see CHANGELOG.md

ThoHiller · Feb 17, 2022 · e639437 · e639437
1 parent 2086284
commit e639437
Show file tree

Hide file tree

Showing 402 changed files with 14,321 additions and 9,190 deletions.
diff --git a/.gitignore b/.gitignore
@@ -4,3 +4,4 @@
 *.log
 *.toc
 *.sty
+/old_functions
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,22 @@
 # Changelog
 
+## [0.1.12] - latest
+
+### Added
+- New *SNR*-option in **NUCLEUSmod** to set the noise of the forward modelled NMR data either by noise level or signal-to-noise ratio (SNR)
+- New *Multi modal* fitting option in **NUCLEUSinv** (only in Expert mode) with built-in uncertainty estimation for the final RTD
+- New import routines to **NUCLEUSinv** for *BGR* devices (*Mouse* and *Helios*)
+- Difussion relaxation time *T<sub>diff</sub>*  is now considered in **NUCLEUSmod** (*NMR* panel) and **NUCLEUSinv** (*Petro Parameter* panel)
+- Added an `AUTHORS.md` file to the repository.
+
+### Changed
+- Changed the default export path and file name for graphics files in **NUCLEUSinv** to the current import path and data file
+- Changed the visualization of the imaginary part of the raw data (if available)
+- Minor internal changes
+
+### Fixed
+- Fixed an issue regarding the import of T<sub>1</sub> data without noise (noise is now estimated on-the-fly via a fit with five free exponents)
+
 ## [0.1.11] - 2021-03-12
 
 ### Added
@@ -75,13 +92,13 @@
 ## [0.1.6] - 2019-06-24
 
 ### Added
-- Added a new *PhaseView*  subGUI to view and change the phase between real and imaginary part of a T2 signal. **NUCLEUSinv**
+- Added a new *PhaseView*  subGUI to view and change the phase between real and imaginary part of a T<sub>2</sub> signal. **NUCLEUSinv**
 - Added a new import filter for the BAM NMR tomograph. **NUCLEUSinv**
-- Added an export feature that allows to save T2 raw data into a csv-file (e.g. LIAG format); during save it is possible to overwrite the imaginary part with zeros. **NUCLEUSinv**
+- Added an export feature that allows to save T<sub>2</sub> raw data into a csv-file (e.g. LIAG format); during save it is possible to overwrite the imaginary part with zeros. **NUCLEUSinv**
 
 ### Changed
 
-- If a T2 signal is imported it is automatically rotated to minimize its imaginary part (the fit incorporates real and imag. part of the signal). **NUCLEUSinv**
+- If a T<sub>2</sub> signal is imported it is automatically rotated to minimize its imaginary part (the fit incorporates real and imag. part of the signal). **NUCLEUSinv**
 - The *FitStatistics* window layout is now in line with the *PhaseView* layout for consistency reasons. **NUCLEUSinv**
 
 ### Fixed
@@ -115,7 +132,7 @@
 - Due to the new error weights there is no default gating method anymore for the *free exp. inversion*. **NUCLEUSinv**
 
 ### Fixed
-- T1 inversion recovery factor (1 or 2 depending on inversion or saturation recovery) was missing in *free exp. inversion* and *free joint inversion* (in Jacobian calculation for angular pores). **NUCLEUSinv**
+- T<sub>1</sub> inversion recovery factor (1 or 2 depending on inversion or saturation recovery) was missing in *free exp. inversion* and *free joint inversion* (in Jacobian calculation for angular pores). **NUCLEUSinv**
 
 ## [0.1.3] - 2019-02-22
 
@@ -154,6 +171,7 @@
 
 Initial Version
 
+[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
 [0.1.10]: https://github.com/ThoHiller/nmr-nucleus/compare/v.0.1.9...v.0.1.10
 [0.1.9]: https://github.com/ThoHiller/nmr-nucleus/compare/v.0.1.8...v.0.1.9

diff --git a/NUCLEUSinv/NUCLEUSinv.m b/NUCLEUSinv/NUCLEUSinv.m
@@ -27,8 +27,8 @@
 %       none
 %
 % See also NUCLEUSmod
-% Author: Thomas Hiller
-% email: thomas.hiller[at]leibniz-liag.de
+% Author: see AUTHORS.md
+% email: see AUTHORS.md
 % License: MIT License (at end)
 
 %------------- BEGIN CODE --------------
@@ -38,10 +38,10 @@
 if ~isempty(h0); close(h0); end
 
 %% GUI 'header' info and defaults
-myui.version = '0.1.11';
-myui.date = '12.03.2021';
-myui.author = {'Thomas Hiller','Stephan Costabel'};
-myui.email = 'thomas.hiller[at]leibniz-liag.de';
+myui.version = '0.1.12';
+myui.date = '17.02.2022';
+myui.author = {'Stephan Costabel','Thomas Hiller'};
+myui.email = 'thomas.hiller[at]bgr.de';
 myui.fontsize = 10;
 myui.inifile = 'NUCLEUSinv.ini';
 

diff --git a/NUCLEUSinv/NUCLEUSinv_createGUI.m b/NUCLEUSinv/NUCLEUSinv_createGUI.m
@@ -36,8 +36,8 @@ function NUCLEUSinv_createGUI(h,wbon)
 %       none
 %
 % See also: NUCLEUSinv
-% Author: Thomas Hiller
-% email: thomas.hiller[at]leibniz-liag.de
+% Author: see AUTHORS.md
+% email: see AUTHORS.md
 % License: MIT License (at end)
 
 %------------- BEGIN CODE --------------
@@ -118,7 +118,7 @@ function NUCLEUSinv_createGUI(h,wbon)
     'TitleColor',myui.colors.BoxCPS,'ForegroundColor',myui.colors.BoxTitle);
 
 % adjust the heights of all left-column-panels
-myui.heights = [250 22 22 22 22; -1 109 137 190 299];
+myui.heights = [250 22 22 22 22; -1 109 165 190 299];
 % panel header is always 22 high
 set(gui.panels.main,'Heights',myui.heights(2,:),...
     'MinimumHeights',[250 22 22 22 22]);
@@ -199,7 +199,7 @@ function NUCLEUSinv_createGUI(h,wbon)
 % otherwise "fixAxes" throws an error (in NUCLEUSmod); strangely here it
 % also works without it, but I put it for consistency reasons
 setappdata(h,'gui',gui);
-% changeColorTheme('INV',myui.colors.theme);
+changeColorTheme('INV',myui.colors.theme);
 set(gui.main,'Visible','on');
 
 %% enable all menus

diff --git a/NUCLEUSinv/NUCLEUSinv_createMenus.m b/NUCLEUSinv/NUCLEUSinv_createMenus.m
@@ -24,8 +24,8 @@
 %       none
 %
 % See also: NUCLEUSinv
-% Author: Thomas Hiller
-% email: thomas.hiller[at]leibniz-liag.de
+% Author: see AUTHORS.md
+% email: see AUTHORS.md
 % License: MIT License (at end)
 
 %------------- BEGIN CODE --------------
@@ -61,12 +61,23 @@
 % 1.1.1.2.1 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 org
-gui.menu.file_import_lab_bgr_org = uimenu(gui.menu.file_import_lab_bgr,...
-    'Label','BGR org','Tag','Lab','Callback',@onMenuImport);
-% 1.1.1.2.3 BGR mat
+% 1.1.1.2.2 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
+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,...
+% 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);
 
 % 1.1.1.3 LIAG
 gui.menu.file_import_lab_liag = uimenu(gui.menu.file_import_lab,...

diff --git a/NUCLEUSinv/NUCLEUSinv_createPanelData.m b/NUCLEUSinv/NUCLEUSinv_createPanelData.m
@@ -25,8 +25,8 @@
 %       none
 %
 % See also: NUCLEUSinv
-% Author: Thomas Hiller
-% email: thomas.hiller[at]leibniz-liag.de
+% Author: see AUTHORS.md
+% email: see AUTHORS.md
 % License: MIT License (at end)
 
 %------------- BEGIN CODE --------------
@@ -78,7 +78,7 @@
 uimenu(gui.cm_handles.data_list_single,...
     'Label','save','Tag','single','Callback',@onContextSignalList);
 uimenu(gui.cm_handles.data_list_single,...
-    'Label','remove','Tag','single','Separator','on',...
+    'Label','\remove','Tag','single','Separator','on',...
     'Callback',@onContextSignalList);
 uimenu(gui.cm_handles.data_list_single,...
     'Label','use as calib.','Tag','single','Separator','on',...

diff --git a/NUCLEUSinv/NUCLEUSinv_createPanelInfo.m b/NUCLEUSinv/NUCLEUSinv_createPanelInfo.m
@@ -23,8 +23,8 @@
 %       none
 %
 % See also: NUCLEUSinv
-% Author: Thomas Hiller
-% email: thomas.hiller[at]leibniz-liag.de
+% Author: see AUTHORS.md
+% email: see AUTHORS.md
 % License: MIT License (at end)
 
 %------------- BEGIN CODE --------------

diff --git a/NUCLEUSinv/NUCLEUSinv_createPanelInversionJoint.m b/NUCLEUSinv/NUCLEUSinv_createPanelInversionJoint.m
@@ -26,8 +26,8 @@
 %       none
 %
 % See also: NUCLEUSinv
-% Author: Thomas Hiller
-% email: thomas.hiller[at]leibniz-liag.de
+% Author: see AUTHORS.md
+% email: see AUTHORS.md
 % License: MIT License (at end)
 
 %------------- BEGIN CODE --------------

diff --git a/NUCLEUSinv/NUCLEUSinv_createPanelInversionStd.m b/NUCLEUSinv/NUCLEUSinv_createPanelInversionStd.m
@@ -26,8 +26,8 @@
 %       none
 %
 % See also: NUCLEUSinv
-% Author: Thomas Hiller
-% email: thomas.hiller[at]leibniz-liag.de
+% Author: see AUTHORS.md
+% email: see AUTHORS.md
 % License: MIT License (at end)
 
 %------------- BEGIN CODE --------------
@@ -62,10 +62,10 @@
 switch data.info.ExpertMode
     case 'on'
         tstr = ' ';
-        istring = {'Mono exp.','Several free exp. (2-5)','Multi exp. (LSQ)','Multi exp. (LU decomp.)'};
+        istring = {'Mono exp.','N free exp. (2-5)','Multi exp. (LSQ)','Multi exp. (LU decomp.)','Multi modal'};
     case 'off'
         tstr = ' ';
-        istring = {'Mono exp.','Several free exp. (2-5)','Multi exp. (LSQ)'};
+        istring = {'Mono exp.','N free exp. (2-5)','Multi exp. (LSQ)'};
 end
 gui.popup_handles.invstd_InvType = uicontrol('Parent',gui.panels.invstd.HBox1,...
     'Style','popup','String',istring,'FontSize',myui.fontsize,'Enable','off','Value',3,...
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,3 +4,4 @@ @@
     *.log
     *.toc
     *.sty
+    /old_functions