Added

- New sub GUI 2DInv in NUCLEUSinv for 2D T1-T2 inversion (works so far for HELIOS, DART and JAVELIN (Vista Clara) and RockCoreAnalyzer (Magritek) data) - New import routines in NUCLEUSinv for the NMR Dart Logging tool - New Extra menu entry in NUCLEUSinv to find duplicate NMR signals in the file list - New fitting options in the PhaseView sub GUI of NUCLEUSinv Changed - Unified the appearance along several sub GUIs for consistency - Updated the wait bar increments for very long batch runs - When HELIOS data is imported, the user can now decide if several files should be stacked together Fixed - Fixed a bug when importing data and the Statistics Toolbox is not available
ThoHiller · Nov 27, 2024 · 0ec7056 · 0ec7056
1 parent 9408835
commit 0ec7056
Show file tree

Hide file tree

Showing 147 changed files with 21,188 additions and 8,030 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,21 @@
 # Changelog
 
+## [0.3.0] - 2024-11-27
+
+### Added
+- New sub GUI *2DInv* in **NUCLEUSinv** for 2D T1-T2 inversion (works so far for HELIOS, DART and JAVELIN (Vista Clara) and RockCoreAnalyzer (Magritek) data)
+- New import routines in **NUCLEUSinv** for the NMR Dart Logging tool
+- New *Extra* menu entry in **NUCLEUSinv** to find duplicate NMR signals in the file list
+- New fitting options in the *PhaseView* sub GUI of **NUCLEUSinv**
+
+### Changed
+- Unified the appearance along several sub GUIs for consistency
+- Updated the wait bar increments for very long batch runs
+- When *HELIOS* data is imported, the user can now decide if several files should be stacked together
+
+### Fixed
+- Fixed a bug when importing data and the Statistics Toolbox is not available
+
 ## [0.2.1] - 2024-02-11
 
 ### Added
@@ -215,6 +231,7 @@
 
 Initial Version
 
+[0.3.0]: https://github.com/ThoHiller/nmr-nucleus/compare/v.0.2.1...v.0.3.0
 [0.2.1]: https://github.com/ThoHiller/nmr-nucleus/compare/v.0.2.0...v.0.2.1
 [0.2.0]: https://github.com/ThoHiller/nmr-nucleus/compare/v.0.1.14...v.0.2.0
 [0.1.14]: https://github.com/ThoHiller/nmr-nucleus/compare/v.0.1.13...v.0.1.14

diff --git 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 = '0.2.1';
-myui.date = '11.02.2024';
+myui.version = '0.3.0';
+myui.date = '27.11.2024';
 myui.author = {'Stephan Costabel','Thomas Hiller'};
 myui.email = 'thomas.hiller[at]bgr.de';
 myui.fontsize = 10;
@@ -68,6 +68,7 @@
 data.uncert = defaults.uncert;
 data.calib = defaults.calib;
 data.invjoint = defaults.invjoint;
+data.inv2D = defaults.inv2D;
 data.pressure = defaults.pressure;
 gui.myui = myui;
 

diff --git a/NUCLEUSinv/NUCLEUSinv_createMenus.m b/NUCLEUSinv/NUCLEUSinv_createMenus.m
@@ -48,88 +48,108 @@
 gui.menu.file_import_lab = uimenu(gui.menu.file_import,...
     'Label','Lab');
 
-% 1.1.1.1 BAM
+% 1.1.1.1 AARHUS
+gui.menu.file_import_lab_aarhus = uimenu(gui.menu.file_import_lab,...
+    'Label','AARHUS');
+% 1.1.1.1.1 AARHUS Dart T1T2
+gui.menu.file_import_lab_aarhus_dartT1T2 = uimenu(gui.menu.file_import_lab_aarhus,...
+    'Label','Dart T1T2','Tag','Lab','Callback',@onMenuImport);
+% 1.1.1.1.2 AARHUS Dart T2 logging
+gui.menu.file_import_lab_aarhus_dartT2 = uimenu(gui.menu.file_import_lab_aarhus,...
+    'Label','Dart T2 logging','Tag','Lab','Callback',@onMenuImport);
+
+% 1.1.1.2 BAM
 gui.menu.file_import_lab_bam = uimenu(gui.menu.file_import_lab,...
     'Label','BAM');
-% 1.1.1.1.1 BAM TOM
+% 1.1.1.2.1 BAM TOM
 gui.menu.file_import_lab_bam_tom = uimenu(gui.menu.file_import_lab_bam,...
     'Label','BAM TOM','Tag','Lab','Callback',@onMenuImport);
 
-% 1.1.1.2 BGR
+% 1.1.1.3 BGR
 gui.menu.file_import_lab_bgr = uimenu(gui.menu.file_import_lab,...
     'Label','BGR');
-% 1.1.1.2.1 BGR std
+% 1.1.1.3.1 BGR std
 gui.menu.file_import_lab_bgr_std = uimenu(gui.menu.file_import_lab_bgr,...
     'Label','BGR std','Tag','Lab','Callback',@onMenuImport);
-% 1.1.1.2.2 BGR mat
+% 1.1.1.3.2 BGR mat
 gui.menu.file_import_lab_bgr_mat = uimenu(gui.menu.file_import_lab_bgr,...
     'Label','BGR mat','Tag','Lab','Callback',@onMenuImport);
-% 1.1.1.2.3 Mouse CPMG data, single data subfolders from CPMG
+% 1.1.1.3.3 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, all data subfolders from t1test,...
+% 1.1.1.3.4 Mouse plus Lift, all data subfolders from t1test,...
 % cpmgfastautotest, or (old Prospa Versions) cpmgfastauto
 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
+% 1.1.1.3.5 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
+% 1.1.1.3.6 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
+% 1.1.1.4 LIAG
 gui.menu.file_import_lab_liag = uimenu(gui.menu.file_import_lab,...
     'Label','LIAG');
-% 1.1.1.3.1 LIAG
+% 1.1.1.4.1 LIAG
 gui.menu.file_import_lab_liag_single = uimenu(gui.menu.file_import_lab_liag,...
     'Label','LIAG single','Tag','Lab','Callback',@onMenuImport);
-% 1.1.1.3.2 LIAG
+% 1.1.1.4.2 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
+% 1.1.1.4.3 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
+% 1.1.1.5 RUTGERS
+gui.menu.file_import_lab_rutgers = uimenu(gui.menu.file_import_lab,...
+    'Label','RUTGERS');
+% 1.1.1.5.1 RUTGERS
+gui.menu.file_import_lab_rutgers_T1T2 = uimenu(gui.menu.file_import_lab_rutgers,...
+    'Label','RoCA T1T2','Tag','Lab','Callback',@onMenuImport);
+
+% 1.1.1.6 RWTH
 gui.menu.file_import_lab_rwth = uimenu(gui.menu.file_import_lab,...
     'Label','RWTH');
-% 1.1.1.4.1 IBAC
+% 1.1.1.6.1 IBAC
 gui.menu.file_import_lab_ibac = uimenu(gui.menu.file_import_lab_rwth,...
     'Label','IBAC');
-% 1.1.1.4.1.1 IBAC
+% 1.1.1.6.1.1 IBAC
 gui.menu.file_import_lab_ibac_pm5 = uimenu(gui.menu.file_import_lab_ibac,...
     'Label','PM5','Tag','Lab','Callback',@onMenuImport);
-% 1.1.1.4.1.2 IBAC
+% 1.1.1.6.1.2 IBAC
 gui.menu.file_import_lab_ibac_pm25 = uimenu(gui.menu.file_import_lab_ibac,...
     'Label','PM25','Tag','Lab','Callback',@onMenuImport);
 
-% 1.1.1.4.2 GGE
+% 1.1.1.6.2 GGE
 gui.menu.file_import_lab_gge = uimenu(gui.menu.file_import_lab_rwth,...
     'Label','GGE');
-% 1.1.1.4.2.1 GGE ascii
+% 1.1.1.6.2.1 GGE ascii
 gui.menu.file_import_lab_gge_ascii = uimenu(gui.menu.file_import_lab_gge,...
     'Label','GGE ascii','Tag','Lab','Callback',@onMenuImport);
-% 1.1.1.4.2.2 GGE field
+% 1.1.1.6.2.2 GGE field
 gui.menu.file_import_lab_gge_field = uimenu(gui.menu.file_import_lab_gge,...
     'Label','GGE field','Tag','Lab','Callback',@onMenuImport);
-% 1.1.1.4.2.3 GGE Dart
+% 1.1.1.6.2.3 GGE Dart
 gui.menu.file_import_lab_gge_dart = uimenu(gui.menu.file_import_lab_gge,...
     'Label','GGE Dart','Tag','Lab','Callback',@onMenuImport);
 
-% 1.1.1.5 OTHER
+% 1.1.1.7 OTHER
 gui.menu.file_import_lab_other = uimenu(gui.menu.file_import_lab,...
     'Label','OTHER');
-% 1.1.1.5.1 CoreLab ascii
+% 1.1.1.7.1 CoreLab ascii
 gui.menu.file_import_lab_corelab = uimenu(gui.menu.file_import_lab_other,...
     'Label','CoreLab ascii','Tag','Lab','Callback',@onMenuImport);
-% 1.1.1.5.2 MOUSE
+% 1.1.1.7.2 MOUSE
 gui.menu.file_import_lab_mouse = uimenu(gui.menu.file_import_lab_other,...
     'Label','MOUSE','Tag','Lab','Callback',@onMenuImport);
-% 1.1.1.5.3 DART (University of Vienna)
+% 1.1.1.7.3 DART (University of Vienna)
 gui.menu.file_import_lab_dart = uimenu(gui.menu.file_import_lab_other,...
     'Label','DART','Tag','Lab','Callback',@onMenuImport);
+% 1.1.1.7.4 DART (incl. Burst echoes)
+gui.menu.file_import_lab_dartburst = uimenu(gui.menu.file_import_lab_other,...
+    'Label','DART (+Burst)','Tag','Lab','Callback',@onMenuImport);
 
 % 1.1.2 Ascii
 gui.menu.file_import_ascii = uimenu(gui.menu.file_import,...
@@ -167,6 +187,9 @@
 % 1.1.5.2 NUCLEUSmod from GUI
 gui.menu.file_import_nmrmod_gui = uimenu(gui.menu.file_import_nmrmod,....
     'Label','GUI','Tag','NUCLEUSmod','Callback',@onMenuImport);
+% 1.1.5.3 NUCLEUSmod from 2D GUI
+gui.menu.file_import_nmrmod_gui2d = uimenu(gui.menu.file_import_nmrmod,....
+    'Label','2D GUI','Tag','NUCLEUSmod2d','Callback',@onMenuImport);
 
 % 1.2 Export
 gui.menu.file_export = uimenu(gui.menu.file,...
@@ -318,6 +341,9 @@
 % 2.9 UncertaintyVIEW GUI
 gui.menu.extra_uncert = uimenu(gui.menu.view,...
     'Label','UncertView GUI','Enable','off','Callback',@onMenuSubGUIs);
+% 2.9 2DInv GUI
+gui.menu.extra_T1T2map = uimenu(gui.menu.view,...
+    'Label','2DInv GUI','Enable','off','Callback',@onMenuSubGUIs);
 
 %% 3. Extras
 gui.menu.extra = uimenu(gui.figh,...
@@ -374,6 +400,11 @@
     'Label','Surface relaxivity bounds','Enable','off',...
     'Callback',@onMenuExtraRhoBounds);
 
+% 3.6 find duplicate data
+gui.menu.extra_find_duplicates = uimenu(gui.menu.extra,...
+    'Label','Find duplicate signals','Enable','on',...
+    'Callback',@onMenuExtraFindDuplicates);
+
 
 %% 4. Color theme
 gui.menu.color_theme = uimenu(gui.figh,...

diff --git a/NUCLEUSinv/NUCLEUSinv_createPanelInversionStd.m b/NUCLEUSinv/NUCLEUSinv_createPanelInversionStd.m
@@ -184,7 +184,7 @@
 gui.push_handles.uncert = uicontrol('Parent',gui.panels.invstd.HBox7,'Enable','off',...
     'String','CALC.','FontSize',myui.fontsize,'BackGroundColor','g',...
     'Tag','uncert','UserData',1,'Callback',@onPushRun);
-set(gui.panels.invstd.HBox7,'Widths',[200 -1 -1]);
+set(gui.panels.invstd.HBox7,'Widths',[200 -1 -2]);
 
 %% Java Hack to adjust vertical alignment of text fields
 jh = findjobj(gui.text_handles.invstd_InvType);

diff --git a/NUCLEUSinv/NUCLEUSinv_loadDefaults.m b/NUCLEUSinv/NUCLEUSinv_loadDefaults.m
@@ -195,6 +195,65 @@
 % corresponding scale factors - 1 | 1e-3 | 1e-6 | 1e-5
 out.pressure.unitfac = 1;
 
+%% 2D inversion GUI settings
+% system / fluid properties
+% diffusion coefficient [m²/s]
+out.inv2D.prop.D = 2.025e-9;
+% gradient [T/m]
+out.inv2D.prop.G0 = 0;
+% echo time [s]
+out.inv2D.prop.te = 200e-6;
+% start echo
+out.inv2D.prop.first = 1;
+% last echo
+out.inv2D.prop.last = 1;
+
+% inversion settings
+% IR/SR factor
+out.inv2D.inv.T1IRfac = 2;
+% IR kernel type (1 or 2)
+out.inv2D.inv.IRtype = 1;
+% T1 range minimum [s]
+out.inv2D.inv.T1min = 1e-4;
+% T1 range maximum [s]
+out.inv2D.inv.T1max = 10;
+% T1 number of points in range
+out.inv2D.inv.T1N = 51;
+% T2 range minimum [s]
+out.inv2D.inv.T2min = 1e-4;
+% T2 range maximum [s]
+out.inv2D.inv.T2max = 10;
+% T2 number of points in range
+out.inv2D.inv.T2N = 51;
+% T1 regularization parameter lambda
+out.inv2D.inv.T1lambda = 5;
+% T1 order of smoothness constraint
+out.inv2D.inv.T1order = 1;
+% T2 regularization parameter lambda
+out.inv2D.inv.T2lambda = 2;
+% T2 order of smoothness constraint
+out.inv2D.inv.T2order = 1;
+
+% information settings / properties
+% T1 minimum [s]
+out.inv2D.info.T1min = 1e-3;
+% T1 maximum [s]
+out.inv2D.info.T1max = 1;
+% T2 minimum [s]
+out.inv2D.info.T2min = 1e-3;
+% T2 minimum [s]
+out.inv2D.info.T2max = 1;
+% initial amplitude E0 [a.u.]
+out.inv2D.info.E0 = 0;
+% T1 log mean time
+out.inv2D.info.T1tlgm = 0;
+% T2 log mean time
+out.inv2D.info.T2tlgm = 0;
+% T1 maximum time
+out.inv2D.info.T1tmax = 0;
+% T2 maximum time
+out.inv2D.info.T2tmax = 0;
+
 return
 
 %------------- END OF CODE --------------

diff --git 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 = '0.2.1';
-myui.date = '11.02.2024';
+myui.version = '0.3.0';
+myui.date = '27.11.2024';
 myui.author = {'Stephan Costabel','Thomas Hiller'};
 myui.email = 'thomas.hiller[at]bgr.de';
 myui.fontsize = 10;
@@ -65,6 +65,7 @@
 data.geometry = defaults.geometry;
 data.pressure = defaults.pressure;
 data.nmr = defaults.nmr;
+data.mod2D = defaults.mod2D;
 gui.myui = myui;
 
 % save the data struct within the GUI

diff --git a/NUCLEUSmod/NUCLEUSmod_createMenus.m b/NUCLEUSmod/NUCLEUSmod_createMenus.m
@@ -99,9 +99,13 @@
 % 2.2 Figure Toolbar
 gui.menu.view_toolbar = uimenu(gui.menu.view,...
     'Label','Figure Toolbar','Callback',@onMenuView);
-% 2.3 hydraulic conductivity
+% 2.3 2D modelling GUI
+gui.menu.view_2dmod = uimenu(gui.menu.view,...
+    'Label','2DMod GUI','Separator','on','Enable','on',...
+    'Callback',@onMenuSubGUIs);
+% 2.4 hydraulic conductivity
 gui.menu.view_conduct = uimenu(gui.menu.view,...
-    'Label','ConductView GUI','Separator','on','Enable','off',...
+    'Label','ConductView GUI','Enable','off',...
     'Callback',@onMenuSubGUIs);
 
 %% 3. Color theme

diff --git a/NUCLEUSmod/NUCLEUSmod_createPanelNMR.m b/NUCLEUSmod/NUCLEUSmod_createPanelNMR.m
@@ -114,7 +114,6 @@
 set(gui.panels.nmr.HBox3,'Widths',[200 -1]);
 
 %% noise & porosity
-
 tstr = ['<HTML>NMR data noise method.<br><br>',...
     'A noise level will be used globally for all NMR signals.<br>',...
     'A signal-to-ratio will be used individually on every single NMR signal.<br><br>',...

diff --git a/NUCLEUSmod/NUCLEUSmod_loadDefaults.m b/NUCLEUSmod/NUCLEUSmod_loadDefaults.m
@@ -92,6 +92,57 @@
 % use linear y-axes as default (log=1, lin=2)
 out.nmr.logliny = 2;
 
+%% 2D settings
+% system / fluid properties
+% diffusion coefficient [m²/s]
+out.mod2D.prop.D = 2.025e-9;
+% gradient [T/m]
+out.mod2D.prop.G0 = 0;
+% echo time [s]
+out.mod2D.prop.te = 0;
+% bulk relaxation [s]
+out.mod2D.prop.Tbulk = 1e6;
+
+% model space settings
+% 2D type
+out.mod2D.mod.type = 'T1T2';
+% T1 range minimum [s]
+out.mod2D.mod.T1min = 1e-4;
+% T1 range maximum [s]
+out.mod2D.mod.T1max = 10;
+% T1 number of points in range
+out.mod2D.mod.T1N = 151;
+% T2 range minimum [s]
+out.mod2D.mod.T2min = 1e-4;
+% T2 range maximum [s]
+out.mod2D.mod.T2max = 10;
+% T2 number of points in range
+out.mod2D.mod.T2N = 151;
+
+% number of 2D distribution
+out.mod2D.mod.Ndist = 3;
+% center point of 2D distribution
+out.mod2D.mod.mu = [1 1;0.01 0.03;0.5 0.005];
+% covariance matrix of 2D distribution
+out.mod2D.mod.sigma{1} = [0.1 0;0 0.1];
+out.mod2D.mod.sigma{2} = [0.2 0.3;0 0.2];
+out.mod2D.mod.sigma{3} = [0.3 0;0 0.01];
+% amplitude of 2D distribution
+out.mod2D.mod.amp = [1 1 1];
+
+% NMR data
+out.mod2D.nmr.T1IRfac = 2;
+out.mod2D.nmr.IRtype = 1;
+out.mod2D.nmr.T1trmin = 1e-3;
+out.mod2D.nmr.T1trmax = 1;
+out.mod2D.nmr.T1trN = 21;
+out.mod2D.nmr.T2te = 200e-6;
+out.mod2D.nmr.T2teN = 500;
+% noise creation type 'level' or 'SNR'
+out.mod2D.nmr.noisetype = 'level';
+% noise level [0:1] or SNR [-]
+out.mod2D.nmr.noise = 0;
+
 return
 
 %------------- END OF CODE --------------