see CHANGELOG.md

CHANGELOG.md

@@ -1,6 +1,16 @@
 # Changelog
 
-## [0.1.12] - latest
+## [0.1.13] - 2022-08-11
+
+### Changed
+- Changed the way the uncertainty region is displayed when the *Multi modal* fitting option in **NUCLEUSinv** is used (now it is `[mean-2*std mean+2*std]` before it was `[min max]`)
+
+### Fixed
+- Fixed an issue in **NUCLEUSmod** when calculating forward NMR data for single capillaries with corners (*right angular* and *polygon*)
+- Fixed an issue in the **NUCLEUSmod** example scripts (*T<sub>diff</sub>* was not initialized)
+- Fixed an issue in **NUCLEUSinv** regarding the fitting routine `fitDataFree` in combination with the Optimization Toolbox in Matlab Versions newer than R2019b
+
+## [0.1.12] - 2022-02-17
 
 ### 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)
@@ -171,6 +181,7 @@
 
 Initial Version
 
+[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
 [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

NUCLEUSinv/NUCLEUSinv.m

@@ -38,8 +38,8 @@
 if ~isempty(h0); close(h0); end
 
 %% GUI 'header' info and defaults
-myui.version = '0.1.12';
-myui.date = '17.02.2022';
+myui.version = '0.1.13';
+myui.date = '11.08.2022';
 myui.author = {'Stephan Costabel','Thomas Hiller'};
 myui.email = 'thomas.hiller[at]bgr.de';
 myui.fontsize = 10;

NUCLEUSinv/NUCLEUSinv_createMenus.m

@@ -124,6 +124,9 @@
 % 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);
+% 1.1.1.5.3 DART (University of Vienna)
+gui.menu.file_import_lab_dart = uimenu(gui.menu.file_import_lab_other,...
+    'Label','DART','Tag','Lab','Callback',@onMenuImport);
 
 % 1.1.2 Ascii
 gui.menu.file_import_ascii = uimenu(gui.menu.file_import,...

NUCLEUSmod/NUCLEUSmod.m

@@ -41,8 +41,8 @@
 if ~isempty(h0); close(h0); end
 
 %% GUI 'header' info and defaults
-myui.version = '0.1.12';
-myui.date = '17.02.2022';
+myui.version = '0.1.13';
+myui.date = '11.08.2022';
 myui.author = {'Stephan Costabel','Thomas Hiller'};
 myui.email = 'thomas.hiller[at]bgr.de';
 myui.fontsize = 10;

README.md

@@ -62,7 +62,7 @@ If you do not have the Optimization or Statistics toolboxes then not all feature
 
 #### Operating System
 
-I tested it successfully under Windows 7 (64bit) and 10 (64bit) with Matlab R2014b and newer. Always with the latest version of the GUI Layout Toolbox (current version is v2.3.5)
+I tested it successfully under Windows 7 (64bit) and 10 (64bit) with Matlab R2016b and newer. Always with the latest version of the GUI Layout Toolbox (current version is v2.3.5)
 
 **NOTE:** So far I did not test anything on Linux or a Mac. If you get it to work on either of the two systems (which it basically should I guess) please let me know.
 
@@ -108,7 +108,7 @@ 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. (2021, March 12). ThoHiller/nmr-nucleus: v0.1.12 (Version v0.1.12). Zenodo. [https://doi.org/10.5281/zenodo.4022195]
+Thomas Hiller. (2022, Aug 11). ThoHiller/nmr-nucleus: v0.1.13 (Version v0.1.13). 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.
 

doc/nucleus/NUCLEUSinv/NUCLEUSinv.html

@@ -111,8 +111,8 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0038 <span class="keyword">if</span> ~isempty(h0); close(h0); <span class="keyword">end</span>
 0039 
 0040 <span class="comment">%% GUI 'header' info and defaults</span>
-0041 myui.version = <span class="string">'0.1.12'</span>;
-0042 myui.date = <span class="string">'17.02.2022'</span>;
+0041 myui.version = <span class="string">'0.1.13'</span>;
+0042 myui.date = <span class="string">'11.08.2022'</span>;
 0043 myui.author = {<span class="string">'Stephan Costabel'</span>,<span class="string">'Thomas Hiller'</span>};
 0044 myui.email = <span class="string">'thomas.hiller[at]bgr.de'</span>;
 0045 myui.fontsize = 10;

doc/nucleus/NUCLEUSinv/NUCLEUSinv_createPanelInversionJoint.html

@@ -295,10 +295,10 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0223 <span class="comment">%% angles</span>
 0224 gui.text_handles.invjoint_angles = uicontrol(<span class="string">'Parent'</span>,gui.panels.invjoint.HBox7,<span class="keyword">...</span>
 0225     <span class="string">'Style'</span>,<span class="string">'text'</span>,<span class="string">'FontSize'</span>,myui.fontsize,<span class="string">'HorizontalAlignment'</span>,<span class="string">'center'</span>,<span class="keyword">...</span>
-0226     <span class="string">'String'</span>,[<span class="string">'angles  -  '</span>,char(hex2dec(<span class="string">'03B1'</span>)),<span class="string">' [°] | '</span>,<span class="keyword">...</span>
-0227     char(hex2dec(<span class="string">'03B2'</span>)),<span class="string">' [°] | '</span>,char(hex2dec(<span class="string">'03B3'</span>)),<span class="string">' [°]'</span>]);
+0226     <span class="string">'String'</span>,[<span class="string">'angles  -  '</span>,char(hex2dec(<span class="string">'03B1'</span>)),<span class="string">' [°] | '</span>,<span class="keyword">...</span>
+0227     char(hex2dec(<span class="string">'03B2'</span>)),<span class="string">' [°] | '</span>,char(hex2dec(<span class="string">'03B3'</span>)),<span class="string">' [°]'</span>]);
 0228 tstr = [<span class="string">'&lt;HTML&gt;For &lt;b&gt;right angular&lt;/b&gt; geometry:&lt;br&gt;&lt;br&gt;'</span>,<span class="keyword">...</span>
-0229     <span class="string">'angle '</span>,char(hex2dec(<span class="string">'03B1'</span>)),<span class="string">' is always 90°&lt;br&gt;'</span>,<span class="keyword">...</span>
+0229     <span class="string">'angle '</span>,char(hex2dec(<span class="string">'03B1'</span>)),<span class="string">' is always 90°&lt;br&gt;'</span>,<span class="keyword">...</span>
 0230     <span class="string">'angle '</span>,char(hex2dec(<span class="string">'03B2'</span>)),<span class="string">' is adjustable&lt;br&gt;'</span>,<span class="keyword">...</span>
 0231     <span class="string">'angle '</span>,char(hex2dec(<span class="string">'03B3'</span>)),<span class="string">' gets calculated from the other two.&lt;br&gt;&lt;br&gt;'</span>,<span class="keyword">...</span>
 0232     <span class="string">'&lt;u&gt;Default value:&lt;/u&gt;&lt;br&gt;'</span>,<span class="keyword">...</span>
@@ -322,7 +322,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0250 <span class="comment">%% start values for rho and angle</span>
 0251 gui.text_handles.invjoint_startvalues = uicontrol(<span class="string">'Parent'</span>,gui.panels.invjoint.HBox8,<span class="keyword">...</span>
 0252     <span class="string">'Style'</span>,<span class="string">'text'</span>,<span class="string">'FontSize'</span>,myui.fontsize,<span class="string">'HorizontalAlignment'</span>,<span class="string">'center'</span>,<span class="keyword">...</span>
-0253     <span class="string">'String'</span>,[<span class="string">'start values - '</span>,char(hex2dec(<span class="string">'03C1'</span>)),<span class="string">' [µm/s] | '</span>,char(hex2dec(<span class="string">'03B2'</span>)),<span class="string">' [°]'</span>]);
+0253     <span class="string">'String'</span>,[<span class="string">'start values - '</span>,char(hex2dec(<span class="string">'03C1'</span>)),<span class="string">' [µm/s] | '</span>,char(hex2dec(<span class="string">'03B2'</span>)),<span class="string">' [°]'</span>]);
 0254 tstr = <span class="string">'tba'</span>;
 0255 gui.edit_handles.invjoint_rhostart = uicontrol(<span class="string">'Parent'</span>,gui.panels.invjoint.HBox8,<span class="keyword">...</span>
 0256     <span class="string">'Style'</span>,<span class="string">'edit'</span>,<span class="string">'String'</span>,num2str(data.invjoint.rhostart),<span class="string">'FontSize'</span>,myui.fontsize,<span class="keyword">...</span>

doc/nucleus/NUCLEUSinv/NUCLEUSinv_createPanelPetro.html

@@ -156,8 +156,8 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0084 <span class="comment">%% surface relaxivity rho and geometry factor a</span>
 0085 gui.text_handles.petro_rho = uicontrol(<span class="string">'Parent'</span>,gui.panels.petro.HBox2,<span class="keyword">...</span>
 0086     <span class="string">'Style'</span>,<span class="string">'text'</span>,<span class="string">'FontSize'</span>,myui.fontsize,<span class="string">'HorizontalAlignment'</span>,<span class="string">'center'</span>,<span class="keyword">...</span>
-0087     <span class="string">'String'</span>,[char(hex2dec(<span class="string">'03C1'</span>)),<span class="string">' [µm/s]   |   geom  '</span>]);
-0088 tstr = [<span class="string">'&lt;HTML&gt;Surface relaxivity in [µm/s].&lt;br&gt;&lt;br&gt;'</span>,<span class="keyword">...</span>
+0087     <span class="string">'String'</span>,[char(hex2dec(<span class="string">'03C1'</span>)),<span class="string">' [µm/s]   |   geom  '</span>]);
+0088 tstr = [<span class="string">'&lt;HTML&gt;Surface relaxivity in [µm/s].&lt;br&gt;&lt;br&gt;'</span>,<span class="keyword">...</span>
 0089     <span class="string">'1/Ts = &lt;b&gt;rho&lt;/b&gt;*S/V = &lt;b&gt;rho&lt;/b&gt;*a/R.&lt;br&gt;&lt;br&gt;'</span>,<span class="keyword">...</span>
 0090     <span class="string">'&lt;u&gt;Default value:&lt;/u&gt;&lt;br&gt;'</span>,<span class="keyword">...</span>
 0091     <span class="string">'&lt;b&gt;10&lt;/b&gt;&lt;br&gt;'</span>];
@@ -171,9 +171,9 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0099     <span class="string">'&lt;b&gt;2&lt;/b&gt; capillaries with circular cross section&lt;br&gt;'</span>,<span class="keyword">...</span>
 0100     <span class="string">'&lt;b&gt;3&lt;/b&gt; spheres&lt;br&gt;&lt;br&gt;'</span>,<span class="keyword">...</span>
 0101     <span class="string">'For &lt;b&gt;right angular&lt;/b&gt; and &lt;b&gt;polygonal&lt;/b&gt; cross-sections &quot;a&quot; converts to the area-equivalent cylinder radius e.g.:&lt;br&gt;'</span>,<span class="keyword">...</span>
-0102     <span class="string">'&lt;b&gt;2.57&lt;/b&gt; capillaries with 60°-60°-60° equilateral cross section&lt;br&gt;'</span>,<span class="keyword">...</span>
-0103     <span class="string">'&lt;b&gt;2.72-12.18&lt;/b&gt; capillaries with 90°-a°-(90-a)° right angular cross section&lt;br&gt;'</span>,<span class="keyword">...</span>
-0104     <span class="string">'e.g. &lt;b&gt;2.72&lt;/b&gt; is 90°-45°-45° | &lt;b&gt;2.87&lt;/b&gt; is 90°-60°-30° | &lt;b&gt;5.64&lt;/b&gt; is 90°-85°-5°&lt;br&gt;&lt;br&gt;'</span>,<span class="keyword">...</span>
+0102     <span class="string">'&lt;b&gt;2.57&lt;/b&gt; capillaries with 60°-60°-60° equilateral cross section&lt;br&gt;'</span>,<span class="keyword">...</span>
+0103     <span class="string">'&lt;b&gt;2.72-12.18&lt;/b&gt; capillaries with 90°-a°-(90-a)° right angular cross section&lt;br&gt;'</span>,<span class="keyword">...</span>
+0104     <span class="string">'e.g. &lt;b&gt;2.72&lt;/b&gt; is 90°-45°-45° | &lt;b&gt;2.87&lt;/b&gt; is 90°-60°-30° | &lt;b&gt;5.64&lt;/b&gt; is 90°-85°-5°&lt;br&gt;&lt;br&gt;'</span>,<span class="keyword">...</span>
 0105     <span class="string">'&lt;u&gt;Default value:&lt;/u&gt;&lt;br&gt;'</span>,<span class="keyword">...</span>
 0106     <span class="string">'&lt;b&gt;2&lt;/b&gt;&lt;br&gt;'</span>];
 0107 gui.edit_handles.param_geom = uicontrol(<span class="string">'Parent'</span>,gui.panels.petro.HBox2,<span class="keyword">...</span>

doc/nucleus/NUCLEUSinv/NUCLEUSinv_loadDefaults.html

@@ -141,7 +141,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0072 out.process.timefac = 1;
 0073 
 0074 <span class="comment">%% petrophysical parameters panel</span>
-0075 <span class="comment">% surface relaxivity [µm/s]</span>
+0075 <span class="comment">% surface relaxivity [µm/s]</span>
 0076 out.param.rho = 10;  
 0077 <span class="comment">% surface to volume ratio factor a [-] 1/T = rho*(S/V) = rho*a/R</span>
 0078 out.param.a = 2;      
@@ -230,15 +230,15 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0161 out.invjoint.geometry_type = <span class="string">'cyl'</span>;
 0162 <span class="comment">% number of polygon sides for geometry 'poly' (3 to 12)</span>
 0163 out.invjoint.polyN = 3;
-0164 <span class="comment">% angle alpha [deg] - fixed to 90°</span>
+0164 <span class="comment">% angle alpha [deg] - fixed to 90°</span>
 0165 out.invjoint.alpha = 90;
 0166 <span class="comment">% angle beta [deg] - changed by user</span>
 0167 out.invjoint.beta = 60;
 0168 <span class="comment">% gamma [deg] - alpha-beta</span>
 0169 out.invjoint.gamma = 30;
-0170 <span class="comment">% start value rho [µm/s]</span>
+0170 <span class="comment">% start value rho [µm/s]</span>
 0171 out.invjoint.rhostart = 20;
-0172 <span class="comment">% lower and upper boundary for rho [µm/s]</span>
+0172 <span class="comment">% lower and upper boundary for rho [µm/s]</span>
 0173 out.invjoint.rhobounds = [0.01 1000];
 0174 <span class="comment">% sart value beta [deg]</span>
 0175 out.invjoint.anglestart = 25;

doc/nucleus/NUCLEUSinv/NUCLEUSinv_updateInterface.html

@@ -804,15 +804,15 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0724         set(gui.text_handles.invstd_RTDtimes,<span class="string">'String'</span>,<span class="string">'RTD - min [s] | max [s] | # / dec'</span>,<span class="keyword">...</span>
 0725             <span class="string">'FontSize'</span>,10);
 0726         set(gui.text_handles.petro_Tbulk,<span class="string">'String'</span>,<span class="string">'Tbulk [s]   |   Tdiff [s]'</span>);
-0727         set(gui.text_handles.petro_rho,<span class="string">'String'</span>,[char(hex2dec(<span class="string">'03C1'</span>)),<span class="string">' [µm/s]   |   geom  '</span>]);
+0727         set(gui.text_handles.petro_rho,<span class="string">'String'</span>,[char(hex2dec(<span class="string">'03C1'</span>)),<span class="string">' [µm/s]   |   geom  '</span>]);
 0728         
 0729     <span class="keyword">case</span> <span class="string">'ms'</span>        
 0730         set(gui.radio_handles.process_timescale_s,<span class="string">'Enable'</span>,<span class="string">'on'</span>,<span class="string">'Value'</span>,0);
 0731         set(gui.radio_handles.process_timescale_ms,<span class="string">'Enable'</span>,<span class="string">'on'</span>,<span class="string">'Value'</span>,1);
 0732         set(gui.text_handles.invstd_RTDtimes,<span class="string">'String'</span>,<span class="string">'RTD - min [ms] | max [ms] | # / dec'</span>,<span class="keyword">...</span>
 0733             <span class="string">'FontSize'</span>,9);
 0734         set(gui.text_handles.petro_Tbulk,<span class="string">'String'</span>,<span class="string">'Tbulk [ms]   |   Tdiff [ms]'</span>);
-0735         set(gui.text_handles.petro_rho,<span class="string">'String'</span>,[char(hex2dec(<span class="string">'03C1'</span>)),<span class="string">' [µm/s]   |   geom  '</span>]);
+0735         set(gui.text_handles.petro_rho,<span class="string">'String'</span>,[char(hex2dec(<span class="string">'03C1'</span>)),<span class="string">' [µm/s]   |   geom  '</span>]);
 0736 <span class="keyword">end</span>
 0737 
 0738 <span class="keyword">end</span>

doc/nucleus/NUCLEUSmod/NUCLEUSmod.html

@@ -117,8 +117,8 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0041 <span class="keyword">if</span> ~isempty(h0); close(h0); <span class="keyword">end</span>
 0042 
 0043 <span class="comment">%% GUI 'header' info and defaults</span>
-0044 myui.version = <span class="string">'0.1.12'</span>;
-0045 myui.date = <span class="string">'17.02.2022'</span>;
+0044 myui.version = <span class="string">'0.1.13'</span>;
+0045 myui.date = <span class="string">'11.08.2022'</span>;
 0046 myui.author = {<span class="string">'Stephan Costabel'</span>,<span class="string">'Thomas Hiller'</span>};
 0047 myui.email = <span class="string">'thomas.hiller[at]bgr.de'</span>;
 0048 myui.fontsize = 10;

doc/nucleus/NUCLEUSmod/NUCLEUSmod_createPanelCPS.html

@@ -136,12 +136,12 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0066     <span class="string">'Tag'</span>,<span class="string">'pressure_sigma'</span>,<span class="string">'Enable'</span>,<span class="string">'on'</span>,<span class="string">'Callback'</span>,@<a href="../../nucleus/callbacks/edits/onEditValue.html" class="code" title="function onEditValue(src,~)">onEditValue</a>);
 0067 gui.text_handles.theta = uicontrol(<span class="string">'Parent'</span>,gui.panels.cps.HBox1,<span class="keyword">...</span>
 0068     <span class="string">'Style'</span>,<span class="string">'text'</span>,<span class="string">'FontSize'</span>,myui.fontsize,<span class="string">'HorizontalAlignment'</span>,<span class="string">'center'</span>,<span class="keyword">...</span>
-0069     <span class="string">'String'</span>,[<span class="string">'CA '</span>,char(hex2dec(<span class="string">'03B8'</span>)),<span class="string">' [°]'</span>]);
+0069     <span class="string">'String'</span>,[<span class="string">'CA '</span>,char(hex2dec(<span class="string">'03B8'</span>)),<span class="string">' [°]'</span>]);
 0070 tstr = [<span class="string">'&lt;HTML&gt;Set surface contact angle &amp;theta of water&lt;br&gt;&lt;br&gt;'</span>,<span class="keyword">...</span>
 0071     <span class="string">'&lt;u&gt;Available options:&lt;/u&gt;&lt;br&gt;'</span>,<span class="keyword">...</span>
-0072     <span class="string">'&lt;b&gt;0°&lt;/b&gt; to &lt;b&gt; &amp;lt 90°&lt;/b&gt; &lt;br&gt;&lt;br&gt;'</span>,<span class="keyword">...</span>
+0072     <span class="string">'&lt;b&gt;0°&lt;/b&gt; to &lt;b&gt; &amp;lt 90°&lt;/b&gt; &lt;br&gt;&lt;br&gt;'</span>,<span class="keyword">...</span>
 0073     <span class="string">'&lt;u&gt;Default value:&lt;/u&gt;&lt;br&gt;'</span>,<span class="keyword">...</span>
-0074     <span class="string">'&lt;b&gt;0°&lt;/b&gt;&lt;br&gt;'</span>];
+0074     <span class="string">'&lt;b&gt;0°&lt;/b&gt;&lt;br&gt;'</span>];
 0075 gui.edit_handles.theta = uicontrol(<span class="string">'Parent'</span>,gui.panels.cps.HBox1,<span class="keyword">...</span>
 0076     <span class="string">'Style'</span>,<span class="string">'edit'</span>,<span class="string">'String'</span>,num2str(data.pressure.theta),<span class="string">'FontSize'</span>,myui.fontsize,<span class="keyword">...</span>
 0077     <span class="string">'UserData'</span>,struct(<span class="string">'Tooltipstr'</span>,tstr,<span class="string">'defaults'</span>,[data.pressure.theta 1 1]),<span class="keyword">...</span>