see CHANGELOG.md

AUTHORS.md

@@ -0,0 +1,4 @@
+**NUCLEUS** is developed by
+
+* Stephan Costabel (since 2020), [email protected]
+* Thomas Hiller (since 2018), [email protected]

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

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;

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,...

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';

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);

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;

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.
 

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');

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'

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');

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 --------------

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

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

doc/menu.html

@@ -16,7 +16,7 @@ <h1>Matlab Index</h1>
 <h2>Matlab Directories</h2>
 <ul style="list-style-image:url(./matlabicon.gif)">
 <li><a href="nucleus/NUCLEUSinv/menu.html" target="menu">nucleus\NUCLEUSinv</a></li><li><a href="nucleus/NUCLEUSmod/menu.html" target="menu">nucleus\NUCLEUSmod</a></li><li><a href="nucleus/callbacks/contextmenus/menu.html" target="menu">nucleus\callbacks\contextmenus</a></li><li><a href="nucleus/callbacks/edits/menu.html" target="menu">nucleus\callbacks\edits</a></li><li><a href="nucleus/callbacks/listboxes/menu.html" target="menu">nucleus\callbacks\listboxes</a></li><li><a href="nucleus/callbacks/menus/menu.html" target="menu">nucleus\callbacks\menus</a></li><li><a href="nucleus/callbacks/popup/menu.html" target="menu">nucleus\callbacks\popup</a></li><li><a href="nucleus/callbacks/push/menu.html" target="menu">nucleus\callbacks\push</a></li><li><a href="nucleus/callbacks/radio/menu.html" target="menu">nucleus\callbacks\radio</a></li><li><a href="nucleus/functions/import/menu.html" target="menu">nucleus\functions\import</a></li><li><a href="nucleus/functions/interface/menu.html" target="menu">nucleus\functions\interface</a></li><li><a href="nucleus/functions/inversion/menu.html" target="menu">nucleus\functions\inversion</a></li><li><a href="nucleus/functions/modeling/menu.html" target="menu">nucleus\functions\modeling</a></li></ul>
-<!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- -->
+<!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- -->
 
 <hr><address>Generated by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" target="_parent">m2html</a></strong> &copy; 2005</address>
 </body>

doc/nucleus/NUCLEUSinv/NUCLEUSinv.html

@@ -111,8 +111,8 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0038 <span class="keyword">if</span> ~isempty(h0); close(h0); <span class="keyword">end</span>
 0039 
 0040 <span class="comment">%% GUI 'header' info and defaults</span>
-0041 myui.version = <span class="string">'0.1.13'</span>;
-0042 myui.date = <span class="string">'11.08.2022'</span>;
+0041 myui.version = <span class="string">'0.1.14'</span>;
+0042 myui.date = <span class="string">'27.09.2023'</span>;
 0043 myui.author = {<span class="string">'Stephan Costabel'</span>,<span class="string">'Thomas Hiller'</span>};
 0044 myui.email = <span class="string">'thomas.hiller[at]bgr.de'</span>;
 0045 myui.fontsize = 10;