see CHANGELOG.md

ThoHiller · Mar 12, 2021 · 2086284 · 2086284
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,24 @@
 # Changelog
 
+## [0.1.11] - 2021-03-12
+
+### Added
+- New *ConductView* figure in **NUCLEUSinv** and **NUCLEUSmod** that shows the hydraulic conductivity and permeability
+- New import routines to **NUCLEUSinv** for *IBAC* institute
+- New parameter file values in **NUCLEUSinv** for the *BAM TOM* import 
+
+### Changed
+- Changed the behavior of the *number of echoes per gate* field. Zero is no longer allowed and will be automatically set to 1
+- Rearrangement of some menues regarding the *ConductView* implementation
+- Restructured the import menu of **NUCLEUSinv** so that the *GGE* and *IBAC* institute are now in *RWTH*
+- The y-axis label of the RTD and PSD plots in **NUCLEUSinv** now only shows *water content [vol %]* if the porosity is not 1. This is much more intuitive
+
+### Fixed
+- Fixed two import bugs for *LIAG single/project* data in **NUCLEUSinv** (time scale conversion and background signal treatment)
+- Fixed output data when using the *LU* inversion in **NUCLEUSinv** (before the wrong kernel matrix was stored)
+- Fixed an internal data managment bug when activating/deactivating the joint inversion options
+- Fixed an issue regarding the use of only a single signal for the joint inversion and the inversion-geometry exhibits corners
+
 ## [0.1.10] - 2020-09-10
 
 ### Added
@@ -135,6 +154,7 @@
 
 Initial Version
 
+[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
 [0.1.8]: https://github.com/ThoHiller/nmr-nucleus/compare/v.0.1.7...v.0.1.8

diff --git a/NUCLEUSinv/NUCLEUSinv.m b/NUCLEUSinv/NUCLEUSinv.m
@@ -38,9 +38,9 @@
 if ~isempty(h0); close(h0); end
 
 %% GUI 'header' info and defaults
-myui.version = '0.1.10';
-myui.date = '10.09.2020';
-myui.author = 'Thomas Hiller';
+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.fontsize = 10;
 myui.inifile = 'NUCLEUSinv.ini';

diff --git a/NUCLEUSinv/NUCLEUSinv_createMenus.m b/NUCLEUSinv/NUCLEUSinv_createMenus.m
@@ -47,12 +47,14 @@
 % 1.1.1 Lab
 gui.menu.file_import_lab = uimenu(gui.menu.file_import,...
     'Label','Lab');
+
 % 1.1.1.1 BAM
 gui.menu.file_import_lab_bam = uimenu(gui.menu.file_import_lab,...
     'Label','BAM');
 % 1.1.1.1.1 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
 gui.menu.file_import_lab_bgr = uimenu(gui.menu.file_import_lab,...
     'Label','BGR');
@@ -65,33 +67,52 @@
 % 1.1.1.2.3 BGR mat
 gui.menu.file_import_lab_bgr_mat = uimenu(gui.menu.file_import_lab_bgr,...
     'Label','BGR mat','Tag','Lab','Callback',@onMenuImport);
-% 1.1.1.3 CoreLab ascii
-gui.menu.file_import_lab_corelab = uimenu(gui.menu.file_import_lab,...
-    'Label','CoreLab ascii','Tag','Lab','Callback',@onMenuImport);
-% 1.1.1.4 LIAG
+
+% 1.1.1.3 LIAG
 gui.menu.file_import_lab_liag = uimenu(gui.menu.file_import_lab,...
     'Label','LIAG');
-% 1.1.1.4.1 LIAG
+% 1.1.1.3.1 LIAG
 gui.menu.file_import_lab_liag_single = uimenu(gui.menu.file_import_lab_liag,...
     'Label','LIAG single','Tag','Lab','Callback',@onMenuImport);
-% 1.1.1.4.2 LIAG
+% 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);
-% 1.1.1.5 MOUSE
-gui.menu.file_import_lab_mouse = uimenu(gui.menu.file_import_lab,...
-    'Label','MOUSE','Tag','Lab','Callback',@onMenuImport);
-% 1.1.1.6 RWTH
+
+% 1.1.1.4 RWTH
 gui.menu.file_import_lab_rwth = uimenu(gui.menu.file_import_lab,...
     'Label','RWTH');
-% 1.1.1.6.1 RWTH ascii
-gui.menu.file_import_lab_rwth_ascii = uimenu(gui.menu.file_import_lab_rwth,...
-    'Label','RWTH ascii','Tag','Lab','Callback',@onMenuImport);
-% 1.1.1.6.2 RWTH field
-gui.menu.file_import_lab_rwth_field = uimenu(gui.menu.file_import_lab_rwth,...
-    'Label','RWTH field','Tag','Lab','Callback',@onMenuImport);
-% 1.1.1.6.3 Dart
-gui.menu.file_import_lab_rwth_dart = uimenu(gui.menu.file_import_lab_rwth,...
-    'Label','Dart','Tag','Lab','Callback',@onMenuImport);
+% 1.1.1.4.1 IBAC
+gui.menu.file_import_lab_ibac = uimenu(gui.menu.file_import_lab_rwth,...
+    'Label','IBAC');
+% 1.1.1.4.1.1 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
+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
+gui.menu.file_import_lab_gge = uimenu(gui.menu.file_import_lab_rwth,...
+    'Label','GGE');
+% 1.1.1.4.2.1 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
+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
+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
+gui.menu.file_import_lab_other = uimenu(gui.menu.file_import_lab,...
+    'Label','OTHER');
+% 1.1.1.5.1 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
+gui.menu.file_import_lab_mouse = uimenu(gui.menu.file_import_lab_other,...
+    'Label','MOUSE','Tag','Lab','Callback',@onMenuImport);
 
 % 1.1.2 Ascii
 gui.menu.file_import_ascii = uimenu(gui.menu.file_import,...
@@ -262,13 +283,15 @@
             'Label','AMP vs TLGM','Enable','off','Callback',@onMenuViewFigures);
         % 2.5.5 relaxation time distribution over time
         gui.menu.extra_graphics_rtd = uimenu(gui.menu.extra_graphics,...
-            'Label','RTD','Enable','off','Callback',@onMenuViewFigures);
+            'Label','RTD','Enable','off','Callback',@onMenuViewFigures);   
 end
 
 % 2.6 PhaseView
 gui.menu.extra_phaseview = uimenu(gui.menu.view,...
-    'Label','PhaseView GUI','Callback',@PhaseView);
-
+    'Label','PhaseView GUI','Enable','off','Callback',@PhaseView);
+% 2.7 ConductVIEW -> hydraulic conductivity
+gui.menu.extra_conduct = uimenu(gui.menu.view,...
+    'Label','ConductView GUI','Enable','off','Callback',@onMenuViewFigures);
 
 %% 3. Extras
 gui.menu.extra = uimenu(gui.figh,...

diff --git a/NUCLEUSmod/NUCLEUSmod.m b/NUCLEUSmod/NUCLEUSmod.m
@@ -41,9 +41,9 @@
 if ~isempty(h0); close(h0); end
 
 %% GUI 'header' info and defaults
-myui.version = '0.1.10';
-myui.date = '10.09.2020';
-myui.author = 'Thomas Hiller';
+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.fontsize = 10;
 
@@ -76,7 +76,6 @@
 
 %% Calculate Initial Geometry
 calculateGeometry;
-
 end
 
 %------------- END OF CODE --------------

diff --git a/NUCLEUSmod/NUCLEUSmod_createMenus.m b/NUCLEUSmod/NUCLEUSmod_createMenus.m
@@ -99,6 +99,10 @@
 % 2.2 Figure Toolbar
 gui.menu.view_toolbar = uimenu(gui.menu.view,...
     'Label','Figure Toolbar','Callback',@onMenuView);
+% 2.3 hydraulic conductivity
+gui.menu.view_conduct = uimenu(gui.menu.view,...
+    'Label','ConductView GUI','Separator','on','Enable','off',...
+    'Callback',@onMenuViewFigures);
 
 %% 3. Color theme
 gui.menu.color_theme = uimenu(gui.figh,...

diff --git a/NUCLEUSmod/NUCLEUSmod_createPanelCPS.m b/NUCLEUSmod/NUCLEUSmod_createPanelCPS.m
@@ -108,7 +108,7 @@
 %% pressure range and number of total points
 gui.text_handles.press_range = uicontrol('Parent',gui.panels.cps.HBox3,...
     'Style','text','FontSize',myui.fontsize,'HorizontalAlignment','center',...
-    'String','pressure - min | max | total steps');
+    'String','pressure - min | max | # steps');
 tstr = ['<HTML>Set minimum pressure value<br><br>',...
     '<u>Default value:</u><br>',...
     '<b>1000 Pa</b><br>'];
@@ -142,7 +142,7 @@
 set(gui.panels.cps.HBox4,'Widths',[200 -1]);
 
 %% drainage & imbibition lists
-tstr = ['<HTML>Choose <b>drainage</b> and <b>drainage</b> saturation levels for NMR forward calculation.<br><br>',...
+tstr = ['<HTML>Choose <b>drainage</b> and <b>imbibition</b> saturation levels for NMR forward calculation.<br><br>',...
     '<u>Hint:</u><br>',...
     'You can select multiple values with a context menu.<br>'];
 gui.cm_handles.select = uicontextmenu(gui.figh);

diff --git a/README.md b/README.md
@@ -73,6 +73,8 @@ I tested it successfully under Windows 7 (64bit) and 10 (64bit) with Matlab R201
 1. It is recommended to install the GUI Layout Toolbox directly into MATLAB<sup>TM</sup> via the mltbx-file (but it should also work via the old-school way of adding the toolbox folders to the MATLAB<sup>TM</sup> path)
 2. To use **NUCLEUS** you just need to place the `nucleus` folder from  the git repository on your hard drive and use the start scripts `startNUCLEUSinv` and `startNUCLEUSmod`, respectively (within these scripts all necessary **NUCLEUS** folders are added to the MATLAB<sup>TM</sup> path)
 
+**NOTE:** It is recommended to have only *one* version of **NUCLEUS** on your current  MATLAB<sup>TM</sup> path.
+
 - - -
 <a name="usage"></a>
 ### Usage
@@ -106,12 +108,13 @@ 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. (2020, September 10). ThoHiller/nmr-nucleus: v0.1.10 (Version v0.1.10). Zenodo. [https://doi.org/10.5281/zenodo.4022195]
+Thomas Hiller. (2021, March 12). ThoHiller/nmr-nucleus: v0.1.11 (Version v0.1.11). 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.
 ### References
 
-1. Hiller, T. and Klitzsch, N., "Joint inversion of nuclear magnetic resonance data from partially saturated rocks using a triangular pore model", GEOPHYSICS **83**(4), JM15-JM28, 2018, [DOI](https://doi.org/10.1190/geo2017-0697.1)
+1. Hiller, T. and Klitzsch, N., "Joint inversion of nuclear magnetic resonance data from partially saturated rocks using a triangular pore model", *GEOPHYSICS* **83**(4), JM15-JM28, 2018, [DOI](https://doi.org/10.1190/geo2017-0697.1)
+2. Costabel, S. and Hiller, T., "Soil hydraulic interpretation of nuclear magnetic resonance measurements based on circular and triangular capillary models", *Vadose Zone Journal*, 2021, e20104, [DOI](https://doi.org/10.1002/vzj2.20104)
 
 - - -
 <p style="text-align: center;"> MATLAB is a registered trademark of The Mathworks, Inc. </p>
diff --git a/callbacks/edits/onEditValue.m b/callbacks/edits/onEditValue.m
@@ -83,40 +83,39 @@ function onEditValue(src,~)
         % switch depending on the parent panel
         switch out.panel
             case 'process'
+                % remove temporary data fields
+                data = removeInversionFields(data);
+                setappdata(fig,'data',data);
+                % process the current selected signal
+                id = get(gui.listbox_handles.signal,'Value');
                 switch out.field
-                    case {'start','Nechoes'}
-                        % remove temporary data fields
-                        data = removeInversionFields(data);
-                        setappdata(fig,'data',data);
-                        % process the current selected signal
-                        id = get(gui.listbox_handles.signal,'Value');
-                        processNMRDataControl(fig,id);
-                        updatePlotsSignal;
-                        updateInfo(src);
-                        % clear axes
-                        clearSingleAxis(gui.axes_handles.rtd);
-                        clearSingleAxis(gui.axes_handles.psd);
-                        % set focus on data
-                        set(gui.plots.SignalPanel,'Selection',1);
+                    case {'Nechoes'}
+                        if value == 0
+                            data.process.Nechoes = 1;
+                            set(src,'String',num2str(data.process.Nechoes));
+                            setappdata(fig,'data',data);
+                        end
                     case 'end'
-                        % remove temporary data fields
-                        data = removeInversionFields(data);
-                        setappdata(fig,'data',data);
                         % check if the first sample is really smaller than
                         % the last one; if not reset everything
                         first = str2double(get(gui.edit_handles.process_start,'String'));
                         last = value;
-                        id = get(gui.listbox_handles.signal,'Value');
                         maxL = length(data.import.NMR.data{id}.signal);
                         if last == 0 || last <= first || last > maxL
                             data.process.end = maxL;
                             set(src,'String',num2str(data.process.end));
                             setappdata(fig,'data',data);
                         end
-                        % process the current selected signal
-                        processNMRDataControl(fig,id);
-                        updatePlotsSignal;
                 end
+                % process the current selected signal
+                processNMRDataControl(fig,id);
+                updatePlotsSignal;
+                updateInfo(src);
+                % clear axes
+                clearSingleAxis(gui.axes_handles.rtd);
+                clearSingleAxis(gui.axes_handles.psd);
+                % set focus on data
+                set(gui.plots.SignalPanel,'Selection',1);
             case 'param'
                 switch out.field
                     case {'rho','a','CBWcutoff','BVIcutoff'}

diff --git a/callbacks/menus/onMenuHelp.m b/callbacks/menus/onMenuHelp.m
@@ -43,7 +43,7 @@ function onMenuHelp(src,~)
         header{1,1}  = 'NUCLEUSmod:';
 end
 header{end+1,1}  = ' ';
-header{end+1,1}  = ['author: ',gui.myui.author];
+header{end+1,1}  = ['authors: ',gui.myui.author{1},', ',gui.myui.author{2}];
 header{end+1,1}  = ' ';
 header{end+1,1}  = ['version: ',gui.myui.version];
 header{end+1,1}  = ' ';

diff --git a/callbacks/menus/onMenuImport.m b/callbacks/menus/onMenuImport.m
@@ -38,6 +38,7 @@ function onMenuImport(src,~)
 %% get GUI handle and data
 fig = ancestor(src,'figure','toplevel');
 fig_tag = get(fig,'Tag');
+gui = getappdata(fig,'gui');
 
 label = get(src,'Label');
 menu_tag = get(src,'Tag');
@@ -53,19 +54,27 @@ function onMenuImport(src,~)
             case 'NUCLEUSinv'
                 importINV2INV(src);
             case 'NUCLEUSmod'
-                importMOD2INV(src);
+                importMOD2INV(src);                
             case 'Excel'
                 importEXCELdata(src);
             case 'Ascii'
                 importASCIIdata(src);
             case 'Lab'
                 importNMRdata(src);
             otherwise
-                helpdlg({'function: onMenuImport','Menu tag no known.'},...
+                helpdlg({'function: onMenuImport','Menu tag not known.'},...
                     'menu not known')
         end
-        % update the "last import" value within the ini-file
-        gui = getappdata(fig,'gui');
+
+        % activate the PhaseView GUI in case real data is imported
+        switch menu_tag
+            case {'NUCLEUSinv','NUCLEUSmod'}
+                set(gui.menu.extra_phaseview,'Enable','off');
+            otherwise
+                set(gui.menu.extra_phaseview,'Enable','on');
+        end
+
+        % update the "last import" value within the ini-file        
         gui.myui.inidata.lastimport = [menu_tag,'_',label];
         setappdata(fig,'gui',gui);
         gui = makeINIfile(gui,'update');

diff --git a/callbacks/menus/onMenuJointInversion.m b/callbacks/menus/onMenuJointInversion.m
@@ -90,14 +90,16 @@ function onMenuJointInversion(src,~)
 
         % clear axes
         clearSingleAxis(gui.axes_handles.all);
+        clearSingleAxis(gui.axes_handles.err_joint);
         clearSingleAxis(gui.axes_handles.psdj);
         clearSingleAxis(gui.axes_handles.cps);
 
         % menu entries
         set(gui.menu.extra_joint,'Checked','off');
         set(gui.menu.extra_joint_rhobounds,'Enable','off');
-        set(gui.menu.file_export_data_invjoint_mat,'Enable','off');        
-
+        set(gui.menu.file_export_data_invjoint_mat,'Enable','off');
+        set(gui.menu.extra_conduct,'Enable','off');
+
         % settings panel
         set(gui.popup_handles.invjoint_InvType,'Enable','off');
         set(gui.popup_handles.invjoint_geometry_type,'Enable','off');
@@ -181,6 +183,7 @@ function onMenuJointInversion(src,~)
 end
 
 setappdata(fig,'data',data);
+setappdata(fig,'INVdata',INVdata);
 setappdata(fig,'gui',gui);
 NUCLEUSinv_updateInterface;
 updateStatusInformation(fig);

diff --git a/callbacks/menus/onMenuViewFigures.m b/callbacks/menus/onMenuViewFigures.m
@@ -45,6 +45,8 @@ function onMenuViewFigures(src,~)
         showExtraGraphics('ampvst');
     case 'RTD'    
         showExtraGraphics('rtd');
+    case 'ConductView GUI'
+        ConductView(src);
 end
 
 end