see CHANGELOG

ThoHiller · Feb 1, 2024 · d792649 · d792649
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,15 @@
 # Changelog
 
+## [0.2.0] - 2024-02-01
+
+### Added
+- New functionality to estimate the uncertainty of relaxation time distributions (RTDs) by using a simple bootstrapping method
+- New sub GUI *UncertView* in **NUCLEUSinv** to process and evaluate the uncertainty data
+
+### Fixed
+ - Fixed an issue when importing **NUCLEUSinv** session files older than version v.0.1.14 (there is a new general *T* field for *mono* and *N free exp. (2-5)* inversion results which was not initialized)
+- Several minor improvements in GUI handling, usability and visualization.
+
 ## [0.1.14] - 2023-09-27
 
 ### Added
@@ -190,6 +200,7 @@
 
 Initial Version
 
+[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
 [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

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 = '0.1.14';
-myui.date = '27.09.2023';
+myui.version = '0.2.0';
+myui.date = '01.02.2024';
 myui.author = {'Stephan Costabel','Thomas Hiller'};
 myui.email = 'thomas.hiller[at]bgr.de';
 myui.fontsize = 10;
@@ -65,6 +65,7 @@
 data.process = defaults.process;
 data.param = defaults.param;
 data.invstd = defaults.invstd;
+data.uncert = defaults.uncert;
 data.calib = defaults.calib;
 data.invjoint = defaults.invjoint;
 data.pressure = defaults.pressure;

diff --git a/NUCLEUSinv/NUCLEUSinv_createGUI.m b/NUCLEUSinv/NUCLEUSinv_createGUI.m
@@ -118,11 +118,11 @@ 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; -1 109 165 190 299];
+myui.heights = [250 22 22 22 22; -1 109 165 221 299];
 % panel header is always 22 high
 set(gui.panels.main,'Heights',myui.heights(2,:),...
     'MinimumHeights',[250 22 22 22 22]);
-set(gui.left,'Heights',-1,'MinimumHeights',250+109+22+190+22);
+set(gui.left,'Heights',-1,'MinimumHeights',250+109+22+221+22);
 
 % 1. data panel
 if wbon

diff --git a/NUCLEUSinv/NUCLEUSinv_createMenus.m b/NUCLEUSinv/NUCLEUSinv_createMenus.m
@@ -315,6 +315,9 @@
 % 2.8 FixedTime VIEW
 gui.menu.extra_fixedtime = uimenu(gui.menu.view,...
     'Label','FixedTimeView GUI','Enable','off','Callback',@FixedTimeView);
+% 2.9 Uncertainty VIEW
+gui.menu.extra_uncert = uimenu(gui.menu.view,...
+    'Label','UncertView GUI','Enable','off','Callback',@UncertView);
 
 %% 3. Extras
 gui.menu.extra = uimenu(gui.figh,...

diff --git a/NUCLEUSinv/NUCLEUSinv_createPanelInversionStd.m b/NUCLEUSinv/NUCLEUSinv_createPanelInversionStd.m
@@ -54,6 +54,9 @@
 % RUN button
 gui.panels.invstd.HBox6 = uix.HBox('Parent',gui.panels.invstd.VBox,...
     'Spacing',3);
+% RTD uncertainty
+gui.panels.invstd.HBox7 = uix.HBox('Parent',gui.panels.invstd.VBox,...
+    'Spacing',3);
 
 %% inversion method
 gui.text_handles.invstd_InvType = uicontrol('Parent',gui.panels.invstd.HBox1,...
@@ -168,6 +171,21 @@
     'Tag','std','UserData',1,'Callback',@onPushRun);
 set(gui.panels.invstd.HBox6,'Widths',[200 -1]);
 
+%% RTD uncertainty
+gui.text_handles.uncert = uicontrol('Parent',gui.panels.invstd.HBox7,...
+    'Style','text','FontSize',myui.fontsize,'HorizontalAlignment','center',...
+    'String','RTD uncertainty | # models');
+tstr = 'Number of uncertainty models to calculate.';
+gui.edit_handles.uncert_N = uicontrol('Parent',gui.panels.invstd.HBox7,...
+    'Style','edit','String',num2str(data.uncert.N),...
+    'UserData',struct('Tooltipstr',tstr,'defaults',[data.uncert.N 1 1]),...
+    'Tag','uncert_N','FontSize',myui.fontsize,...
+    'Enable','off','Callback',@onEditValue);
+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]);
+
 %% Java Hack to adjust vertical alignment of text fields
 jh = findjobj(gui.text_handles.invstd_InvType);
 jh.setVerticalAlignment(javax.swing.JLabel.CENTER);
@@ -181,6 +199,8 @@
 jh.setVerticalAlignment(javax.swing.JLabel.CENTER);
 jh = findjobj(gui.text_handles.invstd_run);
 jh.setVerticalAlignment(javax.swing.JLabel.CENTER);
+jh = findjobj(gui.text_handles.uncert);
+jh.setVerticalAlignment(javax.swing.JLabel.CENTER);
 
 return
 

diff --git a/NUCLEUSinv/NUCLEUSinv_createPanelPlots.m b/NUCLEUSinv/NUCLEUSinv_createPanelPlots.m
@@ -155,6 +155,13 @@
 gui.cm_handles.axes_rtd_view_cum = uimenu(gui.cm_handles.axes_rtd_view,...
     'Label','cum','Tag','view','Callback',@onContextPlotsRTD);
 set(gui.axes_handles.rtd,'UIContextMenu',gui.cm_handles.axes_rtd);
+gui.cm_handles.axes_rtd_uncert = uimenu(gui.cm_handles.axes_rtd,...
+    'Label','uncert','Enable','off');
+gui.cm_handles.axes_rtd_uncert_lines = uimenu(gui.cm_handles.axes_rtd_uncert,...
+    'Label','lines','Tag','uncert','Checked','on','Callback',@onContextPlotsRTD);
+gui.cm_handles.axes_rtd_uncert_patch = uimenu(gui.cm_handles.axes_rtd_uncert,...
+    'Label','patch','Tag','uncert','Callback',@onContextPlotsRTD);
+set(gui.axes_handles.rtd,'UIContextMenu',gui.cm_handles.axes_rtd);
 
 %% 2.2 the PSD panel
 gui.plots.Dist.PSD.box = uicontainer('Parent',gui.plots.Dist.PSDTab);

diff --git a/NUCLEUSinv/NUCLEUSinv_loadDefaults.m b/NUCLEUSinv/NUCLEUSinv_loadDefaults.m
@@ -40,6 +40,8 @@
 out.info.RTDflag = 'freq';
 out.info.PSDflag = 'freq';
 out.info.PSDJflag = 'freq';
+% plot switch for uncertainty line / patch plot
+out.info.RTDuncert = 'lines';
 % flags indicating expert mode / joint inversion / inversion info / tool
 % tips
 out.info.ExpertMode = 'off';
@@ -60,6 +62,8 @@
 % re-sampling (gating) of the raw signal 'log' | 'lin' | 'none'
 % depends on signal type 'T1' or 'T2'
 out.process.gatetype = 'log';
+% gateing flag for convenience
+out.process.isgated = false;
 % maximum number of echoes per gate
 out.process.Nechoes = 50;
 % normalize signal to 1 (no=0, yes=1)
@@ -135,12 +139,16 @@
 % porosity value between 0 and 1 [-]
 out.invstd.porosity = 1;
 
-out.invstd.useUncert = 1;
-out.invstd.uncertMethod = 'thresh';
-out.invstd.uncertThresh = 0.05;
-out.invstd.uncertChi2 = 0.005;
-out.invstd.uncertN = 100;
-out.invstd.uncertMax = 1e4;
+% uncertainty flag (intended for batch use)
+out.uncert.use = 1;
+% default uncertainty calculation method
+out.uncert.Method = 'RMS_bound';
+% uncertaintyx treshold (only need for method 'threshold')
+out.uncert.Thresh = 0.05;
+% number of uncertainty models to calculate
+out.uncert.N = 10;
+% number of unsuccesful tries before calculation stops
+out.uncert.Max = 1e4;
 
 %% joint inversion panel defaults
 % joint inversion methods to choose 'free' | 'fixed' | 'shape'

diff --git a/NUCLEUSinv/NUCLEUSinv_updateInterface.m b/NUCLEUSinv/NUCLEUSinv_updateInterface.m
@@ -86,6 +86,11 @@
                 gui = updateLambda(gui,data.invstd.regtype,0,0,0);
                 gui = updateLorder(gui,data.invstd.invtype,data.invstd.Lorder);
                 gui = updateInvstdTime(gui,data.invstd.invtype,0,0);
+
+                % RTD uncertainty
+                set(gui.edit_handles.uncert_N,'Enable','off',...
+                    'String',num2str(data.uncert.N));
+                set(gui.push_handles.uncert,'Enable','off');
 
                 % Tbulk & Tdiff
                 set(gui.edit_handles.invstd_Tbulk,'Enable','off',...
@@ -108,6 +113,11 @@
                 gui = updateLambda(gui,data.invstd.regtype,0,0,0);
                 gui = updateLorder(gui,data.invstd.invtype,data.invstd.Lorder);
                 gui = updateInvstdTime(gui,data.invstd.invtype,0,0);
+
+                % RTD uncertainty
+                set(gui.edit_handles.uncert_N,'Enable','off',...
+                    'String',num2str(data.uncert.N));
+                set(gui.push_handles.uncert,'Enable','off');
 
                 % Tbulk & Tdiff
                 set(gui.edit_handles.invstd_Tbulk,'Enable','off',...
@@ -148,7 +158,12 @@
                 gui = updateLorder(gui,data.invstd.invtype,data.invstd.Lorder);
                 gui = updateInvstdTime(gui,data.invstd.invtype,data.invstd.time,...
                     data.invstd.Ntime);
-
+
+                % RTD uncertainty
+                set(gui.edit_handles.uncert_N,'Enable','on',...
+                    'String',num2str(data.uncert.N));
+                set(gui.push_handles.uncert,'Enable','on');
+
                 % Tbulk & Tdiff
                 set(gui.edit_handles.invstd_Tbulk,'Enable','on',...
                     'String',num2str(data.invstd.Tbulk));
@@ -180,6 +195,11 @@
                 gui = updateLorder(gui,data.invstd.invtype,data.invstd.Lorder);
                 gui = updateInvstdTime(gui,data.invstd.invtype,data.invstd.time,...
                     data.invstd.Ntime);
+
+                % RTD uncertainty
+                set(gui.edit_handles.uncert_N,'Enable','on',...
+                    'String',num2str(data.uncert.N));
+                set(gui.push_handles.uncert,'Enable','on');
 
                 % Tbulk & Tdiff
                 set(gui.edit_handles.invstd_Tbulk,'Enable','on',...
@@ -208,6 +228,11 @@
                 % lambda, smoothness constraint and RTD limits
                 gui = updateLambda(gui,data.invstd.regtype,0,0,0);
                 gui = updateLorder(gui,data.invstd.invtype,data.invstd.Lorder);
+
+                % RTD uncertainty
+                set(gui.edit_handles.uncert_N,'Enable','on',...
+                    'String',num2str(data.uncert.N));
+                set(gui.push_handles.uncert,'Enable','on');
 
                 % Tbulk & Tdiff
                 set(gui.edit_handles.invstd_Tbulk,'Enable','on',...
@@ -570,6 +595,11 @@
                 gui = updateLambda(gui,data.invstd.regtype,0,0,0);
                 gui = updateLorder(gui,data.invstd.invtype,data.invstd.Lorder);
                 gui = updateInvstdTime(gui,data.invstd.invtype,0,0);
+
+                % RTD uncertainty
+                set(gui.edit_handles.uncert_N,'Enable','off',...
+                    'String',num2str(data.uncert.N));
+                set(gui.push_handles.uncert,'Enable','off');
 
                 % Tbulk & Tdiff
                 set(gui.edit_handles.invstd_Tbulk,'Enable','off',...
@@ -586,12 +616,17 @@
                     'Value',data.invstd.freeDT,...
                     'String',{'1','2','3','4','5'});
                 set(gui.text_handles.invstd_InvTypeOpt,...
-                    'String','No. of relaxation 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);
                 gui = updateLorder(gui,data.invstd.invtype,data.invstd.Lorder);
                 gui = updateInvstdTime(gui,data.invstd.invtype,0,0);
+
+                % RTD uncertainty
+                set(gui.edit_handles.uncert_N,'Enable','off',...
+                    'String',num2str(data.uncert.N));
+                set(gui.push_handles.uncert,'Enable','off');
 
                 % Tbulk & Tdiff
                 set(gui.edit_handles.invstd_Tbulk,'Enable','off',...
@@ -631,6 +666,11 @@
                     'String',num2str(data.invstd.time(2)));
                 set(gui.edit_handles.invstd_Ntime,'Enable','off',...
                     'String',num2str(data.invstd.Ntime));
+
+                % RTD uncertainty
+                set(gui.edit_handles.uncert_N,'Enable','on',...
+                    'String',num2str(data.uncert.N));
+                set(gui.push_handles.uncert,'Enable','on');
 
                 % Tbulk & Tdiff
                 set(gui.edit_handles.invstd_Tbulk,'Enable','on',...

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 = '0.1.14';
-myui.date = '27.09.2023';
+myui.version = '0.2.0';
+myui.date = '01.02.2024';
 myui.author = {'Stephan Costabel','Thomas Hiller'};
 myui.email = 'thomas.hiller[at]bgr.de';
 myui.fontsize = 10;