see CHANGELOG

CHANGELOG.md

@@ -1,5 +1,20 @@
 # Changelog
 
+## [0.2.1] - 2024-02-11
+
+### Added
+- Added uncertainty data do Excel export in **NUCLEUSinv**
+- Added uncertainty calculation to batch mode in **NUCLEUSinv**
+- Added a new flag to the *Extra* menu of **NUCLEUSinv** that allows to set all relaxation times < *TE/5* to zero when `lsqlin` is used for the RTD inversion
+
+### Changed
+- Changed the default settings for NMR signal calculation in **NUCLEUSmod** (more realistic echo time *TE* of 200µs and the first echo within the time vector is actually *TE* or *TE/2* and not 0)
+
+### Fixed
+- Fixed an issue when exporting data from *UncertView* GUI to **NUCLEUSinv** main GUI
+- Re-factored a few of the uncertainty calculation functions
+- More seamless integration of *UncertView* GUI
+
 ## [0.2.0] - 2024-02-01
 
 ### Added
@@ -200,6 +215,7 @@
 
 Initial Version
 
+[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
 [0.1.13]: https://github.com/ThoHiller/nmr-nucleus/compare/v.0.1.12...v.0.1.13

NUCLEUSinv/NUCLEUSinv.m

@@ -38,8 +38,8 @@
 if ~isempty(h0); close(h0); end
 
 %% GUI 'header' info and defaults
-myui.version = '0.2.0';
-myui.date = '01.02.2024';
+myui.version = '0.2.1';
+myui.date = '11.02.2024';
 myui.author = {'Stephan Costabel','Thomas Hiller'};
 myui.email = 'thomas.hiller[at]bgr.de';
 myui.fontsize = 10;

NUCLEUSinv/NUCLEUSinv_createMenus.m

@@ -306,18 +306,18 @@
             'Label','RTD','Enable','off','Callback',@onMenuViewFigures);   
 end
 
-% 2.6 PhaseView
+% 2.6 PhaseView GUI
 gui.menu.extra_phaseview = uimenu(gui.menu.view,...
-    'Label','PhaseView GUI','Enable','off','Callback',@PhaseView);
-% 2.7 ConductVIEW -> hydraulic conductivity
+    'Label','PhaseView GUI','Enable','off','Separator','on','Callback',@onMenuSubGUIs);
+% 2.7 ConductVew GUI -> hydraulic conductivity
 gui.menu.extra_conduct = uimenu(gui.menu.view,...
-    'Label','ConductView GUI','Enable','off','Callback',@onMenuViewFigures);
-% 2.8 FixedTime VIEW
+    'Label','ConductView GUI','Enable','off','Callback',@onMenuSubGUIs);
+% 2.8 FixedTimeView GUI
 gui.menu.extra_fixedtime = uimenu(gui.menu.view,...
-    'Label','FixedTimeView GUI','Enable','off','Callback',@FixedTimeView);
-% 2.9 Uncertainty VIEW
+    'Label','FixedTimeView GUI','Enable','off','Callback',@onMenuSubGUIs);
+% 2.9 UncertaintyVIEW GUI
 gui.menu.extra_uncert = uimenu(gui.menu.view,...
-    'Label','UncertView GUI','Enable','off','Callback',@UncertView);
+    'Label','UncertView GUI','Enable','off','Callback',@onMenuSubGUIs);
 
 %% 3. Extras
 gui.menu.extra = uimenu(gui.figh,...
@@ -353,7 +353,12 @@
 gui.menu.extra_solver_lsqnonneg = uimenu(gui.menu.extra_solver,...
     'Label','LSQNONNEG (default)','Checked','on','Callback',@onMenuSolver);
 
-% 3.3 joint inversion (on/off)
+% 3.3 flag for LSQLIN option to set RTs smaller than min(TE)/5 to 0
+gui.menu.extra_lsqlin_echoflag = uimenu(gui.menu.extra,...
+    'Label','RTD<TE/5=0','Enable','off',...
+    'Callback',@onMenuExtraEchoFlag);
+
+% 3.4 joint inversion (on/off)
 gui.menu.extra_joint = uimenu(gui.menu.extra,...
     'Label','Joint Inversion','Checked','off','Separator','on',...
     'Callback',@onMenuJointInversion);
@@ -364,7 +369,7 @@
         set(gui.menu.extra_joint,'Enable','off');
 end
 
-% 3.4 set inversion bounds for surface relaxivity rho
+% 3.5 set inversion bounds for surface relaxivity rho
 gui.menu.extra_joint_rhobounds = uimenu(gui.menu.extra,...
     'Label','Surface relaxivity bounds','Enable','off',...
     'Callback',@onMenuExtraRhoBounds);

NUCLEUSinv/NUCLEUSinv_loadDefaults.m

@@ -53,6 +53,8 @@
 out.info.has_optim = 'off';
 out.info.solver = 'lsqnonneg';
 out.info.stat = 'off';
+% LSQLIN Echo flag: RTDs<TE/5=0 (default is off)
+out.info.EchoFlag = 'off';
 
 %% process panel defaults
 % first data sample of the signal

NUCLEUSmod/NUCLEUSmod.m

@@ -41,8 +41,8 @@
 if ~isempty(h0); close(h0); end
 
 %% GUI 'header' info and defaults
-myui.version = '0.2.0';
-myui.date = '01.02.2024';
+myui.version = '0.2.1';
+myui.date = '11.02.2024';
 myui.author = {'Stephan Costabel','Thomas Hiller'};
 myui.email = 'thomas.hiller[at]bgr.de';
 myui.fontsize = 10;

NUCLEUSmod/NUCLEUSmod_createMenus.m

@@ -102,7 +102,7 @@
 % 2.3 hydraulic conductivity
 gui.menu.view_conduct = uimenu(gui.menu.view,...
     'Label','ConductView GUI','Separator','on','Enable','off',...
-    'Callback',@onMenuViewFigures);
+    'Callback',@onMenuSubGUIs);
 
 %% 3. Color theme
 gui.menu.color_theme = uimenu(gui.figh,...

NUCLEUSmod/NUCLEUSmod_loadDefaults.m

@@ -70,9 +70,9 @@
 
 %% NMR panel defaults
 % echo time [µs]
-out.nmr.TE = 1000;
+out.nmr.TE = 200;
 % number of echoes
-out.nmr.echosN = 1001;
+out.nmr.echosN = 1000;
 % noise creation type 'level' or 'SNR'
 out.nmr.noisetype = 'level';
 % noise level [0:1] or SNR [-]
@@ -82,7 +82,7 @@
 % diffusion relaxation time [s]
 out.nmr.Tdiff = 1e6;
 % surface relaxivity [µm/s]
-out.nmr.rho = 10;
+out.nmr.rho = 100;
 % porosity value between 0 and 1 [-]
 out.nmr.porosity = 1;
 % plot T2 data as default

README.md

@@ -5,7 +5,7 @@
 modeling and i**N**version of n**UCL**ear magnetic r**E**sonance data with ang**U**lar pore**S**
 
 [![release](https://img.shields.io/github/release/NMR-NUCLEUS/nmr-nucleus.svg)](https://github.com/NMR-NUCLEUS/nmr-nucleus/releases/latest)
-[![DOI](https://zenodo.org/badge/165993294.svg)](https://zenodo.org/badge/latestdoi/165993294)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4022195.svg)](https://doi.org/10.5281/zenodo.4022195)
 - - -
 
 ## Table of Contents
@@ -61,7 +61,7 @@ In order to work properly you need to meet the following requirements:
 4. `findjobj` (get it from [FEX](https://de.mathworks.com/matlabcentral/fileexchange/14317-findjobj-find-java-handles-of-matlab-graphic-objects)) (<span style="color:red">required</span>)
 5. `fminsearchbnd` (get it from [FEX](https://de.mathworks.com/matlabcentral/fileexchange/8277-fminsearchbnd-fminsearchcon)) (<span style="color:red">required</span>)
 6. `dynamicDateTicks` (get it from [FEX](https://de.mathworks.com/matlabcentral/fileexchange/27075-intelligent-dynamic-date-ticks)) (<span style="color:green">optional</span>)
-7. `kde` kernel density estimator (get it from [FEX](https://de.mathworks.com/matlabcentral/fileexchange/14034-kernel-density-estimator)) (<span style="color:green">optional</span>)
+7. `kde` kernel density estimator (get it from [FEX](https://de.mathworks.com/matlabcentral/fileexchange/14034-kernel-density-estimator)) (<span style="color:green">optional; not needed for R2023b and newer</span>)
 
 If you do not have the Optimization or Statistics toolboxes then not all features are available (especially parts of the joint inversion). However, the general functionality of obtaining relaxation time distributions (RTDs) form NMR relaxometry data is of course working.
 
@@ -123,7 +123,7 @@ 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. (2024, Feb 01). ThoHiller/nmr-nucleus: v0.2.0 (Version v0.2.0). Zenodo. [https://doi.org/10.5281/zenodo.4022195]
+Thomas Hiller. (2024, Feb 11). ThoHiller/nmr-nucleus: v0.2.1 (Version v0.2.1). 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

@@ -70,7 +70,7 @@ function onListboxData(src,~)
             data_upd.pressure = data.pressure;
             data = data_upd;
 
-            % if "mono" or "free" inversion is chossen update the internal
+            % if "mono" or "free" inversion is chosen update the internal
             % fixed relaxation times field
             if strcmp(data.invstd.invtype,'mono') ||...
                     strcmp(data.invstd.invtype,'free')
@@ -120,6 +120,9 @@ function onListboxData(src,~)
 
             % take all echoes
             data.process.end = length(data.import.NMR.data{id}.signal);
+
+            % set default number of uncertainty runs
+            data.uncert.N = 10;
 
             % ---
             % special treatments
@@ -204,6 +207,10 @@ function onListboxData(src,~)
         if ~isempty(findobj('Tag','FIXEDTIMEVIEW'))
             FixedTimeView(gui.menu.extra_fixedtime);
         end
+        % if the UncertView window is open update it
+        if ~isempty(findobj('Tag','UNCERTVIEW'))
+            UncertView(gui.menu.extra_uncert);
+        end
     else
         helpdlg({'onListboxData:','Only choose one data set at a time.'},...
             'too many data');

callbacks/menus/onMenuExtraEchoFlag.m

@@ -0,0 +1,87 @@
+function onMenuExtraEchoFlag(src,~)
+%onMenuExtraEchoFlag handles the call from the menu that swicth the "EchoFlag"
+%
+% Syntax:
+%       onMenuExtraEchoFlag
+%
+% Inputs:
+%       src - handle of the calling object
+%
+% Outputs:
+%       none
+%
+% Example:
+%       onMenuExtraEchoFlag(src,~)
+%
+% Other m-files required:
+%       NUCLEUSinv_updateInterface
+%       updateStatusInformation
+%
+% Subfunctions:
+%       none
+%
+% MAT-files required:
+%       none
+%
+% See also: NUCLEUSinv
+% Author: see AUTHORS.md
+% email: see AUTHORS.md
+% License: MIT License (at end)
+
+%------------- BEGIN CODE --------------
+
+%% get GUI handle and data
+fig = findobj('Tag','INV');
+gui = getappdata(fig,'gui');
+data = getappdata(fig,'data');
+
+% on / off switch
+onoff = get(src,'Checked');
+
+% deactivate or activate the "EchoFlag"
+switch onoff
+    case 'on' % if it's on, switch it off
+        data.info.EchoFlag = 'off';
+        % menu entry
+        set(gui.menu.extra_lsqlin_echoflag,'Checked','off');
+    case 'off'  % if it's off, switch it on
+        data.info.EchoFlag = 'on';
+        % menu entry
+        set(gui.menu.extra_lsqlin_echoflag,'Checked','on');
+end
+
+% update GUI data
+setappdata(fig,'data',data);
+setappdata(fig,'gui',gui);
+% update interface
+NUCLEUSinv_updateInterface;
+% update status information
+updateStatusInformation(fig);
+updateToolTips;
+
+end
+
+%------------- END OF CODE --------------
+
+%% License:
+% MIT License
+%
+% Copyright (c) 2019 Thomas Hiller
+%
+% Permission is hereby granted, free of charge, to any person obtaining a copy
+% of this software and associated documentation files (the "Software"), to deal
+% in the Software without restriction, including without limitation the rights
+% to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+% copies of the Software, and to permit persons to whom the Software is
+% furnished to do so, subject to the following conditions:
+%
+% The above copyright notice and this permission notice shall be included in all
+% copies or substantial portions of the Software.
+%
+% THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+% IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+% FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+% AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+% LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+% OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+% SOFTWARE.

callbacks/menus/onMenuSolver.m

@@ -45,14 +45,16 @@ function onMenuSolver(src,~)
         % menu entry
         set(gui.menu.extra_solver_lsqlin,'Checked','on');
         set(gui.menu.extra_solver_lsqnonneg,'Checked','off');
-        
-        % update the tooltips
+
+        set(gui.menu.extra_lsqlin_echoflag,'Enable','on');
 
 elseif strfind(solver,'LSQNONNEG')
         data.info.solver = 'lsqnonneg';
         % menu entry
         set(gui.menu.extra_solver_lsqlin,'Checked','off');
         set(gui.menu.extra_solver_lsqnonneg,'Checked','on');
+
+        set(gui.menu.extra_lsqlin_echoflag,'Enable','off');
 end
 
 % update GUI data