getNMRPathFile(label,data.import);
+0107     
+0108     % only continue if user didn't cancel
+0109     if sum([NMRpath NMRfile]) > 0
+0110         %  remove old fields and data
+0111         data = cleanupGUIData(data);
+0112         
+0113         % check for mat-file with GUI rawdata and import data
+0114         isfile = dir(fullfile(NMRpath,'NUCLEUSinv_raw.mat'));
+0115         
+0116         % if there is no raw-file import from folder/file
+0117         if isempty(isfile)
+0118             % import data
+0119             data.import.path = NMRpath;
+0120             data.import.file = -1;
+0121             displayStatusText(gui,'Reading NMR Data ...');
+0122             % call the corresponding subroutines
+0123             switch label
+0124                 case {'BAM TOM','BGR std','CoreLab ascii','GGE ascii',...
+0125                         'GGE field'}
+0126                     [data,gui] = importDataGeneral(data,gui);
+0127                 case 'GGE Dart'
+0128                     data.import.file = NMRfile;
+0129                     % the data in the example folder is an older type
+0130                     if contains(NMRpath,'nucleus\example_data\dart')
+0131                         data.import.version = 1;
+0132                     else
+0133                         data.import.version = 2;
+0134                     end
+0135                     [data,gui] = importDataDart(data,gui);
+0136                 case 'DART'
+0137                     data.import.file = NMRfile;
+0138                     data.import.version = 3;
+0139                     [data,gui] = importDataDart(data,gui);    
+0140                 case 'MOUSE'
+0141                     [data,gui] = importDataMouse(data,gui);
+0142                 case 'LIAG single'
+0143                     [data,gui] = importDataLIAG(data,gui);
+0144                 case 'LIAG core'
+0145                     [data,gui] = importDataLIAGcore(data,gui);    
+0146                 case {'LIAG from project','LIAG last project'}
+0147                     [data,gui] = importDataLIAGproject(data,gui);
+0148                     % make the Petro Panel visible as default
+0149                     tmp_h = gui.myui.heights(2,:);
+0150                     tmp_h(3) = gui.myui.heights(2,3);
+0151                     % but the CPS panel stays minimized
+0152                     tmp_h(5) = gui.myui.heights(1,3);
+0153                     set(gui.panels.main,'Heights',tmp_h);
+0154                     set(gui.panels.petro.main,'Minimized',false);
+0155                 case 'BGR mat'
+0156                     data.import.file = NMRfile;
+0157                     [data,gui] = importDataBGRmat(data,gui);
+0158                 case 'MouseCPMG'
+0159                     [data,gui] = importDataMouseCPMG(data,gui);
+0160                 case 'MouseLift'
+0161                     [data,gui] = importDataBGRlift(data,gui);
+0162                 case 'HeliosCPMG'
+0163                     data.import.file = NMRfile;
+0164                     [data,gui] = importDataHeliosCPMG(data,gui);
+0165                 case 'HeliosSeries'
+0166                     data.import.file = NMRfile;
+0167                     [data,gui] = importDataHeliosSeries(data,gui);
+0168                 case {'PM5','PM25'}
+0169                     data.import.file = NMRfile;
+0170                     [data,gui] = importDataIBAC(data,gui);
+0171             end
+0172             displayStatusText(gui,'Reading NMR Data ... done');
+0173         else
+0174             % import from mat-file
+0175             displayStatusText(gui,'Importing NMR raw data from mat-file ...');
+0176             data = loadGUIrawdata(data,NMRpath,NMRfile);
+0177             displayStatusText(gui,'Importing NMR raw data from mat-file ... done');
+0178         end
+0179         
+0180         % update the path info field with "NMRpath" ("NMRfile")
+0181         if NMRfile > 0
+0182             tmpstr = fullfile(NMRpath,NMRfile);
+0183         else
+0184             tmpstr = NMRpath;
+0185         end
+0186         if length(tmpstr)>50
+0187             set(gui.text_handles.data_path,'String',['...',tmpstr(end-50:end)],...
+0188                 'HorizontalAlignment','left');
+0189         else
+0190             set(gui.text_handles.data_path,'String',tmpstr,...
+0191                 'HorizontalAlignment','left');
+0192         end
+0193         set(gui.text_handles.data_path,'TooltipString',tmpstr);
+0194         
+0195         % update the ini-file
+0196         gui.myui.inidata.importpath = data.import.path;
+0197         gui = makeINIfile(gui,'update');
+0198         
+0199         % update the list of file names
+0200         set(gui.listbox_handles.signal,'String',data.import.NMR.filesShort);
+0201         set(gui.listbox_handles.signal,'Value',[],'Max',2,'Min',0);
+0202         
+0203         % create a global INVdata struct for every file in the list
+0204         if isstruct(getappdata(fig,'INVdata'))
+0205             setappdata(fig,'INVdata',[]);
+0206         end
+0207         INVdata = cell(length(data.import.NMR.filesShort),1);
+0208         setappdata(fig,'INVdata',INVdata);
+0209         
+0210         % clear all axes
+0211         clearAllAxes(gui.figh);
 0212         
-0213         % special treatment of LIAG projects
-0214         switch label
-0215             case {'LIAG from project','LIAG last project'}
-0216                 cpath = data.import.LIAG.calibrationpath;
-0217                 % check if this calibration file was already used
-0218                 isfile = dir(fullfile(cpath,'NUCLEUS_calibData.mat'));
-0219                 if ~isempty(isfile)
-0220                     id = 2;
-0221                     % if data is there reuse it
-0222                     calib = load(fullfile(cpath,isfile.name),'calib');
-0223                     INVdata{id} = calib.calib;
-0224                     data.calib = INVdata{id}.calib;
-0225                     data.import.LIAG.Tbulk = INVdata{id}.results.invstd.T2;
-0226                     setappdata(fig,'INVdata',INVdata);
-0227                     setappdata(fig,'data',data);
-0228                     % color the list entry
-0229                     strL = get(gui.listbox_handles.signal,'String');
-0230                     str1 = strL{id};
-0231                     str2 = ['<HTML><BODY bgcolor="rgb(',...
-0232                         sprintf('%d,%d,%d',gui.myui.colors.listINV.*255),')">',...
-0233                         str1,'</BODY></HTML>'];
-0234                     strL{id} = str2;
-0235                     set(gui.listbox_handles.signal,'String',strL);
-0236                 end
-0237             otherwise
-0238         end
-0239         % update GUI interface
-0240         NUCLEUSinv_updateInterface;
-0241     end
-0242     
-0243 catch ME
-0244     % show error message in case import fails
-0245     errmsg = {ME.message;[ME.stack(1).name,' Line: ',num2str(ME.stack(1).line)];...
-0246         'Check File Format settings.'};
-0247     errordlg(errmsg,'importNMRdata: Error!');
-0248     
-0249 end
-0250 
-0251 end
-0252 
-0253 %%
-0254 function [NMRpath,NMRfile] = getNMRPathFile(label,import)
-0255 
-0256 NMRpath = -1;
-0257 NMRfile = -1;
-0258 % for almost all import cases we load a folder ... but not for all
-0259 switch label
-0260     case {'GGE ascii','GGE field','CoreLab ascii','MOUSE','LIAG single',...
-0261             'BGR std','MouseCPMG','MouseLiftSingle','MouseLiftAll','Helios','BAM TOM','PM25'}
-0262         % if there is already a data folder present we start from here
-0263         if isfield(import,'path')
-0264             NMRpath = uigetdir(import.path,'Choose Data Path');
-0265         else
-0266             % otherwise we start at the current working dircetory
-0267             % 'NMRpath' holds the name of the choosen data path
-0268             here = mfilename('fullpath');
-0269             [pathstr,~,~] = fileparts(here);
-0270             NMRpath = uigetdir(pathstr,'Choose Data Path');
-0271         end
-0272     case 'LIAG from project'
-0273         % if there is already a data folder present we start from here
-0274         if isfield(import,'path')
-0275             NMRpath = uigetdir(import.path,'Choose Project Path');
-0276         else
-0277             % otherwise we start at the current working dircetory
-0278             % 'NMRpath' holds the name of the choosen data path
-0279             here = mfilename('fullpath');
-0280             [pathstr,~,~] = fileparts(here);
-0281             NMRpath = uigetdir(pathstr,'Choose Project Path');
-0282         end
-0283     case 'LIAG last project'
-0284         % there is already a data folder and we use this one
-0285         if isfield(import,'path')
-0286             NMRpath = import.path;
-0287         else
-0288             % otherwise we start at the current working dircetory
-0289             % 'NMRpath' holds the name of the choosen data path
-0290             here = mfilename('fullpath');
-0291             [pathstr,~,~] = fileparts(here);
-0292             NMRpath = uigetdir(pathstr,'Choose Project Path');
-0293         end
-0294     case {'GGE Dart','DART','BGR mat','NMR mat'}
-0295         % if there is already a data folder present we start from here
-0296         if isfield(import,'path')
-0297             [NMRfile,NMRpath] = uigetfile(import.path,'Choose Data file');
-0298         else
-0299             % otherwise we start at the current working dircetory
-0300             % 'foldername' hold s the name of the choosen data path
-0301             here = mfilename('fullpath');
-0302             [pathstr,~,~] = fileparts(here);
-0303             [NMRfile,NMRpath] = uigetfile(pathstr,'Choose Data file');
-0304         end
-0305     case 'PM5'
-0306         % if there is already a data folder present we start from here
-0307         if isfield(import,'path')
-0308             NMRpath = uigetdir(import.path,'Choose PM5 Data Path');
-0309         else
-0310             % otherwise we start at the current working dircetory
-0311             % 'NMRpath' holds the name of the choosen data path
-0312             here = mfilename('fullpath');
-0313             [pathstr,~,~] = fileparts(here);
-0314             NMRpath = uigetdir(pathstr,'Choose PM5 Data Path');
-0315         end
-0316         
-0317         % check if there are multiple inf-files available
-0318         % if yes -> choose one
-0319         inffiles = dir(fullfile(NMRpath,'*.inf'));
-0320         if numel(inffiles) > 1
-0321             [NMRfile,NMRpath] = uigetfile(fullfile(NMRpath,'*.inf'),...
-0322                 'Choose INF file');
-0323         elseif numel(inffiles) == 1
-0324             NMRfile = inffiles.name;            
-0325         end
-0326 end
-0327 
-0328 end
-0329 
-0330 %%
-0331 function [data,gui] = importDataMouseCPMG(data,gui)
+0213         % update GUI data and interface
+0214         setappdata(fig,'data',data);
+0215         setappdata(fig,'gui',gui);
+0216         enableGUIelements('NMR');
+0217         
+0218         % special treatment of LIAG projects
+0219         switch label
+0220             case {'LIAG from project','LIAG last project'}
+0221                 cpath = data.import.LIAG.calibrationpath;
+0222                 % check if this calibration file was already used
+0223                 isfile = dir(fullfile(cpath,'NUCLEUS_calibData.mat'));
+0224                 if ~isempty(isfile)
+0225                     id = 2;
+0226                     % if data is there reuse it
+0227                     calib = load(fullfile(cpath,isfile.name),'calib');
+0228                     INVdata{id} = calib.calib;
+0229                     data.calib = INVdata{id}.calib;
+0230                     data.import.LIAG.Tbulk = INVdata{id}.results.invstd.T2;
+0231                     setappdata(fig,'INVdata',INVdata);
+0232                     setappdata(fig,'data',data);
+0233                     % color the list entry
+0234                     strL = get(gui.listbox_handles.signal,'String');
+0235                     str1 = strL{id};
+0236                     str2 = ['<HTML><BODY bgcolor="rgb(',...
+0237                         sprintf('%d,%d,%d',gui.myui.colors.listINV.*255),')">',...
+0238                         str1,'</BODY></HTML>'];
+0239                     strL{id} = str2;
+0240                     set(gui.listbox_handles.signal,'String',strL);
+0241                 end
+0242             otherwise
+0243         end
+0244         % update GUI interface
+0245         NUCLEUSinv_updateInterface;
+0246     end
+0247     
+0248 catch ME
+0249     % show error message in case import fails
+0250     errmsg = {ME.message;[ME.stack(1).name,' Line: ',num2str(ME.stack(1).line)];...
+0251         'Check File Format settings.'};
+0252     errordlg(errmsg,'importNMRdata: Error!');    
+0253 end
+0254 
+0255 end
+0256 
+0257 %%
+0258 function [NMRpath,NMRfile] = getNMRPathFile(label,import)
+0259 
+0260 NMRpath = -1;
+0261 NMRfile = -1;
+0262 % for almost all import cases we load a folder ... but not for all
+0263 switch label
+0264     case {'BAM TOM','BGR std','CoreLab ascii','GGE ascii','GGE field',...
+0265             'HeliosCPMG','HeliosSeries','LIAG core','LIAG single',...
+0266             'MOUSE','MouseCPMG','MouseLift','PM25'}
+0267         % if there is already a data folder present we start from here
+0268         if isfield(import,'path')
+0269             NMRpath = uigetdir(import.path,'Choose Data Path');
+0270         else
+0271             % otherwise we start at the current working dircetory
+0272             % 'NMRpath' holds the name of the choosen data path
+0273             here = mfilename('fullpath');
+0274             [pathstr,~,~] = fileparts(here);
+0275             NMRpath = uigetdir(pathstr,'Choose Data Path');
+0276         end
+0277     case 'LIAG from project'
+0278         % if there is already a data folder present we start from here
+0279         if isfield(import,'path')
+0280             NMRpath = uigetdir(import.path,'Choose Project Path');
+0281         else
+0282             % otherwise we start at the current working dircetory
+0283             % 'NMRpath' holds the name of the choosen data path
+0284             here = mfilename('fullpath');
+0285             [pathstr,~,~] = fileparts(here);
+0286             NMRpath = uigetdir(pathstr,'Choose Project Path');
+0287         end
+0288     case 'LIAG last project'
+0289         % there is already a data folder and we use this one
+0290         if isfield(import,'path')
+0291             NMRpath = import.path;
+0292         else
+0293             % otherwise we start at the current working dircetory
+0294             % 'NMRpath' holds the name of the choosen data path
+0295             here = mfilename('fullpath');
+0296             [pathstr,~,~] = fileparts(here);
+0297             NMRpath = uigetdir(pathstr,'Choose Project Path');
+0298         end
+0299     case {'GGE Dart','DART','BGR mat','NMR mat'}
+0300         % if there is already a data folder present we start from here
+0301         if isfield(import,'path')
+0302             [NMRfile,NMRpath] = uigetfile(import.path,'Choose Data file');
+0303         else
+0304             % otherwise we start at the current working dircetory
+0305             % 'foldername' hold s the name of the choosen data path
+0306             here = mfilename('fullpath');
+0307             [pathstr,~,~] = fileparts(here);
+0308             [NMRfile,NMRpath] = uigetfile(pathstr,'Choose Data file');
+0309         end
+0310     case 'PM5'
+0311         % if there is already a data folder present we start from here
+0312         if isfield(import,'path')
+0313             NMRpath = uigetdir(import.path,'Choose PM5 Data Path');
+0314         else
+0315             % otherwise we start at the current working dircetory
+0316             % 'NMRpath' holds the name of the choosen data path
+0317             here = mfilename('fullpath');
+0318             [pathstr,~,~] = fileparts(here);
+0319             NMRpath = uigetdir(pathstr,'Choose PM5 Data Path');
+0320         end
+0321         
+0322         % check if there are multiple inf-files available
+0323         % if yes -> choose one
+0324         inffiles = dir(fullfile(NMRpath,'*.inf'));
+0325         if numel(inffiles) > 1
+0326             [NMRfile,NMRpath] = uigetfile(fullfile(NMRpath,'*.inf'),...
+0327                 'Choose INF file');
+0328         elseif numel(inffiles) == 1
+0329             NMRfile = inffiles.name;            
+0330         end
+0331 end
 0332 
-0333 csv_t2path = dir(fullfile(data.import.path,'CPMG'));
-0334 csv_t2path = csv_t2path(~ismember({csv_t2path.name},{'.','..'}));
-0335 
-0336 fnames = struct;
-0337 % shownames is just a dummy to hold all data file names that
-0338 % will be shown in the listbox
-0339 shownames = cell(1,1);
+0333 end
+0334 
+0335 %%
+0336 function [data,gui] = importDataMouseCPMG(data,gui)
+0337 
+0338 csv_t2path = dir(fullfile(data.import.path,'CPMG'));
+0339 csv_t2path = csv_t2path(~ismember({csv_t2path.name},{'.','..'}));
 0340 
-0341 c = 0;
-0342 if ~isempty(csv_t2path)
-0343     for i = 1:size(csv_t2path,1)
-0344         in.T1T2 = 'T2';
-0345         in.path = fullfile(data.import.path,'CPMG',csv_t2path(i).name);
-0346         in.fileformat = data.import.fileformat;
-0347         out = LoadNMRData_driver(in);
-0348         
-0349         for j = 1:size(out.nmrData,2)
-0350             % the individual file names
-0351             c = c + 1;
-0352             fnames(c).parfile = 'acqu.par';
-0353             fnames(c).datafile = out.nmrData{j}.datfile;
-0354             fnames(c).T2specfile = '';
-0355             
-0356             shownames{c} = ['T2_',csv_t2path(i).name,'_',fnames(c).datafile];
-0357             
-0358             % the NMR data
-0359             % here we fix the time scale from [ms] to [s]
-0360             if max(out.nmrData{j}.time) > 100
-0361                 out.nmrData{j}.time = out.nmrData{j}.time/1000;
-0362                 out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1000;
-0363             end
-0364             data.import.NMR.data{c} = out.nmrData{j};
-0365             data.import.NMR.para{c} = out.parData;
-0366         end
-0367     end
-0368 end
-0369 
-0370 if isempty(csv_t2path)
-0371     helpdlg('No data folders in the given directory.','onMenuImport: No data.');
-0372 else
-0373     % update the global data structure
-0374     data.import.NMR.files = fnames;
-0375     data.import.NMR.filesShort = shownames;
-0376 end
-0377 
-0378 end
-0379 
-0380 %%
-0381 function [data,gui] = importDataBGRmat(data,gui)
+0341 fnames = struct;
+0342 % shownames is just a dummy to hold all data file names that
+0343 % will be shown in the listbox
+0344 shownames = cell(1,1);
+0345 
+0346 c = 0;
+0347 if ~isempty(csv_t2path)
+0348     for i = 1:size(csv_t2path,1)
+0349         in.T1T2 = 'T2';
+0350         in.path = fullfile(data.import.path,'CPMG',csv_t2path(i).name);
+0351         in.fileformat = data.import.fileformat;
+0352         out = LoadNMRData_driver(in);
+0353         
+0354         for j = 1:size(out.nmrData,2)
+0355             % the individual file names
+0356             c = c + 1;
+0357             fnames(c).parfile = 'acqu.par';
+0358             fnames(c).datafile = out.nmrData{j}.datfile;
+0359             fnames(c).T2specfile = '';
+0360             
+0361             shownames{c} = ['T2_',csv_t2path(i).name,'_',fnames(c).datafile];
+0362             
+0363             % the NMR data
+0364             % here we fix the time scale from [ms] to [s]
+0365             if max(out.nmrData{j}.time) > 100
+0366                 out.nmrData{j}.time = out.nmrData{j}.time/1000;
+0367                 out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1000;
+0368             end
+0369             data.import.NMR.data{c} = out.nmrData{j};
+0370             data.import.NMR.para{c} = out.parData;
+0371         end
+0372     end
+0373 end
+0374 
+0375 if isempty(csv_t2path)
+0376     helpdlg('No data folders in the given directory.','onMenuImport: No data.');
+0377 else
+0378     % update the global data structure
+0379     data.import.NMR.files = fnames;
+0380     data.import.NMR.filesShort = shownames;
+0381 end
 0382 
-0383 in.path = fullfile(data.import.path);
-0384 in.name = data.import.file;
-0385 in.fileformat = data.import.fileformat;
-0386 out = LoadNMRData_driver(in);
+0383 end
+0384 
+0385 %%
+0386 function [data,gui] = importDataBGRmat(data,gui)
 0387 
-0388 fnames = struct;
-0389 % shownames is just a dummy to hold all data file names that
-0390 % will be shown in the listbox
-0391 shownames = cell(1,1);
+0388 in.path = fullfile(data.import.path);
+0389 in.name = data.import.file;
+0390 in.fileformat = data.import.fileformat;
+0391 out = LoadNMRData_driver(in);
 0392 
-0393 c = 0;
-0394 table = {true,0,1,'D'};
-0395 for j = 1:size(out.nmrData,2)
-0396     % the individual file names
-0397     c = c + 1;
-0398     fnames(c).parfile = '';
-0399     fnames(c).datafile = data.import.file;
-0400     fnames(c).T2specfile = '';
-0401     
-0402     shownames{c} = out.parData{j}.file;
-0403     
-0404     data.import.NMR.data{c} = out.nmrData{j};
-0405     data.import.NMR.para{c} = out.parData{j};
+0393 fnames = struct;
+0394 % shownames is just a dummy to hold all data file names that
+0395 % will be shown in the listbox
+0396 shownames = cell(1,1);
+0397 
+0398 c = 0;
+0399 table = {true,0,1,'D'};
+0400 for j = 1:size(out.nmrData,2)
+0401     % the individual file names
+0402     c = c + 1;
+0403     fnames(c).parfile = '';
+0404     fnames(c).datafile = data.import.file;
+0405     fnames(c).T2specfile = '';
 0406     
-0407     if isfield(out,'pressData')
-0408         % convert hPa to Pa
-0409         table{c,1} = true;
-0410         table{c,2} = out.pressData.p(j)*1e2;
-0411         table{c,3} = out.pressData.S(j);
-0412         table{c,4} = 'D';
-0413     end
-0414 end
-0415 
-0416 % global Tbulk
-0417 data.invstd.Tbulk = out.parData{1}.Tbulk;
-0418 % global porosity
-0419 data.import.BGR.porosity = out.parData{1}.porosity;
+0407     shownames{c} = out.parData{j}.file;
+0408     
+0409     data.import.NMR.data{c} = out.nmrData{j};
+0410     data.import.NMR.para{c} = out.parData{j};
+0411     
+0412     if isfield(out,'pressData')
+0413         % convert hPa to Pa
+0414         table{c,1} = true;
+0415         table{c,2} = out.pressData.p(j)*1e2;
+0416         table{c,3} = out.pressData.S(j);
+0417         table{c,4} = 'D';
+0418     end
+0419 end
 0420 
-0421 data.import.NMR.files = fnames;
-0422 data.import.NMR.filesShort = shownames;
-0423 
-0424 % import pressure / saturation data
-0425 if isfield(out,'pressData')
-0426     data.pressure.unit = 'kPa';
-0427     data.pressure.unitfac = 1e-3;
-0428     data.pressure.table = table;
-0429 end
-0430 
-0431 end
-0432 
-0433 %%
-0434 function [data,gui] = importDataBGRliftSingle(data,gui)
+0421 % global Tbulk
+0422 data.invstd.Tbulk = out.parData{1}.Tbulk;
+0423 % global porosity
+0424 data.import.BGR.porosity = out.parData{1}.porosity;
+0425 
+0426 data.import.NMR.files = fnames;
+0427 data.import.NMR.filesShort = shownames;
+0428 
+0429 % import pressure / saturation data
+0430 if isfield(out,'pressData')
+0431     data.pressure.unit = 'kPa';
+0432     data.pressure.unitfac = 1e-3;
+0433     data.pressure.table = table;
+0434 end
 0435 
-0436 % first check whether T1 or T2 was measured...
-0437 % by analyzing the name of data folder
-0438 indiz = find(data.import.path == filesep);
-0439 checkT1T2 = data.import.path(indiz(end-1)+1:indiz(end)-1);
-0440 if strcmp(checkT1T2,'t1test')
-0441     in.T1T2 = 'T1';
-0442 elseif strcmp(checkT1T2,'cpmgfastautotest')
-0443     in.T1T2 = 'T2'; 
-0444 elseif strcmp(checkT1T2,'cpmgfastauto')
-0445     in.T1T2 = 'T2'; 
-0446 else
-0447     disp('Please chose an original Prospa folder for Mouse Lift data!');
-0448 end
-0449 
-0450 % % there should be folders with integer values in their names
-0451 % t1t2path = data.import.path;
-0452 
-0453 fnames = struct;
-0454 % shownames is just a dummy to hold all data file names that
-0455 % will be shown in the listbox
-0456 shownames = cell(1,1);
-0457 
-0458 c = 0;
-0459 if ~isempty(data.import.path)
-0460 %    for i = 1:size(t1t2path,1)
-0461         in.path = data.import.path;
-0462         in.fileformat = data.import.fileformat;
-0463         out = LoadNMRData_driver(in);
-0464         
-0465         for j = 1:size(out.nmrData,2)
-0466             % the individual file names
-0467             c = c + 1;
-0468             fnames(c).parfile = 'acq.par';
-0469             fnames(c).datafile = out.nmrData{j}.datfile;
-0470             
-0471             shownames{c} = [in.T1T2,'_',fnames(c).datafile];
-0472             
-0473             % the NMR data
-0474             % here we fix the time scale from [ms] to [s]
-0475             if max(out.nmrData{j}.time) > 100
-0476                 out.nmrData{j}.time = out.nmrData{j}.time/1000;
-0477                 out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1000;
-0478             end
-0479             data.import.NMR.data{c} = out.nmrData{j};
-0480             data.import.NMR.para{c} = out.parData;
-0481         end
-0482 else
-0483     helpdlg('No data folders in the given directory.','onMenuImport: No data.');
-0484 end
-0485 
-0486 
-0487     % update the global data structure
-0488     data.import.NMR.files = fnames;
-0489     data.import.NMR.filesShort = shownames;
-0490 
+0436 end
+0437 
+0438 %%
+0439 function [data,gui] = importDataBGRliftSingle(data,gui)
+0440 
+0441 % first check whether T1 or T2 was measured...
+0442 % by analyzing the name of data folder
+0443 ind = find(data.import.path == filesep);
+0444 checkT1T2 = data.import.path(ind(end-1)+1:ind(end)-1);
+0445 if strcmp(checkT1T2,'t1test')
+0446     in.T1T2 = 'T1';
+0447 elseif strcmp(checkT1T2,'T1auto')
+0448     in.T1T2 = 'T1'; 
+0449 elseif strcmp(checkT1T2,'cpmgfastautotest')
+0450     in.T1T2 = 'T2'; 
+0451 elseif strcmp(checkT1T2,'cpmgfastauto')
+0452     in.T1T2 = 'T2'; 
+0453 else
+0454     disp('Please chose an original Prospa folder for Mouse Lift data!');
+0455 end
+0456 
+0457 % % there should be folders with integer values in their names
+0458 % t1t2path = data.import.path;
+0459 
+0460 fnames = struct;
+0461 % shownames is just a dummy to hold all data file names that
+0462 % will be shown in the listbox
+0463 shownames = cell(1,1);
+0464 
+0465 c = 0;
+0466 if ~isempty(data.import.path)
+0467 %    for i = 1:size(t1t2path,1)
+0468         in.path = data.import.path;
+0469         in.fileformat = data.import.fileformat;
+0470         out = LoadNMRData_driver(in);
+0471         
+0472         for j = 1:size(out.nmrData,2)
+0473             % the individual file names
+0474             c = c + 1;
+0475             fnames(c).parfile = 'acq.par';
+0476             fnames(c).datafile = out.nmrData{j}.datfile;
+0477             
+0478             shownames{c} = [in.T1T2,'_',fnames(c).datafile];
+0479             
+0480             % the NMR data
+0481             % here we fix the time scale from [ms] to [s]
+0482             if max(out.nmrData{j}.time) > 100
+0483                 out.nmrData{j}.time = out.nmrData{j}.time/1000;
+0484                 out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1000;
+0485             end
+0486             data.import.NMR.data{c} = out.nmrData{j};
+0487             data.import.NMR.para{c} = out.parData;
+0488         end
+0489 else
+0490     helpdlg('No data folders in the given directory.','onMenuImport: No data.');
 0491 end
-0492 %%
-0493 function [data,gui] = importDataBGRliftAll(data,gui)
-0494 
-0495 % first check whether T1 or T2 was measured
-0496 indiz = find(data.import.path == filesep);
-0497 checkT1T2 = data.import.path(indiz(end)+1:end);
-0498 if strcmp(checkT1T2,'t1test')
-0499     in.T1T2 = 'T1';
-0500 elseif strcmp(checkT1T2,'cpmgfastautotest')
-0501     in.T1T2 = 'T2'; 
-0502 elseif strcmp(checkT1T2,'cpmgfastauto')
-0503     in.T1T2 = 'T2'; 
-0504 else
-0505     helpdlg('No original data folder','onMenuImport: No data.');
-0506 end
-0507 
-0508 % there should be folders with integer values in their names
-0509 t1t2path = dir(data.import.path);
-0510 t1t2path = t1t2path(~ismember({t1t2path.name},{'.','..'}));
-0511 
-0512 fnames = struct;
-0513 % shownames is just a dummy to hold all data file names that
-0514 % will be shown in the listbox
-0515 shownames = cell(1,1);
-0516 
-0517 c = 0;
-0518 if ~isempty(t1t2path)
-0519     for i = 1:size(t1t2path,1)
-0520         in.path = fullfile(data.import.path,t1t2path(i).name);
-0521         in.fileformat = data.import.fileformat;
-0522         out = LoadNMRData_driver(in);
-0523         
-0524         for j = 1:size(out.nmrData,2)
-0525             % the individual file names
-0526             c = c + 1;
-0527             fnames(c).parfile = 'acq.par';
-0528             fnames(c).datafile = out.nmrData{j}.datfile;
-0529             
-0530             shownames{c} = [in.T1T2,'_',t1t2path(i).name,'_',fnames(c).datafile];
-0531             
-0532             % the NMR data
-0533             % here we fix the time scale from [ms] to [s]
-0534             if max(out.nmrData{j}.time) > 100
-0535                 out.nmrData{j}.time = out.nmrData{j}.time/1000;
-0536                 out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1000;
-0537             end
-0538             data.import.NMR.data{c} = out.nmrData{j};
-0539             data.import.NMR.para{c} = out.parData;
-0540         end
-0541     end
-0542 else
-0543     helpdlg('No data folders in the given directory.','onMenuImport: No data.');
-0544 end
-0545     % update the global data structure
-0546     data.import.NMR.files = fnames;
-0547     data.import.NMR.filesShort = shownames;
-0548 
-0549 end
-0550 
-0551 %%
-0552 function [data,gui] = importDataHelios(data,gui)
-0553 
-0554 % first check the subpaths
-0555 % there should be some folders with names ...
-0556 % ... similar to the data filenames inside them
-0557 datpath = dir(data.import.path);
-0558 datpath = datpath(~ismember({datpath.name},{'.','..'}));
-0559 
-0560 fnames = struct;
-0561 % shownames is just a dummy to hold all data file names that
-0562 % will be shown in the listbox
-0563 shownames = cell(1,1);
+0492 
+0493 % update the global data structure
+0494 data.import.NMR.files = fnames;
+0495 data.import.NMR.filesShort = shownames;
+0496 
+0497 end
+0498 %%
+0499 function [data,gui] = importDataBGRlift(data,gui)
+0500 
+0501 % 1) show all folders and ask for sample
+0502 subdirs = dir(data.import.path);
+0503 % remove the dot-dirs
+0504 subdirs = subdirs(~ismember({subdirs.name},{'.','..'}));
+0505 
+0506 fnames = {subdirs.name};
+0507 [indx,~] = listdlg('PromptString','Choose data set:',...
+0508     'SelectionMode','multiple',...
+0509     'ListString',fnames);
+0510 
+0511 % first check whether T1 or T2 was measured
+0512 ind = find(data.import.path == filesep);
+0513 checkT1T2 = data.import.path(ind(end)+1:end);
+0514 if strcmp(checkT1T2,'t1test')
+0515     in.T1T2 = 'T1';
+0516 elseif strcmp(checkT1T2,'T1auto')
+0517     in.T1T2 = 'T1'; 
+0518 elseif strcmp(checkT1T2,'cpmgfastautotest')
+0519     in.T1T2 = 'T2'; 
+0520 elseif strcmp(checkT1T2,'cpmgfastauto')
+0521     in.T1T2 = 'T2'; 
+0522 else
+0523     helpdlg('No original data folder','onMenuImport: No data.');
+0524 end
+0525 
+0526 % now ask for stacking
+0527 answer = questdlg('Do you want to stack the slices?');
+0528 switch answer
+0529     case 'Yes'
+0530         doSliceStack = true;
+0531         % if stacking ask for stack-rotate-order
+0532         answer = questdlg('Select stack-rotate-order:',...
+0533             'Select order', ...
+0534             'stack-rotate (default)','rotate-stack','Cancel','stack-rotate (default)');
+0535         switch answer
+0536             case 'stack-rotate'
+0537                 StackFirst = true;
+0538             case 'rotate-stack'
+0539                 StackFirst = false;
+0540             otherwise
+0541                 StackFirst = true;
+0542         end
+0543     otherwise
+0544         doSliceStack = false;
+0545 end
+0546 
+0547 fnames = struct;
+0548 % shownames is just a dummy to hold all data file names that
+0549 % will be shown in the listbox
+0550 shownames = cell(1,1);
+0551 
+0552 c = 0;
+0553 if ~isempty(indx)
+0554     for i = indx
+0555         in.path = fullfile(data.import.path,subdirs(i).name);
+0556         in.fileformat = data.import.fileformat;
+0557         out = LoadNMRData_driver(in);
+0558 
+0559         if doSliceStack
+0560             % the individual file names
+0561             c = c + 1;
+0562             fnames(c).parfile = 'acq.par';
+0563             fnames(c).datafile = out.nmrData{1}.datfile;
 0564 
-0565 c = 0;
-0566 if ~isempty(datpath)
-0567     for i = 1:size(datpath,1)
-0568         % does datpath.name points to a folder?
-0569         if datpath(i).isdir    
-0570             % check if datpath.name includes regular Helios data files
-0571             content = dir([data.import.path,filesep,datpath(i).name]);
-0572             content = content(~ismember({content.name},{'.','..'}));
-0573             for j = 1:size(content,1)
-0574                 if strcmp(content(j).name,[datpath(i).name,'_1.hrd'])
-0575                     in.T1T2 = 'T2';
-0576                     in.name = content(j).name;
-0577                     in.path = fullfile(data.import.path,filesep,datpath(i).name);
-0578                     in.fileformat = data.import.fileformat;
-0579                     out = LoadNMRData_driver(in);
-0580                     
-0581                     % the individual file names
-0582                     c = c + 1;
-0583                     fnames(c).parfile = '';
-0584                     fnames(c).datafile = out.nmrData.datfile;
-0585                     fnames(c).T2specfile = '';
-0586                     shownames{c} = ['T2_',datpath(i).name];
-0587             
-0588                     data.import.NMR.data{c} = out.nmrData;
-0589                     data.import.NMR.para{c} = out.parData;
-0590                 end
-0591             end
-0592         end
-0593     end
-0594 end
-0595 
-0596 data.import.NMR.files = fnames;
-0597 data.import.NMR.filesShort = shownames;
-0598 
-0599 end
-0600 
-0601 %%
-0602 function [data,gui] = importDataDart(data,gui)
-0603 
-0604 in.path = fullfile(data.import.path);
-0605 in.name = data.import.file;
-0606 in.fileformat = data.import.fileformat;
-0607 in.version = data.import.version;
-0608 out = LoadNMRData_driver(in);
+0565             shownames{c} = [in.T1T2,'_',subdirs(i).name];
+0566 
+0567             % use the meta data from the first slice
+0568             % fix the time scale from [ms] to [s]
+0569             if max(out.nmrData{1}.time) > 100
+0570                 out.nmrData{1}.time = out.nmrData{1}.time/1000;
+0571                 out.nmrData{1}.raw.time = out.nmrData{1}.raw.time/1000;
+0572             end
+0573             % import into GUI data struct
+0574             data.import.NMR.data{c} = out.nmrData{1};
+0575 
+0576             % stacking
+0577             for j = 1:size(out.nmrData,2)
+0578                 if j == 1
+0579                     signal = out.nmrData{j}.signal;
+0580                 else
+0581                     signal = signal + out.nmrData{j}.signal;
+0582                 end
+0583             end
+0584             signal = signal./size(out.nmrData,2);
+0585 
+0586             % now rotate after the stacking
+0587             if StackFirst
+0588                 [signal,phase] = rotateT2phase(signal);
+0589                 data.import.NMR.data{c}.phase = phase;
+0590                 data.import.NMR.data{c}.signal = signal;
+0591                 data.import.NMR.data{c}.raw.signal = signal;
+0592             else
+0593                 % no rotation after stacking
+0594                 data.import.NMR.data{c}.signal = signal;
+0595                 data.import.NMR.data{c}.raw.signal = signal;
+0596             end
+0597             
+0598             % parameter data
+0599             data.import.NMR.para{c} = out.parData;
+0600         else
+0601 
+0602             for j = 1:size(out.nmrData,2)
+0603                 % the individual file names
+0604                 c = c + 1;
+0605                 fnames(c).parfile = 'acq.par';
+0606                 fnames(c).datafile = out.nmrData{j}.datfile;
+0607 
+0608                 shownames{c} = [in.T1T2,'_',subdirs(i).name,'_',fnames(c).datafile];
 0609 
-0610 fnames = struct;
-0611 % shownames is just a dummy to hold all data file names that
-0612 % will be shown in the listbox
-0613 shownames = cell(1,1);
-0614 
-0615 c = 0;
-0616 for j = 1:size(out.nmrData,2)
-0617     % the individual file names
-0618     c = c + 1;
-0619     fnames(c).parfile = '';
-0620     fnames(c).datafile = data.import.file;
-0621     fnames(c).T2specfile = '';
-0622     
-0623     shownames{c} = ['depth_',sprintf('%04.3f',out.parData{j}.depth)];
-0624     
-0625     % the NMR data
-0626     % here we fix the time scale from [ms] to [s]
-0627     if max(out.nmrData{j}.time) > 100
-0628         out.nmrData{j}.time = out.nmrData{j}.time/1000;
-0629         out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1000;
-0630     end
-0631     data.import.NMR.data{c} = out.nmrData{j};
-0632     data.import.NMR.para{c} = out.parData{j};
-0633 end
-0634 
-0635 data.import.NMR.files = fnames;
-0636 data.import.NMR.filesShort = shownames;
-0637 
-0638 end
+0610                 % the NMR data
+0611                 % here we fix the time scale from [ms] to [s]
+0612                 if max(out.nmrData{j}.time) > 100
+0613                     out.nmrData{j}.time = out.nmrData{j}.time/1000;
+0614                     out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1000;
+0615                 end
+0616                 data.import.NMR.data{c} = out.nmrData{j};
+0617                 data.import.NMR.para{c} = out.parData;
+0618             end
+0619         end
+0620     end
+0621 else
+0622     helpdlg('No data folders in the given directory.','onMenuImport: No data.');
+0623 end
+0624 
+0625 % update the global data structure
+0626 data.import.NMR.files = fnames;
+0627 data.import.NMR.filesShort = shownames;
+0628 
+0629 end
+0630 
+0631 %%
+0632 function [data,gui] = importDataHeliosCPMG(data,gui)
+0633 
+0634 % first check the subpaths
+0635 % there should be some folders with names ...
+0636 % ... similar to the data filenames inside them
+0637 datpath = dir(data.import.path);
+0638 datpath = datpath(~ismember({datpath.name},{'.','..'}));
 0639 
-0640 %%
-0641 function [data,gui] = importDataGeneral(data,gui)
-0642 
-0643 % look for all files ending with '.par'
-0644 % should exist for T1 and T2 measurements
-0645 filenames = dir(fullfile(data.import.path,'*.par'));
-0646 
-0647 fnames = struct;
-0648 % shownames is just a dummy to hold all data file names that
-0649 % will be shown in the listbox
-0650 shownames = cell(1,1);
-0651 
-0652 % loop over all found files and import the data
-0653 c = 0;
-0654 in.path = data.import.path;
-0655 for i = 1:size(filenames,1)
-0656     ind = strfind(filenames(i).name,'.');
-0657     ind = max(ind);
-0658     in.name = filenames(i).name(1:ind-1);
-0659     in.fileformat = data.import.fileformat;
-0660     out = LoadNMRData_driver(in);
-0661     
-0662     for j = 1:size(out.nmrData,2)
-0663         % the individual file names
-0664         c = c + 1;
-0665         fnames(c).parfile = filenames(i).name;
-0666         fnames(c).datafile = out.nmrData{j}.datfile;
-0667         if strcmp(out.nmrData{j}.flag,'T2') && isfield(out.nmrData{j},'specfile')
-0668             fnames(c).T2specfile = out.nmrData{j}.specfile;
-0669         else
-0670             fnames(c).T2specfile = '';
-0671         end
-0672         shownames{c} = fnames(c).datafile;
-0673         
-0674         % the NMR data
-0675         % here we fix the time scale from [ms] to [s]
-0676         if max(out.nmrData{j}.time) > 100
-0677             out.nmrData{j}.time = out.nmrData{j}.time/1000;
-0678             out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1000;
-0679         end
-0680         data.import.NMR.data{c} = out.nmrData{j};
-0681         data.import.NMR.para{c} = out.parData;
-0682     end
-0683 end
-0684 
-0685 switch data.import.fileformat
-0686     case 'bamtom'
-0687         nslices = out.parData.nSlices;
-0688         ncsvfiles = numel(fnames);
-0689         
-0690         % check for background file ("Leermessung")
-0691         has_bg = false;
-0692         for i = 1:numel(fnames)
-0693             if ~isempty(strfind(fnames(i).datafile,'000'))
-0694                 has_bg = true;
-0695                 index_bg = i;
-0696                 break;
-0697             end
-0698         end
-0699         
-0700         if has_bg
-0701             % background data set
-0702             bg = data.import.NMR.data{index_bg};
-0703             
-0704             % vector of indices of the files that get corrected
-0705             ind_files = 1:1:ncsvfiles;
-0706             ind_files(ind_files==index_bg) = [];
-0707             
-0708             for i = ind_files                
-0709                 % subtract the background signal
-0710                 s = data.import.NMR.data{i}.signal;
-0711                 s_bg = bg.signal;
-0712                 % if the background signal is longer than the signal cut it
-0713                 if numel(s_bg) > numel(s)
-0714                     tmp_s = s_bg(1:numel(s));
-0715                 else % if not pad it with zeros
-0716                     tmp_s = zeros(size(s));
-0717                     tmp_s(1:numel(s_bg)) = s_bg;
-0718                 end
-0719                 s = complex(real(s)-real(tmp_s),imag(s)-imag(tmp_s));
-0720                 % update original data set
-0721                 data.import.NMR.data{i}.signal = s;                
-0722             end
-0723             
-0724             % check if the number of slices is equal to the number of files
-0725             % (excluding the background file)
-0726             if nslices == numel(ind_files)
-0727                 % create z-vector
-0728                 p = out.parData;
-0729                 zslice = linspace(p.startPos,p.endPos,p.nSlices)';
-0730                 data.import.BAM.use_z = true;
-0731                 data.import.BAM.zslice = zslice;
-0732                 if numel(zslice) > 1
-0733                     c = 0;
-0734                     for i = ind_files
-0735                         c = c + 1;
-0736                         tmp = shownames{i};
-0737                         shownames{i} = [tmp,' z:',sprintf('%5.4f',zslice(c))];
-0738                     end
-0739                 end
-0740             else
-0741                 data.import.BAM.use_z = false;
-0742                 data.import.BAM.zslice = 1:1:max([numel(ind_files) 1]);
-0743             end
-0744             
-0745         else
-0746             if nslices == ncsvfiles
-0747                 % create z-vector
-0748                 p = out.parData;
-0749                 zslice = linspace(p.startPos,p.endPos,p.nSlices)';
-0750                 data.import.BAM.use_z = true;
-0751                 data.import.BAM.zslice = zslice;
-0752                 if numel(zslice) > 1
-0753                     for i = 1:numel(zslice)
-0754                         tmp = shownames{i};
-0755                         shownames{i} = [tmp,' z:',sprintf('%5.4f',zslice(i))];
-0756                     end
-0757                 end
-0758             else
-0759                 data.import.BAM.use_z = false;
-0760                 data.import.BAM.zslice = 1:1:ncsvfiles;
-0761             end
-0762         end    
-0763 end
-0764 
-0765 % update the global data structure
-0766 data.import.NMR.files = fnames;
-0767 data.import.NMR.filesShort = shownames;
-0768 
-0769 end
+0640 fnames = struct;
+0641 % shownames is just a dummy to hold all data file names that
+0642 % will be shown in the listbox
+0643 shownames = cell(1,1);
+0644 
+0645 c = 0;
+0646 if ~isempty(datpath)
+0647     for i = 1:size(datpath,1)
+0648         % does datpath.name points to a folder?
+0649         if datpath(i).isdir    
+0650             % check if datpath.name includes regular Helios data files
+0651             content = dir([data.import.path,filesep,datpath(i).name]);
+0652             content = content(~ismember({content.name},{'.','..'}));
+0653             for j = 1:size(content,1)
+0654                 if strcmp(content(j).name,[datpath(i).name,'.hrd'])
+0655                     if ~strcmp(content(j).name,[datpath(i).name,'_ref'])
+0656                         in.T1T2 = 'T2';
+0657                         in.name = content(j).name;
+0658                         in.path = fullfile(data.import.path,filesep,datpath(i).name);
+0659                         in.fileformat = data.import.fileformat;
+0660                         out = LoadNMRData_driver(in);
+0661                         
+0662                         % the individual file names
+0663                         c = c + 1;
+0664                         fnames(c).parfile = '';
+0665                         fnames(c).datafile = out.nmrData.datfile;
+0666                         fnames(c).T2specfile = '';
+0667                         shownames{c} = ['T2_',datpath(i).name];
+0668                         
+0669                         data.import.NMR.data{c} = out.nmrData;
+0670                         data.import.NMR.para{c} = out.parData;
+0671                     end
+0672                 end
+0673             end
+0674         end
+0675     end
+0676 end
+0677 
+0678 % update the global data structure
+0679 data.import.NMR.files = fnames;
+0680 data.import.NMR.filesShort = shownames;
+0681 
+0682 end
+0683 
+0684 %%
+0685 function [data,gui] = importDataHeliosSeries(data,gui)
+0686 
+0687 % first check the subpaths
+0688 % there should be some folders with names ...
+0689 % ... similar to the data filenames inside them
+0690 datpath = dir(data.import.path);
+0691 datpath = datpath(~ismember({datpath.name},{'.','..'}));
+0692 
+0693 fnames = struct;
+0694 % shownames is just a dummy to hold all data file names that
+0695 % will be shown in the listbox
+0696 shownames = cell(1,1);
+0697 
+0698 c = 0;
+0699 if ~isempty(datpath)
+0700     content = datpath;
+0701     for j = 1:size(content,1)
+0702         if ~strcmp(content(j).name(end-7:end),'_ref.hrd')
+0703             in.T1T2 = 'T2';
+0704             in.name = content(j).name;
+0705             in.path = fullfile(data.import.path);
+0706             in.fileformat = data.import.fileformat;
+0707             out = LoadNMRData_driver(in);
+0708             % the individual file names
+0709             c = c + 1;
+0710             fnames(c).parfile = '';
+0711             fnames(c).datafile = out.nmrData.datfile;
+0712             fnames(c).T2specfile = '';
+0713             shownames{c} = ['T2_',content(j).name];
+0714             
+0715             data.import.NMR.data{c} = out.nmrData;
+0716             data.import.NMR.para{c} = out.parData;
+0717         end
+0718         
+0719     end
+0720 end
+0721 
+0722 % update the global data structure
+0723 data.import.NMR.files = fnames;
+0724 data.import.NMR.filesShort = shownames;
+0725 
+0726 end
+0727 
+0728 %%
+0729 function [data,gui] = importDataDart(data,gui)
+0730 
+0731 in.path = fullfile(data.import.path);
+0732 in.name = data.import.file;
+0733 in.fileformat = data.import.fileformat;
+0734 in.version = data.import.version;
+0735 out = LoadNMRData_driver(in);
+0736 
+0737 fnames = struct;
+0738 % shownames is just a dummy to hold all data file names that
+0739 % will be shown in the listbox
+0740 shownames = cell(1,1);
+0741 
+0742 c = 0;
+0743 for j = 1:size(out.nmrData,2)
+0744     % the individual file names
+0745     c = c + 1;
+0746     fnames(c).parfile = '';
+0747     fnames(c).datafile = data.import.file;
+0748     fnames(c).T2specfile = '';
+0749     
+0750     shownames{c} = ['depth_',sprintf('%04.3f',out.parData{j}.depth)];
+0751     
+0752     % the NMR data
+0753     % here we fix the time scale from [ms] to [s]
+0754     if max(out.nmrData{j}.time) > 100
+0755         out.nmrData{j}.time = out.nmrData{j}.time/1000;
+0756         out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1000;
+0757     end
+0758     data.import.NMR.data{c} = out.nmrData{j};
+0759     data.import.NMR.para{c} = out.parData{j};
+0760 end
+0761 
+0762 % update the global data structure
+0763 data.import.NMR.files = fnames;
+0764 data.import.NMR.filesShort = shownames;
+0765 
+0766 end
+0767 
+0768 %%
+0769 function [data,gui] = importDataGeneral(data,gui)
 0770 
-0771 %%
-0772 function [data,gui] = importDataLIAG(data,gui)
-0773 
-0774 in.path = fullfile(data.import.path);
-0775 in.fileformat = data.import.fileformat;
-0776 out = LoadNMRData_driver(in);
-0777 
-0778 fnames = struct;
-0779 % shownames is just a dummy to hold all data file names that
-0780 % will be shown in the listbox
-0781 shownames = cell(1,1);
-0782 
-0783 c = 0;
-0784 for j = 1:size(out.nmrData,2)
-0785     % the individual file names
-0786     c = c + 1;
-0787     fnames(c).parfile = 'acqu.par';
-0788     fnames(c).datafile = out.nmrData{j}.datfile;
-0789     fnames(c).T2specfile = '';
-0790     
-0791     shownames{c} = fnames(c).datafile;
-0792     
-0793     % the NMR data
-0794     % here we fix the time scale to [s] if neccessary
-0795     TE = out.parData.echoTime; % [µs]
-0796     if out.nmrData{j}.time(1)== TE/1e3
-0797         % change [ms] to [s]
-0798         out.nmrData{j}.time = out.nmrData{j}.time/1e3;
-0799         out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1e3;
-0800     elseif out.nmrData{j}.time(1)== TE
-0801         % change [µs] to [s] -> very unlikely
-0802         out.nmrData{j}.time = out.nmrData{j}.time/1e6;
-0803         out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1e6;
-0804     end
-0805     data.import.NMR.data{c} = out.nmrData{j};
-0806     data.import.NMR.para{c} = out.parData;
-0807 end
-0808 
-0809 % update the global data structure
-0810 data.import.NMR.files = fnames;
-0811 data.import.NMR.filesShort = shownames;
+0771 % look for all files ending with '.par'
+0772 % should exist for T1 and T2 measurements
+0773 filenames = dir(fullfile(data.import.path,'*.par'));
+0774 
+0775 fnames = struct;
+0776 % shownames is just a dummy to hold all data file names that
+0777 % will be shown in the listbox
+0778 shownames = cell(1,1);
+0779 
+0780 % loop over all found files and import the data
+0781 c = 0;
+0782 in.path = data.import.path;
+0783 for i = 1:size(filenames,1)
+0784     ind = strfind(filenames(i).name,'.');
+0785     ind = max(ind);
+0786     in.name = filenames(i).name(1:ind-1);
+0787     in.fileformat = data.import.fileformat;
+0788     out = LoadNMRData_driver(in);
+0789     
+0790     for j = 1:size(out.nmrData,2)
+0791         % the individual file names
+0792         c = c + 1;
+0793         fnames(c).parfile = filenames(i).name;
+0794         fnames(c).datafile = out.nmrData{j}.datfile;
+0795         if strcmp(out.nmrData{j}.flag,'T2') && isfield(out.nmrData{j},'specfile')
+0796             fnames(c).T2specfile = out.nmrData{j}.specfile;
+0797         else
+0798             fnames(c).T2specfile = '';
+0799         end
+0800         shownames{c} = fnames(c).datafile;
+0801         
+0802         % the NMR data
+0803         % here we fix the time scale from [ms] to [s]
+0804         if max(out.nmrData{j}.time) > 100
+0805             out.nmrData{j}.time = out.nmrData{j}.time/1000;
+0806             out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1000;
+0807         end
+0808         data.import.NMR.data{c} = out.nmrData{j};
+0809         data.import.NMR.para{c} = out.parData;
+0810     end
+0811 end
 0812 
-0813 end
-0814 
-0815 %%
-0816 function [data,gui] = importDataLIAGproject(data,gui)
-0817 
-0818 % 1) show all folders and ask for sample
-0819 subdirs = dir(data.import.path);
-0820 % remove the dot-dirs
-0821 subdirs = subdirs(~ismember({subdirs.name},{'.','..'}));
-0822 
-0823 fnames = {subdirs.name};
-0824 [indx,~] = listdlg('PromptString','Select Sample:',...
-0825     'SelectionMode','single',...
-0826     'ListString',fnames);
-0827 
-0828 if ~isempty(indx)
-0829     % 2) check corresponding SampleParameter.par file for reference and
-0830     % calibration sample and other parameters
-0831     datapath = fullfile(data.import.path,fnames{indx});
-0832     % load SampleParameter file for sample
-0833     [SampleParameter] = loadGUIParameters(datapath,'SampleParameters.par');
-0834     if isfield(SampleParameter,'sampleVolume')
-0835         dataVol = SampleParameter.sampleVolume;
-0836     else
-0837         dataVol = 1;
-0838     end
-0839     
-0840     % 2a) background file #1
-0841     backgroundFile1 = SampleParameter.backgroundFile;
-0842     if isempty(backgroundFile1)
-0843         bnames = {subdirs.name};
-0844         bnames(indx) = [];
-0845         [indb,~] = listdlg('PromptString','Select Background File:',...
-0846             'SelectionMode','single',...
-0847             'ListString',bnames);
-0848         if ~isempty(indb)
-0849             backgroundFile1 = bnames{indb};
-0850         else
-0851             backgroundFile1 = '';
-0852         end
-0853     end
-0854     if ~isempty(backgroundFile1)
-0855         ind = strfind(backgroundFile1,filesep);
-0856         if ~isempty(ind)
-0857             backgroundFile1 = backgroundFile1(ind(end)+1:end);
-0858         end
-0859         fileInList = ismember(fnames,{backgroundFile1});
-0860         if any(fileInList)
-0861             backgroundpath1 = fullfile(data.import.path,fnames{fileInList});
-0862         end
-0863     else
-0864         backgroundpath1 = '';
-0865         backgroundFile1 = '';
-0866     end
-0867     backVol = 1;
-0868     
-0869     % 2b) calibration file
-0870     c = 0;
-0871     if isfield(SampleParameter,'calibrationFile0')
-0872         c = c + 1;
-0873         calibrationFiles{c} = SampleParameter.calibrationFile0;
-0874     end
-0875     if isfield(SampleParameter,'calibrationFile1')
-0876         c = c + 1;
-0877         calibrationFiles{c} = SampleParameter.calibrationFile1;
-0878     end
-0879     if isfield(SampleParameter,'calibrationFile2')
-0880         c = c + 1;
-0881         calibrationFiles{c} = SampleParameter.calibrationFile2;
-0882     end
-0883     if isfield(SampleParameter,'calibrationFile3')
-0884         c = c + 1;
-0885         calibrationFiles{c} = SampleParameter.calibrationFile3;
-0886     end
-0887     
-0888     % find the non-empty one
-0889     ind = ismember(calibrationFiles,{''});
-0890     % there are three possibilities: 0, 1 and more than 1 calib. files
-0891     calibrationFiles(ind) = [];
-0892     if isempty(calibrationFiles)
-0893         cnames = {subdirs.name};
-0894         cnames(indx) = [];
-0895         [indc,~] = listdlg('PromptString','Select Calibration File:',...
-0896             'SelectionMode','single',...
-0897             'ListString',cnames);
-0898         if ~isempty(indc)
-0899             calibrationFiles = cnames{indc};
-0900         else
-0901             calibrationFiles = '';
-0902         end        
-0903     else
-0904         % if there are more than one let the user select the correct one
-0905         if numel(calibrationFiles) > 1
-0906             [ind,~] = listdlg('PromptString','Select Calibration File:',...
-0907                 'SelectionMode','single',...
-0908                 'ListString',calibrationFiles);
-0909             calibrationFiles = calibrationFiles{ind};
-0910         else
-0911             calibrationFiles = calibrationFiles{1};
-0912         end
-0913     end
-0914     if ~isempty(calibrationFiles)
-0915         ind = strfind(calibrationFiles,filesep);
-0916         if ~isempty(ind)
-0917             calibrationFiles = calibrationFiles(ind(end)+1:end);
-0918         end
-0919         fileInList = ismember(fnames,{calibrationFiles});
-0920         if any(fileInList)
-0921             calibrationpath = fullfile(data.import.path,fnames{fileInList});
-0922         end
-0923     else
-0924         calibrationpath = '';
-0925         calibrationFiles = '';
-0926     end
-0927     
-0928     if ~isempty(calibrationpath)
-0929         [SampleParameterC] = loadGUIParameters(calibrationpath,'SampleParameters.par');
-0930         if isfield(SampleParameterC,'sampleVolume')
-0931             calibVol = SampleParameterC.sampleVolume;
-0932         else
-0933             calibVol = 1;
-0934         end
-0935         
-0936         % 2a) background file #2
-0937         backgroundFile2 = SampleParameterC.backgroundFile;
-0938         if isempty(backgroundFile2)
-0939             bnames = {subdirs.name};
-0940             bnames(indx) = [];
-0941             [indb,~] = listdlg('PromptString','Select Background File for Calibration:',...
-0942                 'SelectionMode','single',...
-0943                 'ListString',bnames);
-0944             if ~isempty(indb)
-0945                 backgroundFile2 = bnames{indb};
-0946             else
-0947                 backgroundFile2 = '';
-0948             end  
-0949         end
-0950         if ~isempty(backgroundFile2)
-0951             ind = strfind(backgroundFile2,filesep);
-0952             if ~isempty(ind)
-0953                 backgroundFile2 = backgroundFile2(ind(end)+1:end);
-0954             end
-0955             fileInList = ismember(fnames,{backgroundFile2});
-0956             if any(fileInList)
-0957                 backgroundpath2 = fullfile(data.import.path,fnames{fileInList});
-0958             end
-0959         else
-0960             backgroundpath2 = '';
-0961             backgroundFile2 = '';
-0962         end
-0963     else
-0964         calibVol = 1;
-0965         backgroundpath2 = '';
-0966         backgroundFile2 = '';
-0967     end
-0968     
-0969     % 3) now load the data
-0970     workpaths = {datapath,calibrationpath,backgroundpath1,backgroundpath2};
-0971     workfiles = {fnames{indx},[calibrationFiles,' - calibration'],...
-0972         [backgroundFile1,' - backgroundS'],[backgroundFile2,' - backgroundC']};
-0973     out = cell(size(workpaths));
-0974     count = 0;
-0975     keep = false(size(workpaths));
-0976     for i = 1:numel(workpaths)
-0977         if ~isempty(workpaths{i})
-0978             workdirs = dir(workpaths{i});
-0979             workdirs = workdirs(~ismember({workdirs.name},{'.','..'}));
-0980             isT2 = ismember({workdirs.name},{'T2CPMG'});
-0981             if any(isT2)
-0982                 keep(i) = true;
-0983                 count = count + 1;
-0984                 T2path = fullfile(workdirs(isT2).folder,workdirs(isT2).name);
-0985                 in.path = T2path;
-0986                 in.fileformat = data.import.fileformat;
-0987                 out{i} = LoadNMRData_driver(in);
-0988             end
-0989         end
-0990     end    
-0991     
-0992     if isempty(backgroundpath1)
-0993         ref1 = struct;
-0994     else
-0995         background1 = out{3};
-0996         % get the background data 1
-0997         ref1.t = background1.nmrData{1}.time;
-0998         ref1.s = background1.nmrData{1}.signal;
-0999         [ref1.s,~] = rotateT2phase(ref1.s);
-1000     end
-1001     
-1002     if isempty(backgroundpath2)
-1003         ref2 = struct;
-1004     else
-1005         background2 = out{4};
-1006         % get the background data 2
-1007         ref2.t = background2.nmrData{1}.time;
-1008         ref2.s = background2.nmrData{1}.signal;
-1009         [ref2.s,~] = rotateT2phase(ref2.s);
-1010     end
-1011     
-1012     workpaths = workpaths(keep);
-1013     workfiles = workfiles(keep);
-1014     out = out(keep);
-1015     
-1016     ffnames = struct;
-1017     % shownames is just a dummy to hold all data file names that
-1018     % will be shown in the listbox
-1019     shownames = cell(1,1);
-1020     
-1021     for i = 1:count
-1022         ffnames(i).parfile = 'acqu.par';
-1023         ffnames(i).datafile = workfiles{i};
-1024         ffnames(i).T2specfile = '';
-1025         
-1026         shownames{i} = ffnames(i).datafile;
-1027         
-1028         % the NMR data
-1029         % here we fix the time scale to [s] if neccessary
-1030         TE = out{i}.parData.echoTime; % [µs]
-1031         if out{i}.nmrData{1}.time(1)== TE/1e3
-1032             % change [ms] to [s]
-1033             out{i}.nmrData{1}.time = out{i}.nmrData{1}.time/1e3;
-1034             out{i}.nmrData{1}.raw.time = out{i}.nmrData{1}.raw.time/1e3;
-1035         elseif out{i}.nmrData{1}.time(1)== TE
-1036             % change [µs] to [s] -> very unlikely
-1037             out{i}.nmrData{1}.time = out{i}.nmrData{1}.time/1e6;
-1038         out{i}.nmrData{1}.raw.time = out{i}.nmrData{1}.raw.time/1e6;
-1039         end
-1040         
-1041         data.import.NMR.data{i} = out{i}.nmrData{1};
-1042         data.import.NMR.para{i} = out{i}.parData;
-1043         data.import.NMR.para{i}.SampleParameter = SampleParameter;
-1044         
-1045         % subtract the background signal
-1046         s = data.import.NMR.data{i}.signal;
-1047         if i==1 && isfield(ref1,'s')
-1048             % if the background signal is longer than the signal cut it, if
-1049             % not extend it with zeros
-1050             if numel(ref1.s) > numel(s)
-1051                 tmp_r = ref1.s(1:numel(s));
-1052             else
-1053                 tmp_r = zeros(size(s));
-1054                 tmp_r(1:numel(ref1.s)) = ref1.s;
-1055             end
-1056             s = complex(real(s)-real(tmp_r),imag(s)-imag(tmp_r));
-1057         elseif i==2 && isfield(ref2,'s')
-1058             % if the background signal is longer than the signal cut it, if
-1059             % not extend it with zeros
-1060             if numel(ref2.s) > numel(s)
-1061                 tmp_r = ref2.s(1:numel(s));
-1062             else
-1063                 tmp_r = zeros(size(s));
-1064                 tmp_r(1:numel(ref2.s)) = ref2.s;
-1065             end
-1066             s = complex(real(s)-real(tmp_r),imag(s)-imag(tmp_r));
-1067         end        
-1068         data.import.NMR.data{i}.signal = s;
-1069         data.import.NMR.data{i}.raw.signal = s;
-1070         
-1071         if ~isempty(strfind(workfiles{i},' - background'))
-1072             data.import.LIAG.sampleVol(i) = backVol;
-1073         elseif ~isempty(strfind(workfiles{i},' - calibration'))
-1074             data.import.LIAG.sampleVol(i) = calibVol;
-1075         elseif isempty(strfind(workfiles{i},' - background')) &&...
-1076                 isempty(strfind(workfiles{i},' - calibration'))
-1077             data.import.LIAG.sampleVol(i) = dataVol;
-1078         end
-1079     end
-1080     data.import.LIAG.Tbulk = 1e6;
-1081     data.import.LIAG.workpaths = workpaths;
-1082     data.import.LIAG.datapath = datapath;
-1083     data.import.LIAG.calibrationpath = calibrationpath;
-1084     data.import.LIAG.backgroundpath1 = backgroundpath1;
-1085     data.import.LIAG.backgroundpath2 = backgroundpath2;
-1086     
-1087     % update the global data structure
-1088     data.import.NMR.files = ffnames;
-1089     data.import.NMR.filesShort = shownames;
-1090     
-1091 end
-1092 
-1093 end
-1094 
-1095 %%
-1096 function [data,gui] = importDataMouse(data,gui)
-1097 
-1098 in.path = fullfile(data.import.path);
-1099 in.fileformat = data.import.fileformat;
-1100 out = LoadNMRData_driver(in);
-1101 
-1102 fnames = struct;
-1103 % shownames is just a dummy to hold all data file names that
-1104 % will be shown in the listbox
-1105 shownames = cell(1,1);
-1106 
-1107 c = 0;
-1108 for j = 1:size(out.nmrData,2)
-1109     % the individual file names
-1110     c = c + 1;
-1111     fnames(c).parfile = 'acq.par';
-1112     fnames(c).datafile = out.nmrData{j}.datfile;
-1113     fnames(c).T2specfile = '';
-1114     
-1115     shownames{c} = ['T2_',fnames(c).datafile];
-1116     
-1117     % the NMR data
-1118     % here we fix the time scale from [ms] to [s]
-1119     if max(out.nmrData{j}.time) > 100
-1120         out.nmrData{j}.time = out.nmrData{j}.time/1000;
-1121         out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1000;
-1122     end
-1123     data.import.NMR.data{c} = out.nmrData{j};
-1124     data.import.NMR.para{c} = out.parData;
-1125 end
-1126 
-1127 % update the global data structure
-1128 data.import.NMR.files = fnames;
-1129 data.import.NMR.filesShort = shownames;
-1130 
-1131 end
-1132 
-1133 %%
-1134 function [data,gui] = importDataIBAC(data,gui)
-1135 
-1136 in.path = fullfile(data.import.path);
-1137 in.name = data.import.file;
-1138 in.fileformat = data.import.fileformat;
-1139 out = LoadNMRData_driver(in);
-1140 
-1141 nslices = out.parData.depths;
-1142 nfiles = size(out.nmrData,2);
-1143 
-1144 fnames = struct;
-1145 % shownames is just a dummy to hold all data file names that
-1146 % will be shown in the listbox
-1147 shownames = cell(1,1);
-1148 
-1149 c = 0;
-1150 for j = 1:size(out.nmrData,2)
-1151     % the individual file names
-1152     c = c + 1;
-1153     fnames(c).parfile = out.parData.parfile;
-1154     fnames(c).datafile = out.nmrData{j}.datfile;
-1155     fnames(c).T2specfile = '';
+0813 switch data.import.fileformat
+0814     case 'bamtom'
+0815         nslices = out.parData.nSlices;
+0816         ncsvfiles = numel(fnames);
+0817         
+0818         % check for background file ("Leermessung")
+0819         has_bg = false;
+0820         for i = 1:numel(fnames)
+0821             if ~isempty(strfind(fnames(i).datafile,'000'))
+0822                 has_bg = true;
+0823                 index_bg = i;
+0824                 break;
+0825             end
+0826         end
+0827         
+0828         if has_bg
+0829             % background data set
+0830             bg = data.import.NMR.data{index_bg};
+0831             
+0832             % vector of indices of the files that get corrected
+0833             ind_files = 1:1:ncsvfiles;
+0834             ind_files(ind_files==index_bg) = [];
+0835             
+0836             for i = ind_files                
+0837                 % subtract the background signal
+0838                 s = data.import.NMR.data{i}.signal;
+0839                 s_bg = bg.signal;
+0840                 % if the background signal is longer than the signal cut it
+0841                 if numel(s_bg) > numel(s)
+0842                     tmp_s = s_bg(1:numel(s));
+0843                 else % if not pad it with zeros
+0844                     tmp_s = zeros(size(s));
+0845                     tmp_s(1:numel(s_bg)) = s_bg;
+0846                 end
+0847                 s = complex(real(s)-real(tmp_s),imag(s)-imag(tmp_s));
+0848                 % update original data set
+0849                 data.import.NMR.data{i}.signal = s;                
+0850             end
+0851             
+0852             % check if the number of slices is equal to the number of files
+0853             % (excluding the background file)
+0854             if nslices == numel(ind_files)
+0855                 % create z-vector
+0856                 p = out.parData;
+0857                 zslice = linspace(p.startPos,p.endPos,p.nSlices)';
+0858                 data.import.BAM.use_z = true;
+0859                 data.import.BAM.zslice = zslice;
+0860                 if numel(zslice) > 1
+0861                     c = 0;
+0862                     for i = ind_files
+0863                         c = c + 1;
+0864                         tmp = shownames{i};
+0865                         shownames{i} = [tmp,' z:',sprintf('%5.4f',zslice(c))];
+0866                     end
+0867                 end
+0868             else
+0869                 data.import.BAM.use_z = false;
+0870                 data.import.BAM.zslice = 1:1:max([numel(ind_files) 1]);
+0871             end
+0872             
+0873         else
+0874             if nslices == ncsvfiles
+0875                 % create z-vector
+0876                 p = out.parData;
+0877                 zslice = linspace(p.startPos,p.endPos,p.nSlices)';
+0878                 data.import.BAM.use_z = true;
+0879                 data.import.BAM.zslice = zslice;
+0880                 if numel(zslice) > 1
+0881                     for i = 1:numel(zslice)
+0882                         tmp = shownames{i};
+0883                         shownames{i} = [tmp,' z:',sprintf('%5.4f',zslice(i))];
+0884                     end
+0885                 end
+0886             else
+0887                 data.import.BAM.use_z = false;
+0888                 data.import.BAM.zslice = 1:1:ncsvfiles;
+0889             end
+0890         end    
+0891 end
+0892 
+0893 % update the global data structure
+0894 data.import.NMR.files = fnames;
+0895 data.import.NMR.filesShort = shownames;
+0896 
+0897 end
+0898 
+0899 %%
+0900 function [data,gui] = importDataLIAG(data,gui)
+0901 
+0902 in.path = fullfile(data.import.path);
+0903 in.fileformat = data.import.fileformat;
+0904 out = LoadNMRData_driver(in);
+0905 
+0906 fnames = struct;
+0907 % shownames is just a dummy to hold all data file names that
+0908 % will be shown in the listbox
+0909 shownames = cell(1,1);
+0910 
+0911 c = 0;
+0912 for j = 1:size(out.nmrData,2)
+0913     % the individual file names
+0914     c = c + 1;
+0915     fnames(c).parfile = 'acqu.par';
+0916     fnames(c).datafile = out.nmrData{j}.datfile;
+0917     fnames(c).T2specfile = '';
+0918     
+0919     shownames{c} = fnames(c).datafile;
+0920     
+0921     % the NMR data
+0922     % here we fix the time scale to [s] if neccessary
+0923     TE = out.parData.echoTime; % [µs]
+0924     if out.nmrData{j}.time(1)== TE/1e3
+0925         % change [ms] to [s]
+0926         out.nmrData{j}.time = out.nmrData{j}.time/1e3;
+0927         out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1e3;
+0928     elseif out.nmrData{j}.time(1)== TE
+0929         % change [µs] to [s] -> very unlikely
+0930         out.nmrData{j}.time = out.nmrData{j}.time/1e6;
+0931         out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1e6;
+0932     end
+0933     data.import.NMR.data{c} = out.nmrData{j};
+0934     data.import.NMR.para{c} = out.parData;
+0935 end
+0936 
+0937 % update the global data structure
+0938 data.import.NMR.files = fnames;
+0939 data.import.NMR.filesShort = shownames;
+0940 
+0941 end
+0942 
+0943 %%
+0944 function [data,gui] = importDataLIAGcore(data,gui)
+0945 
+0946 % get all subfolders containing a measurement at a certain heigth
+0947 subdirs = dir(data.import.path);
+0948 % remove the dot-dirs
+0949 subdirs = subdirs(~ismember({subdirs.name},{'.','..'}));
+0950 
+0951 % now get the background data ("Leermessung")
+0952 bgPath = uigetdir(data.import.path,'Choose Background Data Path');
+0953 isbgPath = false;
+0954 if bgPath == 0
+0955     disp('NUCLEUSinv: LIAG core import: No background file provided.');
+0956 else
+0957     isbgPath = true;
+0958     in.path = fullfile(bgPath);
+0959     in.fileformat = data.import.fileformat;
+0960     bgout = LoadNMRData_driver(in);
+0961     ref1.t = bgout.nmrData{1}.time;
+0962     ref1.s = bgout.nmrData{1}.signal;
+0963     [ref1.s,~] = rotateT2phase(ref1.s);
+0964 end
+0965 
+0966 % get the Position file
+0967 [posFile,posFilePath] = uigetfile('*.*','Choose Lift Position File',data.import.path);
+0968 isposFile = false;
+0969 if posFilePath == 0
+0970     disp('NUCLEUSinv: LIAG core import: No position file provided.');
+0971 else
+0972     isposFile = true;
+0973     % import LIAG lift file
+0974     buffer = fileread(fullfile(posFilePath,posFile));
+0975 
+0976     % get the time stamps of the lift positions
+0977     substr = 'Zeit:' ;
+0978     loc = strfind(buffer, substr);
+0979     timepoint = cell(1,1);
+0980     for i = 1:length(loc)
+0981         timestr = strtrim(buffer(loc(i)+numel(substr):loc(i)+numel(substr)+19));
+0982         timepoint{i} = datetime(timestr,'InputFormat','dd.MM.yyyy HH:mm:ss');
+0983     end
+0984     % ignore the first time stamp
+0985     t_range = [datenum(timepoint{2}), datenum(timepoint{3})];
+0986     % get the z coords
+0987     substr = 'Z1=';
+0988     loc = strfind(buffer, substr) ;
+0989     z_range(1) = sscanf(buffer(loc+numel(substr):loc+numel(substr)+10),'%f',1);
+0990     substr = 'Z2=';
+0991     loc = strfind(buffer, substr) ;
+0992     z_range(2) =  sscanf(buffer(loc+numel(substr):loc+numel(substr)+10),'%f',1);
+0993 end
+0994 
+0995 % import the NMR data
+0996 count = 0;
+0997 levels = zeros(size(subdirs));
+0998 nmrDataTMP = cell(1,1);
+0999 for i = 1:numel(subdirs)
+1000     if ~isnan(str2double(subdirs(i).name))
+1001 
+1002         % import the NMR file
+1003         in.path = fullfile(data.import.path,subdirs(i).name,'T2CPMG');
+1004         in.fileformat = data.import.fileformat;
+1005         out = LoadNMRData_driver(in);
+1006 
+1007         % if there is a position file
+1008         if isposFile
+1009             % keep only files within the correct time range
+1010             if out.nmrData{1}.datenum > t_range(1) && out.nmrData{1}.datenum < t_range(2)
+1011                 count = count + 1;
+1012                 % interpolate the z position via the time stamp of the NMR file
+1013                 levels(count) = interp1(t_range,z_range,out.nmrData{1}.datenum,'linear');
+1014                 nmrDataTMP{count} = out;
+1015             end
+1016         else % just read everything
+1017             count = count + 1;
+1018             levels(count) = str2double(subdirs(i).name);
+1019             nmrDataTMP{count} = out;
+1020         end
+1021     end
+1022 end
+1023 % cut off data that is not part of the scan
+1024 levels = levels(1:count);
+1025 % sort in ascending order
+1026 [levels,idx] = sort(levels);
+1027 
+1028 % sort the NMR data accordingly
+1029 fnames = struct;
+1030 % shownames is just a dummy to hold all data file names that
+1031 % will be shown in the listbox
+1032 shownames = cell(1,1);
+1033 for c = 1:numel(levels)
+1034     % the individual file names
+1035     fnames(c).parfile = 'acqu.par';
+1036     fnames(c).datafile = nmrDataTMP{idx(c)}.nmrData{1}.datfile;
+1037     fnames(c).T2specfile = '';
+1038     
+1039     shownames{c} = fnames(c).datafile;
+1040     tmp = shownames{c};
+1041     if isposFile
+1042         shownames{c} = [tmp,': ',sprintf('%4d',floor(levels(c))),'mm'];
+1043     else
+1044         shownames{c} = [tmp,' level:',sprintf('%d',levels(c))];
+1045     end
+1046     out = nmrDataTMP{idx(c)};
+1047     
+1048     % the NMR data
+1049     % here we fix the time scale to [s] if neccessary
+1050     TE = out.parData.echoTime; % [µs]
+1051     if out.nmrData{1}.time(1) == TE/1e3
+1052         % change [ms] to [s]
+1053         out.nmrData{1}.time = out.nmrData{1}.time/1e3;
+1054         out.nmrData{1}.raw.time = out.nmrData{1}.raw.time/1e3;
+1055     elseif out.nmrData{1}.time(1) == TE
+1056         % change [µs] to [s] -> very unlikely
+1057         out.nmrData{1}.time = out.nmrData{1}.time/1e6;
+1058         out.nmrData{1}.raw.time = out.nmrData{1}.raw.time/1e6;
+1059     end
+1060     data.import.NMR.data{c} = out.nmrData{1};
+1061     data.import.NMR.para{c} = out.parData;
+1062 
+1063     % subtract the background signal is one is available
+1064     if isbgPath
+1065         % get the original signal
+1066         s = data.import.NMR.data{c}.signal;
+1067         % if the background signal is longer than the signal cut it, if
+1068         % not extend it with zeros
+1069         if numel(ref1.s) > numel(s)
+1070             tmp_r = ref1.s(1:numel(s));
+1071         else
+1072             tmp_r = zeros(size(s));
+1073             tmp_r(1:numel(ref1.s)) = ref1.s;
+1074         end
+1075         s = complex(real(s)-real(tmp_r),imag(s)-imag(tmp_r));
+1076 
+1077         % sign check
+1078         if real(s(1:3))<0
+1079             s = s*-1;
+1080         end
+1081 
+1082         % rotate phase again - TEST
+1083         [s,~] = rotateT2phase(s);
+1084 
+1085         % update signal
+1086         data.import.NMR.data{c}.signal = s;
+1087         data.import.NMR.data{c}.raw.signal = s;
+1088     end
+1089 end
+1090 if isposFile
+1091     data.import.LIAGCORE.use_z = true;
+1092 else
+1093     data.import.LIAGCORE.use_z = false;
+1094 end
+1095 data.import.LIAGCORE.zslice = levels;
+1096 
+1097 % update the global data structure
+1098 data.import.NMR.files = fnames;
+1099 data.import.NMR.filesShort = shownames;
+1100 
+1101 end
+1102 
+1103 %%
+1104 function [data,gui] = importDataLIAGproject(data,gui)
+1105 
+1106 % 1) show all folders and ask for sample
+1107 subdirs = dir(data.import.path);
+1108 % remove the dot-dirs
+1109 subdirs = subdirs(~ismember({subdirs.name},{'.','..'}));
+1110 
+1111 fnames = {subdirs.name};
+1112 [indx,~] = listdlg('PromptString','Select Sample:',...
+1113     'SelectionMode','single',...
+1114     'ListString',fnames);
+1115 
+1116 if ~isempty(indx)
+1117     % 2) check corresponding SampleParameter.par file for reference and
+1118     % calibration sample and other parameters
+1119     datapath = fullfile(data.import.path,fnames{indx});
+1120     % load SampleParameter file for sample
+1121     [SampleParameter] = loadGUIParameters(datapath,'SampleParameters.par');
+1122     if isfield(SampleParameter,'sampleVolume')
+1123         dataVol = SampleParameter.sampleVolume;
+1124     else
+1125         dataVol = 1;
+1126     end
+1127     
+1128     % 2a) background file #1
+1129     backgroundFile1 = SampleParameter.backgroundFile;
+1130     if isempty(backgroundFile1)
+1131         bnames = {subdirs.name};
+1132         bnames(indx) = [];
+1133         [indb,~] = listdlg('PromptString','Select Background File:',...
+1134             'SelectionMode','single',...
+1135             'ListString',bnames);
+1136         if ~isempty(indb)
+1137             backgroundFile1 = bnames{indb};
+1138         else
+1139             backgroundFile1 = '';
+1140         end
+1141     end
+1142     if ~isempty(backgroundFile1)
+1143         ind = strfind(backgroundFile1,filesep);
+1144         if ~isempty(ind)
+1145             backgroundFile1 = backgroundFile1(ind(end)+1:end);
+1146         end
+1147         fileInList = ismember(fnames,{backgroundFile1});
+1148         if any(fileInList)
+1149             backgroundpath1 = fullfile(data.import.path,fnames{fileInList});
+1150         end
+1151     else
+1152         backgroundpath1 = '';
+1153         backgroundFile1 = '';
+1154     end
+1155     backVol = 1;
 1156     
-1157     shownames{c} = [fnames(c).datafile];
-1158 
-1159     data.import.NMR.data{c} = out.nmrData{j};
-1160     data.import.NMR.para{c} = out.parData;
-1161 end
-1162 
-1163 % check if the number of depth levels is equal to the number of
-1164 % measurements
-1165 if nslices == nfiles
-1166     % create z-vector
-1167     p = out.parData;
-1168     zslice = linspace(p.initialdepth,p.finaldepth,p.depths)';
-1169     data.import.IBAC.use_z = true;
-1170     data.import.IBAC.zslice = zslice;
-1171     if numel(zslice) > 1
-1172         c = 0;
-1173         for i = 1:nfiles
-1174             c = c + 1;
-1175             tmp = shownames{i};
-1176             shownames{i} = [tmp,' z:',sprintf('%05d',zslice(c))];
-1177         end
-1178     end
-1179 else
-1180     data.import.IBAC.use_z = false;
-1181     data.import.IBAC.zslice = 1:1:max([nfiles 1]);
-1182 end
-1183 
-1184 % update the global data structure
-1185 data.import.NMR.files = fnames;
-1186 data.import.NMR.filesShort = shownames;
-1187 
-1188 end
-1189 
-1190 %%
-1191 function data = loadGUIParameters(datapath,fname)
-1192 fid = fopen(fullfile(datapath,fname));
-1193 d = textscan(fid,'%s','Delimiter','\n');
-1194 fclose(fid);
-1195 data = struct;
-1196 for i = 1:size(d{1},1)
-1197     str = char(d{1}(i));
-1198     str = fixParameterString(str);
-1199     eval(['data.',str,';']);
-1200 end
-1201 
-1202 end
-1203 
-1204 %%
-1205 function data = loadGUIrawdata(data,NMRpath,NMRfile)
-1206 
-1207 load(fullfile(NMRpath,'NUCLEUSinv_raw.mat'),'savedata');
-1208 
-1209 data.import.file = NMRfile;
-1210 data.import.path = NMRpath;
-1211 data.import.NMR = savedata;
-1212 
-1213 end
-1214 
-1215 %------------- END OF CODE --------------
-1216 
-1217 %% License:
-1218 % MIT License
-1219 %
-1220 % Copyright (c) 2018 Thomas Hiller
-1221 %
-1222 % Permission is hereby granted, free of charge, to any person obtaining a copy
-1223 % of this software and associated documentation files (the "Software"), to deal
-1224 % in the Software without restriction, including without limitation the rights
-1225 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-1226 % copies of the Software, and to permit persons to whom the Software is
-1227 % furnished to do so, subject to the following conditions:
-1228 %
-1229 % The above copyright notice and this permission notice shall be included in all
-1230 % copies or substantial portions of the Software.
-1231 %
-1232 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-1233 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-1234 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-1235 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-1236 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-1237 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-1238 % SOFTWARE.
    +1157 % 2b) calibration file +1158 c = 0; +1159 if isfield(SampleParameter,'calibrationFile0') +1160 c = c + 1; +1161 calibrationFiles{c} = SampleParameter.calibrationFile0; +1162 end +1163 if isfield(SampleParameter,'calibrationFile1') +1164 c = c + 1; +1165 calibrationFiles{c} = SampleParameter.calibrationFile1; +1166 end +1167 if isfield(SampleParameter,'calibrationFile2') +1168 c = c + 1; +1169 calibrationFiles{c} = SampleParameter.calibrationFile2; +1170 end +1171 if isfield(SampleParameter,'calibrationFile3') +1172 c = c + 1; +1173 calibrationFiles{c} = SampleParameter.calibrationFile3; +1174 end +1175 +1176 % find the non-empty one +1177 ind = ismember(calibrationFiles,{''}); +1178 % there are three possibilities: 0, 1 and more than 1 calib. files +1179 calibrationFiles(ind) = []; +1180 if isempty(calibrationFiles) +1181 cnames = {subdirs.name}; +1182 cnames(indx) = []; +1183 [indc,~] = listdlg('PromptString','Select Calibration File:',... +1184 'SelectionMode','single',... +1185 'ListString',cnames); +1186 if ~isempty(indc) +1187 calibrationFiles = cnames{indc}; +1188 else +1189 calibrationFiles = ''; +1190 end +1191 else +1192 % if there are more than one let the user select the correct one +1193 if numel(calibrationFiles) > 1 +1194 [ind,~] = listdlg('PromptString','Select Calibration File:',... +1195 'SelectionMode','single',... +1196 'ListString',calibrationFiles); +1197 calibrationFiles = calibrationFiles{ind}; +1198 else +1199 calibrationFiles = calibrationFiles{1}; +1200 end +1201 end +1202 if ~isempty(calibrationFiles) +1203 ind = strfind(calibrationFiles,filesep); +1204 if ~isempty(ind) +1205 calibrationFiles = calibrationFiles(ind(end)+1:end); +1206 end +1207 fileInList = ismember(fnames,{calibrationFiles}); +1208 if any(fileInList) +1209 calibrationpath = fullfile(data.import.path,fnames{fileInList}); +1210 end +1211 else +1212 calibrationpath = ''; +1213 calibrationFiles = ''; +1214 end +1215 +1216 if ~isempty(calibrationpath) +1217 [SampleParameterC] = loadGUIParameters(calibrationpath,'SampleParameters.par'); +1218 if isfield(SampleParameterC,'sampleVolume') +1219 calibVol = SampleParameterC.sampleVolume; +1220 else +1221 calibVol = 1; +1222 end +1223 +1224 % 2a) background file #2 +1225 backgroundFile2 = SampleParameterC.backgroundFile; +1226 if isempty(backgroundFile2) +1227 bnames = {subdirs.name}; +1228 bnames(indx) = []; +1229 [indb,~] = listdlg('PromptString','Select Background File for Calibration:',... +1230 'SelectionMode','single',... +1231 'ListString',bnames); +1232 if ~isempty(indb) +1233 backgroundFile2 = bnames{indb}; +1234 else +1235 backgroundFile2 = ''; +1236 end +1237 end +1238 if ~isempty(backgroundFile2) +1239 ind = strfind(backgroundFile2,filesep); +1240 if ~isempty(ind) +1241 backgroundFile2 = backgroundFile2(ind(end)+1:end); +1242 end +1243 fileInList = ismember(fnames,{backgroundFile2}); +1244 if any(fileInList) +1245 backgroundpath2 = fullfile(data.import.path,fnames{fileInList}); +1246 end +1247 else +1248 backgroundpath2 = ''; +1249 backgroundFile2 = ''; +1250 end +1251 else +1252 calibVol = 1; +1253 backgroundpath2 = ''; +1254 backgroundFile2 = ''; +1255 end +1256 +1257 % 3) now load the data +1258 workpaths = {datapath,calibrationpath,backgroundpath1,backgroundpath2}; +1259 workfiles = {fnames{indx},[calibrationFiles,' - calibration'],... +1260 [backgroundFile1,' - backgroundS'],[backgroundFile2,' - backgroundC']}; +1261 out = cell(size(workpaths)); +1262 count = 0; +1263 keep = false(size(workpaths)); +1264 for i = 1:numel(workpaths) +1265 if ~isempty(workpaths{i}) +1266 workdirs = dir(workpaths{i}); +1267 workdirs = workdirs(~ismember({workdirs.name},{'.','..'})); +1268 isT2 = ismember({workdirs.name},{'T2CPMG'}); +1269 if any(isT2) +1270 keep(i) = true; +1271 count = count + 1; +1272 T2path = fullfile(workdirs(isT2).folder,workdirs(isT2).name); +1273 in.path = T2path; +1274 in.fileformat = data.import.fileformat; +1275 out{i} = LoadNMRData_driver(in); +1276 end +1277 end +1278 end +1279 +1280 if isempty(backgroundpath1) +1281 ref1 = struct; +1282 else +1283 background1 = out{3}; +1284 % get the background data 1 +1285 ref1.t = background1.nmrData{1}.time; +1286 ref1.s = background1.nmrData{1}.signal; +1287 [ref1.s,~] = rotateT2phase(ref1.s); +1288 end +1289 +1290 if isempty(backgroundpath2) +1291 ref2 = struct; +1292 else +1293 background2 = out{4}; +1294 % get the background data 2 +1295 ref2.t = background2.nmrData{1}.time; +1296 ref2.s = background2.nmrData{1}.signal; +1297 [ref2.s,~] = rotateT2phase(ref2.s); +1298 end +1299 +1300 workpaths = workpaths(keep); +1301 workfiles = workfiles(keep); +1302 out = out(keep); +1303 +1304 ffnames = struct; +1305 % shownames is just a dummy to hold all data file names that +1306 % will be shown in the listbox +1307 shownames = cell(1,1); +1308 +1309 for i = 1:count +1310 ffnames(i).parfile = 'acqu.par'; +1311 ffnames(i).datafile = workfiles{i}; +1312 ffnames(i).T2specfile = ''; +1313 +1314 shownames{i} = ffnames(i).datafile; +1315 +1316 % the NMR data +1317 % here we fix the time scale to [s] if neccessary +1318 TE = out{i}.parData.echoTime; % [µs] +1319 if out{i}.nmrData{1}.time(1)== TE/1e3 +1320 % change [ms] to [s] +1321 out{i}.nmrData{1}.time = out{i}.nmrData{1}.time/1e3; +1322 out{i}.nmrData{1}.raw.time = out{i}.nmrData{1}.raw.time/1e3; +1323 elseif out{i}.nmrData{1}.time(1)== TE +1324 % change [µs] to [s] -> very unlikely +1325 out{i}.nmrData{1}.time = out{i}.nmrData{1}.time/1e6; +1326 out{i}.nmrData{1}.raw.time = out{i}.nmrData{1}.raw.time/1e6; +1327 end +1328 +1329 data.import.NMR.data{i} = out{i}.nmrData{1}; +1330 data.import.NMR.para{i} = out{i}.parData; +1331 data.import.NMR.para{i}.SampleParameter = SampleParameter; +1332 +1333 % subtract the background signal +1334 s = data.import.NMR.data{i}.signal; +1335 if i==1 && isfield(ref1,'s') +1336 % if the background signal is longer than the signal cut it, if +1337 % not extend it with zeros +1338 if numel(ref1.s) > numel(s) +1339 tmp_r = ref1.s(1:numel(s)); +1340 else +1341 tmp_r = zeros(size(s)); +1342 tmp_r(1:numel(ref1.s)) = ref1.s; +1343 end +1344 s = complex(real(s)-real(tmp_r),imag(s)-imag(tmp_r)); +1345 elseif i==2 && isfield(ref2,'s') +1346 % if the background signal is longer than the signal cut it, if +1347 % not extend it with zeros +1348 if numel(ref2.s) > numel(s) +1349 tmp_r = ref2.s(1:numel(s)); +1350 else +1351 tmp_r = zeros(size(s)); +1352 tmp_r(1:numel(ref2.s)) = ref2.s; +1353 end +1354 s = complex(real(s)-real(tmp_r),imag(s)-imag(tmp_r)); +1355 end +1356 data.import.NMR.data{i}.signal = s; +1357 data.import.NMR.data{i}.raw.signal = s; +1358 +1359 if ~isempty(strfind(workfiles{i},' - background')) +1360 data.import.LIAG.sampleVol(i) = backVol; +1361 elseif ~isempty(strfind(workfiles{i},' - calibration')) +1362 data.import.LIAG.sampleVol(i) = calibVol; +1363 elseif isempty(strfind(workfiles{i},' - background')) &&... +1364 isempty(strfind(workfiles{i},' - calibration')) +1365 data.import.LIAG.sampleVol(i) = dataVol; +1366 end +1367 end +1368 data.import.LIAG.Tbulk = 1e6; +1369 data.import.LIAG.workpaths = workpaths; +1370 data.import.LIAG.datapath = datapath; +1371 data.import.LIAG.calibrationpath = calibrationpath; +1372 data.import.LIAG.backgroundpath1 = backgroundpath1; +1373 data.import.LIAG.backgroundpath2 = backgroundpath2; +1374 +1375 % update the global data structure +1376 data.import.NMR.files = ffnames; +1377 data.import.NMR.filesShort = shownames; +1378 end +1379 +1380 end +1381 +1382 %% +1383 function [data,gui] = importDataMouse(data,gui) +1384 +1385 in.path = fullfile(data.import.path); +1386 in.fileformat = data.import.fileformat; +1387 out = LoadNMRData_driver(in); +1388 +1389 fnames = struct; +1390 % shownames is just a dummy to hold all data file names that +1391 % will be shown in the listbox +1392 shownames = cell(1,1); +1393 +1394 c = 0; +1395 for j = 1:size(out.nmrData,2) +1396 % the individual file names +1397 c = c + 1; +1398 fnames(c).parfile = 'acq.par'; +1399 fnames(c).datafile = out.nmrData{j}.datfile; +1400 fnames(c).T2specfile = ''; +1401 +1402 shownames{c} = ['T2_',fnames(c).datafile]; +1403 +1404 % the NMR data +1405 % here we fix the time scale from [ms] to [s] +1406 if max(out.nmrData{j}.time) > 100 +1407 out.nmrData{j}.time = out.nmrData{j}.time/1000; +1408 out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1000; +1409 end +1410 data.import.NMR.data{c} = out.nmrData{j}; +1411 data.import.NMR.para{c} = out.parData; +1412 end +1413 +1414 % update the global data structure +1415 data.import.NMR.files = fnames; +1416 data.import.NMR.filesShort = shownames; +1417 +1418 end +1419 +1420 %% +1421 function [data,gui] = importDataIBAC(data,gui) +1422 +1423 in.path = fullfile(data.import.path); +1424 in.name = data.import.file; +1425 in.fileformat = data.import.fileformat; +1426 out = LoadNMRData_driver(in); +1427 +1428 nslices = out.parData.depths; +1429 nfiles = size(out.nmrData,2); +1430 +1431 fnames = struct; +1432 % shownames is just a dummy to hold all data file names that +1433 % will be shown in the listbox +1434 shownames = cell(1,1); +1435 +1436 c = 0; +1437 for j = 1:size(out.nmrData,2) +1438 % the individual file names +1439 c = c + 1; +1440 fnames(c).parfile = out.parData.parfile; +1441 fnames(c).datafile = out.nmrData{j}.datfile; +1442 fnames(c).T2specfile = ''; +1443 +1444 shownames{c} = [fnames(c).datafile]; +1445 +1446 data.import.NMR.data{c} = out.nmrData{j}; +1447 data.import.NMR.para{c} = out.parData; +1448 end +1449 +1450 % check if the number of depth levels is equal to the number of +1451 % measurements +1452 if nslices == nfiles +1453 % create z-vector +1454 p = out.parData; +1455 zslice = linspace(p.initialdepth,p.finaldepth,p.depths)'; +1456 data.import.IBAC.use_z = true; +1457 data.import.IBAC.zslice = zslice; +1458 if numel(zslice) > 1 +1459 c = 0; +1460 for i = 1:nfiles +1461 c = c + 1; +1462 tmp = shownames{i}; +1463 shownames{i} = [tmp,' z:',sprintf('%05d',zslice(c))]; +1464 end +1465 end +1466 else +1467 data.import.IBAC.use_z = false; +1468 data.import.IBAC.zslice = 1:1:max([nfiles 1]); +1469 end +1470 +1471 % update the global data structure +1472 data.import.NMR.files = fnames; +1473 data.import.NMR.filesShort = shownames; +1474 +1475 end +1476 +1477 %% +1478 function data = loadGUIParameters(datapath,fname) +1479 fid = fopen(fullfile(datapath,fname)); +1480 d = textscan(fid,'%s','Delimiter','\n'); +1481 fclose(fid); +1482 data = struct; +1483 for i = 1:size(d{1},1) +1484 str = char(d{1}(i)); +1485 str = fixParameterString(str); +1486 eval(['data.',str,';']); %#ok<EVLDOT> +1487 end +1488 +1489 end +1490 +1491 %% +1492 function data = loadGUIrawdata(data,NMRpath,NMRfile) +1493 +1494 load(fullfile(NMRpath,'NUCLEUSinv_raw.mat'),'savedata'); +1495 +1496 data.import.file = NMRfile; +1497 data.import.path = NMRpath; +1498 data.import.NMR = savedata; +1499 +1500 end +1501 +1502 %------------- END OF CODE -------------- +1503 +1504 %% License: +1505 % MIT License +1506 % +1507 % Copyright (c) 2018 Thomas Hiller +1508 % +1509 % Permission is hereby granted, free of charge, to any person obtaining a copy +1510 % of this software and associated documentation files (the "Software"), to deal +1511 % in the Software without restriction, including without limitation the rights +1512 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +1513 % copies of the Software, and to permit persons to whom the Software is +1514 % furnished to do so, subject to the following conditions: +1515 % +1516 % The above copyright notice and this permission notice shall be included in all +1517 % copies or substantial portions of the Software. +1518 % +1519 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +1520 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +1521 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +1522 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +1523 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +1524 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +1525 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/functions/interface/menu.html b/doc/nucleus/functions/interface/menu.html index dd24a64..d9bca19 100644 --- a/doc/nucleus/functions/interface/menu.html +++ b/doc/nucleus/functions/interface/menu.html @@ -18,7 +18,7 @@

    Index for nucleus\functions\interface

    Matlab files in this directory:

    +
  • ConductView
  • FixedTimeView
  • PhaseView
  • beautifyAxes
  • calculateGeometry
  • calculateGuiOnMonitorPosition
  • calculateNMR
  • calibratePorosity
  • caluclatePressureSaturation
  • changeColorTheme
  • checkIfInversionExists
  • cleanupGUIData
  • clearAllAxes
  • clearInversion
  • clearSingleAxis
  • displayStatusText
  • enableGUIelements
  • exportData
  • exportGraphics
  • exportINV
  • findParentOfType
  • fixAxes
  • getColorIndex
  • getColorTheme
  • getVersionNoFromString
  • importASCIIdata
  • importCPSdata
  • importCalibrationData
  • importEXCELdata
  • importINV2INV
  • importMOD2INV
  • importMOD2MOD
  • importNMRdata
  • makeINIfile
  • minimizePanel
  • moveEntryInList
  • onFigureSizeChange
  • processNMRData
  • processNMRDataControl
  • readINIfile
  • removeCalculationFields
  • removeInversionFields
  • removeSignalFromList
  • resortDataList
  • runInversionBatch
  • runInversionJoint
  • runInversionStd
  • showExtraGraphics
  • showFitStatistics
  • showParameterInfo
  • switchToolTips
  • uncheckImportMenus
  • updateCPSTable
  • updateCPSTableSize
  • updateInfo
  • updateNMRsignals
  • updatePlotsCPS
  • updatePlotsDistribution
  • updatePlotsDistributionInfo
  • updatePlotsGeometryType
  • updatePlotsJointInversion
  • updatePlotsLcurve
  • updatePlotsNMR
  • updatePlotsPSD
  • updatePlotsSignal
  • updateStatusInformation
  • updateToolTips
  • useSignalAsCalibration

    • Other Matlab-specific files in this directory:

    This function is called by: @@ -286,256 +286,266 @@

    SOURCE CODE ^if isfield(data.results.nmrproc,'W') -0202 param.W = data.results.nmrproc.W; -0203 end -0204 % status bar information -0205 switch data.info.has_optim -0206 case 'on' -0207 infostring = 'Inversion using ''Optimization Toolbox'' ... '; -0208 case 'off' -0209 infostring = 'Inversion using ''fminsearchbnd'' ... '; -0210 end -0211 displayStatusText(gui,infostring); -0212 invstd = fitDataFree(data.results.nmrproc.t,... -0213 data.results.nmrproc.s,flag,param,1); -0214 -0215 case 'free' % N free single-exponential inversion -0216 flag = data.results.nmrproc.T1T2; -0217 param.T1IRfac = data.results.nmrproc.T1IRfac; -0218 param.noise = data.results.nmrproc.noise; -0219 param.optim = data.info.has_optim; -0220 if isfield(data.results.nmrproc,'W') -0221 param.W = data.results.nmrproc.W; -0222 end -0223 % status bar information -0224 switch data.info.has_optim -0225 case 'on' -0226 infostring = 'Inversion using ''Optimization Toolbox'' ... '; -0227 case 'off' -0228 infostring = 'Inversion using ''fminsearchbnd'' ... '; -0229 end -0230 displayStatusText(gui,infostring); -0231 invstd = fitDataFree(data.results.nmrproc.t,... -0232 data.results.nmrproc.s,flag,param,data.invstd.freeDT); -0233 -0234 case 'LU' % multi-exponential inversion -0235 % general parameter -0236 param.T1T2 = data.results.nmrproc.T1T2; -0237 param.T1IRfac = data.results.nmrproc.T1IRfac; -0238 param.Tb = data.invstd.Tbulk; -0239 param.Td = data.invstd.Tdiff; -0240 param.Tint = [log10(data.invstd.time) data.invstd.Ntime]; -0241 param.Lorder = data.invstd.Lorder; -0242 param.lambda = data.invstd.lambda; -0243 param.noise = data.results.nmrproc.noise; -0244 if isfield(data.results.nmrproc,'W') -0245 param.W = data.results.nmrproc.W; -0246 end -0247 % status bar information -0248 infostring = 'Inversion using LU decomposition ... '; -0249 displayStatusText(gui,infostring); -0250 invstd = fitDataLUdecomp(data.results.nmrproc.t,... -0251 data.results.nmrproc.s,param); -0252 -0253 case 'NNLS' % multi-exponential inversion with manual regularization -0254 % general parameter -0255 param.T1T2 = data.results.nmrproc.T1T2; -0256 param.T1IRfac = data.results.nmrproc.T1IRfac; -0257 param.Tb = data.invstd.Tbulk; -0258 param.Td = data.invstd.Tdiff; -0259 param.Tint = [log10(data.invstd.time) data.invstd.Ntime]; -0260 param.regMethod = data.invstd.regtype; -0261 param.Lorder = data.invstd.Lorder; -0262 param.lambda = data.invstd.lambda; -0263 param.noise = data.results.nmrproc.noise; -0264 param.solver = data.info.solver; -0265 if isfield(data.results.nmrproc,'W') -0266 param.W = data.results.nmrproc.W; -0267 end -0268 -0269 % status bar information -0270 switch data.info.solver -0271 case 'lsqlin' -0272 infostring = 'Inversion using ''Optimization Toolbox'' ... '; -0273 case 'lsqnonneg' -0274 infostring = 'Inversion using ''lsqnonneg'' ... '; -0275 end -0276 displayStatusText(gui,infostring); -0277 invstd = fitDataLSQ(data.results.nmrproc.t,... -0278 data.results.nmrproc.s,param); -0279 -0280 case 'MUMO' % N free distribution inversion -0281 param.T1T2 = data.results.nmrproc.T1T2; -0282 param.T1IRfac = data.results.nmrproc.T1IRfac; -0283 param.Tb = data.invstd.Tbulk; -0284 param.Td = data.invstd.Tdiff; -0285 param.Tint = [log10(data.invstd.time) data.invstd.Ntime]; -0286 param.noise = data.results.nmrproc.noise; -0287 param.optim = data.info.has_optim; -0288 if isfield(data.results.nmrproc,'W') -0289 param.W = data.results.nmrproc.W; -0290 end -0291 -0292 % status bar information -0293 switch data.info.solver -0294 case 'lsqlin' -0295 infostring = 'Inversion using ''Optimization Toolbox'' ... '; -0296 case 'lsqnonneg' -0297 infostring = 'Inversion using ''fminsearchbnd'' ... '; -0298 end -0299 displayStatusText(gui,infostring); -0300 invstd = fitDataMultiModal(data.results.nmrproc.t,... -0301 data.results.nmrproc.s,param,data.invstd.freeDT); -0302 -0303 % estimate uncertainty -0304 if data.invstd.useUncert -0305 % original fit parameter -0306 iparam = param; -0307 % uncertainty parameter -0308 uparam.time = data.results.nmrproc.t; -0309 uparam.signal = data.results.nmrproc.s; -0310 uparam.uncertMethod = data.invstd.uncertMethod; -0311 uparam.uncertThresh = data.invstd.uncertThresh; -0312 uparam.uncertChi2 = data.invstd.uncertChi2; -0313 uparam.uncertN = data.invstd.uncertN; -0314 uparam.uncertMax = data.invstd.uncertMax; -0315 invstd = estimateUncertainty(data.invstd.invtype,invstd,iparam,uparam); -0316 end -0317 end -0318 % normalize to 1 -0319 if data.process.norm == 1 -0320 switch data.invstd.invtype -0321 case {'LU','NNLS','MUMO'} -0322 % normalization with sum() -> sum(f)=1 -0323 % this is the standard way of doing it -0324 invstd.T1T2f = invstd.T1T2f./sum(invstd.T1T2f); -0325 % alternatives depending on the objective: -0326 % 1.) normalization with sum(f*dt) -> area~=1 -0327 % dt = log10(invstd.T1T2me(2))-log10(invstd.T1T2me(1)); -0328 % invstd.T1T2f = invstd.T1T2f/sum(invstd.T1T2f*dt); -0329 % 2.) normalization with trapz() -> area=1 but sum(f)>1 -0330 % invstd.T1T2f = invstd.T1T2f./trapz(invstd.T1T2me,invstd.T1T2f); -0331 otherwise -0332 % nothing to do -0333 end -0334 end -0335 runtime = toc; -0336 displayStatusText(gui,[infostring,'done | inversion took ',... -0337 sprintf('%5.2f',runtime),' s']); -0338 % save inversion results -0339 data.results.invstd = invstd; -0340 setappdata(fig,'data',data); -0341 end -0342 % as long as the "UserData" is 1 the STOP button was not pressed and -0343 % the inversion result gets saved in "INVdata" -0344 if get(gui.push_handles.invstd_run,'UserData') == 1 && ... -0345 ( isfield(data.results,'invstd') || ... -0346 isfield(data.results,'lcurve') ) -0347 INVdata{id} = []; -0348 INVdata{id} = data; -0349 INVdata{id} = rmfield(INVdata{id},'import'); -0350 INVdata{id} = rmfield(INVdata{id},'info'); -0351 INVdata{id} = rmfield(INVdata{id},'calib'); -0352 INVdata{id} = rmfield(INVdata{id},'pressure'); -0353 -0354 % color the list entries that already have an inversion result -0355 strL = get(gui.listbox_handles.signal,'String'); -0356 str1 = strL{id}; -0357 str2 = ['<HTML><BODY bgcolor="rgb(',... -0358 sprintf('%d,%d,%d',gui.myui.colors.listINV.*255),')">',str1,'</BODY></HTML>']; -0359 strL{id} = str2; -0360 set(gui.listbox_handles.signal,'String',strL); -0361 -0362 % update GUI INVdata -0363 setappdata(fig,'INVdata',INVdata); -0364 -0365 % --- -0366 % special treatment for LIAG processing -0367 if isfield(data.import,'LIAG') && ~strcmp(data.invstd.regtype,'lcurve') -0368 if contains(str1,' - calibration') -0369 % save Tbulk from the calibration sample -0370 btn1 = 'Yes keep it'; -0371 btn2 = 'No, reset to 1e6 [s]'; -0372 if data.results.invstd.T2 < 0.2 -0373 answer = questdlg(['Tbulk seems very short with ',... -0374 sprintf('%4.3f',data.results.invstd.T2),' [s] ',... -0375 'Do you want to keep it?'], ... -0376 'Keep relaxation time as Tbulk', ... -0377 btn1,btn2,btn2); -0378 % Handle response -0379 switch answer -0380 case btn1 -0381 data.import.LIAG.Tbulk = data.results.invstd.T2; -0382 case btn2 -0383 data.import.LIAG.Tbulk = 1e6; -0384 end -0385 else -0386 data.import.LIAG.Tbulk = data.results.invstd.T2; -0387 end -0388 % update GUI data -0389 setappdata(fig,'data',data); -0390 % save calibration data -0391 useSignalAsCalibration(id); -0392 else -0393 calibratePorosity; -0394 end -0395 end -0396 % --- -0397 else % STOP was pressed (because "UserData" is 0) -0398 % reset "UserData" -0399 set(gui.push_handles.invstd_run,'UserData',1); -0400 end -0401 % update plots and INFO fields -0402 updatePlotsSignal; -0403 updatePlotsDistribution; -0404 updateInfo(gui.plots.SignalPanel); -0405 % set focus on results -0406 set(gui.plots.SignalPanel,'Selection',1); -0407 set(gui.plots.DistPanel,'Selection',1); -0408 % open INFO field -0409 set(gui.push_handles.info,'String','<'); -0410 onPushShowHide(gui.push_handles.info); -0411 if ~isempty(findobj('Tag','FITSTATS')) -0412 showFitStatistics; -0413 end -0414 NUCLEUSinv_updateInterface; -0415 else -0416 helpdlg('Cannot start inversion because no data set is selected!',... -0417 'Select NMR data first.'); -0418 end -0419 -0420 %% at the end, no matter what reset the RUN button -0421 set(gui.push_handles.invstd_run,'String','<HTML><u>R</u>UN',... -0422 'BackgroundColor','g','Enable','on','Callback',@onPushRun); -0423 setappdata(fig,'gui',gui); -0424 -0425 end -0426 -0427 %------------- END OF CODE -------------- -0428 -0429 %% License: -0430 % MIT License -0431 % -0432 % Copyright (c) 2018 Thomas Hiller -0433 % -0434 % Permission is hereby granted, free of charge, to any person obtaining a copy -0435 % of this software and associated documentation files (the "Software"), to deal -0436 % in the Software without restriction, including without limitation the rights -0437 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0438 % copies of the Software, and to permit persons to whom the Software is -0439 % furnished to do so, subject to the following conditions: -0440 % -0441 % The above copyright notice and this permission notice shall be included in all -0442 % copies or substantial portions of the Software. +0201 param.Tfixed_bool = data.invstd.Tfixed_bool; +0202 param.Tfixed_val = data.invstd.Tfixed_val; +0203 if isfield(data.results.nmrproc,'W') +0204 param.W = data.results.nmrproc.W; +0205 end +0206 % status bar information +0207 switch data.info.has_optim +0208 case 'on' +0209 infostring = 'Inversion using ''Optimization Toolbox'' ... '; +0210 case 'off' +0211 infostring = 'Inversion using ''fminsearchbnd'' ... '; +0212 end +0213 displayStatusText(gui,infostring); +0214 invstd = fitDataFree(data.results.nmrproc.t,... +0215 data.results.nmrproc.s,flag,param,1); +0216 data.invstd.Tfixed_val = [invstd.T zeros(1,4)]; +0217 +0218 case 'free' % N free single-exponential inversion +0219 flag = data.results.nmrproc.T1T2; +0220 param.T1IRfac = data.results.nmrproc.T1IRfac; +0221 param.noise = data.results.nmrproc.noise; +0222 param.optim = data.info.has_optim; +0223 param.Tfixed_bool = data.invstd.Tfixed_bool; +0224 param.Tfixed_val = data.invstd.Tfixed_val; +0225 if isfield(data.results.nmrproc,'W') +0226 param.W = data.results.nmrproc.W; +0227 end +0228 % status bar information +0229 switch data.info.has_optim +0230 case 'on' +0231 infostring = 'Inversion using ''Optimization Toolbox'' ... '; +0232 case 'off' +0233 infostring = 'Inversion using ''fminsearchbnd'' ... '; +0234 end +0235 displayStatusText(gui,infostring); +0236 invstd = fitDataFree(data.results.nmrproc.t,... +0237 data.results.nmrproc.s,flag,param,data.invstd.freeDT); +0238 data.invstd.Tfixed_val = [invstd.T(1:data.invstd.freeDT)... +0239 zeros(1,5-data.invstd.freeDT)]; +0240 +0241 case 'LU' % multi-exponential inversion +0242 % general parameter +0243 param.T1T2 = data.results.nmrproc.T1T2; +0244 param.T1IRfac = data.results.nmrproc.T1IRfac; +0245 param.Tb = data.invstd.Tbulk; +0246 param.Td = data.invstd.Tdiff; +0247 param.Tint = [log10(data.invstd.time) data.invstd.Ntime]; +0248 param.Lorder = data.invstd.Lorder; +0249 param.lambda = data.invstd.lambda; +0250 param.noise = data.results.nmrproc.noise; +0251 if isfield(data.results.nmrproc,'W') +0252 param.W = data.results.nmrproc.W; +0253 end +0254 % status bar information +0255 infostring = 'Inversion using LU decomposition ... '; +0256 displayStatusText(gui,infostring); +0257 invstd = fitDataLUdecomp(data.results.nmrproc.t,... +0258 data.results.nmrproc.s,param); +0259 +0260 case 'NNLS' % multi-exponential inversion with manual regularization +0261 % general parameter +0262 param.T1T2 = data.results.nmrproc.T1T2; +0263 param.T1IRfac = data.results.nmrproc.T1IRfac; +0264 param.Tb = data.invstd.Tbulk; +0265 param.Td = data.invstd.Tdiff; +0266 param.Tint = [log10(data.invstd.time) data.invstd.Ntime]; +0267 param.regMethod = data.invstd.regtype; +0268 param.Lorder = data.invstd.Lorder; +0269 param.lambda = data.invstd.lambda; +0270 param.noise = data.results.nmrproc.noise; +0271 param.solver = data.info.solver; +0272 if isfield(data.results.nmrproc,'W') +0273 param.W = data.results.nmrproc.W; +0274 end +0275 +0276 % status bar information +0277 switch data.info.solver +0278 case 'lsqlin' +0279 infostring = 'Inversion using ''Optimization Toolbox'' ... '; +0280 case 'lsqnonneg' +0281 infostring = 'Inversion using ''lsqnonneg'' ... '; +0282 end +0283 displayStatusText(gui,infostring); +0284 invstd = fitDataLSQ(data.results.nmrproc.t,... +0285 data.results.nmrproc.s,param); +0286 +0287 case 'MUMO' % N free distribution inversion +0288 param.T1T2 = data.results.nmrproc.T1T2; +0289 param.T1IRfac = data.results.nmrproc.T1IRfac; +0290 param.Tb = data.invstd.Tbulk; +0291 param.Td = data.invstd.Tdiff; +0292 param.Tint = [log10(data.invstd.time) data.invstd.Ntime]; +0293 param.noise = data.results.nmrproc.noise; +0294 param.optim = data.info.has_optim; +0295 if isfield(data.results.nmrproc,'W') +0296 param.W = data.results.nmrproc.W; +0297 end +0298 +0299 % status bar information +0300 switch data.info.solver +0301 case 'lsqlin' +0302 infostring = 'Inversion using ''Optimization Toolbox'' ... '; +0303 case 'lsqnonneg' +0304 infostring = 'Inversion using ''fminsearchbnd'' ... '; +0305 end +0306 displayStatusText(gui,infostring); +0307 invstd = fitDataMultiModal(data.results.nmrproc.t,... +0308 data.results.nmrproc.s,param,data.invstd.freeDT); +0309 +0310 % estimate uncertainty +0311 if data.invstd.useUncert +0312 % original fit parameter +0313 iparam = param; +0314 % uncertainty parameter +0315 uparam.time = data.results.nmrproc.t; +0316 uparam.signal = data.results.nmrproc.s; +0317 uparam.uncertMethod = data.invstd.uncertMethod; +0318 uparam.uncertThresh = data.invstd.uncertThresh; +0319 uparam.uncertChi2 = data.invstd.uncertChi2; +0320 uparam.uncertN = data.invstd.uncertN; +0321 uparam.uncertMax = data.invstd.uncertMax; +0322 invstd = estimateUncertainty(data.invstd.invtype,invstd,iparam,uparam); +0323 end +0324 end +0325 % normalize to 1 +0326 if data.process.norm == 1 +0327 switch data.invstd.invtype +0328 case {'LU','NNLS','MUMO'} +0329 % normalization with sum() -> sum(f)=1 +0330 % this is the standard way of doing it +0331 invstd.T1T2f = invstd.T1T2f./sum(invstd.T1T2f); +0332 % alternatives depending on the objective: +0333 % 1.) normalization with sum(f*dt) -> area~=1 +0334 % dt = log10(invstd.T1T2me(2))-log10(invstd.T1T2me(1)); +0335 % invstd.T1T2f = invstd.T1T2f/sum(invstd.T1T2f*dt); +0336 % 2.) normalization with trapz() -> area=1 but sum(f)>1 +0337 % invstd.T1T2f = invstd.T1T2f./trapz(invstd.T1T2me,invstd.T1T2f); +0338 otherwise +0339 % nothing to do +0340 end +0341 end +0342 runtime = toc; +0343 displayStatusText(gui,[infostring,'done | inversion took ',... +0344 sprintf('%5.2f',runtime),' s']); +0345 % save inversion results +0346 data.results.invstd = invstd; +0347 setappdata(fig,'data',data); +0348 end +0349 % as long as the "UserData" is 1 the STOP button was not pressed and +0350 % the inversion result gets saved in "INVdata" +0351 if get(gui.push_handles.invstd_run,'UserData') == 1 && ... +0352 ( isfield(data.results,'invstd') || ... +0353 isfield(data.results,'lcurve') ) +0354 INVdata{id} = []; +0355 INVdata{id} = data; +0356 INVdata{id} = rmfield(INVdata{id},'import'); +0357 INVdata{id} = rmfield(INVdata{id},'info'); +0358 INVdata{id} = rmfield(INVdata{id},'calib'); +0359 INVdata{id} = rmfield(INVdata{id},'pressure'); +0360 +0361 % color the list entries that already have an inversion result +0362 strL = get(gui.listbox_handles.signal,'String'); +0363 str1 = strL{id}; +0364 str2 = ['<HTML><BODY bgcolor="rgb(',... +0365 sprintf('%d,%d,%d',gui.myui.colors.listINV.*255),')">',str1,'</BODY></HTML>']; +0366 strL{id} = str2; +0367 set(gui.listbox_handles.signal,'String',strL); +0368 +0369 % update GUI INVdata +0370 setappdata(fig,'INVdata',INVdata); +0371 +0372 % --- +0373 % special treatment for LIAG processing +0374 if isfield(data.import,'LIAG') && ~strcmp(data.invstd.regtype,'lcurve') +0375 if contains(str1,' - calibration') +0376 % save Tbulk from the calibration sample +0377 btn1 = 'Yes keep it'; +0378 btn2 = 'No, reset to 1e6 [s]'; +0379 if data.results.invstd.T2 < 0.2 +0380 answer = questdlg(['Tbulk seems very short with ',... +0381 sprintf('%4.3f',data.results.invstd.T2),' [s] ',... +0382 'Do you want to keep it?'], ... +0383 'Keep relaxation time as Tbulk', ... +0384 btn1,btn2,btn2); +0385 % Handle response +0386 switch answer +0387 case btn1 +0388 data.import.LIAG.Tbulk = data.results.invstd.T2; +0389 case btn2 +0390 data.import.LIAG.Tbulk = 1e6; +0391 end +0392 else +0393 data.import.LIAG.Tbulk = data.results.invstd.T2; +0394 end +0395 % update GUI data +0396 setappdata(fig,'data',data); +0397 % save calibration data +0398 useSignalAsCalibration(id); +0399 else +0400 calibratePorosity; +0401 end +0402 end +0403 % --- +0404 else % STOP was pressed (because "UserData" is 0) +0405 % reset "UserData" +0406 set(gui.push_handles.invstd_run,'UserData',1); +0407 end +0408 % update plots and INFO fields +0409 updatePlotsSignal; +0410 updatePlotsDistribution; +0411 updateInfo(gui.plots.SignalPanel); +0412 % set focus on results +0413 set(gui.plots.SignalPanel,'Selection',1); +0414 set(gui.plots.DistPanel,'Selection',1); +0415 % open INFO field +0416 set(gui.push_handles.info,'String','<'); +0417 onPushShowHide(gui.push_handles.info); +0418 if ~isempty(findobj('Tag','FITSTATS')) +0419 showFitStatistics; +0420 end +0421 if ~isempty(findobj('Tag','FIXEDTIMEVIEW')) +0422 FixedTimeView(gui.menu.extra_fixedtime); +0423 end +0424 NUCLEUSinv_updateInterface; +0425 else +0426 helpdlg('Cannot start inversion because no data set is selected!',... +0427 'Select NMR data first.'); +0428 end +0429 +0430 %% at the end, no matter what reset the RUN button +0431 set(gui.push_handles.invstd_run,'String','<HTML><u>R</u>UN',... +0432 'BackgroundColor','g','Enable','on','Callback',@onPushRun); +0433 setappdata(fig,'gui',gui); +0434 +0435 end +0436 +0437 %------------- END OF CODE -------------- +0438 +0439 %% License: +0440 % MIT License +0441 % +0442 % Copyright (c) 2018 Thomas Hiller 0443 % -0444 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0445 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0446 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0447 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0448 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0449 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0450 % SOFTWARE. +0444 % Permission is hereby granted, free of charge, to any person obtaining a copy +0445 % of this software and associated documentation files (the "Software"), to deal +0446 % in the Software without restriction, including without limitation the rights +0447 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0448 % copies of the Software, and to permit persons to whom the Software is +0449 % furnished to do so, subject to the following conditions: +0450 % +0451 % The above copyright notice and this permission notice shall be included in all +0452 % copies or substantial portions of the Software. +0453 % +0454 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0455 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0456 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0457 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0458 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0459 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0460 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/functions/interface/showExtraGraphics.html b/doc/nucleus/functions/interface/showExtraGraphics.html index 4fb400e..bd15978 100644 --- a/doc/nucleus/functions/interface/showExtraGraphics.html +++ b/doc/nucleus/functions/interface/showExtraGraphics.html @@ -104,7 +104,7 @@

    SOURCE CODE ^%% get GUI handle and data 0034 fig = findobj('Tag','INV'); -0035 fig_tag = get(fig,'Tag'); +0035 % fig_tag = get(fig,'Tag'); 0036 data = getappdata(fig,'data'); 0037 INVdata = getappdata(fig,'INVdata'); 0038 gui = getappdata(fig,'gui'); @@ -200,203 +200,229 @@

    SOURCE CODE ^if data.import.BAM.use_z 0129 xval = data.import.BAM.zslice; 0130 xlabelstr = 'position'; -0131 else -0132 xlabelstr = 'date' ; -0133 end -0134 elseif isfield(data.import,'IBAC') -0135 if data.import.IBAC.use_z -0136 xval = data.import.IBAC.zslice; -0137 xlabelstr = 'position'; -0138 else -0139 xlabelstr = 'date' ; -0140 end -0141 else -0142 xlabelstr = 'date' ; -0143 end -0144 -0145 % plot it -0146 switch method -0147 case 'amp' -0148 f = figure; -0149 ax1 = subplot(311,'Parent',f); -0150 ax2 = subplot(312,'Parent',f); -0151 ax3 = subplot(313,'Parent',f); -0152 -0153 hold(ax1,'on'); -0154 switch data.invstd.invtype -0155 case {'mono','free'} -0156 errorbar(xval,E0,E0er,'o','Parent',ax1); -0157 otherwise -0158 plot(xval,E0,'o','Parent',ax1); -0159 end -0160 grid(ax1,'on'); -0161 set(get(ax1,'YLabel'),'String','E0'); -0162 -0163 hold(ax2,'on'); -0164 switch data.invstd.invtype -0165 case 'mono' -0166 errorbar(xval,T,Ter,'ko','Parent',ax2); -0167 set(get(ax2,'YLabel'),'String',['T [',timescale,']']); -0168 case 'free' -0169 for i = 1:size(T,2) -0170 semilogy(xval,T(:,i),'ko','Parent',ax2); -0171 end -0172 set(get(ax2,'YLabel'),'String',['T_x [',timescale,']']); -0173 set(ax2,'YScale','log'); -0174 otherwise -0175 for i = 1:size(T,2) -0176 semilogy(xval,T(:,i),'ko','Parent',ax2); -0177 end -0178 set(get(ax2,'YLabel'),'String',['TLGM [',timescale,']']); -0179 end -0180 grid(ax2,'on'); -0181 -0182 hold(ax3,'on'); -0183 plot(xval,SNR,'o','Parent',ax3); -0184 grid on; -0185 xlabel(xlabelstr); -0186 set(get(ax3,'YLabel'),'String','signal-to-noise ratio'); -0187 -0188 linkaxes([ax1 ax2 ax3], 'x'); -0189 -0190 if strcmp(xlabelstr,'date') -0191 isfile = which('dynamicDateTicks'); -0192 if ~isempty(isfile) -0193 dynamicDateTicks([ax1 ax2 ax3],'link','dd.mm. HH:MM'); -0194 else -0195 datetick(ax1,'x','dd.mm. HH:MM','keepticks'); -0196 datetick(ax2,'x','dd.mm. HH:MM','keepticks'); -0197 datetick(ax3,'x','dd.mm. HH:MM','keepticks'); -0198 end -0199 end +0131 ylabelstr = 'position [µm]'; +0132 else +0133 xlabelstr = 'date' ; +0134 end +0135 elseif isfield(data.import,'IBAC') +0136 if data.import.IBAC.use_z +0137 xval = data.import.IBAC.zslice; +0138 xlabelstr = 'position'; +0139 ylabelstr = 'position [µm]'; +0140 else +0141 xlabelstr = 'date' ; +0142 end +0143 elseif isfield(data.import,'LIAGCORE') +0144 xval = data.import.LIAGCORE.zslice; +0145 if data.import.LIAGCORE.use_z +0146 xlabelstr = 'position [mm]'; +0147 ylabelstr = 'position [mm]'; +0148 else +0149 xlabelstr = 'level'; +0150 ylabelstr = 'level'; +0151 end +0152 else +0153 xlabelstr = 'date' ; +0154 end +0155 +0156 % plot it +0157 switch method +0158 case 'amp' +0159 f = figure; +0160 ax1 = subplot(311,'Parent',f); +0161 ax2 = subplot(312,'Parent',f); +0162 ax3 = subplot(313,'Parent',f); +0163 +0164 hold(ax1,'on'); +0165 switch data.invstd.invtype +0166 case {'mono','free'} +0167 errorbar(xval,E0,E0er,'o','Parent',ax1); +0168 otherwise +0169 plot(xval,E0,'o','Parent',ax1); +0170 end +0171 grid(ax1,'on'); +0172 set(get(ax1,'YLabel'),'String','E0'); +0173 +0174 hold(ax2,'on'); +0175 switch data.invstd.invtype +0176 case 'mono' +0177 errorbar(xval,T,Ter,'ko','Parent',ax2); +0178 set(get(ax2,'YLabel'),'String',['T [',timescale,']']); +0179 case 'free' +0180 for i = 1:size(T,2) +0181 semilogy(xval,T(:,i),'ko','Parent',ax2); +0182 end +0183 set(get(ax2,'YLabel'),'String',['T_x [',timescale,']']); +0184 set(ax2,'YScale','log'); +0185 otherwise +0186 for i = 1:size(T,2) +0187 semilogy(xval,T(:,i),'ko','Parent',ax2); +0188 end +0189 set(get(ax2,'YLabel'),'String',['TLGM [',timescale,']']); +0190 end +0191 grid(ax2,'on'); +0192 +0193 hold(ax3,'on'); +0194 plot(xval,SNR,'o','Parent',ax3); +0195 grid on; +0196 xlabel(xlabelstr); +0197 set(get(ax3,'YLabel'),'String','signal-to-noise ratio'); +0198 +0199 linkaxes([ax1 ax2 ax3], 'x'); 0200 -0201 case 'ampvst' -0202 f = figure; -0203 ax1 = axes('Parent',f); -0204 -0205 plot(E0,T,'ko','Parent',ax1), -0206 set(get(ax1,'XLabel'),'String','E0'); -0207 set(get(ax1,'YLabel'),'String',['T [',timescale,']']); -0208 -0209 case 'rtd' -0210 switch data.invstd.invtype -0211 case {'LU','NNLS'} -0212 if strcmp(xlabelstr,'date') -0213 mycol = jet(size(Tspec,1)); -0214 [time,ix] = sort(xval); -0215 Tspec = Tspec(ix,:); -0216 f = figure; -0217 ax = axes('Parent',f); -0218 hold(ax,'on') -0219 for i = 1:size(Tspec,1) -0220 plot3(time(i)*ones(size(Tt)),Tt,Tspec(i,:),... -0221 'Color',mycol(i,:),'Parent',ax); -0222 end -0223 grid on; box on; -0224 xlabel('date'); -0225 ylabel(['relaxation time [',timescale,']']); -0226 zlabel('amplitude [-]'); -0227 -0228 set(ax,'YScale','log'); -0229 isfile = which('dynamicDateTicks'); -0230 if ~isempty(isfile) -0231 dynamicDateTicks(ax,'dd.mm. HH:MM'); -0232 else -0233 datetick(ax,'x','dd.mm. HH:MM','keepticks'); -0234 end -0235 view([90 0]); -0236 else -0237 dx = xval(2)-xval(1); -0238 [xx,yy] = meshgrid(Tt',[xval-dx/2; xval(end)+dx/2]); -0239 f = figure; -0240 ax = axes('Parent',f); -0241 hold(ax,'on') -0242 -0243 % remove the backgound file -0244 Tspec(isnan(Tspec)) = []; -0245 xi = numel(Tspec)/numel(Tt); -0246 Tspec = reshape(Tspec,[xi numel(Tt)]); -0247 -0248 surf(xx,yy,zeros(size(xx)),Tspec./max(Tspec(:)),'Parent',ax); -0249 shading(ax,'flat'); -0250 xticks = log10(min(Tt)):1:log10(max(Tt)); -0251 set(ax,'XScale','log','XLim',[10^xticks(1) 10^xticks(end)],... -0252 'XTick',10.^xticks,'Layer','top','Box','on'); -0253 set(ax,'YLim',[min(yy(:)) max(yy(:))],'YDir','normal') -0254 cmap = jet; cmap = flipud(cmap); -0255 colormap(ax,cmap); -0256 xlabel(['relaxation time [',timescale,']']); -0257 ylabel('position [µm]'); -0258 cb = colorbar; -0259 set(get(cb,'YLabel'),'String','norm. amplitude'); -0260 -0261 % context menu to flip y-axis direction -0262 axes_cm = uicontextmenu(f); -0263 gui.cm_handles.axes_proc_xaxis = uimenu(axes_cm,... -0264 'Label','flip y-axis','Tag','flip','Enable','on',... -0265 'Callback',@onContextFlip); -0266 set(ax,'UIContextMenu',axes_cm); -0267 -0268 end -0269 otherwise -0270 helpdlg({'function: showExtraGraphics',... -0271 'Cannot plot RTDs because the inversion was not multi exponential'},... -0272 'Invert NMR data first.'); -0273 end -0274 end -0275 -0276 catch ME -0277 % show error message in case import fails -0278 errmsg = {ME.message;[ME.stack(1).name,' Line: ',num2str(ME.stack(1).line)];... -0279 'Cannot show figure.'}; -0280 errordlg(errmsg,'showExtraGraphics: Error!'); -0281 end -0282 else -0283 helpdlg({'function: showExtraGraphics',... -0284 'Cannot continue because there need to be at least two NMR measurements.'},... -0285 'Not enough data to show'); -0286 end -0287 -0288 end -0289 -0290 function onContextFlip(src,~) -0291 f = ancestor(src,'Figure','toplevel'); -0292 ax = findobj(f,'Type','Axes'); -0293 -0294 direction = get(ax,'Ydir'); -0295 switch direction -0296 case 'normal' -0297 set(ax,'Ydir','reverse') -0298 case 'reverse' -0299 set(ax,'Ydir','normal') +0201 if strcmp(xlabelstr,'date') +0202 isfile = which('dynamicDateTicks'); +0203 if ~isempty(isfile) +0204 dynamicDateTicks([ax1 ax2 ax3],'link','dd.mm. HH:MM'); +0205 else +0206 datetick(ax1,'x','dd.mm. HH:MM','keepticks'); +0207 datetick(ax2,'x','dd.mm. HH:MM','keepticks'); +0208 datetick(ax3,'x','dd.mm. HH:MM','keepticks'); +0209 end +0210 end +0211 +0212 case 'ampvst' +0213 f = figure; +0214 ax1 = axes('Parent',f); +0215 +0216 plot(E0,T,'ko','Parent',ax1), +0217 set(get(ax1,'XLabel'),'String','E0'); +0218 set(get(ax1,'YLabel'),'String',['T [',timescale,']']); +0219 +0220 case 'rtd' +0221 switch data.invstd.invtype +0222 case {'LU','NNLS'} +0223 if strcmp(xlabelstr,'date') +0224 mycol = jet(size(Tspec,1)); +0225 [time,ix] = sort(xval); +0226 Tspec = Tspec(ix,:); +0227 f = figure; +0228 ax = axes('Parent',f); +0229 hold(ax,'on') +0230 for i = 1:size(Tspec,1) +0231 plot3(time(i)*ones(size(Tt)),Tt,Tspec(i,:),... +0232 'Color',mycol(i,:),'Parent',ax); +0233 end +0234 grid on; box on; +0235 xlabel('date'); +0236 ylabel(['relaxation time [',timescale,']']); +0237 zlabel('amplitude [-]'); +0238 +0239 set(ax,'YScale','log'); +0240 isfile = which('dynamicDateTicks'); +0241 if ~isempty(isfile) +0242 dynamicDateTicks(ax,'dd.mm. HH:MM'); +0243 else +0244 datetick(ax,'x','dd.mm. HH:MM','keepticks'); +0245 end +0246 view([90 0]); +0247 else +0248 dx = xval(2)-xval(1); +0249 [xx,yy] = meshgrid(Tt',[xval-dx/2; xval(end)+dx/2]); +0250 f = figure; +0251 ax = axes('Parent',f); +0252 hold(ax,'on') +0253 +0254 % remove the backgound file +0255 Tspec(isnan(Tspec)) = []; +0256 xi = numel(Tspec)/numel(Tt); +0257 Tspec = reshape(Tspec,[xi numel(Tt)]); +0258 +0259 surf(xx,yy,zeros(size(xx)),Tspec./max(Tspec(:)),'Parent',ax); +0260 shading(ax,'flat'); +0261 xticks = log10(min(Tt)):1:log10(max(Tt)); +0262 set(ax,'XScale','log','XLim',[10^xticks(1) 10^xticks(end)],... +0263 'XTick',10.^xticks,'Layer','top','Box','on'); +0264 set(ax,'YLim',[min(yy(:)) max(yy(:))],'YDir','normal') +0265 cmap = jet; cmap = flipud(cmap); +0266 colormap(ax,cmap); +0267 xlabel(['relaxation time [',timescale,']']); +0268 ylabel(ylabelstr); +0269 cb = colorbar; +0270 set(get(cb,'YLabel'),'String','norm. amplitude'); +0271 +0272 % context menu to flip y-axis direction +0273 axes_cm = uicontextmenu(f); +0274 gui.cm_handles.axes_proc_xaxis = uimenu(axes_cm,... +0275 'Label','flip y-axis','Tag','flip','Enable','on',... +0276 'Callback',@onContextFlip); +0277 gui.cm_handles.axes_proc_xaxis2 = uimenu(axes_cm,... +0278 'Label','color scale log/lin','Tag','loglin','Enable','on',... +0279 'Callback',@onContextFlip); +0280 set(ax,'UIContextMenu',axes_cm); +0281 +0282 end +0283 otherwise +0284 helpdlg({'function: showExtraGraphics',... +0285 'Cannot plot RTDs because the inversion was not multi exponential'},... +0286 'Invert NMR data first.'); +0287 end +0288 end +0289 +0290 catch ME +0291 % show error message in case import fails +0292 errmsg = {ME.message;[ME.stack(1).name,' Line: ',num2str(ME.stack(1).line)];... +0293 'Cannot show figure.'}; +0294 errordlg(errmsg,'showExtraGraphics: Error!'); +0295 end +0296 else +0297 helpdlg({'function: showExtraGraphics',... +0298 'Cannot continue because there need to be at least two NMR measurements.'},... +0299 'Not enough data to show'); 0300 end 0301 0302 end 0303 -0304 %------------- END OF CODE -------------- -0305 -0306 %% License: -0307 % MIT License -0308 % -0309 % Copyright (c) 2018 Thomas Hiller -0310 % -0311 % Permission is hereby granted, free of charge, to any person obtaining a copy -0312 % of this software and associated documentation files (the "Software"), to deal -0313 % in the Software without restriction, including without limitation the rights -0314 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0315 % copies of the Software, and to permit persons to whom the Software is -0316 % furnished to do so, subject to the following conditions: -0317 % -0318 % The above copyright notice and this permission notice shall be included in all -0319 % copies or substantial portions of the Software. -0320 % -0321 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0322 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0323 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0324 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0325 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0326 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0327 % SOFTWARE. +0304 function onContextFlip(src,~) +0305 f = ancestor(src,'Figure','toplevel'); +0306 ax = findobj(f,'Type','Axes'); +0307 tag = get(src,'Tag'); +0308 +0309 switch tag +0310 case 'loglin' +0311 isscale = get(ax,'ColorScale'); +0312 switch isscale +0313 case 'log' +0314 set(ax,'ColorScale','lin','CLim',[0 1]); +0315 case 'linear' +0316 set(ax,'ColorScale','log','CLim',[0.01 1]); +0317 end +0318 case 'flip' +0319 direction = get(ax,'Ydir'); +0320 switch direction +0321 case 'normal' +0322 set(ax,'Ydir','reverse') +0323 case 'reverse' +0324 set(ax,'Ydir','normal') +0325 end +0326 end +0327 +0328 end +0329 +0330 %------------- END OF CODE -------------- +0331 +0332 %% License: +0333 % MIT License +0334 % +0335 % Copyright (c) 2018 Thomas Hiller +0336 % +0337 % Permission is hereby granted, free of charge, to any person obtaining a copy +0338 % of this software and associated documentation files (the "Software"), to deal +0339 % in the Software without restriction, including without limitation the rights +0340 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0341 % copies of the Software, and to permit persons to whom the Software is +0342 % furnished to do so, subject to the following conditions: +0343 % +0344 % The above copyright notice and this permission notice shall be included in all +0345 % copies or substantial portions of the Software. +0346 % +0347 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0348 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0349 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0350 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0351 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0352 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0353 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/functions/interface/uncheckImportMenus.html b/doc/nucleus/functions/interface/uncheckImportMenus.html index fba64b6..bdcb707 100644 --- a/doc/nucleus/functions/interface/uncheckImportMenus.html +++ b/doc/nucleus/functions/interface/uncheckImportMenus.html @@ -116,9 +116,9 @@

    SOURCE CODE ^'Checked','off'); 0048 set(gui.menu.file_import_lab_bgr_mat,'Checked','off'); 0049 set(gui.menu.file_import_lab_bgr_mouse_cpmg,'Checked','off'); -0050 set(gui.menu.file_import_lab_bgr_mouse_liftsingle,'Checked','off'); -0051 set(gui.menu.file_import_lab_bgr_mouse_liftall,'Checked','off'); -0052 set(gui.menu.file_import_lab_bgr_helios,'Checked','off'); +0050 set(gui.menu.file_import_lab_bgr_mouse_lift,'Checked','off'); +0051 set(gui.menu.file_import_lab_bgr_helios_cpmg,'Checked','off'); +0052 set(gui.menu.file_import_lab_bgr_helios_series,'Checked','off'); 0053 set(gui.menu.file_import_lab_bam_tom,'Checked','off'); 0054 set(gui.menu.file_import_lab_ascii_T1,'Checked','off'); 0055 set(gui.menu.file_import_lab_ascii_T2,'Checked','off'); diff --git a/doc/nucleus/functions/interface/updateInfo.html b/doc/nucleus/functions/interface/updateInfo.html index d622507..44b354f 100644 --- a/doc/nucleus/functions/interface/updateInfo.html +++ b/doc/nucleus/functions/interface/updateInfo.html @@ -384,233 +384,249 @@

    SOURCE CODE ^' '; 0317 ciT = sum(full(invstd.ci(2:2:end))); -0318 -0319 switch nmrproc.T1T2 -0320 case 'T1' -0321 info{end+1,1} = ['<HTML><BODY>T<sub><font size="',num2str(subfs),'">1</sub> = ',... -0322 sprintf('%5.4f',invstd.T1),... -0323 ' &#8723 (',sprintf('%5.4f',ciT),')','</BODY></HTML>']; -0324 case 'T2' -0325 info{end+1,1} = ['<HTML><BODY>T<sub><font size="',num2str(subfs),'">2</sub> = ',... -0326 sprintf('%5.4f',invstd.T2),... -0327 ' &#8723 (',sprintf('%5.4f',ciT),')','</BODY></HTML>']; -0328 end -0329 info{end+1,1} = ' '; -0330 -0331 case 'free' -0332 str = [invtype,' ',num2str(data.invstd.freeDT)]; -0333 info{end+1,1} = str; -0334 info{end+1,1} = ' '; -0335 -0336 E0 = invstd.E0; -0337 ciE0 = full(invstd.ci(1:2:end)); -0338 ciT = full(invstd.ci(2:2:end)); -0339 -0340 switch nmrproc.T1T2 -0341 case 'T1' -0342 T = invstd.T1; -0343 case 'T2' -0344 T = invstd.T2; -0345 end -0346 -0347 for i = 1:length(T) -0348 info{end+1,1} = ['<HTML><BODY>T(',num2str(i),') = ',sprintf('%5.4f',T(i)),... -0349 ' &#8723 (',sprintf('%5.4f',ciT(i)),')','</BODY></HTML>']; %#ok<*AGROW> -0350 info{end+1,1} = ['<HTML><BODY>E(',num2str(i),') = ',sprintf('%5.4f',E0(i)),... -0351 ' &#8723 (',sprintf('%5.4f',ciE0(i)),')','</BODY></HTML>']; -0352 info{end+1,1} = ' '; +0318 +0319 if data.invstd.Tfixed_bool(1) +0320 col = gui.myui.colors.listINV.*255; +0321 else +0322 col = [1 1 1].*255; +0323 end +0324 +0325 switch nmrproc.T1T2 +0326 case 'T1' +0327 info{end+1,1} = ['<HTML><BODY bgcolor="rgb(',... +0328 sprintf('%d,%d,%d',col),')">T<sub><font size="',num2str(subfs),'">1</sub> = ',... +0329 sprintf('%5.4f',invstd.T1),... +0330 ' &#8723 (',sprintf('%5.4f',ciT),')','</BODY></HTML>']; +0331 case 'T2' +0332 info{end+1,1} = ['<HTML><BODY bgcolor="rgb(',... +0333 sprintf('%d,%d,%d',col),')">T<sub><font size="',num2str(subfs),'">2</sub> = ',... +0334 sprintf('%5.4f',invstd.T2),... +0335 ' &#8723 (',sprintf('%5.4f',ciT),')','</BODY></HTML>']; +0336 end +0337 info{end+1,1} = ' '; +0338 +0339 case 'free' +0340 str = [invtype,' ',num2str(data.invstd.freeDT)]; +0341 info{end+1,1} = str; +0342 info{end+1,1} = ' '; +0343 +0344 E0 = invstd.E0; +0345 ciE0 = full(invstd.ci(1:2:end)); +0346 ciT = full(invstd.ci(2:2:end)); +0347 +0348 switch nmrproc.T1T2 +0349 case 'T1' +0350 T = invstd.T1; +0351 case 'T2' +0352 T = invstd.T2; 0353 end 0354 -0355 case {'LU','NNLS'} -0356 % info is a cell array -0357 str = [invtype,' ',data.invstd.regtype,' ',num2str(data.invstd.Lorder)]; -0358 info{end+1,1} = str; -0359 info{end+1,1} = ' '; -0360 -0361 % TLGM -0362 info{end+1,1} = ['<HTML><BODY>TLGM</sub> = ',sprintf('%5.4f',invstd.Tlgm),'</BODY></HTML>']; -0363 info{end+1,1} = ' '; -0364 -0365 % clay-bound water CBW < tcut ms -0366 % irreducible water / capillary water BVI ccut - tcut ms -0367 % movable water BVM > tcut ms -0368 switch data.process.timescale -0369 case 's' -0370 ccut = data.param.CBWcutoff/1000; -0371 tcut = data.param.BVIcutoff/1000; -0372 case 'ms' -0373 ccut = data.param.CBWcutoff; -0374 tcut = data.param.BVIcutoff; -0375 end -0376 por = data.invstd.porosity; -0377 CBW = abs(sum(invstd.T1T2f(invstd.T1T2me<=ccut))/sum(invstd.T1T2f)); -0378 BVI = abs(sum(invstd.T1T2f(invstd.T1T2me>ccut & invstd.T1T2me<=tcut))/sum(invstd.T1T2f)); -0379 BVM = abs(sum(invstd.T1T2f(invstd.T1T2me>tcut))/sum(invstd.T1T2f)); -0380 info{end+1,1} = ['CBW(',sprintf('%2d',data.param.CBWcutoff),... -0381 ') = ',sprintf('%5.2f',por*CBW*100),' [vol. %]']; -0382 -0383 info{end+1,1} = ['BVI(',sprintf('%2d',data.param.BVIcutoff),... -0384 ') = ',sprintf('%5.2f',por*BVI*100),' [vol. %]']; -0385 info{end+1,1} = ['BVM = ',sprintf('%5.2f',por*BVM*100),' [vol. %]']; -0386 -0387 case {'MUMO'} -0388 -0389 % info is a cell array -0390 str = [invtype,' ',num2str(data.invstd.freeDT)]; -0391 info{end+1,1} = str; -0392 info{end+1,1} = ' '; -0393 -0394 % TLGM -0395 info{end+1,1} = ['<HTML><BODY>TLGM</sub> = ',sprintf('%5.4f',invstd.Tlgm),'</BODY></HTML>']; -0396 info{end+1,1} = ' '; -0397 -0398 % clay-bound water CBW < tcut ms -0399 % irreducible water / capillary water BVI ccut - tcut ms -0400 % movable water BVM > tcut ms -0401 switch data.process.timescale -0402 case 's' -0403 ccut = data.param.CBWcutoff/1000; -0404 tcut = data.param.BVIcutoff/1000; -0405 case 'ms' -0406 ccut = data.param.CBWcutoff; -0407 tcut = data.param.BVIcutoff; -0408 end -0409 por = data.invstd.porosity; -0410 CBW = abs(sum(invstd.T1T2f(invstd.T1T2me<=ccut))/sum(invstd.T1T2f)); -0411 BVI = abs(sum(invstd.T1T2f(invstd.T1T2me>ccut & invstd.T1T2me<=tcut))/sum(invstd.T1T2f)); -0412 BVM = abs(sum(invstd.T1T2f(invstd.T1T2me>tcut))/sum(invstd.T1T2f)); -0413 info{end+1,1} = ['CBW(',sprintf('%2d',data.param.CBWcutoff),... -0414 ') = ',sprintf('%5.2f',por*CBW*100),' [vol. %]']; -0415 -0416 info{end+1,1} = ['BVI(',sprintf('%2d',data.param.BVIcutoff),... -0417 ') = ',sprintf('%5.2f',por*BVI*100),' [vol. %]']; -0418 info{end+1,1} = ['BVM = ',sprintf('%5.2f',por*BVM*100),' [vol. %]']; -0419 info{end+1,1} = ' '; -0420 -0421 % values for T, sigma and amplitude -0422 T = invstd.T; ciT = invstd.ci(1:3:end); -0423 S = invstd.S; ciS = invstd.ci(2:3:end); -0424 E = invstd.E; ciE = invstd.ci(3:3:end); -0425 % transform ciT because it is in log scale -0426 tmpT = log(T)-ciT'; -0427 ciT = T - exp(tmpT); -0428 -0429 for i = 1:length(T) -0430 info{end+1,1} = ['<HTML><BODY>T(',num2str(i),') = ',sprintf('%5.4f',T(i)),... -0431 ' &#8723 (',sprintf('%5.4f',ciT(i)),')','</BODY></HTML>']; %#ok<*AGROW> -0432 info{end+1,1} = ['<HTML><BODY>S(',num2str(i),') = ',sprintf('%5.4f',S(i)),... -0433 ' &#8723 (',sprintf('%5.4f',ciS(i)),')','</BODY></HTML>']; -0434 info{end+1,1} = ['<HTML><BODY>E(',num2str(i),') = ',sprintf('%5.4f',E(i)),... -0435 ' &#8723 (',sprintf('%5.4f',ciE(i)),')','</BODY></HTML>']; -0436 info{end+1,1} = ' '; -0437 end -0438 end -0439 end -0440 end -0441 -0442 case 2 % PSD -0443 info{end+1,1} = 'PSD'; -0444 info{end+1,1} = ' '; -0445 -0446 case 3 % PSDJ -0447 if isfield(data,'results') -0448 if isfield(data.results,'invjoint') -0449 invjoint = data.results.invjoint; -0450 -0451 info{end+1,1} = ['Inversion type: ',data.invjoint.invtype]; -0452 info{end+1,1} = ' '; -0453 switch data.invjoint.geometry_type -0454 case 'cyl' -0455 info{end+1,1} = ['Shape: ',data.invjoint.geometry_type]; -0456 info{end+1,1} = ['Geom.: ',sprintf('%4.2f',invjoint.iGEOM.a)]; -0457 case 'ang' -0458 info{end+1,1} = ['Shape: ',data.invjoint.geometry_type,' ',... -0459 num2str(invjoint.iGEOM.angles(1)),' ',... -0460 num2str(invjoint.iGEOM.angles(2)),' ',... -0461 num2str(invjoint.iGEOM.angles(3))]; -0462 info{end+1,1} = ['Geom.: ',sprintf('%4.2f',invjoint.iGEOM.a)]; -0463 case 'poly' -0464 info{end+1,1} = ['Shape: ',data.invjoint.geometry_type,... -0465 ' ',num2str(data.invjoint.polyN),' sides']; -0466 info{end+1,1} = ['Geom.: ',sprintf('%4.2f',invjoint.iGEOM.a)]; -0467 end +0355 for i = 1:length(T) +0356 +0357 if data.invstd.Tfixed_bool(i) +0358 col = gui.myui.colors.listINV.*255; +0359 else +0360 col = [1 1 1].*255; +0361 end +0362 +0363 info{end+1,1} = ['<HTML><BODY bgcolor="rgb(',... +0364 sprintf('%d,%d,%d',col),')">T(',num2str(i),') = ',sprintf('%5.4f',T(i)),... +0365 ' &#8723 (',sprintf('%5.4f',ciT(i)),')','</BODY></HTML>']; %#ok<*AGROW> +0366 info{end+1,1} = ['<HTML><BODY>E(',num2str(i),') = ',sprintf('%5.4f',E0(i)),... +0367 ' &#8723 (',sprintf('%5.4f',ciE0(i)),')','</BODY></HTML>']; +0368 info{end+1,1} = ' '; +0369 end +0370 +0371 case {'LU','NNLS'} +0372 % info is a cell array +0373 str = [invtype,' ',data.invstd.regtype,' ',num2str(data.invstd.Lorder)]; +0374 info{end+1,1} = str; +0375 info{end+1,1} = ' '; +0376 +0377 % TLGM +0378 info{end+1,1} = ['<HTML><BODY>TLGM</sub> = ',sprintf('%5.4f',invstd.Tlgm),'</BODY></HTML>']; +0379 info{end+1,1} = ' '; +0380 +0381 % clay-bound water CBW < tcut ms +0382 % irreducible water / capillary water BVI ccut - tcut ms +0383 % movable water BVM > tcut ms +0384 switch data.process.timescale +0385 case 's' +0386 ccut = data.param.CBWcutoff/1000; +0387 tcut = data.param.BVIcutoff/1000; +0388 case 'ms' +0389 ccut = data.param.CBWcutoff; +0390 tcut = data.param.BVIcutoff; +0391 end +0392 por = data.invstd.porosity; +0393 CBW = abs(sum(invstd.T1T2f(invstd.T1T2me<=ccut))/sum(invstd.T1T2f)); +0394 BVI = abs(sum(invstd.T1T2f(invstd.T1T2me>ccut & invstd.T1T2me<=tcut))/sum(invstd.T1T2f)); +0395 BVM = abs(sum(invstd.T1T2f(invstd.T1T2me>tcut))/sum(invstd.T1T2f)); +0396 info{end+1,1} = ['CBW(',sprintf('%2d',data.param.CBWcutoff),... +0397 ') = ',sprintf('%5.2f',por*CBW*100),' [vol. %]']; +0398 +0399 info{end+1,1} = ['BVI(',sprintf('%2d',data.param.BVIcutoff),... +0400 ') = ',sprintf('%5.2f',por*BVI*100),' [vol. %]']; +0401 info{end+1,1} = ['BVM = ',sprintf('%5.2f',por*BVM*100),' [vol. %]']; +0402 +0403 case {'MUMO'} +0404 +0405 % info is a cell array +0406 str = [invtype,' ',num2str(data.invstd.freeDT)]; +0407 info{end+1,1} = str; +0408 info{end+1,1} = ' '; +0409 +0410 % TLGM +0411 info{end+1,1} = ['<HTML><BODY>TLGM</sub> = ',sprintf('%5.4f',invstd.Tlgm),'</BODY></HTML>']; +0412 info{end+1,1} = ' '; +0413 +0414 % clay-bound water CBW < tcut ms +0415 % irreducible water / capillary water BVI ccut - tcut ms +0416 % movable water BVM > tcut ms +0417 switch data.process.timescale +0418 case 's' +0419 ccut = data.param.CBWcutoff/1000; +0420 tcut = data.param.BVIcutoff/1000; +0421 case 'ms' +0422 ccut = data.param.CBWcutoff; +0423 tcut = data.param.BVIcutoff; +0424 end +0425 por = data.invstd.porosity; +0426 CBW = abs(sum(invstd.T1T2f(invstd.T1T2me<=ccut))/sum(invstd.T1T2f)); +0427 BVI = abs(sum(invstd.T1T2f(invstd.T1T2me>ccut & invstd.T1T2me<=tcut))/sum(invstd.T1T2f)); +0428 BVM = abs(sum(invstd.T1T2f(invstd.T1T2me>tcut))/sum(invstd.T1T2f)); +0429 info{end+1,1} = ['CBW(',sprintf('%2d',data.param.CBWcutoff),... +0430 ') = ',sprintf('%5.2f',por*CBW*100),' [vol. %]']; +0431 +0432 info{end+1,1} = ['BVI(',sprintf('%2d',data.param.BVIcutoff),... +0433 ') = ',sprintf('%5.2f',por*BVI*100),' [vol. %]']; +0434 info{end+1,1} = ['BVM = ',sprintf('%5.2f',por*BVM*100),' [vol. %]']; +0435 info{end+1,1} = ' '; +0436 +0437 % values for T, sigma and amplitude +0438 T = invstd.T; ciT = invstd.ci(1:3:end); +0439 S = invstd.S; ciS = invstd.ci(2:3:end); +0440 E = invstd.E; ciE = invstd.ci(3:3:end); +0441 % transform ciT because it is in log scale +0442 tmpT = log(T)-ciT'; +0443 ciT = T - exp(tmpT); +0444 +0445 for i = 1:length(T) +0446 info{end+1,1} = ['<HTML><BODY>T(',num2str(i),') = ',sprintf('%5.4f',T(i)),... +0447 ' &#8723 (',sprintf('%5.4f',ciT(i)),')','</BODY></HTML>']; %#ok<*AGROW> +0448 info{end+1,1} = ['<HTML><BODY>S(',num2str(i),') = ',sprintf('%5.4f',S(i)),... +0449 ' &#8723 (',sprintf('%5.4f',ciS(i)),')','</BODY></HTML>']; +0450 info{end+1,1} = ['<HTML><BODY>E(',num2str(i),') = ',sprintf('%5.4f',E(i)),... +0451 ' &#8723 (',sprintf('%5.4f',ciE(i)),')','</BODY></HTML>']; +0452 info{end+1,1} = ' '; +0453 end +0454 end +0455 end +0456 end +0457 +0458 case 2 % PSD +0459 info{end+1,1} = 'PSD'; +0460 info{end+1,1} = ' '; +0461 +0462 case 3 % PSDJ +0463 if isfield(data,'results') +0464 if isfield(data.results,'invjoint') +0465 invjoint = data.results.invjoint; +0466 +0467 info{end+1,1} = ['Inversion type: ',data.invjoint.invtype]; 0468 info{end+1,1} = ' '; -0469 info{end+1,1} = ['rho (INV): ',sprintf('%5.3f',invjoint.irho*1e6),' [µm/s]']; -0470 if isfield(data.import,'NMRMOD') -0471 info{end+1,1} = ['rho (MOD): ',... -0472 sprintf('%5.3f',data.import.NMRMOD.nmr.rho*1e6),' [µm/s]']; -0473 end -0474 end -0475 end -0476 end -0477 % and update the text box -0478 set(gui.listbox_handles.info_dist,'String',info,'Value',[],'Max',2,'Min',0); -0479 -0480 %% CPS panel info -0481 % check if the CPS panel is maximized -0482 isminimized = get(gui.plots.CPSPanel,'Minimized'); -0483 if ~isminimized -0484 clear info; -0485 info{1,1} = ' '; -0486 if isfield(data,'results') -0487 if isfield(data.results,'invjoint') -0488 invjoint = data.results.invjoint; -0489 nmr = invjoint.idata.nmr; -0490 levels = invjoint.levels; -0491 -0492 for i = 1:numel(levels) -0493 info{end+1,1} = nmr{levels(i)}.name; -0494 info{end+1,1} = ['press. : ',... -0495 sprintf('%5.4f',invjoint.p0(levels(i))*data.pressure.unitfac),... -0496 ' [',data.pressure.unit,']']; -0497 switch invjoint.T1T2 -0498 case 'T1' -0499 info{end+1,1} = ['sat. (INV) : ',... -0500 sprintf('%4.2f',invjoint.idata.nmr{levels(i)}.fit_g(end))]; -0501 case 'T2' -0502 info{end+1,1} = ['sat. (INV) : ',... -0503 sprintf('%4.2f',invjoint.idata.nmr{levels(i)}.fit_g(1))]; -0504 end -0505 info{end+1,1} = ['sat. (MOD) : ',... -0506 sprintf('%4.2f',invjoint.S0(levels(i)))]; -0507 info{end+1,1} = ' '; -0508 end -0509 end -0510 end -0511 set(gui.listbox_handles.info_cps,'String',info,'Value',[],'Max',2,'Min',0); -0512 end -0513 -0514 % update GUI data -0515 setappdata(fig,'data',data); -0516 setappdata(fig,'gui',gui); -0517 end -0518 -0519 end -0520 -0521 %------------- END OF CODE -------------- -0522 -0523 %% License: -0524 % MIT License -0525 % -0526 % Copyright (c) 2018 Thomas Hiller -0527 % -0528 % Permission is hereby granted, free of charge, to any person obtaining a copy -0529 % of this software and associated documentation files (the "Software"), to deal -0530 % in the Software without restriction, including without limitation the rights -0531 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0532 % copies of the Software, and to permit persons to whom the Software is -0533 % furnished to do so, subject to the following conditions: -0534 % -0535 % The above copyright notice and this permission notice shall be included in all -0536 % copies or substantial portions of the Software. -0537 % -0538 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0539 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0540 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0541 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0542 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0543 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0544 % SOFTWARE. +0469 switch data.invjoint.geometry_type +0470 case 'cyl' +0471 info{end+1,1} = ['Shape: ',data.invjoint.geometry_type]; +0472 info{end+1,1} = ['Geom.: ',sprintf('%4.2f',invjoint.iGEOM.a)]; +0473 case 'ang' +0474 info{end+1,1} = ['Shape: ',data.invjoint.geometry_type,' ',... +0475 num2str(invjoint.iGEOM.angles(1)),' ',... +0476 num2str(invjoint.iGEOM.angles(2)),' ',... +0477 num2str(invjoint.iGEOM.angles(3))]; +0478 info{end+1,1} = ['Geom.: ',sprintf('%4.2f',invjoint.iGEOM.a)]; +0479 case 'poly' +0480 info{end+1,1} = ['Shape: ',data.invjoint.geometry_type,... +0481 ' ',num2str(data.invjoint.polyN),' sides']; +0482 info{end+1,1} = ['Geom.: ',sprintf('%4.2f',invjoint.iGEOM.a)]; +0483 end +0484 info{end+1,1} = ' '; +0485 info{end+1,1} = ['rho (INV): ',sprintf('%5.3f',invjoint.irho*1e6),' [µm/s]']; +0486 if isfield(data.import,'NMRMOD') +0487 info{end+1,1} = ['rho (MOD): ',... +0488 sprintf('%5.3f',data.import.NMRMOD.nmr.rho*1e6),' [µm/s]']; +0489 end +0490 end +0491 end +0492 end +0493 % and update the text box +0494 set(gui.listbox_handles.info_dist,'String',info,'Value',[],'Max',2,'Min',0); +0495 +0496 %% CPS panel info +0497 % check if the CPS panel is maximized +0498 isminimized = get(gui.plots.CPSPanel,'Minimized'); +0499 if ~isminimized +0500 clear info; +0501 info{1,1} = ' '; +0502 if isfield(data,'results') +0503 if isfield(data.results,'invjoint') +0504 invjoint = data.results.invjoint; +0505 nmr = invjoint.idata.nmr; +0506 levels = invjoint.levels; +0507 +0508 for i = 1:numel(levels) +0509 info{end+1,1} = nmr{levels(i)}.name; +0510 info{end+1,1} = ['press. : ',... +0511 sprintf('%5.4f',invjoint.p0(levels(i))*data.pressure.unitfac),... +0512 ' [',data.pressure.unit,']']; +0513 switch invjoint.T1T2 +0514 case 'T1' +0515 info{end+1,1} = ['sat. (INV) : ',... +0516 sprintf('%4.2f',invjoint.idata.nmr{levels(i)}.fit_g(end))]; +0517 case 'T2' +0518 info{end+1,1} = ['sat. (INV) : ',... +0519 sprintf('%4.2f',invjoint.idata.nmr{levels(i)}.fit_g(1))]; +0520 end +0521 info{end+1,1} = ['sat. (MOD) : ',... +0522 sprintf('%4.2f',invjoint.S0(levels(i)))]; +0523 info{end+1,1} = ' '; +0524 end +0525 end +0526 end +0527 set(gui.listbox_handles.info_cps,'String',info,'Value',[],'Max',2,'Min',0); +0528 end +0529 +0530 % update GUI data +0531 setappdata(fig,'data',data); +0532 setappdata(fig,'gui',gui); +0533 end +0534 +0535 end +0536 +0537 %------------- END OF CODE -------------- +0538 +0539 %% License: +0540 % MIT License +0541 % +0542 % Copyright (c) 2018 Thomas Hiller +0543 % +0544 % Permission is hereby granted, free of charge, to any person obtaining a copy +0545 % of this software and associated documentation files (the "Software"), to deal +0546 % in the Software without restriction, including without limitation the rights +0547 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0548 % copies of the Software, and to permit persons to whom the Software is +0549 % furnished to do so, subject to the following conditions: +0550 % +0551 % The above copyright notice and this permission notice shall be included in all +0552 % copies or substantial portions of the Software. +0553 % +0554 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0555 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0556 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0557 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0558 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0559 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0560 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/functions/inversion/fitDataFree.html b/doc/nucleus/functions/inversion/fitDataFree.html index 852332a..f4a69e7 100644 --- a/doc/nucleus/functions/inversion/fitDataFree.html +++ b/doc/nucleus/functions/inversion/fitDataFree.html @@ -180,140 +180,187 @@

    SOURCE CODE ^'off'; 0081 end 0082 -0083 % start values for E and T -0084 x0 = zeros(1,2*nExp); -0085 for i = 1:nExp -0086 x0(2*i-1) = i*max(signal)/nExp; -0087 x0(2*i) = i*max(t)/nExp; -0088 end -0089 -0090 switch parameter.optim -0091 case 'on' -0092 switch flag -0093 case 'T1' -0094 % solver options -0095 options = optimoptions('lsqcurvefit'); -0096 options.Display = parameter.info; -0097 % options.OptimalityTolerance = 1e-18; -0098 % options.StepTolerance = 1e-18; -0099 % options.MaxIterations = 1e3; -0100 [x,~,~,~,output,~,jacobian] = lsqcurvefit(@(x,t)fcn_fitFreeT1(x,t,IRfac),... -0101 x0,t,s,zeros(size(x0)),[],options); -0102 case 'T2' -0103 % solver options -0104 options = optimoptions('lsqnonlin'); -0105 options.Display = parameter.info; -0106 % options.OptimalityTolerance = 1e-18; -0107 % options.StepTolerance = 1e-18; -0108 % options.MaxIterations = 1e3; -0109 -0110 iparam.t = t; -0111 iparam.s = s; -0112 [x,~,~,~,output,~,jacobian] = lsqnonlin(@(x)fcn_fitFreeT2w(x,iparam),... -0113 x0,zeros(size(x0)),[],options); -0114 % [x,~,~,~,output,~,jacobian] = lsqcurvefit(@fcn_fitFreeT2,... -0115 % x0,t,s,zeros(size(x0)),[],options); -0116 end -0117 case 'off' -0118 % solver options -0119 options = optimset('Display',parameter.info,'MaxFunEvals',10^6,... -0120 'MaxIter',5000,'TolFun',1e-12,'TolX',1e-12); -0121 switch flag -0122 case 'T1' -0123 [x,~,~,output] = fminsearchbnd(@(x) fcn_fitFreeT1_fmin(x,t,s,IRfac),... -0124 x0,zeros(size(x0)),[],options); -0125 case 'T2' -0126 [x,~,~,output] = fminsearchbnd(@(x) fcn_fitFreeT2_fmin(x,t,s,e),... -0127 x0,zeros(size(x0)),[],options); -0128 end -0129 end -0130 -0131 % get the fit -0132 fit_t = t; -0133 switch flag -0134 case 'T1' -0135 fit_s = fcn_fitFreeT1(x,fit_t,IRfac); -0136 case 'T2' -0137 fit_s = fcn_fitFreeT2(x,fit_t); -0138 end -0139 -0140 % get residuals and error measures -0141 if isfield(parameter,'W') -0142 % when signal gating was used the error estimates need to be adjusted -0143 out = getFitErrors(signal,fit_s,parameter.noise,parameter.W); -0144 else -0145 out = getFitErrors(signal,fit_s,parameter.noise); -0146 end -0147 -0148 % get Jacobian -0149 switch parameter.optim -0150 case 'on' -0151 % nothing to do because the Optim. Toolbox gives the jacobian as -0152 % output -0153 case 'off' -0154 jacobian = getFitFreeJacobian(x,t,flag,IRfac); -0155 end -0156 -0157 % confidence interval -0158 ci = getConfInterval(out.resnorm,jacobian,0.05); -0159 -0160 % sort the relaxation times in ascending order -0161 E0 = x(1:2:end); -0162 T = x(2:2:end); -0163 [T,idx] = sort(T); -0164 E0 = E0(idx); -0165 ciT = ci(2:2:end); -0166 ciE = ci(1:2:end); -0167 ciT = ciT(idx); -0168 ciE = ciE(idx); -0169 ci(2:2:end) = ciT; -0170 ci(1:2:end) = ciE; -0171 -0172 % output struct -0173 fitdata.E0 = E0; -0174 switch flag -0175 case 'T1' -0176 fitdata.T1 = T; -0177 case 'T2' -0178 fitdata.T2 = T; -0179 end -0180 fitdata.fit_t = fit_t; -0181 fitdata.fit_s = fit_s; -0182 fitdata.resnorm = out.resnorm; -0183 fitdata.residual = out.residual; -0184 fitdata.errornorm = out.errnorm1; -0185 fitdata.rms = out.rms; -0186 fitdata.chi2 = out.chi2; -0187 fitdata.ci = ci; -0188 fitdata.x = x; -0189 fitdata.output = output; -0190 -0191 return -0192 -0193 %------------- END OF CODE -------------- -0194 -0195 %% License: -0196 % MIT License -0197 % -0198 % Copyright (c) 2018 Thomas Hiller -0199 % -0200 % Permission is hereby granted, free of charge, to any person obtaining a copy -0201 % of this software and associated documentation files (the "Software"), to deal -0202 % in the Software without restriction, including without limitation the rights -0203 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0204 % copies of the Software, and to permit persons to whom the Software is -0205 % furnished to do so, subject to the following conditions: -0206 % -0207 % The above copyright notice and this permission notice shall be included in all -0208 % copies or substantial portions of the Software. -0209 % -0210 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0211 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0212 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0213 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0214 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0215 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0216 % SOFTWARE. +0083 % check if any relaxation time is fixed +0084 if any(parameter.Tfixed_bool) +0085 +0086 % start values for E and T +0087 x0 = zeros(1,2*nExp); +0088 for i = 1:nExp +0089 x0(2*i-1) = i*max(signal)/nExp; +0090 if parameter.Tfixed_bool(i) +0091 x0(2*i) = parameter.Tfixed_val(i); +0092 else +0093 x0(2*i) = i*max(t)/nExp; +0094 end +0095 end +0096 +0097 % bounds for E and T +0098 lb = zeros(1,2*nExp); +0099 ub = zeros(1,2*nExp); +0100 for i = 1:nExp +0101 lb(2*i-1) = 0; +0102 ub(2*i-1) = 2*i*max(signal); +0103 if parameter.Tfixed_bool(i) +0104 lb(2*i) = parameter.Tfixed_val(i); +0105 ub(2*i) = parameter.Tfixed_val(i); +0106 else +0107 lb(2*i) = 0; +0108 ub(2*i) = 2*i*max(t); +0109 end +0110 end +0111 +0112 else % if not proceed with the standard version +0113 +0114 % start values for E and T +0115 x0 = zeros(1,2*nExp); +0116 for i = 1:nExp +0117 x0(2*i-1) = i*max(signal)/nExp; +0118 x0(2*i) = i*max(t)/nExp; +0119 end +0120 +0121 % bounds for E and T +0122 lb = zeros(1,2*nExp); +0123 ub = zeros(1,2*nExp); +0124 for i = 1:nExp +0125 lb(2*i-1) = 0; +0126 ub(2*i-1) = 2*i*max(signal); +0127 lb(2*i) = 0; +0128 ub(2*i) = 2*i*max(t); +0129 end +0130 end +0131 +0132 switch parameter.optim +0133 case 'on' +0134 switch flag +0135 case 'T1' +0136 % solver options +0137 options = optimoptions('lsqcurvefit'); +0138 options.Display = parameter.info; +0139 % options.OptimalityTolerance = 1e-18; +0140 % options.StepTolerance = 1e-18; +0141 % options.MaxIterations = 1e3; +0142 [x,~,~,~,output,~,jacobian] = lsqcurvefit(@(x,t)fcn_fitFreeT1(x,t,IRfac),... +0143 x0,t,s,lb,ub,options); +0144 case 'T2' +0145 % solver options +0146 options = optimoptions('lsqnonlin'); +0147 options.Display = parameter.info; +0148 % options.OptimalityTolerance = 1e-18; +0149 % options.StepTolerance = 1e-18; +0150 % options.MaxIterations = 1e3; +0151 +0152 iparam.t = t; +0153 iparam.s = s; +0154 [x,~,~,~,output,~,jacobian] = lsqnonlin(@(x)fcn_fitFreeT2w(x,iparam),... +0155 x0,lb,ub,options); +0156 % [x,~,~,~,output,~,jacobian] = lsqcurvefit(@fcn_fitFreeT2,... +0157 % x0,t,s,zeros(size(x0)),[],options); +0158 end +0159 case 'off' +0160 % solver options +0161 options = optimset('Display',parameter.info,'MaxFunEvals',10^6,... +0162 'MaxIter',5000,'TolFun',1e-12,'TolX',1e-12); +0163 switch flag +0164 case 'T1' +0165 [x,~,~,output] = fminsearchbnd(@(x) fcn_fitFreeT1_fmin(x,t,s,IRfac),... +0166 x0,lb,ub,options); +0167 case 'T2' +0168 [x,~,~,output] = fminsearchbnd(@(x) fcn_fitFreeT2_fmin(x,t,s,e),... +0169 x0,lb,ub,options); +0170 end +0171 end +0172 +0173 % get the fit +0174 fit_t = t; +0175 switch flag +0176 case 'T1' +0177 fit_s = fcn_fitFreeT1(x,fit_t,IRfac); +0178 case 'T2' +0179 fit_s = fcn_fitFreeT2(x,fit_t); +0180 end +0181 +0182 % get residuals and error measures +0183 if isfield(parameter,'W') +0184 % when signal gating was used the error estimates need to be adjusted +0185 out = getFitErrors(signal,fit_s,parameter.noise,parameter.W); +0186 else +0187 out = getFitErrors(signal,fit_s,parameter.noise); +0188 end +0189 +0190 % get Jacobian +0191 switch parameter.optim +0192 case 'on' +0193 % nothing to do because the Optim. Toolbox gives the jacobian as +0194 % output +0195 case 'off' +0196 jacobian = getFitFreeJacobian(x,t,flag,IRfac); +0197 end +0198 +0199 % confidence interval +0200 ci = getConfInterval(out.resnorm,jacobian,0.05); +0201 +0202 % sort the relaxation times in ascending order +0203 E0 = x(1:2:end); +0204 T = x(2:2:end); +0205 if any(parameter.Tfixed_bool) +0206 idx = 1:1:nExp; +0207 else +0208 [T,idx] = sort(T); +0209 end +0210 E0 = E0(idx); +0211 ciT = ci(2:2:end); +0212 ciE = ci(1:2:end); +0213 ciT = ciT(idx); +0214 ciE = ciE(idx); +0215 ci(2:2:end) = ciT; +0216 ci(1:2:end) = ciE; +0217 +0218 % output struct +0219 fitdata.E0 = E0; +0220 switch flag +0221 case 'T1' +0222 fitdata.T1 = T; +0223 case 'T2' +0224 fitdata.T2 = T; +0225 end +0226 fitdata.T = T; +0227 fitdata.fit_t = fit_t; +0228 fitdata.fit_s = fit_s; +0229 fitdata.resnorm = out.resnorm; +0230 fitdata.residual = out.residual; +0231 fitdata.errornorm = out.errnorm1; +0232 fitdata.rms = out.rms; +0233 fitdata.chi2 = out.chi2; +0234 fitdata.ci = ci; +0235 fitdata.x = x; +0236 fitdata.output = output; +0237 +0238 return +0239 +0240 %------------- END OF CODE -------------- +0241 +0242 %% License: +0243 % MIT License +0244 % +0245 % Copyright (c) 2018 Thomas Hiller +0246 % +0247 % Permission is hereby granted, free of charge, to any person obtaining a copy +0248 % of this software and associated documentation files (the "Software"), to deal +0249 % in the Software without restriction, including without limitation the rights +0250 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0251 % copies of the Software, and to permit persons to whom the Software is +0252 % furnished to do so, subject to the following conditions: +0253 % +0254 % The above copyright notice and this permission notice shall be included in all +0255 % copies or substantial portions of the Software. +0256 % +0257 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0258 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0259 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0260 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0261 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0262 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0263 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/functions/inversion/fitDataMultiModal.html b/doc/nucleus/functions/inversion/fitDataMultiModal.html index bd0ae6e..500034f 100644 --- a/doc/nucleus/functions/inversion/fitDataMultiModal.html +++ b/doc/nucleus/functions/inversion/fitDataMultiModal.html @@ -217,199 +217,201 @@

    SOURCE CODE ^if isfield(parameter,'W') -0108 param0.W = parameter.W; -0109 end -0110 % free exponential fit to get some reasonable start values -0111 invstd0 = fitDataFree(t,s,flag,param0,nModes); -0112 -0113 % start values for E and T -0114 x0 = zeros(1,3*nModes); -0115 lb = zeros(1,3*nModes); -0116 ub = zeros(1,3*nModes); -0117 for i = 1:nModes -0118 % initial values for T, sigma and E -0119 x0(3*i-2) = log(invstd0.x(2*i)); -0120 x0(3*i-1) = 1; -0121 x0(3*i) = invstd0.x(2*i-1); -0122 -0123 % lower bounds for T, sigma and E -0124 lb(3*i-2) = log(1e-6);%log(invstd0.x(2*i)*0.8);%log(invstd0.x(2*i) - 10*invstd0.ci(2*i)); -0125 lb(3*i-1) = 0.01; -0126 lb(3*i) = invstd0.x(2*i-1)*0.8;%invstd0.x(2*i-1) - 10*invstd0.ci(2*i-1); -0127 -0128 % upper bounds for T, sigma and E -0129 ub(3*i-2) = log(10);%log(invstd0.x(2*i) + 50*invstd0.ci(2*i)); -0130 ub(3*i-1) = 3.5; -0131 ub(3*i) = max(invstd0.E0)*1.1;%invstd0.x(2*i-1) + 50*invstd0.ci(2*i-1); -0132 end -0133 -0134 % switch off output if no option is given via 'parameter' -0135 if ~isfield(parameter,'info') -0136 parameter.info = 'off'; -0137 end -0138 -0139 % create the relaxation time vector -0140 T1T2me = logspace(tstart,tend,(tend-tstart)*N); -0141 -0142 % just needed for debugging the Optimization Toolbox availability -0143 % parameter.optim = 'off'; -0144 -0145 switch parameter.optim -0146 case 'on' -0147 % solver options -0148 options = optimoptions('lsqnonlin'); -0149 options.Algorithm = 'levenberg-marquardt'; -0150 options.Display = parameter.info; -0151 options.OptimalityTolerance = 1e-12; -0152 options.StepTolerance = 1e-12; -0153 -0154 iparam.optim = parameter.optim; -0155 iparam.flag = flag; -0156 iparam.T1IRfac = T1IRfac; -0157 iparam.nModes = nModes; -0158 iparam.t = t; -0159 iparam.s = s; -0160 iparam.T = T1T2me; -0161 iparam.Tb = Tb; -0162 iparam.Td = Td; -0163 [x,~,~,~,output,~,jacobian] = lsqnonlin(@(x)fcn_fitMultiModal(x,iparam),... -0164 x0,lb,ub,options); -0165 -0166 case 'off' -0167 % solver options -0168 options = optimset('Display',parameter.info,'MaxFunEvals',10^6,... -0169 'MaxIter',5000,'TolFun',1e-12,'TolX',1e-12); -0170 -0171 iparam.optim = parameter.optim; -0172 iparam.flag = flag; -0173 iparam.T1IRfac = T1IRfac; -0174 iparam.nModes = nModes; -0175 iparam.t = t; -0176 iparam.s = s; -0177 iparam.T = T1T2me; -0178 iparam.Tb = Tb; -0179 iparam.Td = Td; -0180 [x,~,~,output] = fminsearchbnd(@(x) fcn_fitMultiModal(x,iparam),... -0181 x0,lb,ub,options); -0182 -0183 % get Jacobian -0184 % therefore we need to switch the 'optim' on to get the correct -0185 % output of 'fcn_fitMultiModal' -0186 iparam.optim = 'on'; -0187 jacobian = estimateJacobian(@(x)fcn_fitMultiModal(x,iparam),x); -0188 end -0189 -0190 % assemble the final RTD -0191 Tdist = 0; -0192 for i = 1:length(x)/3 -0193 mu = exp(x(3*i-2)); % T -0194 sigma = x(3*i-1); % S -0195 amp = x(3*i); % E -0196 -0197 tmp = 1./( sigma*sqrt(2*pi)).*exp(-((log(T1T2me) - log(mu))/ sqrt(2)/sigma).^2); +0107 param0.Tfixed_bool = [0 0 0 0 0]; +0108 param0.Tfixed_val = [0 0 0 0 0]; +0109 if isfield(parameter,'W') +0110 param0.W = parameter.W; +0111 end +0112 % free exponential fit to get some reasonable start values +0113 invstd0 = fitDataFree(t,s,flag,param0,nModes); +0114 +0115 % start values for E and T +0116 x0 = zeros(1,3*nModes); +0117 lb = zeros(1,3*nModes); +0118 ub = zeros(1,3*nModes); +0119 for i = 1:nModes +0120 % initial values for T, sigma and E +0121 x0(3*i-2) = log(invstd0.x(2*i)); +0122 x0(3*i-1) = 1; +0123 x0(3*i) = invstd0.x(2*i-1); +0124 +0125 % lower bounds for T, sigma and E +0126 lb(3*i-2) = log(1e-6);%log(invstd0.x(2*i)*0.8);%log(invstd0.x(2*i) - 10*invstd0.ci(2*i)); +0127 lb(3*i-1) = 0.01; +0128 lb(3*i) = invstd0.x(2*i-1)*0.8;%invstd0.x(2*i-1) - 10*invstd0.ci(2*i-1); +0129 +0130 % upper bounds for T, sigma and E +0131 ub(3*i-2) = log(10);%log(invstd0.x(2*i) + 50*invstd0.ci(2*i)); +0132 ub(3*i-1) = 3.5; +0133 ub(3*i) = max(invstd0.E0)*1.1;%invstd0.x(2*i-1) + 50*invstd0.ci(2*i-1); +0134 end +0135 +0136 % switch off output if no option is given via 'parameter' +0137 if ~isfield(parameter,'info') +0138 parameter.info = 'off'; +0139 end +0140 +0141 % create the relaxation time vector +0142 T1T2me = logspace(tstart,tend,(tend-tstart)*N); +0143 +0144 % just needed for debugging the Optimization Toolbox availability +0145 % parameter.optim = 'off'; +0146 +0147 switch parameter.optim +0148 case 'on' +0149 % solver options +0150 options = optimoptions('lsqnonlin'); +0151 options.Algorithm = 'levenberg-marquardt'; +0152 options.Display = parameter.info; +0153 options.OptimalityTolerance = 1e-12; +0154 options.StepTolerance = 1e-12; +0155 +0156 iparam.optim = parameter.optim; +0157 iparam.flag = flag; +0158 iparam.T1IRfac = T1IRfac; +0159 iparam.nModes = nModes; +0160 iparam.t = t; +0161 iparam.s = s; +0162 iparam.T = T1T2me; +0163 iparam.Tb = Tb; +0164 iparam.Td = Td; +0165 [x,~,~,~,output,~,jacobian] = lsqnonlin(@(x)fcn_fitMultiModal(x,iparam),... +0166 x0,lb,ub,options); +0167 +0168 case 'off' +0169 % solver options +0170 options = optimset('Display',parameter.info,'MaxFunEvals',10^6,... +0171 'MaxIter',5000,'TolFun',1e-12,'TolX',1e-12); +0172 +0173 iparam.optim = parameter.optim; +0174 iparam.flag = flag; +0175 iparam.T1IRfac = T1IRfac; +0176 iparam.nModes = nModes; +0177 iparam.t = t; +0178 iparam.s = s; +0179 iparam.T = T1T2me; +0180 iparam.Tb = Tb; +0181 iparam.Td = Td; +0182 [x,~,~,output] = fminsearchbnd(@(x) fcn_fitMultiModal(x,iparam),... +0183 x0,lb,ub,options); +0184 +0185 % get Jacobian +0186 % therefore we need to switch the 'optim' on to get the correct +0187 % output of 'fcn_fitMultiModal' +0188 iparam.optim = 'on'; +0189 jacobian = estimateJacobian(@(x)fcn_fitMultiModal(x,iparam),x); +0190 end +0191 +0192 % assemble the final RTD +0193 Tdist = 0; +0194 for i = 1:length(x)/3 +0195 mu = exp(x(3*i-2)); % T +0196 sigma = x(3*i-1); % S +0197 amp = x(3*i); % E 0198 -0199 % scale to amplitude -0200 tmp = (tmp/sum(tmp)) * amp; -0201 % add the tmp per mu to Tdist -0202 Tdist = Tdist + tmp; -0203 end -0204 f = Tdist; -0205 % the fitted signal -0206 K = createKernelMatrix(t,T1T2me,Tb,Td,flag,1); -0207 si = K*f'; -0208 -0209 % get the fit -0210 fit_t = t; -0211 fit_s = si; -0212 -0213 % get residuals and error measures -0214 if isfield(parameter,'W') -0215 % when signal gating was used the error estimates need to be adjusted -0216 out = getFitErrors(signal,fit_s,parameter.noise,parameter.W); -0217 else -0218 out = getFitErrors(signal,fit_s,parameter.noise); -0219 end -0220 -0221 % confidence interval -0222 ci = getConfInterval(out.resnorm,jacobian,0.05); -0223 -0224 % sort the relaxation times in ascending order and adjust the confidence -0225 % interval accordingly -0226 T = exp(x(1:3:end)); -0227 S = x(2:3:end); -0228 E = x(3:3:end); -0229 [T,idx] = sort(T); -0230 S = S(idx); -0231 E = E(idx); -0232 ciT = ci(1:3:end); -0233 ciS = ci(2:3:end); -0234 ciE = ci(3:3:end); -0235 ciT = ciT(idx); -0236 ciS = ciS(idx); -0237 ciE = ciE(idx); -0238 ci(1:3:end) = ciT; -0239 ci(2:3:end) = ciS; -0240 ci(3:3:end) = ciE; -0241 -0242 % get "initial" value E0 -0243 switch flag -0244 case 'T1' -0245 K0 = createKernelMatrix(10*time(end),T1T2me,Tb,Td,flag,T1IRfac); -0246 case 'T2' -0247 K0 = createKernelMatrix(0,T1T2me,Tb,Td,flag,T1IRfac); -0248 end -0249 E0 = K0*f'; -0250 -0251 % output struct -0252 fitdata.fit_t = fit_t; -0253 fitdata.fit_s = fit_s; -0254 fitdata.T1T2me = T1T2me(:); -0255 fitdata.T1T2f = f(:); -0256 fitdata.Tlgm = getTLogMean(T1T2me,f); -0257 fitdata.E0 = E0; -0258 fitdata.ciE0 = NaN; -0259 fitdata.resnorm = out.resnorm; -0260 fitdata.residual = out.residual; -0261 fitdata.errornorm = out.errnorm1; -0262 fitdata.lambda_out = 0; -0263 fitdata.rms = out.rms; -0264 fitdata.chi2 = out.chi2; -0265 fitdata.ci = ci; -0266 fitdata.T = T; -0267 fitdata.S = S; -0268 fitdata.E = E; -0269 fitdata.x = x; -0270 fitdata.lb = lb; -0271 fitdata.ub = ub; -0272 fitdata.output = output; -0273 -0274 return +0199 tmp = 1./( sigma*sqrt(2*pi)).*exp(-((log(T1T2me) - log(mu))/ sqrt(2)/sigma).^2); +0200 +0201 % scale to amplitude +0202 tmp = (tmp/sum(tmp)) * amp; +0203 % add the tmp per mu to Tdist +0204 Tdist = Tdist + tmp; +0205 end +0206 f = Tdist; +0207 % the fitted signal +0208 K = createKernelMatrix(t,T1T2me,Tb,Td,flag,1); +0209 si = K*f'; +0210 +0211 % get the fit +0212 fit_t = t; +0213 fit_s = si; +0214 +0215 % get residuals and error measures +0216 if isfield(parameter,'W') +0217 % when signal gating was used the error estimates need to be adjusted +0218 out = getFitErrors(signal,fit_s,parameter.noise,parameter.W); +0219 else +0220 out = getFitErrors(signal,fit_s,parameter.noise); +0221 end +0222 +0223 % confidence interval +0224 ci = getConfInterval(out.resnorm,jacobian,0.05); +0225 +0226 % sort the relaxation times in ascending order and adjust the confidence +0227 % interval accordingly +0228 T = exp(x(1:3:end)); +0229 S = x(2:3:end); +0230 E = x(3:3:end); +0231 [T,idx] = sort(T); +0232 S = S(idx); +0233 E = E(idx); +0234 ciT = ci(1:3:end); +0235 ciS = ci(2:3:end); +0236 ciE = ci(3:3:end); +0237 ciT = ciT(idx); +0238 ciS = ciS(idx); +0239 ciE = ciE(idx); +0240 ci(1:3:end) = ciT; +0241 ci(2:3:end) = ciS; +0242 ci(3:3:end) = ciE; +0243 +0244 % get "initial" value E0 +0245 switch flag +0246 case 'T1' +0247 K0 = createKernelMatrix(10*time(end),T1T2me,Tb,Td,flag,T1IRfac); +0248 case 'T2' +0249 K0 = createKernelMatrix(0,T1T2me,Tb,Td,flag,T1IRfac); +0250 end +0251 E0 = K0*f'; +0252 +0253 % output struct +0254 fitdata.fit_t = fit_t; +0255 fitdata.fit_s = fit_s; +0256 fitdata.T1T2me = T1T2me(:); +0257 fitdata.T1T2f = f(:); +0258 fitdata.Tlgm = getTLogMean(T1T2me,f); +0259 fitdata.E0 = E0; +0260 fitdata.ciE0 = NaN; +0261 fitdata.resnorm = out.resnorm; +0262 fitdata.residual = out.residual; +0263 fitdata.errornorm = out.errnorm1; +0264 fitdata.lambda_out = 0; +0265 fitdata.rms = out.rms; +0266 fitdata.chi2 = out.chi2; +0267 fitdata.ci = ci; +0268 fitdata.T = T; +0269 fitdata.S = S; +0270 fitdata.E = E; +0271 fitdata.x = x; +0272 fitdata.lb = lb; +0273 fitdata.ub = ub; +0274 fitdata.output = output; 0275 -0276 %------------- END OF CODE -------------- +0276 return 0277 -0278 %% License: -0279 % MIT License -0280 % -0281 % Copyright (c) 2022 Thomas Hiller +0278 %------------- END OF CODE -------------- +0279 +0280 %% License: +0281 % MIT License 0282 % -0283 % Permission is hereby granted, free of charge, to any person obtaining a copy -0284 % of this software and associated documentation files (the "Software"), to deal -0285 % in the Software without restriction, including without limitation the rights -0286 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -0287 % copies of the Software, and to permit persons to whom the Software is -0288 % furnished to do so, subject to the following conditions: -0289 % -0290 % The above copyright notice and this permission notice shall be included in all -0291 % copies or substantial portions of the Software. -0292 % -0293 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -0294 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -0295 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -0296 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -0297 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -0298 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -0299 % SOFTWARE. +0283 % Copyright (c) 2022 Thomas Hiller +0284 % +0285 % Permission is hereby granted, free of charge, to any person obtaining a copy +0286 % of this software and associated documentation files (the "Software"), to deal +0287 % in the Software without restriction, including without limitation the rights +0288 % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +0289 % copies of the Software, and to permit persons to whom the Software is +0290 % furnished to do so, subject to the following conditions: +0291 % +0292 % The above copyright notice and this permission notice shall be included in all +0293 % copies or substantial portions of the Software. +0294 % +0295 % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +0296 % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +0297 % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +0298 % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +0299 % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +0300 % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +0301 % SOFTWARE.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/nucleus/functions/inversion/getConfInterval.html b/doc/nucleus/functions/inversion/getConfInterval.html index 100e87d..eecfcef 100644 --- a/doc/nucleus/functions/inversion/getConfInterval.html +++ b/doc/nucleus/functions/inversion/getConfInterval.html @@ -116,7 +116,7 @@

    SOURCE CODE ^%% degrees of freedom DOF 0041 [i,j] = size(J); -0042 deg_free = i-j; +0042 deg_free = abs(i-j); 0043 0044 %% mean squared error MSE: 0045 mse = sqrt(resnorm/deg_free); @@ -148,7 +148,7 @@

    SOURCE CODE ^if deg_free <= 1000 0072 stud_fac = getStudentInvCDF(1-alpha,deg_free); 0073 else -0074 stud_fac = NaN; +0074 stud_fac = 1;%NaN; 0075 end 0076 end 0077 diff --git a/example_data/bgr/HeliosCPMG/Gna004_15_20A_orig/Gna004_15_20A_orig.hrd b/example_data/bgr/HeliosCPMG/Gna004_15_20A_orig/Gna004_15_20A_orig.hrd new file mode 100644 index 0000000..eaf40c3 --- /dev/null +++ b/example_data/bgr/HeliosCPMG/Gna004_15_20A_orig/Gna004_15_20A_orig.hrd @@ -0,0 +1,3 @@ +26 0.0002 500 465000 128 0 50 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 50 0.8 100 0 0 0 0 0 0 3 1 0 0 0 0 0 0 0 1676027292 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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a/example_data/bgr/MouseCPMG/CPMG/10/acqu.par b/example_data/bgr/MouseCPMG/CPMG/10/acqu.par new file mode 100644 index 0000000..e867433 --- /dev/null +++ b/example_data/bgr/MouseCPMG/CPMG/10/acqu.par @@ -0,0 +1,37 @@ +90Amplitude = -7 +180Amplitude = 0 +accumulate = "yes" +acqTime = 0.016 +alpha = 0.1 +autoPhase = "yes" +autoPhase = "yes" +b1Freq = 13.24d +bandwidth = 2e+003 +dataDirectory = "C:\Costabel.S\Desktop\NMR-Mouse Data\GnaSamples2023_orig" +dwellTime = 0.5 +echoShift = 0.7 +echoTime = 68 +experiment = "CPMG" +expName = "CPMG" +expNr = 10 +filter = "no" +filterType = "sinebellsquared" +fitType = "exp" +flatFilter = "no" +incExpNr = "yes" +normalize = "no" +nrEchoes = 2000 +nrPnts = 32 +nrScans = 8 +position = [75,377] +pulseLength = 12.5 +repTime = 16000 +rxGain = 31 +rxPhase = 3 +saveData = "true" +sumEchoes = "yes" +timeMag = "no" +usePhaseCycle = "yes" +windowSize = "small" +x_maximum = 100 +x_minimum = 0.2 diff --git a/example_data/bgr/MouseCPMG/CPMG/10/data.csv 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4000 +rxGain = 31 +rxPhase = 4 +saveData = "true" +sumEchoes = "yes" +timeMag = "no" +usePhaseCycle = "yes" +windowSize = "small" +x_maximum = 100 +x_minimum = 0.2 diff --git a/example_data/bgr/MouseCPMG/CPMG/11/data.csv b/example_data/bgr/MouseCPMG/CPMG/11/data.csv new file mode 100644 index 0000000..658bec2 --- /dev/null +++ b/example_data/bgr/MouseCPMG/CPMG/11/data.csv @@ -0,0 +1,500 @@ +68,0.904671 +136,1.13246 +204,1.14088 +272,1.10487 +340,1.10046 +408,1.11865 +476,1.06737 +544,1.06453 +612,1.03796 +680,1.08972 +748,1.05525 +816,1.04441 +884,1.06198 +952,1.05133 +1020,1.05347 +1088,0.992228 +1156,1.01966 +1224,1.01425 +1292,0.99627 +1360,1.00283 +1428,0.957667 +1496,0.992358 +1564,1.0101 +1632,0.952219 +1700,0.948924 +1768,0.951205 +1836,0.939005 +1904,0.976147 +1972,0.953217 +2040,0.950168 +2108,0.932947 +2176,0.969026 +2244,0.966497 +2312,0.922206 +2380,0.89693 +2448,0.91324 +2516,0.894929 +2584,0.91726 +2652,0.948545 +2720,0.893941 +2788,0.867858 +2856,0.903905 +2924,0.911382 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"true" +sumEchoes = "yes" +timeMag = "no" +usePhaseCycle = "yes" +windowSize = "small" +x_maximum = 100 +x_minimum = 0.2 diff --git a/example_data/bgr/MouseCPMG/CPMG/12/data.csv b/example_data/bgr/MouseCPMG/CPMG/12/data.csv new file mode 100644 index 0000000..715f38e --- /dev/null +++ b/example_data/bgr/MouseCPMG/CPMG/12/data.csv @@ -0,0 +1,2000 @@ +68,2.67412 +136,3.4323 +204,3.39241 +272,3.39891 +340,3.34132 +408,3.33333 +476,3.29835 +544,3.24572 +612,3.29625 +680,3.25292 +748,3.2462 +816,3.23618 +884,3.24655 +952,3.21752 +1020,3.23975 +1088,3.17745 +1156,3.15781 +1224,3.13821 +1292,3.15703 +1360,3.15264 +1428,3.14877 +1496,3.14997 +1564,3.18078 +1632,3.13739 +1700,3.10504 +1768,3.10991 +1836,3.03936 +1904,3.03926 +1972,3.02913 +2040,3.09235 +2108,3.02442 +2176,3.04249 +2244,2.97798 +2312,2.96691 +2380,3.03365 +2448,2.93215 +2516,2.8836 +2584,2.90021 +2652,2.91154 +2720,2.92519 +2788,2.8866 +2856,2.8769 +2924,2.90198 +2992,2.83963 +3060,2.84556 +3128,2.8692 +3196,2.83446 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+autoPhase = "yes" +b1Freq = 13.24d +bandwidth = 2e+003 +dataDirectory = "C:\Costabel.S\Desktop\NMR-Mouse Data\GnaSamples2023_orig" +dwellTime = 0.5 +echoShift = 0.7 +echoTime = 68 +experiment = "CPMG" +expName = "CPMG" +expNr = 5 +filter = "no" +filterType = "sinebellsquared" +fitType = "exp" +flatFilter = "no" +incExpNr = "yes" +normalize = "no" +nrEchoes = 1000 +nrPnts = 32 +nrScans = 16 +position = [28,470] +pulseLength = 12.5 +repTime = 8000 +rxGain = 31 +rxPhase = 0 +saveData = "true" +sumEchoes = "yes" +timeMag = "no" +usePhaseCycle = "yes" +windowSize = "small" +x_maximum = 100 +x_minimum = 0.2 diff --git a/example_data/bgr/MouseCPMG/CPMG/5/data.csv b/example_data/bgr/MouseCPMG/CPMG/5/data.csv new file mode 100644 index 0000000..9c03428 --- /dev/null +++ b/example_data/bgr/MouseCPMG/CPMG/5/data.csv @@ -0,0 +1,1000 @@ +68,1.52756 +136,1.83104 +204,1.73568 +272,1.63777 +340,1.57905 +408,1.42804 +476,1.48169 +544,1.36099 +612,1.36351 +680,1.28224 +748,1.19992 +816,1.18228 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+acqTime = 0.016 +alpha = 0.1 +autoPhase = "yes" +autoPhase = "yes" +b1Freq = 13.24d +bandwidth = 2e+003 +dataDirectory = "C:\Costabel.S\Desktop\NMR-Mouse Data\GnaSamples2023_orig" +dwellTime = 0.5 +echoShift = 0.7 +echoTime = 68 +experiment = "CPMG" +expName = "CPMG" +expNr = 6 +filter = "no" +filterType = "sinebellsquared" +fitType = "exp" +flatFilter = "no" +incExpNr = "yes" +normalize = "no" +nrEchoes = 1000 +nrPnts = 32 +nrScans = 16 +position = [28,470] +pulseLength = 12.5 +repTime = 8000 +rxGain = 31 +rxPhase = 8 +saveData = "true" +sumEchoes = "yes" +timeMag = "no" +usePhaseCycle = "yes" +windowSize = "small" +x_maximum = 100 +x_minimum = 0.2 diff --git a/example_data/bgr/MouseCPMG/CPMG/6/data.csv b/example_data/bgr/MouseCPMG/CPMG/6/data.csv new file mode 100644 index 0000000..082c7e0 --- /dev/null +++ b/example_data/bgr/MouseCPMG/CPMG/6/data.csv @@ -0,0 +1,1000 @@ +68,1.37664 +136,1.69163 +204,1.62439 +272,1.53074 +340,1.43864 +408,1.397 +476,1.36283 +544,1.268 +612,1.21668 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b/example_data/bgr/MouseLift/cpmgfastautotest/11/GUI.par @@ -0,0 +1,20 @@ +maxDepth = 15000 +nrPntsRemFit = 0 +enableLift = "yes" +refSignal = 1 +refSignalCheck = "no" +nrScans = 8 +fitType = "exp" +x_minimum = 0.1 +x_maximum = 100 +alpha = 0.1 +dataDirectory = "C:\Costabel.S\Desktop\NMR-Mouse Data\GnaSamples2022" +repTime = 8000 +expName = "cpmgfastautotest" +nrEchoes = 1000 +probeHead = "PM25-10mm.par" +resolution = 200 +expNr = 11 +incExpNr = "yes" +depthList = "" +depthListValues = ["8500","7500","6500","5500","4500","3500"] diff --git a/example_data/bgr/MouseLift/cpmgfastautotest/11/T2Axis.dat b/example_data/bgr/MouseLift/cpmgfastautotest/11/T2Axis.dat new file mode 100644 index 0000000..e60076d --- /dev/null +++ b/example_data/bgr/MouseLift/cpmgfastautotest/11/T2Axis.dat @@ -0,0 +1,1000 @@ +0.0725 +0.145 +0.2175 +0.29 +0.3625 +0.435 +0.5075 +0.58 +0.6525 +0.725 +0.7975 +0.87 +0.9425 +1.015 +1.0875 +1.16 +1.2325 +1.305 +1.3775 +1.45 +1.5225 +1.595 +1.6675 +1.74 +1.8125 +1.885 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b/example_data/bgr/MouseLift/cpmgfastautotest/11/acq.par new file mode 100644 index 0000000..1149db3 --- /dev/null +++ b/example_data/bgr/MouseLift/cpmgfastautotest/11/acq.par @@ -0,0 +1,54 @@ +maxDepth = 15000 +nrPntsRemFit = 0 +enableLift = "yes" +refSignal = 1 +refSignalCheck = "no" +nrScans = 8 +fitType = "exp" +x_minimum = 0.1 +x_maximum = 100 +alpha = 0.1 +dataDirectory = "C:\Costabel.S\Desktop\NMR-Mouse Data\GnaSamples2022" +repTime = 8000 +expName = "cpmgfastautotest" +nrEchoes = 1000 +probeHead = "PM25-10mm.par" +resolution = 200 +expNr = 11 +incExpNr = "yes" +depthList = "" +Sensor = "PM25" +Probe = "1H-L" +Spacer = "PM25-10mm.par" +b1Freq = 13.24 +gradient = 300 +echoTime0 = 68 +pulseLength = 12.5 +bestResol = 50 +90Amplitude = -7 +180Amplitude = 0 +echoShift = 0.7 +rxPhase = 2 +last = 0 +accumulate = "yes" +acqTime = 0.0165 +autoPhase = "no" +bandwidth = 2000 +dwellTime = 0.5 +echoTime = 72.5 +experiment = "CPMGFast" +fitMode = "manual" +flatFilter = "no" +normalize = "no" +nrEchoesCut = 0 +nrExp = 1 +nrPnts = 33 +phaseMethod = "maxreal" +position = [198,460] +rxGain = 31 +saveData = "false" +usePhaseCycle = "yes" +windowSize = "small" +bandwidthFile = 0.5 +showFreqDomain = "no" +excecutedBackdoor = "yes" diff --git a/example_data/bgr/MouseLift/cpmgfastautotest/11/acqu.par b/example_data/bgr/MouseLift/cpmgfastautotest/11/acqu.par new file mode 100644 index 0000000..effa8b4 --- /dev/null +++ b/example_data/bgr/MouseLift/cpmgfastautotest/11/acqu.par @@ -0,0 +1,54 @@ +90Amplitude = -7 +180Amplitude = 0 +accumulate = "yes" +acqTime = 0.0165 +alpha = 0.1 +autoPhase = "no" +b1Freq = 13.24 +bandwidth = 2000 +bandwidthFile = 0.5 +bestResol = 50 +dataDirectory = "C:\Costabel.S\Desktop\NMR-Mouse Data\GnaSamples2022" +depthList = "" +dwellTime = 0.5 +echoShift = 0.7 +echoTime = 72.5 +echoTime0 = 68 +enableLift = "yes" +excecutedBackdoor = "yes" +experiment = "CPMGFast" +expName = "cpmgfastautotest" +expNr = 11 +fitMode = "manual" +fitType = "exp" +flatFilter = "no" +gradient = 300 +incExpNr = "yes" +last = 0 +maxDepth = 15000 +normalize = "no" +nrEchoes = 1000 +nrEchoesCut = 0 +nrExp = 1 +nrPnts = 33 +nrPntsRemFit = 0 +nrScans = 8 +phaseMethod = "maxreal" +position = [198,460] +Probe = "1H-L" +probeHead = "PM25-10mm.par" +pulseLength = 12.5 +refSignal = 1 +refSignalCheck = "no" +repTime = 8000 +resolution = 200 +rxGain = 31 +rxPhase = 2 +saveData = "false" +Sensor = "PM25" +showFreqDomain = "no" +Spacer = "PM25-10mm.par" +usePhaseCycle = "yes" +windowSize = "small" +x_maximum = 100 +x_minimum = 0.1 diff --git a/example_data/bgr/MouseLift/cpmgfastautotest/11/data-03500um.dat b/example_data/bgr/MouseLift/cpmgfastautotest/11/data-03500um.dat new file mode 100644 index 0000000..1297403 --- /dev/null +++ b/example_data/bgr/MouseLift/cpmgfastautotest/11/data-03500um.dat @@ -0,0 +1,1000 @@ +7.25e-005 1.67608 0.11923 +0.000145 1.96257 0.108058 +0.0002175 1.94364 0.100004 +0.00029 1.97477 0.0820685 +0.0003625 1.84699 0.0875461 +0.000435 1.87568 0.0899509 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mode 100644 index 0000000..8dbbb58 --- /dev/null +++ b/example_data/bgr/MouseLift/cpmgfastautotest/11/resultsFit.par @@ -0,0 +1,6 @@ +depth = 8500 um, E = (1.941 ± 0.009), T2 = (17.5 ± 0.1) ms +depth = 7500 um, E = (2.011 ± 0.009), T2 = (17.8 ± 0.1) ms +depth = 6500 um, E = (1.870 ± 0.009), T2 = (18.0 ± 0.1) ms +depth = 5500 um, E = (1.872 ± 0.009), T2 = (18.1 ± 0.1) ms +depth = 4500 um, E = (1.893 ± 0.009), T2 = (17.8 ± 0.1) ms +depth = 3500 um, E = (1.766 ± 0.009), T2 = (17.8 ± 0.1) ms diff --git a/example_data/bgr/MouseLift/cpmgfastautotest/6/GUI.par b/example_data/bgr/MouseLift/cpmgfastautotest/6/GUI.par new file mode 100644 index 0000000..0629c86 --- /dev/null +++ b/example_data/bgr/MouseLift/cpmgfastautotest/6/GUI.par @@ -0,0 +1,20 @@ +maxDepth = 15000 +nrPntsRemFit = 0 +enableLift = "yes" +refSignal = 1 +refSignalCheck = "no" +nrScans = 8 +fitType = "exp" +x_minimum = 0.1 +x_maximum = 100 +alpha = 0.1 +dataDirectory = "C:\Costabel.S\Desktop\NMR-Mouse Data\GnaSamples2022" +repTime = 8000 +expName = "cpmgfastautotest" +nrEchoes = 1000 +probeHead = "PM25-10mm.par" +resolution = 200 +expNr = 6 +incExpNr = "yes" +depthList = "" +depthListValues = ["8500","7500","6500","5500","4500","3500"] diff --git a/example_data/bgr/MouseLift/cpmgfastautotest/6/T2Axis.dat b/example_data/bgr/MouseLift/cpmgfastautotest/6/T2Axis.dat new file mode 100644 index 0000000..e60076d --- /dev/null +++ b/example_data/bgr/MouseLift/cpmgfastautotest/6/T2Axis.dat @@ -0,0 +1,1000 @@ +0.0725 +0.145 +0.2175 +0.29 +0.3625 +0.435 +0.5075 +0.58 +0.6525 +0.725 +0.7975 +0.87 +0.9425 +1.015 +1.0875 +1.16 +1.2325 +1.305 +1.3775 +1.45 +1.5225 +1.595 +1.6675 +1.74 +1.8125 +1.885 +1.9575 +2.03 +2.1025 +2.175 +2.2475 +2.32 +2.3925 +2.465 +2.5375 +2.61 +2.6825 +2.755 +2.8275 +2.9 +2.9725 +3.045 +3.1175 +3.19 +3.2625 +3.335 +3.4075 +3.48 +3.5525 +3.625 +3.6975 +3.77 +3.8425 +3.915 +3.9875 +4.06 +4.1325 +4.205 +4.2775 +4.35 +4.4225 +4.495 +4.5675 +4.64 +4.7125 +4.785 +4.8575 +4.93 +5.0025 +5.075 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= 0.1 +x_maximum = 100 +alpha = 0.1 +dataDirectory = "C:\Costabel.S\Desktop\NMR-Mouse Data\GnaSamples2022" +repTime = 8000 +expName = "cpmgfastautotest" +nrEchoes = 1000 +probeHead = "PM25-10mm.par" +resolution = 200 +expNr = 6 +incExpNr = "yes" +depthList = "" +Sensor = "PM25" +Probe = "1H-L" +Spacer = "PM25-10mm.par" +b1Freq = 13.24 +gradient = 300 +echoTime0 = 68 +pulseLength = 12.5 +bestResol = 50 +90Amplitude = -7 +180Amplitude = 0 +echoShift = 0.7 +rxPhase = 2 +last = 0 +accumulate = "yes" +acqTime = 0.0165 +autoPhase = "no" +bandwidth = 2000 +dwellTime = 0.5 +echoTime = 72.5 +experiment = "CPMGFast" +fitMode = "manual" +flatFilter = "no" +normalize = "no" +nrEchoesCut = 0 +nrExp = 1 +nrPnts = 33 +phaseMethod = "maxreal" +position = [198,460] +rxGain = 31 +saveData = "false" +usePhaseCycle = "yes" +windowSize = "small" +bandwidthFile = 0.5 +showFreqDomain = "no" +excecutedBackdoor = "yes" diff --git a/example_data/bgr/MouseLift/cpmgfastautotest/6/acqu.par b/example_data/bgr/MouseLift/cpmgfastautotest/6/acqu.par new file mode 100644 index 0000000..d4012e9 --- /dev/null +++ b/example_data/bgr/MouseLift/cpmgfastautotest/6/acqu.par @@ -0,0 +1,54 @@ +90Amplitude = -7 +180Amplitude = 0 +accumulate = "yes" +acqTime = 0.0165 +alpha = 0.1 +autoPhase = "no" +b1Freq = 13.24 +bandwidth = 2000 +bandwidthFile = 0.5 +bestResol = 50 +dataDirectory = "C:\Costabel.S\Desktop\NMR-Mouse Data\GnaSamples2022" +depthList = "" +dwellTime = 0.5 +echoShift = 0.7 +echoTime = 72.5 +echoTime0 = 68 +enableLift = "yes" +excecutedBackdoor = "yes" +experiment = "CPMGFast" +expName = "cpmgfastautotest" +expNr = 6 +fitMode = "manual" +fitType = "exp" +flatFilter = "no" +gradient = 300 +incExpNr = "yes" +last = 0 +maxDepth = 15000 +normalize = "no" +nrEchoes = 1000 +nrEchoesCut = 0 +nrExp = 1 +nrPnts = 33 +nrPntsRemFit = 0 +nrScans = 8 +phaseMethod = "maxreal" +position = [198,460] +Probe = "1H-L" +probeHead = "PM25-10mm.par" +pulseLength = 12.5 +refSignal = 1 +refSignalCheck = "no" +repTime = 8000 +resolution = 200 +rxGain = 31 +rxPhase = 2 +saveData = "false" +Sensor = "PM25" +showFreqDomain = "no" +Spacer = "PM25-10mm.par" +usePhaseCycle = "yes" +windowSize = "small" +x_maximum = 100 +x_minimum = 0.1 diff --git a/example_data/bgr/MouseLift/cpmgfastautotest/6/data-03500um.dat b/example_data/bgr/MouseLift/cpmgfastautotest/6/data-03500um.dat new file mode 100644 index 0000000..44a4fab --- /dev/null +++ b/example_data/bgr/MouseLift/cpmgfastautotest/6/data-03500um.dat @@ -0,0 +1,1000 @@ +7.25e-005 2.2718 0.0899843 +0.000145 3.04452 0.0624918 +0.0002175 2.99681 0.108342 +0.00029 2.86874 0.167894 +0.0003625 2.98016 0.157899 +0.000435 2.88558 0.198589 +0.0005075 2.76797 0.111832 +0.00058 2.78448 0.142176 +0.0006525 2.88877 0.113323 +0.000725 2.84583 0.0323147 +0.0007975 2.84607 0.14317 +0.00087 2.77791 0.151942 +0.0009425 2.86391 0.229768 +0.001015 2.80866 0.292982 +0.0010875 2.74947 0.0370867 +0.00116 2.82412 0.088594 +0.0012325 2.87226 0.205148 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0.334657 0.421323 0.338127 0.412927 0.383292 0.397884 0.345266 0.256129 0.390252 0.330023 0.34072 0.347212 0.391659 0.355428 0.32599 0.351015 0.2664 0.264425 0.242068 0.346373 0.338152 0.247061 0.206797 0.426992 0.23204 0.259862 0.370508 0.370037 0.278791 0.416129 0.461766 0.304522 0.358405 0.366054 0.433969 0.353224 0.254489 0.424166 0.290431 0.392878 0.432349 0.36531 0.420287 0.38943 0.344794 0.242176 0.300748 0.436286 0.264183 0.479677 0.243404 0.348285 0.374274 0.218262 diff --git a/example_data/bgr/MouseLift/cpmgfastautotest/6/resultsFit.par b/example_data/bgr/MouseLift/cpmgfastautotest/6/resultsFit.par new file mode 100644 index 0000000..4fc2bde --- /dev/null +++ b/example_data/bgr/MouseLift/cpmgfastautotest/6/resultsFit.par @@ -0,0 +1,6 @@ +depth = 8500 um, E = (2.845 ± 0.007), T2 = (31.5 ± 0.1) ms +depth = 7500 um, E = (2.829 ± 0.008), T2 = (33.4 ± 0.1) ms +depth = 6500 um, E = (2.806 ± 0.007), T2 = (34.9 ± 0.1) ms +depth = 5500 um, E = (2.818 ± 0.007), T2 = (35.3 ± 0.1) ms +depth = 4500 um, E = (2.811 ± 0.007), T2 = (34.0 ± 0.1) ms +depth = 3500 um, E = (2.754 ± 0.008), T2 = (31.5 ± 0.1) ms diff --git a/example_data/bgr/MouseLift/cpmgfastautotest/8/GUI.par b/example_data/bgr/MouseLift/cpmgfastautotest/8/GUI.par new file mode 100644 index 0000000..97f9319 --- /dev/null +++ b/example_data/bgr/MouseLift/cpmgfastautotest/8/GUI.par @@ -0,0 +1,20 @@ +maxDepth = 15000 +nrPntsRemFit = 0 +enableLift = "yes" +refSignal = 1 +refSignalCheck = "no" +nrScans = 8 +fitType = "exp" +x_minimum = 0.1 +x_maximum = 100 +alpha = 0.1 +dataDirectory = "C:\Costabel.S\Desktop\NMR-Mouse Data\GnaSamples2022" +repTime = 8000 +expName = "cpmgfastautotest" +nrEchoes = 1000 +probeHead = "PM25-10mm.par" +resolution = 200 +expNr = 8 +incExpNr = "yes" +depthList = "" +depthListValues = ["8500","7500","6500","5500","4500","3500"] diff --git a/example_data/bgr/MouseLift/cpmgfastautotest/8/T2Axis.dat b/example_data/bgr/MouseLift/cpmgfastautotest/8/T2Axis.dat new file mode 100644 index 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+70.615 +70.6875 +70.76 +70.8325 +70.905 +70.9775 +71.05 +71.1225 +71.195 +71.2675 +71.34 +71.4125 +71.485 +71.5575 +71.63 +71.7025 +71.775 +71.8475 +71.92 +71.9925 +72.065 +72.1375 +72.21 +72.2825 +72.355 +72.4275 +72.5 diff --git a/example_data/bgr/MouseLift/cpmgfastautotest/8/acq.par b/example_data/bgr/MouseLift/cpmgfastautotest/8/acq.par new file mode 100644 index 0000000..b437fdc --- /dev/null +++ b/example_data/bgr/MouseLift/cpmgfastautotest/8/acq.par @@ -0,0 +1,54 @@ +maxDepth = 15000 +nrPntsRemFit = 0 +enableLift = "yes" +refSignal = 1 +refSignalCheck = "no" +nrScans = 8 +fitType = "exp" +x_minimum = 0.1 +x_maximum = 100 +alpha = 0.1 +dataDirectory = "C:\Costabel.S\Desktop\NMR-Mouse Data\GnaSamples2022" +repTime = 8000 +expName = "cpmgfastautotest" +nrEchoes = 1000 +probeHead = "PM25-10mm.par" +resolution = 200 +expNr = 8 +incExpNr = "yes" +depthList = "" +Sensor = "PM25" +Probe = "1H-L" +Spacer = "PM25-10mm.par" +b1Freq = 13.24 +gradient = 300 +echoTime0 = 68 +pulseLength = 12.5 +bestResol = 50 +90Amplitude = -7 +180Amplitude = 0 +echoShift = 0.7 +rxPhase = 2 +last = 0 +accumulate = "yes" +acqTime = 0.0165 +autoPhase = "no" +bandwidth = 2000 +dwellTime = 0.5 +echoTime = 72.5 +experiment = "CPMGFast" +fitMode = "manual" +flatFilter = "no" +normalize = "no" +nrEchoesCut = 0 +nrExp = 1 +nrPnts = 33 +phaseMethod = "maxreal" +position = [198,460] +rxGain = 31 +saveData = "false" +usePhaseCycle = "yes" +windowSize = "small" +bandwidthFile = 0.5 +showFreqDomain = "no" +excecutedBackdoor = "yes" diff --git a/example_data/bgr/MouseLift/cpmgfastautotest/8/acqu.par b/example_data/bgr/MouseLift/cpmgfastautotest/8/acqu.par new file mode 100644 index 0000000..840b835 --- /dev/null +++ b/example_data/bgr/MouseLift/cpmgfastautotest/8/acqu.par @@ -0,0 +1,54 @@ +90Amplitude = -7 +180Amplitude = 0 +accumulate = "yes" +acqTime = 0.0165 +alpha = 0.1 +autoPhase = "no" +b1Freq = 13.24 +bandwidth = 2000 +bandwidthFile = 0.5 +bestResol = 50 +dataDirectory = "C:\Costabel.S\Desktop\NMR-Mouse Data\GnaSamples2022" +depthList = "" +dwellTime = 0.5 +echoShift = 0.7 +echoTime = 72.5 +echoTime0 = 68 +enableLift = "yes" +excecutedBackdoor = "yes" +experiment = "CPMGFast" +expName = "cpmgfastautotest" +expNr = 8 +fitMode = "manual" +fitType = "exp" +flatFilter = "no" +gradient = 300 +incExpNr = "yes" +last = 0 +maxDepth = 15000 +normalize = "no" +nrEchoes = 1000 +nrEchoesCut = 0 +nrExp = 1 +nrPnts = 33 +nrPntsRemFit = 0 +nrScans = 8 +phaseMethod = "maxreal" +position = [198,460] +Probe = "1H-L" +probeHead = "PM25-10mm.par" +pulseLength = 12.5 +refSignal = 1 +refSignalCheck = "no" +repTime = 8000 +resolution = 200 +rxGain = 31 +rxPhase = 2 +saveData = "false" +Sensor = "PM25" +showFreqDomain = "no" +Spacer = "PM25-10mm.par" +usePhaseCycle = "yes" +windowSize = "small" +x_maximum = 100 +x_minimum = 0.1 diff --git a/example_data/bgr/MouseLift/cpmgfastautotest/8/data-03500um.dat b/example_data/bgr/MouseLift/cpmgfastautotest/8/data-03500um.dat new file mode 100644 index 0000000..51801da --- /dev/null +++ b/example_data/bgr/MouseLift/cpmgfastautotest/8/data-03500um.dat @@ -0,0 +1,1000 @@ +7.25e-005 2.49068 0.174128 +0.000145 3.05982 0.174913 +0.0002175 3.02664 0.120433 +0.00029 3.08839 0.186348 +0.0003625 2.96085 0.108183 +0.000435 3.0026 0.186636 +0.0005075 3.0098 0.0434077 +0.00058 2.87628 0.101399 +0.0006525 2.90296 0.0666668 +0.000725 2.92511 0.0859471 +0.0007975 2.86324 0.246594 +0.00087 2.89134 0.179793 +0.0009425 2.92197 0.135697 +0.001015 2.8673 0.100555 +0.0010875 2.95206 0.0738437 +0.00116 2.85683 0.215147 +0.0012325 2.86628 0.108793 +0.001305 2.79626 0.104906 +0.0013775 2.8451 0.197541 +0.00145 2.7927 0.126224 +0.0015225 2.88994 0.255361 +0.001595 2.84778 0.246652 +0.0016675 2.76579 0.111907 +0.00174 2.81747 0.108221 +0.0018125 2.83331 0.14965 +0.001885 2.84755 0.0391951 +0.0019575 2.75753 0.167343 +0.00203 2.75218 0.196406 +0.0021025 2.68886 0.160471 +0.002175 2.78821 0.184256 +0.0022475 2.71483 0.127059 +0.00232 2.73955 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0.541576 0.389759 0.320742 0.40476 0.37622 0.448732 0.475089 0.404176 0.411703 0.364192 0.369389 0.39183 0.410668 0.374525 0.337989 0.423602 0.497717 0.321393 0.393592 0.392106 0.491425 0.428245 0.501951 0.353053 0.281267 diff --git a/example_data/bgr/MouseLift/cpmgfastautotest/8/resultsFit.par b/example_data/bgr/MouseLift/cpmgfastautotest/8/resultsFit.par new file mode 100644 index 0000000..87a59b0 --- /dev/null +++ b/example_data/bgr/MouseLift/cpmgfastautotest/8/resultsFit.par @@ -0,0 +1,6 @@ +depth = 8500 um, E = (2.857 ± 0.007), T2 = (32.6 ± 0.1) ms +depth = 7500 um, E = (2.865 ± 0.007), T2 = (33.2 ± 0.1) ms +depth = 6500 um, E = (2.843 ± 0.007), T2 = (33.5 ± 0.1) ms +depth = 5500 um, E = (2.865 ± 0.007), T2 = (34.8 ± 0.1) ms +depth = 4500 um, E = (2.872 ± 0.007), T2 = (35.5 ± 0.1) ms +depth = 3500 um, E = (2.813 ± 0.007), T2 = (34.0 ± 0.1) ms diff --git a/example_data/bgr/std/sample_T1.dat b/example_data/bgr/std/sample_T1.dat new file mode 100644 index 0000000..825e354 --- /dev/null +++ b/example_data/bgr/std/sample_T1.dat @@ -0,0 +1,30 @@ +0.0179527 0.0570798 0 +0.0299937 0.061475 0 +0.0424638 0.0703219 0 +0.0553947 0.0988175 0 +0.0688217 0.109881 0 +0.0827844 0.119812 0 +0.0973273 0.136375 0 +0.112501 0.154137 0 +0.128362 0.154389 0 +0.144976 0.164147 0 +0.162419 0.17181 0 +0.180777 0.187818 0 +0.20015 0.213492 0 +0.22066 0.213368 0 +0.242447 0.221974 0 +0.26568 0.235361 0 +0.290566 0.243323 0 +0.317358 0.253344 0 +0.346372 0.255927 0 +0.37801 0.271413 0 +0.412795 0.271762 0 +0.451422 0.289986 0 +0.494848 0.294341 0 +0.544435 0.298221 0 +0.602225 0.321101 0 +0.671483 0.315926 0 +0.757912 0.329307 0 +0.87294 0.322243 0 +1.04542 0.355889 0 +1.4 0.364782 0 diff --git a/example_data/bgr/std/sample_T1.par b/example_data/bgr/std/sample_T1.par new file mode 100644 index 0000000..9039795 --- /dev/null +++ b/example_data/bgr/std/sample_T1.par @@ -0,0 +1,54 @@ +90Amplitude = -7 +180Amplitude = 0 +accumulate = "yes" +acqTime = 0.0245 +b1Freq = 13.05 +bandwidth = 2000 +bandwidthFile = 0.5 +bestResol = 50 +dataDirectory = "C:\NMRMouse_data\Fe_soils_MA_Robin\FBS8510" +depthList = "" +dispRange = 0 +dwellTime = 0.5 +echoShift = 1.0 +echoTime = 101 +echoTime0 = 100 +enableLift = "yes" +excecutedBackdoor = "yes" +experiment = "T1Sat" +expName = "t1test" +expNr = 1 +fdPhaseCorr = "mag" +filter = "no" +filterType = "" +flatFilter = "no" +gradient = 273 +incExpNr = "yes" +index = "exp" +last = 0 +maxDepth = 20200 +nrEchoes = 10 +nrExp = 1 +nrPnts = 49 +nrPntsT1 = 30 +nrScans = 25 +position = [624,388] +Probe = "1H-L" +probeHead = "PM25-05mm.par" +pulseLength = 24 +refSignal = 1 +refSignalCheck = "no" +repTime = 400 +resolution = 150 +rxGain = 31 +rxPhase = 145 +saveData = "false" +Sensor = "PM25" +showFreqDomain = "no" +showTimeDomain = "yes" +Spacer = "PM25-05mm.par" +t1Est = 350 +tdPhaseCorr = "none" +tMax = 1400 +usePhaseCycle = "yes" +windowSize = "small" diff --git a/example_data/bgr/std/sample_T2.dat b/example_data/bgr/std/sample_T2.dat new file 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0.112967 -0.0046819 +0.070296 0.0923129 -0.0105118 +0.070397 0.122716 -0.00420712 +0.070498 0.117018 0.0085326 +0.070599 0.122761 0.00141434 +0.0707 0.128949 -0.00660127 diff --git a/example_data/bgr/std/sample_T2.par b/example_data/bgr/std/sample_T2.par new file mode 100644 index 0000000..c482f3c --- /dev/null +++ b/example_data/bgr/std/sample_T2.par @@ -0,0 +1,52 @@ +90Amplitude = -7 +180Amplitude = 0 +accumulate = "yes" +acqTime = 0.0245 +alpha = 1e10 +autoPhase = "no" +b1Freq = 13.05 +bandwidth = 2000 +bandwidthFile = 0.5 +bestResol = 50 +dataDirectory = "C:\NMRMouse_data\Fe_soils_MA_Robin\FBS8510" +depthList = "" +dwellTime = 0.5 +echoShift = 1.0 +echoTime = 101 +echoTime0 = 100 +enableLift = "yes" +excecutedBackdoor = "yes" +experiment = "CPMGFast" +expName = "cpmgfastauto" +expNr = 1 +fitMode = "manual" +fitType = "exp" +flatFilter = "no" +gradient = 273 +incExpNr = "yes" +last = 0 +maxDepth = 20200 +normalize = "no" +nrEchoes = 700 +nrPnts = 49 +nrPntsRemFit = 1 +nrScans = 100 +phaseMethod = "maxreal" +position = [699,169] +Probe = "1H-L" +probeHead = "PM25-05mm.par" +pulseLength = 24 +refSignal = 1 +refSignalCheck = "no" +repTime = 14000 +resolution = 150 +rxGain = 31 +rxPhase = 145 +saveData = "false" +Sensor = "PM25" +showFreqDomain = "no" +Spacer = "PM25-05mm.par" +usePhaseCycle = "yes" +windowSize = "small" +x_maximum = 10000 +x_minimum = 0.01 diff --git a/externals/GUI_Layout_Toolbox/GUI Layout Toolbox 2.3.6.mltbx b/externals/GUI_Layout_Toolbox/GUI Layout Toolbox 2.3.6.mltbx new file mode 100644 index 0000000..b77e000 Binary files /dev/null and b/externals/GUI_Layout_Toolbox/GUI Layout Toolbox 2.3.6.mltbx differ diff --git a/externals/dynamicDateTicks/dynamicDateTicks.m b/externals/dynamicDateTicks/dynamicDateTicks.m new file mode 100644 index 0000000..f4aa654 --- /dev/null +++ b/externals/dynamicDateTicks/dynamicDateTicks.m @@ -0,0 +1,163 @@ +function dynamicDateTicks(axH, link, mdformat) +% DYNAMICDATETICKS is a wrapper function around DATETICK which creates +% dynamic date tick labels for plots with dates on the X-axis. The date +% ticks intelligently include year/month/day information on specific ticks +% as appropriate. The ticks are dynamic with respect to zooming and +% panning. They update as the timescale changes (from years to seconds). +% Data tips on the plot also show intelligently as dates. +% +% The function may be used with linked axes as well as with multiple +% independent date and non-date axes within a plot. +% +% USAGE: +% dynamicDateTicks() +% makes the current axes a date axes with dynamic properties +% +% dynamicDateTicks(axH) +% makes all the axes handles in vector axH dynamic date axes +% +% dynamicDateTicks(axH, 'link') +% additionally specifies that all the axes in axH are linked. This +% option should be used in conjunction with LINKAXES. +% +% dynamicDateTicks(axH, 'link', 'dd/mm') +% additionally specifies the format of all ticks that include both +% date and month information. The default value is 'mm/dd' but any +% valid date string format can be specified. The first two options +% may be empty [] if only specifying format. +% +% EXAMPLES: +% load integersignal +% dates = datenum('July 1, 2008'):1/24:datenum('May 11, 2009 1:00 PM'); +% subplot(2,1,1), plot(dates, Signal1); +% dynamicDateTicks +% subplot(2,1,2), plot(dates, Signal4); +% dynamicDateTicks([], [], 'dd/mm'); +% +% figure +% ax1 = subplot(2,1,1); plot(dates, Signal1); +% ax2 = subplot(2,1,2); plot(dates, Signal4); +% linkaxes([ax1 ax2], 'x'); +% dynamicDateTicks([ax1 ax2], 'linked') + +if nargin < 1 || isempty(axH) % If no axes is specified, use the current axes + axH = gca; +end + +if nargin < 3 % Default mm/dd format + mdformat = 'mm/dd'; +end + +% Apply datetick to all axes in axH, and store any linking information +axesInfo.Type = 'dateaxes'; % Information stored in axes userdata indicating that these are date axes +for i = 1:length(axH) + datetick(axH(i), 'x'); + if nargin > 1 && ~isempty(link) % If axes are linked, + axesInfo.Linked = axH; % Need to modify all axes at once + else + axesInfo.Linked = axH(i); % Need to modify only 1 axes + end + axesInfo.mdformat = mdformat; % Remember mm/dd format for each axes + set(axH(i), 'UserData', axesInfo); % Store the fact that this is a date axes and its link & mm/dd information in userdata + updateDateLabel('', struct('Axes', axH(i)), 0); % Call once to ensure proper formatting +end + +% Set the zoom, pan and datacursor callbacks +figH = get(axH, 'Parent'); +if iscell(figH) + figH = unique([figH{:}]); +end +if length(figH) > 1 + error('Axes should be part of the same plot (have the same figure parent)'); +end + +z = zoom(figH); +p = pan(figH); +d = datacursormode(figH); + +set(z,'ActionPostCallback',@updateDateLabel); +set(p,'ActionPostCallback',@updateDateLabel); +set(d,'UpdateFcn',@dateTip); + +% ------------ End of dynamicDateTicks----------------------- + + + function output_txt = dateTip(gar, ev) + pos = ev.Position; + axHandle = get(ev.Target, 'Parent'); % Which axes is the data cursor on + axesInfo = get(axHandle, 'UserData'); % Get the axes info for that axes + try % If it is a date axes, create a date-friendly data tip + if strcmp(axesInfo.Type, 'dateaxes') + output_txt = sprintf('X: %s\nY: %0.4g', datestr(pos(1)), pos(2)); + else + output_txt = sprintf('X: %0.4g\nY: %0.4g', pos(1), pos(2)); + end + catch % It's not a date axes, create a generic data tip + output_txt = sprintf('X: %0.4g\nY: %0.4g', pos(1), pos(2)); + end + end + + function updateDateLabel(obj, ev, varargin) + ax1 = ev.Axes; % On which axes has the zoom/pan occurred + axesInfo = get(ev.Axes, 'UserData'); + % Check if this axes is a date axes. If not, do nothing more (return) + try + if ~strcmp(axesInfo.Type, 'dateaxes') + return; + end + catch + return; + end + + % Re-apply date ticks, but keep limits (unless called the first time) + if nargin < 3 + datetick(ax1, 'x', 'keeplimits'); + end + + + % Get the current axes ticks & labels + ticks = get(ax1, 'XTick'); + labels = get(ax1, 'XTickLabel'); + + % Sometimes the first tick can be outside axes limits. If so, remove it & its label + if all(ticks(1) < get(ax1,'xlim')) + ticks(1) = []; + labels(1,:) = []; + end + + [yr, mo, da] = datevec(ticks); % Extract year & day information (necessary for ticks on the boundary) + newlabels = cell(size(labels,1), 1); % Initialize cell array of new tick label information + + if regexpi(labels(1,:), '[a-z]{3}', 'once') % Tick format is mmm + + % Add year information to first tick & ticks where the year changes + ind = [1 find(diff(yr))+1]; + newlabels(ind) = cellstr(datestr(ticks(ind), '/yy')); + labels = strcat(labels, newlabels); + + elseif regexpi(labels(1,:), '\d\d/\d\d', 'once') % Tick format is mm/dd + + % Change mm/dd to dd/mm if necessary + labels = datestr(ticks, axesInfo.mdformat); + % Add year information to first tick & ticks where the year changes + ind = [1 find(diff(yr))+1]; + newlabels(ind) = cellstr(datestr(ticks(ind), '/yy')); + labels = strcat(labels, newlabels); + + elseif any(labels(1,:) == ':') % Tick format is HH:MM + + % Add month/day/year information to the first tick and month/day to other ticks where the day changes + ind = find(diff(da))+1; + newlabels{1} = datestr(ticks(1), [axesInfo.mdformat '/yy-']); % Add month/day/year to first tick + newlabels(ind) = cellstr(datestr(ticks(ind), [axesInfo.mdformat '-'])); % Add month/day to ticks where day changes + labels = strcat(newlabels, labels); + + end + + set(axesInfo.Linked, 'XTick', ticks, 'XTickLabel', labels); + end +end +%#ok<*CTCH> +%#ok<*ASGLU> +%#ok<*INUSL> +%#ok<*INUSD> \ No newline at end of file diff --git a/externals/dynamicDateTicks/license.txt b/externals/dynamicDateTicks/license.txt new file mode 100644 index 0000000..cae4cd5 --- /dev/null +++ b/externals/dynamicDateTicks/license.txt @@ -0,0 +1,27 @@ +Copyright (c) 2016, The MathWorks, Inc. +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in + the documentation and/or other materials provided with the distribution. + * In all cases, the software is, and all modifications and derivatives + of the software shall be, licensed to you solely for use in conjunction + with MathWorks products and service offerings. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. diff --git a/externals/dynamicDateTicks/setDateAxes.m b/externals/dynamicDateTicks/setDateAxes.m new file mode 100644 index 0000000..aea5e4b --- /dev/null +++ b/externals/dynamicDateTicks/setDateAxes.m @@ -0,0 +1,98 @@ +function varargout = setDateAxes(varargin) +% setDateAxes is a convenience function that allows you to programmatically +% set properties of axes that contain dates and automatically update the +% date ticks. This function should be used in lieu of SET for date axes. +% +% This function is intended to be used after an initial call to +% DYNAMICDATETICKS. For more information on this function please see the +% help for dynamicDateTicks +% +% The calling syntax for this function is the same as that of SET. For more +% information see the documentation for SET +% +% Example: +% load integersignal +% dates = datenum('July 1, 2008'):1/24:datenum('May 11, 2009 1:00 PM'); +% subplot(2,1,1), plot(dates, Signal1); +% dynamicDateTicks +% subplot(2,1,2), plot(dates, Signal1); +% dynamicDateTicks +% setDateAxes(gca, 'XLim', [datenum('July 1, 2008') datenum('August 1, 2008')]); + + +% Call the SET function with all inputs and outputs requested. +[varargout{1:nargout}] = set(varargin{:}); + +% At this point we could return and nothing different from calling SET +% would have occurred. + +% Since this is a date axes convenience function, we should update the +% ticks if appropriate. The updateDateLabels function will automatically +% check if the axes are date axes before making changes +if nargin == 0 + return +end +for i = 1:length(varargin{1}) + updateDateLabel([], struct('Axes',varargin{1}(i))); +end + + +% This subfunction is identical to its namesake in dynamicDateTicks +function updateDateLabel(obj, ev, varargin) %#ok +ax1 = ev.Axes; % On which axes has the zoom/pan occurred +axesInfo = get(ev.Axes, 'UserData'); +% Check if this axes is a date axes. If not, do nothing more (return) +try + if ~strcmp(axesInfo.Type, 'dateaxes') + return; + end +catch %#ok + return; +end + +% Re-apply date ticks, but keep limits (unless called the first time) +if nargin < 3 + datetick(ax1, 'x', 'keeplimits'); +end + + +% Get the current axes ticks & labels +ticks = get(ax1, 'XTick'); +labels = get(ax1, 'XTickLabel'); + +% Sometimes the first tick can be outside axes limits. If so, remove it & its label +if all(ticks(1) < get(ax1,'xlim')) + ticks(1) = []; + labels(1,:) = []; +end + +[yr, mo, da] = datevec(ticks); %#ok % Extract year & day information (necessary for ticks on the boundary) +newlabels = cell(size(labels,1), 1); % Initialize cell array of new tick label information + +if regexpi(labels(1,:), '[a-z]{3}', 'once') % Tick format is mmm + + % Add year information to first tick & ticks where the year changes + ind = [1 find(diff(yr))+1]; + newlabels(ind) = cellstr(datestr(ticks(ind), '/yy')); + labels = strcat(labels, newlabels); + +elseif regexpi(labels(1,:), '\d\d/\d\d', 'once') % Tick format is mm/dd + + % Change mm/dd to dd/mm if necessary + labels = datestr(ticks, axesInfo.mdformat); + % Add year information to first tick & ticks where the year changes + ind = [1 find(diff(yr))+1]; + newlabels(ind) = cellstr(datestr(ticks(ind), '/yy')); + labels = strcat(labels, newlabels); + +elseif any(labels(1,:) == ':') % Tick format is HH:MM + + % Add month/day/year information to the first tick and month/day to other ticks where the day changes + ind = find(diff(da))+1; + newlabels{1} = datestr(ticks(1), [axesInfo.mdformat '/yy-']); % Add month/day/year to first tick + newlabels(ind) = cellstr(datestr(ticks(ind), [axesInfo.mdformat '-'])); % Add month/day to ticks where day changes + labels = strcat(newlabels, labels); + +end + +set(axesInfo.Linked, 'XTick', ticks, 'XTickLabel', labels); diff --git a/externals/findjobj/findjobj.mltbx b/externals/findjobj/findjobj.mltbx new file mode 100644 index 0000000..66f229d Binary files /dev/null and b/externals/findjobj/findjobj.mltbx differ diff --git a/functions/import/LoadNMRData_driver.m b/functions/import/LoadNMRData_driver.m index 6bfb3f7..72e8e1a 100644 --- a/functions/import/LoadNMRData_driver.m +++ b/functions/import/LoadNMRData_driver.m @@ -51,24 +51,24 @@ out = LoadNMRData_bamtom(in); case 'bgr' out = LoadNMRData_bgr(in); - case 'MouseCPMG' - out = LoadNMRData_mousecpmg(in); case 'bgrmat' out = LoadNMRData_bgrmat(in); - case {'MouseLiftSingle','MouseLiftAll'} - out = LoadNMRData_mouselift(in); - case 'helios' - out = LoadNMRData_helios(in); case 'corelab' out = LoadNMRData_corelab(in); case 'dart' out = LoadNMRData_dart(in); case 'field' out = LoadNMRData_field(in); + case {'heliosCPMG','heliosSeries'} + out = LoadNMRData_helios(in); case 'liag' out = LoadNMRData_liag(in); case 'mouse' out = LoadNMRData_mouse(in); + case 'MouseCPMG' + out = LoadNMRData_mousecpmg(in); + case 'MouseLift' + out = LoadNMRData_mouselift(in); case 'rwth' out = LoadNMRData_rwth(in); case 'pm5' @@ -79,13 +79,16 @@ % if an imported T2 signal has no imaginary part, the noise is estimated % from an exponential fit -if ~strcmp(in.fileformat,'helios') +if ~strcmp(in.fileformat,'heliosCPMG') && ~strcmp(in.fileformat,'heliosSeries')... + && (isfield(in,'T1T2') && ~strcmp(in.T1T2,'T1')) for i = 1:numel(out.nmrData) if isreal(out.nmrData{i}.signal) disp('NUCLUESinv import: Estimating noise from exponential fit ...'); param.T1IRfac = out.nmrData{i}.T1IRfac; param.noise = 0; param.optim = 'off'; + param.Tfixed_bool = [0 0 0 0 0]; + param.Tfixed_val = [0 0 0 0 0]; invstd = fitDataFree(out.nmrData{i}.time,out.nmrData{i}.signal,... out.nmrData{i}.flag,param,5); out.nmrData{i}.noise = invstd.rms; diff --git a/functions/import/LoadNMRData_helios.m b/functions/import/LoadNMRData_helios.m index 96bb02c..f6573a7 100644 --- a/functions/import/LoadNMRData_helios.m +++ b/functions/import/LoadNMRData_helios.m @@ -1,6 +1,6 @@ function out = LoadNMRData_helios(in) -%LoadNMRData_helios loads BGR NMR data from a typical folder structure -%produced by the Helios NMR Scanner +%LoadNMRData_helios loads BGR NMR data from a typical folder structure +%produced by the Helios NMR Scanner % % Syntax: % out = LoadNMRData_helios(in) @@ -66,27 +66,50 @@ %% load NMR data file function [data,pardata] = LoadDataFile(datapath,fname,flag) -A = importdata(fullfile(datapath,fname),'\t'); +% importdata is rather slow for row data +% A = importdata(fullfile(datapath,fname),'\t'); + +% first read the file to get the number of echos +fid = fopen(fullfile(datapath,fname)); +A0 = textscan(fid,'%f','Delimiter','\n'); +fclose(fid); +% now read all three lines +fid = fopen(fullfile(datapath,fname)); +A1 = textscan(fid,'%f',A0{1}(3)); +A2 = textscan(fid,'%f',A0{1}(3)); +A3 = textscan(fid,'%f',A0{1}(3)); +fclose(fid); +% and stitch them together +A = [A1{1}';A2{1}';A3{1}']; + t_echo = A(1,2); n_echo = A(1,3); +freq = A(1,4); +Nscans = A(1,5); time = t_echo:t_echo:t_echo*n_echo; time = time(:); -re = -A(2,1:length(time)); -im = -A(3,1:length(time)); +re = A(2,1:length(time)); +im = A(3,1:length(time)); re = re(:); im = im(:); data.flag = flag; -data.time = time; -data.signal = complex(re,im); -[data.signal,data.phase] = rotateT2phase(data.signal); +data.raw.time = time; +data.raw.signal = complex(re,im); +[data.signal,data.phase] = rotateT2phase(data.raw.signal); -data.raw.time = data.time; -data.raw.signal = data.signal; +data.time = data.raw.time; -pardata.t_echo = t_echo; -pardata.n_echo = n_echo; +pardata.t_echo = t_echo; +pardata.n_echo = n_echo; +pardata.freq = freq; +pardata.Nscans = Nscans; +d{1}{1,1} = ['t_echo = ',num2str(t_echo)]; +d{1}{2,1} = ['n_echo = ',num2str(n_echo)]; +d{1}{3,1} = ['freq = ',num2str(freq)]; +d{1}{4,1} = ['Nscans = ',num2str(Nscans)]; +pardata.all = d; end %------------- END OF CODE -------------- diff --git a/functions/import/LoadNMRData_liag.m b/functions/import/LoadNMRData_liag.m index bfb981f..94a9b01 100644 --- a/functions/import/LoadNMRData_liag.m +++ b/functions/import/LoadNMRData_liag.m @@ -119,7 +119,7 @@ for i = 1:size(d{1},1) str = char(d{1}(i)); str = fixParameterString(str); - eval(['data.',str,';']); + eval(['data.',str,';']); %#ok end data.all = d; diff --git a/functions/import/LoadNMRData_mousecpmg.m b/functions/import/LoadNMRData_mousecpmg.m new file mode 100644 index 0000000..7b4c86e --- /dev/null +++ b/functions/import/LoadNMRData_mousecpmg.m @@ -0,0 +1,145 @@ +function out = LoadNMRData_mousecpmg(in) +%LoadNMRData_bgr2 loads BGR NMR data from an original folder structure as +%generated by the NMR MOUSE (the routines are also similar to +%"LoadNMRData_mouse" the only difference is the in.T1T2 input flag) +% +% Syntax: +% out = LoadNMRData_mousecpmg(in) +% +% Inputs: +% in - input structure +% in.path - data path +% in.T1T2 - T1 / T2 flag +% in.fileformat - 'mouse' +% +% Outputs: +% out - output structure +% out.parData - parameter file data +% out.nmrData - NMR data +% +% Example: +% out = LoadNMRData_mousecpmg(in) +% +% Other m-files required: +% fixParameterString +% +% Subfunctions: +% LoadDataFile +% LoadParameterFile +% +% MAT-files required: +% none +% +% See also: NUCLEUSinv +% Author: Stephan Costabel +% email: stephan.costabel[at]bgr.de +% License: MIT License (at end) + +%------------- BEGIN CODE -------------- + +%% start processing the files +% load Parameter file +[parData] = LoadParameterFile(in.path,'acqu.par'); + +% find all data files +files = dir(fullfile(in.path,'*.csv')); + +% remove not needed csv-files +files = files(~ismember({files.name},'data2.csv')); + +nmrData = cell(1,size(files,1)); +for i = 1:size(files,1) + % read the data file + data = Load_csvDataFile(in.path,files(i).name,in.T1T2); + + % get file statistics + nmrData{i}.datfile = files(i).name; + nmrData{i}.date = files(i).date; + nmrData{i}.datenum = files(i).datenum; + nmrData{i}.bytes = files(i).bytes; + + % save the NMR data + nmrData{i}.flag = data.flag; + nmrData{i}.T1IRfac = 1; + nmrData{i}.time = data.time; + nmrData{i}.signal = data.signal; + nmrData{i}.raw = data.raw; + if strcmp(in.T1T2,'T2') + %nmrData{i}.phase = data.phase; + nmrData{i}.phase = 0; + end + clear data +end + +% save data to output struct +out.parData = parData; +out.nmrData = nmrData; + +end + +%% load NMR data file +function [data] = Load_csvDataFile(datapath,fname,flag) + +d = csvread(fullfile(datapath,fname)); + +if size(d,2) == 2 + data.flag = flag; + data.time = d(:,1)/1000000; + data.signal = d(:,2); + +else + data.flag = '0'; + data.time = 0; + data.signal = 0; + data.phase = 0; +end + +data.raw.time = data.time; +data.raw.signal = data.signal; + +end + +%% load parameter file +function [data] = LoadParameterFile(datapath,fname) + +fid = fopen(fullfile(datapath,fname)); +d = textscan(fid,'%s','Delimiter','\n'); +fclose(fid); + +for i = 1:size(d{1},1) + str = char(d{1}(i)); + str = fixParameterString(str); + if strcmp(str(end),'d') + str = str(1:end-1); + %frag nich... + end + eval(['data.',str,';']); +end +data.all = d; + +end + +%------------- END OF CODE -------------- + +%% License: +% MIT License +% +% Copyright (c) 2018 Thomas Hiller +% +% Permission is hereby granted, free of charge, to any person obtaining a copy +% of this software and associated documentation files (the "Software"), to deal +% in the Software without restriction, including without limitation the rights +% to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +% copies of the Software, and to permit persons to whom the Software is +% furnished to do so, subject to the following conditions: +% +% The above copyright notice and this permission notice shall be included in all +% copies or substantial portions of the Software. +% +% THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +% IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +% FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +% AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +% LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +% OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +% SOFTWARE. diff --git a/functions/import/LoadNMRData_mouselift.m b/functions/import/LoadNMRData_mouselift.m index b7e12fd..9dec426 100644 --- a/functions/import/LoadNMRData_mouselift.m +++ b/functions/import/LoadNMRData_mouselift.m @@ -119,7 +119,7 @@ for i = 1:size(d{1},1) str = char(d{1}(i)); str = fixParameterString(str); - eval(['data.',str,';']); + eval(['data.',str,';']); %#ok end data.all = d; diff --git a/functions/import/fixParameterString.m b/functions/import/fixParameterString.m index 05b4a07..fe2e147 100644 --- a/functions/import/fixParameterString.m +++ b/functions/import/fixParameterString.m @@ -45,6 +45,11 @@ %% check for " and make it '' str = strrep(str,'"',''''); +%% check for "d" at the end of a number and delete it +if strncmpi(str,'b1Freq',6) + str = strrep(str,'d',''); +end + return %------------- END OF CODE -------------- diff --git a/functions/interface/FixedTimeView.m b/functions/interface/FixedTimeView.m new file mode 100644 index 0000000..e78db41 --- /dev/null +++ b/functions/interface/FixedTimeView.m @@ -0,0 +1,219 @@ +function FixedTimeView(src,~) +%FixedTimeView is an extra subGUI to fix certain relaxation times during +%the free inversion with #1-5 free relaxation times; thus only the +%amplitude gets fitted +% +% Syntax: +% FixedTimeView +% +% Inputs: +% src - handle of the calling object +% +% Outputs: +% none +% +% Example: +% FixedTimeView(src,~) +% +% Other m-files required: +% none +% +% Subfunctions: +% ft_closeme +% ft_updateChecked +% ft_updateEdit +% +% MAT-files required: +% none +% +% See also: NUCLEUSinv +% Author: see AUTHORS.md +% email: see AUTHORS.md +% License: MIT License (at end) + +%------------- BEGIN CODE -------------- + +%% get GUI handle and data +figh_nucleus = ancestor(src,'figure','toplevel'); +nucleus.data = getappdata(figh_nucleus,'data'); +nucleus.gui = getappdata(figh_nucleus,'gui'); +colors = nucleus.gui.myui.colors; + +%% proceed if the correct inversion type is chosen +if strcmp(nucleus.data.invstd.invtype,'mono') || strcmp(nucleus.data.invstd.invtype,'free') + + % check if the figure is already open + fig_fixedtime = findobj('Tag','FIXEDTIMEVIEW'); + % if not, create it + if isempty(fig_fixedtime) + % draw the figure on top of NUCLEUSinv + fig_fixedtime = figure('Name','NUCLEUSinv - Fix Relaxation Time',... + 'NumberTitle','off','Resize','on','ToolBar','none',... + 'CloseRequestFcn',@ft_closeme,... + 'MenuBar','none','Tag','FIXEDTIMEVIEW'); + pos0 = get(figh_nucleus,'Position'); + cent(1) = (pos0(1)+pos0(3)/2); + cent(2) = (pos0(2)+pos0(4)/2); + posf = [cent(1)-pos0(3)/6 pos0(2)+pos0(4)-pos0(4)/5 pos0(3)/3 pos0(4)/5]; +% posf = [cent(1)-pos0(3)/6 pos0(2)+pos0(4)-140 350 145]; + set(fig_fixedtime,'Position',posf); + + % create the main layout + gui.main = uix.VBox('Parent',fig_fixedtime,'BackGroundColor',colors.panelBG,'Spacing',5,'Padding',5); + gui.row1 = uicontainer('Parent',gui.main,'BackGroundColor',colors.panelBG); % check boxes + gui.row2 = uicontainer('Parent',gui.main,'BackGroundColor',colors.panelBG); % edit fields + gui.row3 = uicontainer('Parent',gui.main,'BackGroundColor',colors.panelBG); % text fields + set(gui.main,'Heights',[-1 -1 -1]); + + % horizontal boxes + gui.hbox1 = uix.HBox('Parent',gui.row1,'BackGroundColor',colors.panelBG,'Spacing',5,'Padding',5); % control elements + gui.hbox2 = uix.HBox('Parent',gui.row2,'BackGroundColor',colors.panelBG,'Spacing',5,'Padding',5); % control elements + gui.hbox3 = uix.HBox('Parent',gui.row3,'BackGroundColor',colors.panelBG,'Spacing',5,'Padding',5); % text + + % create the ui elements inside the horizontal boxes + for i = 1:5 + % check boxes + gui.check(i).fixed = uicontrol('Parent',gui.hbox1,... + 'Style','checkbox','FontSize',nucleus.gui.myui.fontsize,'Tag',num2str(i),... + 'Value',nucleus.data.invstd.Tfixed_bool(i),'String','fix it',... + 'BackGroundColor',colors.panelBG,'ForeGroundColor',colors.panelFG,... + 'Callback',@ft_updateChecked); + jh = findjobj(gui.check(i).fixed); + jh.setHorizontalAlignment(javax.swing.JLabel.CENTER); + + % edit fields + gui.edit(i).fixed = uicontrol('Parent',gui.hbox2,... + 'Style','edit','FontSize',nucleus.gui.myui.fontsize,'Tag',num2str(i),... + 'String',sprintf('%6.4f',nucleus.data.invstd.Tfixed_val(i)),... + 'BackGroundColor',colors.editBG,'ForeGroundColor',colors.panelFG,... + 'Callback',@ft_updateEdit); + + % text fields + gui.text(i).fixed = uicontrol('Parent',gui.hbox3,... + 'Style','text','FontSize',nucleus.gui.myui.fontsize,'Tag',['text',num2str(i)],... + 'HorizontalAlignment','center',... + 'BackGroundColor',colors.panelBG,'ForeGroundColor',colors.panelFG,... + 'String',['#',num2str(i)]); + end + + % store main GUI settings + gui.myui = nucleus.gui.myui; + gui.figh_nucleus = figh_nucleus; + + % save to GUI + setappdata(fig_fixedtime,'gui',gui); + end + + % if the figure is already open load the GUI data + gui = getappdata(fig_fixedtime,'gui'); + + % update all edit fields and check boxes + for i = 1:5 + set(gui.edit(i).fixed,'String',sprintf('%6.4f',nucleus.data.invstd.Tfixed_val(i))); + set(gui.check(i).fixed,'Value',nucleus.data.invstd.Tfixed_bool(i)) + + % enable only the needed ones + if i <=nucleus.data.invstd.freeDT + set(gui.check(i).fixed,'Enable','on'); + set(gui.edit(i).fixed,'Enable','on'); + else + set(gui.check(i).fixed,'Enable','off'); + set(gui.edit(i).fixed,'Enable','off'); + end + end +else + % check if the figure is already open + fig_fixedtime = findobj('Tag','FIXEDTIMEVIEW'); + if ~isempty(fig_fixedtime) + ft_closeme(fig_fixedtime) + else + helpdlg({'function: FixedTimeView',... + 'Cannot continue because wrong inversion method!'},... + 'Wrong inversion method.'); + end +end + +end + +% subfunction to update the check boxes +function ft_updateChecked(src,~) +fig_fixedtime = ancestor(src,'figure','toplevel'); +gui = getappdata(fig_fixedtime,'gui'); +data = getappdata(gui.figh_nucleus,'data'); + +id = str2double(get(src,'Tag')); +value = get(src,'Value'); + +data.invstd.Tfixed_bool(id) = value; + +% update local GUI +setappdata(fig_fixedtime,'gui',gui); + +% update NUCLEUSinv +setappdata(gui.figh_nucleus,'data',data); +end + +% subfunction to update the edit fields +function ft_updateEdit(src,~) +fig_fixedtime = ancestor(src,'figure','toplevel'); +gui = getappdata(fig_fixedtime,'gui'); +data = getappdata(gui.figh_nucleus,'data'); + +id = str2double(get(src,'Tag')); +value = str2double(get(src,'String')); + +data.invstd.Tfixed_val(id) = value; + +% update local GUI +setappdata(fig_fixedtime,'gui',gui); + +% update NUCLEUSinv +setappdata(gui.figh_nucleus,'data',data); +end + +% subfunction to update the edit fields +function ft_closeme(src,~) +fig_fixedtime = ancestor(src,'figure','toplevel'); +% try to close the sub GUI in a clean manner +try + gui = getappdata(fig_fixedtime,'gui'); + data = getappdata(gui.figh_nucleus,'data'); + % reset ui controls + data.invstd.Tfixed_bool = zeros(1,5); + data.invstd.Tfixed_val = zeros(1,5); + + % update NUCLEUSinv + setappdata(gui.figh_nucleus,'data',data); + delete(fig_fixedtime); +catch + % if this is not working: just close it + delete(fig_fixedtime); +end + + +end + +%------------- END OF CODE -------------- + +%% License: +% MIT License +% +% Copyright (c) 2023 Thomas Hiller +% +% Permission is hereby granted, free of charge, to any person obtaining a copy +% of this software and associated documentation files (the "Software"), to deal +% in the Software without restriction, including without limitation the rights +% to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +% copies of the Software, and to permit persons to whom the Software is +% furnished to do so, subject to the following conditions: +% +% The above copyright notice and this permission notice shall be included in all +% copies or substantial portions of the Software. +% +% THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +% IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +% FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +% AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +% LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +% OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +% SOFTWARE. \ No newline at end of file diff --git a/functions/interface/changeColorTheme.m b/functions/interface/changeColorTheme.m index 01dd0e8..0913571 100644 --- a/functions/interface/changeColorTheme.m +++ b/functions/interface/changeColorTheme.m @@ -185,6 +185,23 @@ function changeColorTheme(fig_tag,th) updatePlotsPSD; updatePlotsCPS; updatePlotsNMR; + + case 'FIXEDTIMEVIEW' + % set the background color for all uicontainer (HBox, VBox, etc.) + h = findall(fig,'-depth',inf,'Type','uicontainer'); + set(h,'BackGroundColor',myui.colors.panelBG); + + % chekcbox controls + h = findobj(fig,'Type','uicontrol','-and','Style','checkbox'); + set(h,'BackGroundColor',myui.colors.panelBG,'ForeGroundColor',myui.colors.panelFG); + + % edit field + h = findall(fig,'Type','uicontrol','-and','Style','edit'); + set(h,'BackGroundColor',myui.colors.editBG,'ForeGroundColor',myui.colors.panelFG); + + % text field + h = findobj(fig,'Type','uicontrol','-and','Style','text'); + set(h,'BackGroundColor',myui.colors.panelBG,'ForeGroundColor',myui.colors.panelFG); end end diff --git a/functions/interface/exportData.m b/functions/interface/exportData.m index 3f26a79..d60488a 100644 --- a/functions/interface/exportData.m +++ b/functions/interface/exportData.m @@ -6,7 +6,7 @@ function exportData(fig_tag,format) % % Inputs: % fig_tag - 'MOD' or 'INV' -% format - 'matS', 'matA', 'excelS' or 'LIAG' +% format - 'matS', 'matA', 'excelS', 'LIAG', or 'bgr_repo' % % Outputs: % none @@ -22,6 +22,7 @@ function exportData(fig_tag,format) % checkMOD % exportINV_EXCEL % exportINV_CSV +% exportINV_BGR_repos % exportMOD_EXCEL % findApproxTlgmAmplitude % @@ -130,7 +131,6 @@ function exportData(fig_tag,format) if sum([sfile spath]) > 0 exportINV_EXCEL(gui,INVdata,id,sfile,spath); end - case 'matS' % get the file name [sfile,spath] = uiputfile('*.mat',... @@ -301,6 +301,19 @@ function exportData(fig_tag,format) 'This routine works only on LIAG specific project data.'},... 'No LIAG data'); end + case 'BGR_repos' + + % get the file name + [sfile,spath] = uiputfile('*.csv',... + 'Save measurement and inversion data and parameters csv-file',... + fullfile(data.import.path,[sfilename,'.csv'])); + % if user didn't cancel + if sum([sfile spath]) > 0 + csvname = fullfile(spath,sfile); + exportINV_BGR_repos(INVdata{id},csvname); + end + + end end end @@ -549,6 +562,116 @@ function exportINV_CSV(INVdata,sfile) %write data to end of file dlmwrite(sfile,out,'-append','precision','%.5f'); +end +%% +function exportINV_BGR_repos(INVdata,sfile) +unit = INVdata.process.timescale; + +% gather all data +% raw data +tmp1(:,1) = INVdata.results.nmrraw.t(:); +header1{1} = ['time [',unit,']']; +if isreal(INVdata.results.nmrraw.s(:)) + header1{2} = 'amplitude [a.u.]'; + tmp1(:,2) = INVdata.results.nmrraw.s(:); + + b1 = {'raw data',''}; + b1(2,:) = header1; + b1(3:2+size(tmp1,1),:) = [num2cell(tmp1(:,1)),num2cell(tmp1(:,2))]; +else + header1{2} = 'real [a.u.]'; + header1{3} = 'imag [a.u.]'; + tmp1(:,2) = real(INVdata.results.nmrraw.s(:)); + tmp1(:,3) = imag(INVdata.results.nmrraw.s(:)); + + b1 = {'raw data','',''}; + b1(2,:) = header1; + b1(3:2+size(tmp1,1),:) = [num2cell(tmp1(:,1)),num2cell(tmp1(:,2)),... + num2cell(tmp1(:,3))]; +end +% proc data +tmp2(:,1) = INVdata.results.nmrproc.t(:); +tmp2(:,2) = INVdata.results.nmrproc.s(:); +header2{1} = ['time [',unit,']']; +header2{2} = 'signal [a.u.]'; + +% fit data (incl. residuals) +tmp3(:,1) = INVdata.results.invstd.fit_t(:); +tmp3(:,2) = INVdata.results.invstd.fit_s(:); +tmp3(:,3) = INVdata.results.invstd.residual(:); +header3{1} = ['time [',unit,']']; +header3{2} = 'fit [a.u.]'; +header3{3} = 'residual [-]'; + +% relaxation times +switch INVdata.invstd.invtype + case {'LU','NNLS'} + por = INVdata.invstd.porosity; + F = INVdata.results.invstd.T1T2f(:); + F = 100*por.*F./sum(F); + tmp4 = [INVdata.results.invstd.T1T2me(:)... + INVdata.results.invstd.T1T2f(:) F]; + header4 = {['relaxation times [',unit,']'],'amplitude [-]',... + 'partial water content [vol. %]'}; + + case {'mono','free'} + por = INVdata.invstd.porosity; + F = 100*por.*INVdata.results.invstd.E0./sum(INVdata.results.invstd.E0); + switch INVdata.results.nmrproc.T1T2 + case 'T1' + tmp4 = [INVdata.results.invstd.T1(:)... + INVdata.results.invstd.E0(:) F(:)]; + header4 = {['relaxation time(s) T1 [',unit,']'],... + 'amplitude [a.u.]','partial water content [vol. %]'}; + case 'T2' + tmp4 = [INVdata.results.invstd.T2(:)... + INVdata.results.invstd.E0(:) F(:)]; + header4 = {['relaxation time(s) T2 [',unit,']'],... + 'amplitude [a.u.]','partial water content [vol. %]'}; + end + + otherwise + % Nothing to do +end + +% glue together headers +cHeader = [header1 header2 header3 header4]; +% insert commas +commaHeader = [cHeader;repmat({','},1,numel(cHeader))]; +commaHeader = commaHeader(:)'; +% cHeader as string with commas +textHeader = cell2mat(commaHeader(1:numel(commaHeader)-1)); + +maxrows = max([size(tmp1,1) size(tmp2,1) size(tmp3,1) size(tmp4,1)]); +% glue together data +if size(tmp1,1) < maxrows + tmp1(end+1:maxrows,:) = NaN; +end +if size(tmp2,1) < maxrows + tmp2(end+1:maxrows,:) = NaN; +end +if size(tmp3,1) < maxrows + tmp3(end+1:maxrows,:) = NaN; +end +if size(tmp4,1) < maxrows + tmp4(end+1:maxrows,:) = NaN; +end +out(1:maxrows,1:size(tmp1,2)) = tmp1; +yi = size(tmp1,2)+1; +out(1:maxrows,yi:yi-1+size(tmp2,2)) = tmp2; +yi = yi + size(tmp2,2); +out(1:maxrows,yi:yi-1+size(tmp3,2)) = tmp3; +yi = yi + size(tmp3,2); +out(1:maxrows,yi:yi-1+size(tmp4,2)) = tmp4; + +% save data to file +%write header to file +fid = fopen(sfile,'w'); +fprintf(fid,'%s\n',textHeader); +fclose(fid); +%write data to end of file +dlmwrite(sfile,out,'-append','precision','%.5f'); + end %% diff --git a/functions/interface/getColorTheme.m b/functions/interface/getColorTheme.m index cdba4d7..8f366e0 100644 --- a/functions/interface/getColorTheme.m +++ b/functions/interface/getColorTheme.m @@ -33,7 +33,7 @@ colors.theme = th; %% switch depending on the calling figure switch fig_tag - case 'INV' + case {'INV','FIXEDTIMEVIEW'} % chose selected theme switch th case 'standard' diff --git a/functions/interface/importASCIIdata.m b/functions/interface/importASCIIdata.m index 1a9e05b..1c58c6f 100644 --- a/functions/interface/importASCIIdata.m +++ b/functions/interface/importASCIIdata.m @@ -141,7 +141,8 @@ function importASCIIdata(src) data.import.NMR.data{c}.T1IRfac = 1; data.import.NMR.data{c}.raw.time = data.import.NMR.data{c}.time; data.import.NMR.data{c}.raw.signal = data.import.NMR.data{c}.signal; - + data.import.NMR.data{c}.phase = 0; + % dummy parameter data data.import.NMR.para{c} = 0; end diff --git a/functions/interface/importINV2INV.m b/functions/interface/importINV2INV.m index fc1710a..eb70abb 100644 --- a/functions/interface/importINV2INV.m +++ b/functions/interface/importINV2INV.m @@ -97,6 +97,17 @@ function importINV2INV(src) end end end + if version_in < 114 % changes introduced with v.0.1.14 + % add 'Tfixed_bool' & 'Tfixed_val' field to savedata + savedata.data.invstd.Tfixed_bool = data.invstd.Tfixed_bool; + savedata.data.invstd.Tfixed_val = data.invstd.Tfixed_val; + for i = 1:numel(savedata.INVdata) + if isstruct(savedata.INVdata{i}) + savedata.INVdata{i}.invstd.Tfixed_bool = data.invstd.Tfixed_bool; + savedata.INVdata{i}.invstd.Tfixed_val = data.invstd.Tfixed_val; + end + end + end end % update GUI data from session mat-file diff --git a/functions/interface/importNMRdata.m b/functions/interface/importNMRdata.m index b3f19aa..799c499 100644 --- a/functions/interface/importNMRdata.m +++ b/functions/interface/importNMRdata.m @@ -56,38 +56,40 @@ function importNMRdata(src) label = get(src,'Label'); % set file format for later use - if strcmp(label,'GGE ascii') + if strcmp(label,'BAM TOM') + data.import.fileformat = 'bamtom'; + elseif strcmp(label,'BGR mat') + data.import.fileformat = 'bgrmat'; + elseif strcmp(label,'BGR std') + data.import.fileformat = 'bgr'; + elseif strcmp(label,'CoreLab ascii') + data.import.fileformat = 'corelab'; + elseif strcmp(label,'DART') + data.import.fileformat = 'dart'; + elseif strcmp(label,'GGE ascii') data.import.fileformat = 'rwth'; elseif strcmp(label,'GGE field') data.import.fileformat = 'field'; elseif strcmp(label,'GGE Dart') data.import.fileformat = 'dart'; - elseif strcmp(label,'CoreLab ascii') - data.import.fileformat = 'corelab'; - elseif strcmp(label,'DART') - data.import.fileformat = 'dart'; - elseif strcmp(label,'MOUSE') - data.import.fileformat = 'mouse'; - elseif strcmp(label,'LIAG single') + elseif strcmp(label,'HeliosCPMG') + data.import.fileformat = 'heliosCPMG'; + elseif strcmp(label,'HeliosSeries') + data.import.fileformat = 'heliosSeries'; + elseif strcmp(label,'LIAG core') data.import.fileformat = 'liag'; elseif strcmp(label,'LIAG from project') data.import.fileformat = 'liag'; elseif strcmp(label,'LIAG last project') data.import.fileformat = 'liag'; - elseif strcmp(label,'BGR std') - data.import.fileformat = 'bgr'; + elseif strcmp(label,'LIAG single') + data.import.fileformat = 'liag'; + elseif strcmp(label,'MOUSE') + data.import.fileformat = 'mouse'; elseif strcmp(label,'MouseCPMG') data.import.fileformat = 'MouseCPMG'; - elseif strcmp(label,'BGR mat') - data.import.fileformat = 'bgrmat'; - elseif strcmp(label,'MouseLiftSingle') - data.import.fileformat = 'MouseLiftSingle'; - elseif strcmp(label,'MouseLiftAll') - data.import.fileformat = 'MouseLiftAll'; - elseif strcmp(label,'Helios') - data.import.fileformat = 'helios'; - elseif strcmp(label,'BAM TOM') - data.import.fileformat = 'bamtom'; + elseif strcmp(label,'MouseLift') + data.import.fileformat = 'MouseLift'; elseif strcmp(label,'PM5') data.import.fileformat = 'pm5'; elseif strcmp(label,'PM25') @@ -119,8 +121,8 @@ function importNMRdata(src) displayStatusText(gui,'Reading NMR Data ...'); % call the corresponding subroutines switch label - case {'GGE ascii','GGE field','CoreLab ascii','BGR std',... - 'BAM TOM'} + case {'BAM TOM','BGR std','CoreLab ascii','GGE ascii',... + 'GGE field'} [data,gui] = importDataGeneral(data,gui); case 'GGE Dart' data.import.file = NMRfile; @@ -139,6 +141,8 @@ function importNMRdata(src) [data,gui] = importDataMouse(data,gui); case 'LIAG single' [data,gui] = importDataLIAG(data,gui); + case 'LIAG core' + [data,gui] = importDataLIAGcore(data,gui); case {'LIAG from project','LIAG last project'} [data,gui] = importDataLIAGproject(data,gui); % make the Petro Panel visible as default @@ -153,13 +157,14 @@ function importNMRdata(src) [data,gui] = importDataBGRmat(data,gui); case 'MouseCPMG' [data,gui] = importDataMouseCPMG(data,gui); - case 'MouseLiftSingle' - [data,gui] = importDataBGRliftSingle(data,gui); - case 'MouseLiftAll' - [data,gui] = importDataBGRliftAll(data,gui); - case 'Helios' + case 'MouseLift' + [data,gui] = importDataBGRlift(data,gui); + case 'HeliosCPMG' data.import.file = NMRfile; - [data,gui] = importDataHelios(data,gui); + [data,gui] = importDataHeliosCPMG(data,gui); + case 'HeliosSeries' + data.import.file = NMRfile; + [data,gui] = importDataHeliosSeries(data,gui); case {'PM5','PM25'} data.import.file = NMRfile; [data,gui] = importDataIBAC(data,gui); @@ -244,8 +249,7 @@ function importNMRdata(src) % show error message in case import fails errmsg = {ME.message;[ME.stack(1).name,' Line: ',num2str(ME.stack(1).line)];... 'Check File Format settings.'}; - errordlg(errmsg,'importNMRdata: Error!'); - + errordlg(errmsg,'importNMRdata: Error!'); end end @@ -257,8 +261,9 @@ function importNMRdata(src) NMRfile = -1; % for almost all import cases we load a folder ... but not for all switch label - case {'GGE ascii','GGE field','CoreLab ascii','MOUSE','LIAG single',... - 'BGR std','MouseCPMG','MouseLiftSingle','MouseLiftAll','Helios','BAM TOM','PM25'} + case {'BAM TOM','BGR std','CoreLab ascii','GGE ascii','GGE field',... + 'HeliosCPMG','HeliosSeries','LIAG core','LIAG single',... + 'MOUSE','MouseCPMG','MouseLift','PM25'} % if there is already a data folder present we start from here if isfield(import,'path') NMRpath = uigetdir(import.path,'Choose Data Path'); @@ -435,10 +440,12 @@ function importNMRdata(src) % first check whether T1 or T2 was measured... % by analyzing the name of data folder -indiz = find(data.import.path == filesep); -checkT1T2 = data.import.path(indiz(end-1)+1:indiz(end)-1); +ind = find(data.import.path == filesep); +checkT1T2 = data.import.path(ind(end-1)+1:ind(end)-1); if strcmp(checkT1T2,'t1test') in.T1T2 = 'T1'; +elseif strcmp(checkT1T2,'T1auto') + in.T1T2 = 'T1'; elseif strcmp(checkT1T2,'cpmgfastautotest') in.T1T2 = 'T2'; elseif strcmp(checkT1T2,'cpmgfastauto') @@ -483,20 +490,31 @@ function importNMRdata(src) helpdlg('No data folders in the given directory.','onMenuImport: No data.'); end - - % update the global data structure - data.import.NMR.files = fnames; - data.import.NMR.filesShort = shownames; +% update the global data structure +data.import.NMR.files = fnames; +data.import.NMR.filesShort = shownames; end %% -function [data,gui] = importDataBGRliftAll(data,gui) +function [data,gui] = importDataBGRlift(data,gui) + +% 1) show all folders and ask for sample +subdirs = dir(data.import.path); +% remove the dot-dirs +subdirs = subdirs(~ismember({subdirs.name},{'.','..'})); + +fnames = {subdirs.name}; +[indx,~] = listdlg('PromptString','Choose data set:',... + 'SelectionMode','multiple',... + 'ListString',fnames); % first check whether T1 or T2 was measured -indiz = find(data.import.path == filesep); -checkT1T2 = data.import.path(indiz(end)+1:end); +ind = find(data.import.path == filesep); +checkT1T2 = data.import.path(ind(end)+1:end); if strcmp(checkT1T2,'t1test') in.T1T2 = 'T1'; +elseif strcmp(checkT1T2,'T1auto') + in.T1T2 = 'T1'; elseif strcmp(checkT1T2,'cpmgfastautotest') in.T1T2 = 'T2'; elseif strcmp(checkT1T2,'cpmgfastauto') @@ -505,9 +523,26 @@ function importNMRdata(src) helpdlg('No original data folder','onMenuImport: No data.'); end -% there should be folders with integer values in their names -t1t2path = dir(data.import.path); -t1t2path = t1t2path(~ismember({t1t2path.name},{'.','..'})); +% now ask for stacking +answer = questdlg('Do you want to stack the slices?'); +switch answer + case 'Yes' + doSliceStack = true; + % if stacking ask for stack-rotate-order + answer = questdlg('Select stack-rotate-order:',... + 'Select order', ... + 'stack-rotate (default)','rotate-stack','Cancel','stack-rotate (default)'); + switch answer + case 'stack-rotate' + StackFirst = true; + case 'rotate-stack' + StackFirst = false; + otherwise + StackFirst = true; + end + otherwise + doSliceStack = false; +end fnames = struct; % shownames is just a dummy to hold all data file names that @@ -515,41 +550,86 @@ function importNMRdata(src) shownames = cell(1,1); c = 0; -if ~isempty(t1t2path) - for i = 1:size(t1t2path,1) - in.path = fullfile(data.import.path,t1t2path(i).name); +if ~isempty(indx) + for i = indx + in.path = fullfile(data.import.path,subdirs(i).name); in.fileformat = data.import.fileformat; out = LoadNMRData_driver(in); - - for j = 1:size(out.nmrData,2) + + if doSliceStack % the individual file names c = c + 1; fnames(c).parfile = 'acq.par'; - fnames(c).datafile = out.nmrData{j}.datfile; - - shownames{c} = [in.T1T2,'_',t1t2path(i).name,'_',fnames(c).datafile]; - - % the NMR data - % here we fix the time scale from [ms] to [s] - if max(out.nmrData{j}.time) > 100 - out.nmrData{j}.time = out.nmrData{j}.time/1000; - out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1000; + fnames(c).datafile = out.nmrData{1}.datfile; + + shownames{c} = [in.T1T2,'_',subdirs(i).name]; + + % use the meta data from the first slice + % fix the time scale from [ms] to [s] + if max(out.nmrData{1}.time) > 100 + out.nmrData{1}.time = out.nmrData{1}.time/1000; + out.nmrData{1}.raw.time = out.nmrData{1}.raw.time/1000; end - data.import.NMR.data{c} = out.nmrData{j}; + % import into GUI data struct + data.import.NMR.data{c} = out.nmrData{1}; + + % stacking + for j = 1:size(out.nmrData,2) + if j == 1 + signal = out.nmrData{j}.signal; + else + signal = signal + out.nmrData{j}.signal; + end + end + signal = signal./size(out.nmrData,2); + + % now rotate after the stacking + if StackFirst + [signal,phase] = rotateT2phase(signal); + data.import.NMR.data{c}.phase = phase; + data.import.NMR.data{c}.signal = signal; + data.import.NMR.data{c}.raw.signal = signal; + else + % no rotation after stacking + data.import.NMR.data{c}.signal = signal; + data.import.NMR.data{c}.raw.signal = signal; + end + + % parameter data data.import.NMR.para{c} = out.parData; + else + + for j = 1:size(out.nmrData,2) + % the individual file names + c = c + 1; + fnames(c).parfile = 'acq.par'; + fnames(c).datafile = out.nmrData{j}.datfile; + + shownames{c} = [in.T1T2,'_',subdirs(i).name,'_',fnames(c).datafile]; + + % the NMR data + % here we fix the time scale from [ms] to [s] + if max(out.nmrData{j}.time) > 100 + out.nmrData{j}.time = out.nmrData{j}.time/1000; + out.nmrData{j}.raw.time = out.nmrData{j}.raw.time/1000; + end + data.import.NMR.data{c} = out.nmrData{j}; + data.import.NMR.para{c} = out.parData; + end end end else helpdlg('No data folders in the given directory.','onMenuImport: No data.'); end - % update the global data structure - data.import.NMR.files = fnames; - data.import.NMR.filesShort = shownames; + +% update the global data structure +data.import.NMR.files = fnames; +data.import.NMR.filesShort = shownames; end %% -function [data,gui] = importDataHelios(data,gui) +function [data,gui] = importDataHeliosCPMG(data,gui) % first check the subpaths % there should be some folders with names ... @@ -571,28 +651,75 @@ function importNMRdata(src) content = dir([data.import.path,filesep,datpath(i).name]); content = content(~ismember({content.name},{'.','..'})); for j = 1:size(content,1) - if strcmp(content(j).name,[datpath(i).name,'_1.hrd']) - in.T1T2 = 'T2'; - in.name = content(j).name; - in.path = fullfile(data.import.path,filesep,datpath(i).name); - in.fileformat = data.import.fileformat; - out = LoadNMRData_driver(in); - - % the individual file names - c = c + 1; - fnames(c).parfile = ''; - fnames(c).datafile = out.nmrData.datfile; - fnames(c).T2specfile = ''; - shownames{c} = ['T2_',datpath(i).name]; - - data.import.NMR.data{c} = out.nmrData; - data.import.NMR.para{c} = out.parData; + if strcmp(content(j).name,[datpath(i).name,'.hrd']) + if ~strcmp(content(j).name,[datpath(i).name,'_ref']) + in.T1T2 = 'T2'; + in.name = content(j).name; + in.path = fullfile(data.import.path,filesep,datpath(i).name); + in.fileformat = data.import.fileformat; + out = LoadNMRData_driver(in); + + % the individual file names + c = c + 1; + fnames(c).parfile = ''; + fnames(c).datafile = out.nmrData.datfile; + fnames(c).T2specfile = ''; + shownames{c} = ['T2_',datpath(i).name]; + + data.import.NMR.data{c} = out.nmrData; + data.import.NMR.para{c} = out.parData; + end end end end end end +% update the global data structure +data.import.NMR.files = fnames; +data.import.NMR.filesShort = shownames; + +end + +%% +function [data,gui] = importDataHeliosSeries(data,gui) + +% first check the subpaths +% there should be some folders with names ... +% ... similar to the data filenames inside them +datpath = dir(data.import.path); +datpath = datpath(~ismember({datpath.name},{'.','..'})); + +fnames = struct; +% shownames is just a dummy to hold all data file names that +% will be shown in the listbox +shownames = cell(1,1); + +c = 0; +if ~isempty(datpath) + content = datpath; + for j = 1:size(content,1) + if ~strcmp(content(j).name(end-7:end),'_ref.hrd') + in.T1T2 = 'T2'; + in.name = content(j).name; + in.path = fullfile(data.import.path); + in.fileformat = data.import.fileformat; + out = LoadNMRData_driver(in); + % the individual file names + c = c + 1; + fnames(c).parfile = ''; + fnames(c).datafile = out.nmrData.datfile; + fnames(c).T2specfile = ''; + shownames{c} = ['T2_',content(j).name]; + + data.import.NMR.data{c} = out.nmrData; + data.import.NMR.para{c} = out.parData; + end + + end +end + +% update the global data structure data.import.NMR.files = fnames; data.import.NMR.filesShort = shownames; @@ -632,6 +759,7 @@ function importNMRdata(src) data.import.NMR.para{c} = out.parData{j}; end +% update the global data structure data.import.NMR.files = fnames; data.import.NMR.filesShort = shownames; @@ -812,6 +940,166 @@ function importNMRdata(src) end +%% +function [data,gui] = importDataLIAGcore(data,gui) + +% get all subfolders containing a measurement at a certain heigth +subdirs = dir(data.import.path); +% remove the dot-dirs +subdirs = subdirs(~ismember({subdirs.name},{'.','..'})); + +% now get the background data ("Leermessung") +bgPath = uigetdir(data.import.path,'Choose Background Data Path'); +isbgPath = false; +if bgPath == 0 + disp('NUCLEUSinv: LIAG core import: No background file provided.'); +else + isbgPath = true; + in.path = fullfile(bgPath); + in.fileformat = data.import.fileformat; + bgout = LoadNMRData_driver(in); + ref1.t = bgout.nmrData{1}.time; + ref1.s = bgout.nmrData{1}.signal; + [ref1.s,~] = rotateT2phase(ref1.s); +end + +% get the Position file +[posFile,posFilePath] = uigetfile('*.*','Choose Lift Position File',data.import.path); +isposFile = false; +if posFilePath == 0 + disp('NUCLEUSinv: LIAG core import: No position file provided.'); +else + isposFile = true; + % import LIAG lift file + buffer = fileread(fullfile(posFilePath,posFile)); + + % get the time stamps of the lift positions + substr = 'Zeit:' ; + loc = strfind(buffer, substr); + timepoint = cell(1,1); + for i = 1:length(loc) + timestr = strtrim(buffer(loc(i)+numel(substr):loc(i)+numel(substr)+19)); + timepoint{i} = datetime(timestr,'InputFormat','dd.MM.yyyy HH:mm:ss'); + end + % ignore the first time stamp + t_range = [datenum(timepoint{2}), datenum(timepoint{3})]; + % get the z coords + substr = 'Z1='; + loc = strfind(buffer, substr) ; + z_range(1) = sscanf(buffer(loc+numel(substr):loc+numel(substr)+10),'%f',1); + substr = 'Z2='; + loc = strfind(buffer, substr) ; + z_range(2) = sscanf(buffer(loc+numel(substr):loc+numel(substr)+10),'%f',1); +end + +% import the NMR data +count = 0; +levels = zeros(size(subdirs)); +nmrDataTMP = cell(1,1); +for i = 1:numel(subdirs) + if ~isnan(str2double(subdirs(i).name)) + + % import the NMR file + in.path = fullfile(data.import.path,subdirs(i).name,'T2CPMG'); + in.fileformat = data.import.fileformat; + out = LoadNMRData_driver(in); + + % if there is a position file + if isposFile + % keep only files within the correct time range + if out.nmrData{1}.datenum > t_range(1) && out.nmrData{1}.datenum < t_range(2) + count = count + 1; + % interpolate the z position via the time stamp of the NMR file + levels(count) = interp1(t_range,z_range,out.nmrData{1}.datenum,'linear'); + nmrDataTMP{count} = out; + end + else % just read everything + count = count + 1; + levels(count) = str2double(subdirs(i).name); + nmrDataTMP{count} = out; + end + end +end +% cut off data that is not part of the scan +levels = levels(1:count); +% sort in ascending order +[levels,idx] = sort(levels); + +% sort the NMR data accordingly +fnames = struct; +% shownames is just a dummy to hold all data file names that +% will be shown in the listbox +shownames = cell(1,1); +for c = 1:numel(levels) + % the individual file names + fnames(c).parfile = 'acqu.par'; + fnames(c).datafile = nmrDataTMP{idx(c)}.nmrData{1}.datfile; + fnames(c).T2specfile = ''; + + shownames{c} = fnames(c).datafile; + tmp = shownames{c}; + if isposFile + shownames{c} = [tmp,': ',sprintf('%4d',floor(levels(c))),'mm']; + else + shownames{c} = [tmp,' level:',sprintf('%d',levels(c))]; + end + out = nmrDataTMP{idx(c)}; + + % the NMR data + % here we fix the time scale to [s] if neccessary + TE = out.parData.echoTime; % [µs] + if out.nmrData{1}.time(1) == TE/1e3 + % change [ms] to [s] + out.nmrData{1}.time = out.nmrData{1}.time/1e3; + out.nmrData{1}.raw.time = out.nmrData{1}.raw.time/1e3; + elseif out.nmrData{1}.time(1) == TE + % change [µs] to [s] -> very unlikely + out.nmrData{1}.time = out.nmrData{1}.time/1e6; + out.nmrData{1}.raw.time = out.nmrData{1}.raw.time/1e6; + end + data.import.NMR.data{c} = out.nmrData{1}; + data.import.NMR.para{c} = out.parData; + + % subtract the background signal is one is available + if isbgPath + % get the original signal + s = data.import.NMR.data{c}.signal; + % if the background signal is longer than the signal cut it, if + % not extend it with zeros + if numel(ref1.s) > numel(s) + tmp_r = ref1.s(1:numel(s)); + else + tmp_r = zeros(size(s)); + tmp_r(1:numel(ref1.s)) = ref1.s; + end + s = complex(real(s)-real(tmp_r),imag(s)-imag(tmp_r)); + + % sign check + if real(s(1:3))<0 + s = s*-1; + end + + % rotate phase again - TEST + [s,~] = rotateT2phase(s); + + % update signal + data.import.NMR.data{c}.signal = s; + data.import.NMR.data{c}.raw.signal = s; + end +end +if isposFile + data.import.LIAGCORE.use_z = true; +else + data.import.LIAGCORE.use_z = false; +end +data.import.LIAGCORE.zslice = levels; + +% update the global data structure +data.import.NMR.files = fnames; +data.import.NMR.filesShort = shownames; + +end + %% function [data,gui] = importDataLIAGproject(data,gui) @@ -1087,7 +1375,6 @@ function importNMRdata(src) % update the global data structure data.import.NMR.files = ffnames; data.import.NMR.filesShort = shownames; - end end @@ -1196,7 +1483,7 @@ function importNMRdata(src) for i = 1:size(d{1},1) str = char(d{1}(i)); str = fixParameterString(str); - eval(['data.',str,';']); + eval(['data.',str,';']); %#ok end end diff --git a/functions/interface/runInversionBatch.m b/functions/interface/runInversionBatch.m index 34853b5..92141cc 100644 --- a/functions/interface/runInversionBatch.m +++ b/functions/interface/runInversionBatch.m @@ -108,24 +108,31 @@ param.T1IRfac = data.results.nmrproc.T1IRfac; param.noise = data.results.nmrproc.noise; param.optim = data.info.has_optim; + param.Tfixed_bool = data.invstd.Tfixed_bool; + param.Tfixed_val = data.invstd.Tfixed_val; if isfield(data.results.nmrproc,'W') param.W = data.results.nmrproc.W; end invstd = fitDataFree(data.results.nmrproc.t,... data.results.nmrproc.s,flag,param,1); + data.invstd.Tfixed_val = [invstd.T zeros(1,4)]; case 'free' flag = data.results.nmrproc.T1T2; param.T1IRfac = data.results.nmrproc.T1IRfac; param.noise = data.results.nmrproc.noise; param.optim = data.info.has_optim; + param.Tfixed_bool = data.invstd.Tfixed_bool; + param.Tfixed_val = data.invstd.Tfixed_val; if isfield(data.results.nmrproc,'W') param.W = data.results.nmrproc.W; end invstd = fitDataFree(data.results.nmrproc.t,... data.results.nmrproc.s,flag,param,data.invstd.freeDT); + data.invstd.Tfixed_val = [invstd.T(1:data.invstd.freeDT)... + zeros(1,5-data.invstd.freeDT)]; case 'LU' param.T1T2 = data.results.nmrproc.T1T2; diff --git a/functions/interface/runInversionStd.m b/functions/interface/runInversionStd.m index 9bdcf51..702e0f1 100644 --- a/functions/interface/runInversionStd.m +++ b/functions/interface/runInversionStd.m @@ -198,6 +198,8 @@ param.T1IRfac = data.results.nmrproc.T1IRfac; param.noise = data.results.nmrproc.noise; param.optim = data.info.has_optim; + param.Tfixed_bool = data.invstd.Tfixed_bool; + param.Tfixed_val = data.invstd.Tfixed_val; if isfield(data.results.nmrproc,'W') param.W = data.results.nmrproc.W; end @@ -211,12 +213,15 @@ displayStatusText(gui,infostring); invstd = fitDataFree(data.results.nmrproc.t,... data.results.nmrproc.s,flag,param,1); + data.invstd.Tfixed_val = [invstd.T zeros(1,4)]; case 'free' % N free single-exponential inversion flag = data.results.nmrproc.T1T2; param.T1IRfac = data.results.nmrproc.T1IRfac; param.noise = data.results.nmrproc.noise; param.optim = data.info.has_optim; + param.Tfixed_bool = data.invstd.Tfixed_bool; + param.Tfixed_val = data.invstd.Tfixed_val; if isfield(data.results.nmrproc,'W') param.W = data.results.nmrproc.W; end @@ -230,6 +235,8 @@ displayStatusText(gui,infostring); invstd = fitDataFree(data.results.nmrproc.t,... data.results.nmrproc.s,flag,param,data.invstd.freeDT); + data.invstd.Tfixed_val = [invstd.T(1:data.invstd.freeDT)... + zeros(1,5-data.invstd.freeDT)]; case 'LU' % multi-exponential inversion % general parameter @@ -411,6 +418,9 @@ if ~isempty(findobj('Tag','FITSTATS')) showFitStatistics; end + if ~isempty(findobj('Tag','FIXEDTIMEVIEW')) + FixedTimeView(gui.menu.extra_fixedtime); + end NUCLEUSinv_updateInterface; else helpdlg('Cannot start inversion because no data set is selected!',... diff --git a/functions/interface/showExtraGraphics.m b/functions/interface/showExtraGraphics.m index 3a64831..180680a 100644 --- a/functions/interface/showExtraGraphics.m +++ b/functions/interface/showExtraGraphics.m @@ -32,7 +32,7 @@ function showExtraGraphics(method) %% get GUI handle and data fig = findobj('Tag','INV'); -fig_tag = get(fig,'Tag'); +% fig_tag = get(fig,'Tag'); data = getappdata(fig,'data'); INVdata = getappdata(fig,'INVdata'); gui = getappdata(fig,'gui'); @@ -128,6 +128,7 @@ function showExtraGraphics(method) if data.import.BAM.use_z xval = data.import.BAM.zslice; xlabelstr = 'position'; + ylabelstr = 'position [µm]'; else xlabelstr = 'date' ; end @@ -135,9 +136,19 @@ function showExtraGraphics(method) if data.import.IBAC.use_z xval = data.import.IBAC.zslice; xlabelstr = 'position'; + ylabelstr = 'position [µm]'; else xlabelstr = 'date' ; end + elseif isfield(data.import,'LIAGCORE') + xval = data.import.LIAGCORE.zslice; + if data.import.LIAGCORE.use_z + xlabelstr = 'position [mm]'; + ylabelstr = 'position [mm]'; + else + xlabelstr = 'level'; + ylabelstr = 'level'; + end else xlabelstr = 'date' ; end @@ -254,7 +265,7 @@ function showExtraGraphics(method) cmap = jet; cmap = flipud(cmap); colormap(ax,cmap); xlabel(['relaxation time [',timescale,']']); - ylabel('position [µm]'); + ylabel(ylabelstr); cb = colorbar; set(get(cb,'YLabel'),'String','norm. amplitude'); @@ -263,6 +274,9 @@ function showExtraGraphics(method) gui.cm_handles.axes_proc_xaxis = uimenu(axes_cm,... 'Label','flip y-axis','Tag','flip','Enable','on',... 'Callback',@onContextFlip); + gui.cm_handles.axes_proc_xaxis2 = uimenu(axes_cm,... + 'Label','color scale log/lin','Tag','loglin','Enable','on',... + 'Callback',@onContextFlip); set(ax,'UIContextMenu',axes_cm); end @@ -290,13 +304,25 @@ function showExtraGraphics(method) function onContextFlip(src,~) f = ancestor(src,'Figure','toplevel'); ax = findobj(f,'Type','Axes'); +tag = get(src,'Tag'); -direction = get(ax,'Ydir'); -switch direction - case 'normal' - set(ax,'Ydir','reverse') - case 'reverse' - set(ax,'Ydir','normal') +switch tag + case 'loglin' + isscale = get(ax,'ColorScale'); + switch isscale + case 'log' + set(ax,'ColorScale','lin','CLim',[0 1]); + case 'linear' + set(ax,'ColorScale','log','CLim',[0.01 1]); + end + case 'flip' + direction = get(ax,'Ydir'); + switch direction + case 'normal' + set(ax,'Ydir','reverse') + case 'reverse' + set(ax,'Ydir','normal') + end end end diff --git a/functions/interface/uncheckImportMenus.m b/functions/interface/uncheckImportMenus.m index cd541f0..606d8cb 100644 --- a/functions/interface/uncheckImportMenus.m +++ b/functions/interface/uncheckImportMenus.m @@ -47,9 +47,9 @@ set(gui.menu.file_import_lab_bgr_std,'Checked','off'); set(gui.menu.file_import_lab_bgr_mat,'Checked','off'); set(gui.menu.file_import_lab_bgr_mouse_cpmg,'Checked','off'); -set(gui.menu.file_import_lab_bgr_mouse_liftsingle,'Checked','off'); -set(gui.menu.file_import_lab_bgr_mouse_liftall,'Checked','off'); -set(gui.menu.file_import_lab_bgr_helios,'Checked','off'); +set(gui.menu.file_import_lab_bgr_mouse_lift,'Checked','off'); +set(gui.menu.file_import_lab_bgr_helios_cpmg,'Checked','off'); +set(gui.menu.file_import_lab_bgr_helios_series,'Checked','off'); set(gui.menu.file_import_lab_bam_tom,'Checked','off'); set(gui.menu.file_import_lab_ascii_T1,'Checked','off'); set(gui.menu.file_import_lab_ascii_T2,'Checked','off'); diff --git a/functions/interface/updateInfo.m b/functions/interface/updateInfo.m index 344bc19..d15d8be 100644 --- a/functions/interface/updateInfo.m +++ b/functions/interface/updateInfo.m @@ -315,14 +315,22 @@ function updateInfo(src,~) %#ok info{end+1,1} = invtype; info{end+1,1} = ' '; ciT = sum(full(invstd.ci(2:2:end))); - + + if data.invstd.Tfixed_bool(1) + col = gui.myui.colors.listINV.*255; + else + col = [1 1 1].*255; + end + switch nmrproc.T1T2 case 'T1' - info{end+1,1} = ['T1 = ',... + info{end+1,1} = ['T1 = ',... sprintf('%5.4f',invstd.T1),... ' ∓ (',sprintf('%5.4f',ciT),')','']; case 'T2' - info{end+1,1} = ['T2 = ',... + info{end+1,1} = ['T2 = ',... sprintf('%5.4f',invstd.T2),... ' ∓ (',sprintf('%5.4f',ciT),')','']; end @@ -345,7 +353,15 @@ function updateInfo(src,~) %#ok end for i = 1:length(T) - info{end+1,1} = ['T(',num2str(i),') = ',sprintf('%5.4f',T(i)),... + + if data.invstd.Tfixed_bool(i) + col = gui.myui.colors.listINV.*255; + else + col = [1 1 1].*255; + end + + info{end+1,1} = ['T(',num2str(i),') = ',sprintf('%5.4f',T(i)),... ' ∓ (',sprintf('%5.4f',ciT(i)),')','']; %#ok<*AGROW> info{end+1,1} = ['E(',num2str(i),') = ',sprintf('%5.4f',E0(i)),... ' ∓ (',sprintf('%5.4f',ciE0(i)),')','']; diff --git a/functions/inversion/fitDataFree.m b/functions/inversion/fitDataFree.m index 0f96ba4..449a19e 100644 --- a/functions/inversion/fitDataFree.m +++ b/functions/inversion/fitDataFree.m @@ -80,11 +80,53 @@ parameter.info = 'off'; end -% start values for E and T -x0 = zeros(1,2*nExp); -for i = 1:nExp - x0(2*i-1) = i*max(signal)/nExp; - x0(2*i) = i*max(t)/nExp; +% check if any relaxation time is fixed +if any(parameter.Tfixed_bool) + + % start values for E and T + x0 = zeros(1,2*nExp); + for i = 1:nExp + x0(2*i-1) = i*max(signal)/nExp; + if parameter.Tfixed_bool(i) + x0(2*i) = parameter.Tfixed_val(i); + else + x0(2*i) = i*max(t)/nExp; + end + end + + % bounds for E and T + lb = zeros(1,2*nExp); + ub = zeros(1,2*nExp); + for i = 1:nExp + lb(2*i-1) = 0; + ub(2*i-1) = 2*i*max(signal); + if parameter.Tfixed_bool(i) + lb(2*i) = parameter.Tfixed_val(i); + ub(2*i) = parameter.Tfixed_val(i); + else + lb(2*i) = 0; + ub(2*i) = 2*i*max(t); + end + end + +else % if not proceed with the standard version + + % start values for E and T + x0 = zeros(1,2*nExp); + for i = 1:nExp + x0(2*i-1) = i*max(signal)/nExp; + x0(2*i) = i*max(t)/nExp; + end + + % bounds for E and T + lb = zeros(1,2*nExp); + ub = zeros(1,2*nExp); + for i = 1:nExp + lb(2*i-1) = 0; + ub(2*i-1) = 2*i*max(signal); + lb(2*i) = 0; + ub(2*i) = 2*i*max(t); + end end switch parameter.optim @@ -98,7 +140,7 @@ % options.StepTolerance = 1e-18; % options.MaxIterations = 1e3; [x,~,~,~,output,~,jacobian] = lsqcurvefit(@(x,t)fcn_fitFreeT1(x,t,IRfac),... - x0,t,s,zeros(size(x0)),[],options); + x0,t,s,lb,ub,options); case 'T2' % solver options options = optimoptions('lsqnonlin'); @@ -110,7 +152,7 @@ iparam.t = t; iparam.s = s; [x,~,~,~,output,~,jacobian] = lsqnonlin(@(x)fcn_fitFreeT2w(x,iparam),... - x0,zeros(size(x0)),[],options); + x0,lb,ub,options); % [x,~,~,~,output,~,jacobian] = lsqcurvefit(@fcn_fitFreeT2,... % x0,t,s,zeros(size(x0)),[],options); end @@ -121,10 +163,10 @@ switch flag case 'T1' [x,~,~,output] = fminsearchbnd(@(x) fcn_fitFreeT1_fmin(x,t,s,IRfac),... - x0,zeros(size(x0)),[],options); + x0,lb,ub,options); case 'T2' [x,~,~,output] = fminsearchbnd(@(x) fcn_fitFreeT2_fmin(x,t,s,e),... - x0,zeros(size(x0)),[],options); + x0,lb,ub,options); end end @@ -160,7 +202,11 @@ % sort the relaxation times in ascending order E0 = x(1:2:end); T = x(2:2:end); -[T,idx] = sort(T); +if any(parameter.Tfixed_bool) + idx = 1:1:nExp; +else + [T,idx] = sort(T); +end E0 = E0(idx); ciT = ci(2:2:end); ciE = ci(1:2:end); @@ -177,6 +223,7 @@ case 'T2' fitdata.T2 = T; end +fitdata.T = T; fitdata.fit_t = fit_t; fitdata.fit_s = fit_s; fitdata.resnorm = out.resnorm; diff --git a/functions/inversion/fitDataMultiModal.m b/functions/inversion/fitDataMultiModal.m index 9e776e0..4027ebc 100644 --- a/functions/inversion/fitDataMultiModal.m +++ b/functions/inversion/fitDataMultiModal.m @@ -104,6 +104,8 @@ param0.T1IRfac = T1IRfac; param0.noise = parameter.noise; param0.optim = parameter.optim; +param0.Tfixed_bool = [0 0 0 0 0]; +param0.Tfixed_val = [0 0 0 0 0]; if isfield(parameter,'W') param0.W = parameter.W; end diff --git a/functions/inversion/getConfInterval.m b/functions/inversion/getConfInterval.m index 6a6e8ba..0562543 100644 --- a/functions/inversion/getConfInterval.m +++ b/functions/inversion/getConfInterval.m @@ -39,7 +39,7 @@ %% degrees of freedom DOF [i,j] = size(J); -deg_free = i-j; +deg_free = abs(i-j); %% mean squared error MSE: mse = sqrt(resnorm/deg_free); @@ -71,7 +71,7 @@ if deg_free <= 1000 stud_fac = getStudentInvCDF(1-alpha,deg_free); else - stud_fac = NaN; + stud_fac = 1;%NaN; end end diff --git a/scripts/run_Ku_prediction.m b/scripts/run_Ku_prediction.m new file mode 100644 index 0000000..7aa860a --- /dev/null +++ b/scripts/run_Ku_prediction.m @@ -0,0 +1,109 @@ +% example script imports NUCLEUS data files and calculates Ku estimates +% based on capillary bundle model with circular or angular pore cross section + +% For running it, NUCLEUS folder und subfolders must be registered in the +% MATLAB working path +clear all; +% working directory: +%mypath = 'E:\Costabel.S\Papers\KU_triangle_model\figures\Figure2'; +mypath = 'E:\Costabel.S\Projekte\Petromethoden\WRC_from_NMR\Software\NUCLEUS\example data\Documentation\T2inv_maran'; + +[filenames,path] = uigetfile('*.mat','pick NUCLEUS data files',mypath,'MultiSelect','on'); + +pressure = 10.^[1:0.01:7]; + +% check how many files were selected +if iscell(filenames) + ndset = length(filenames); +else + ndset = 1; + file = filenames; +end + +for nfile = 1:ndset + if ndset > 1 + file = filenames{nfile}; + end + load([path,file]); + % check whether file comes from NUCLEUSmod + if exist('data') == 1 + % gather info for feeding the the modified NUCLEUS functions + geom = data.GEOM; + psddata = data.psddata; + wbopts.show = false; + % check whether file comes from NUCLEUSinv... + elseif exist('idata') == 1 + %...and contains results of joint inversion + if isfield(idata.results,'invjoint') + % gather info for feeding the modified NUCLEUS functions + geom = idata.results(1).invjoint.iGEOM; + psddata.r = geom.radius'; + psddata.psd = idata.results(1).invjoint.iF'./sum(idata.results(1).invjoint.iF); + wbopts.show = false; + else + disp(['File <',file,'> does not contain joint inversion results']); + end + else + disp(['File <',file,'> is not a regular NUCLEUS export']); + end + pSAT = getSaturationFromPressureBatch(geom,pressure,psddata,getConstants,wbopts); +% idata.results(1).invjoint.pSAT = pSAT; +% save([path,file(1:end-4),'_corr.mat']); + dset(nfile).pSAT = pSAT; + dset(nfile).file = file; + dset(nfile).PSD = psddata; + dset(nfile).ptype = geom.type; +end + +%% plot WRC and KU data +p_fak = 1/100; %pressure in hPa or h in cm +K_fak = 100*60*60*24; % hydr. conductivity in cm/d +% porosity estimate: +poro = 0.35; % NOTE THAT K-VALUES FROM NUCLEUS COME PURELY, I.E., WITHOUT +% POROSITY AND TORTUOSITY CORRECTION! + +% tolerance for Krel calculation considering possible artefacts at high +% relaxation times: +tolKrel = 0.999; + +for nfile = 1:ndset + pSAT = dset(nfile).pSAT; + PSD = dset(nfile).PSD; + figure; + % Equivalent pore size distribution + subplot(2,2,1); + plot(PSD.r,PSD.psd); + title(['eq. PSD of <',dset(nfile).file,'>']); + xlabel('r_{eq} [m]'); + ylabel('\theta_{part} [a.u.]'); + set(gca,'xscale','log'); + % Water retention curve + subplot(2,2,2); + plot(pSAT.Sdfull,p_fak*pSAT.pressure); + title(['WRC (',dset(nfile).ptype,') of <',dset(nfile).file,'>']); + xlabel('S [-]'); + ylabel('h [cm]'); + set(gca,'yscale','log',... + 'xlim',[0 1]); + % hydraulic conductivity + subplot(2,2,3); + plot(pSAT.Sdfull,K_fak*poro*pSAT.Kdfull,pSAT.Sdfull,K_fak*poro*pSAT.Kd_eff); + title(['K_U (',dset(nfile).ptype,') of <',dset(nfile).file,'>']); + xlabel('S [-]'); + ylabel('K_U [cm/d]'); + set(gca,'yscale','log',... + 'xlim',[0 1],... + 'ylim',[1e-5 1e5]); + legend('K_U (full)','K_U (eff)','Location','SouthEast'); + % relative hydraulic conductivity + subplot(2,2,4); + plot(pSAT.Sdfull,pSAT.Kdfull/pSAT.Kdfull(find(pSAT.Sdfull']); + xlabel('S [-]'); + ylabel('K_{rel} [-]'); + set(gca,'yscale','log',... + 'xlim',[0 1],... + 'ylim',[1e-6 1]); + legend('K_{rel} (full)','K_{rel} (eff)','Location','SouthEast'); +end