Merge commit dev into dev_varRBErobOpt

HomolkaN · Dec 3, 2020 · 4c987aa · 4c987aa
2 parents 52e1d08 + 1d2bc93
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diff --git a/ChangeLog.txt b/ChangeLog.txt
@@ -1,4 +1,21 @@
-Version 2.10.0 "Blaise"
+Version 2.10.1 - Patch release for "Blaise" 
+	Release with small updates, clean-ups and bugfixes    
+    - Bugfix in 3D view due to inconsistent angles in pln & stf
+    - Bugfix for using incorrect dicom UID's and wrong writing order in the dicom export
+    - Bugfix for weird colormap issue in plotting
+    - New handling of environment checking with matRad_cfg (old function is still working)
+    - Code documentation update
+    - Remove hardcoded penumbra width in photon dose calculation -> can now be stored in machine file (machine.data.penumbraFWHMatIso)
+    - Update to ompMC to use virtual Gaussian source (uses measured penumbra value) incld precompiled mex files
+    - remove useless global statements before matRad_cfg
+    - add blue/white/red difference map to colormaps (in the correct way)
+    - Updated TravisCI testing (Sped up by using pre-compiled mex interfaces and including testing with Matlab (on Ubuntu), Azure DevOps as fallback
+    - Github gimmicks added: Stalebot, Issue & PR Templates
+	- code optimization for jacobian evaluation (x10-100 speedup)
+	- New option pln.propDoseCalc.useGivenEqDensityCube (default false) to directly use the literal values from ct.cube and omit HU to WEQ conversion from ct.cubeHU
+	- New option pln.propDoseCalc.ignoreOutsideDensities (default true) to disable/enable inclusion of WEPL outside the patient contour in ray-tracing
+
+Version 2.10.0 - "Blaise"
 	Second Release of matRad. Note that despite major incompatibilities with "Alan" we still chose major version number "2" to have a consistent versioning in the future.
 	we want to thank all new contributing authors (see AUTHORS.txt)
 	The new release contains:

diff --git a/MatRad_Config.m b/MatRad_Config.m
@@ -148,7 +148,7 @@ function setDefaultProperties(obj)
             %   properties
             %  input
 
-            obj.propStf.defaultLongitudinalSpotSpacing = 3;
+            obj.propStf.defaultLongitudinalSpotSpacing = 2;
             obj.propStf.defaultAddMargin = true; %expand target for beamlet finding
 
             obj.propDoseCalc.defaultResolution = struct('x',3,'y',3,'z',3); %[mm]

diff --git a/README.md b/README.md
@@ -6,6 +6,9 @@
 [![TravisCI Build Status](https://travis-ci.org/e0404/matRad.svg?branch=dev_varRBErobOpt)](https://travis-ci.org/e0404/matRad)
 [![Azure Pipelines Build Status](https://dev.azure.com/e0404/matRad/_apis/build/status/e0404.matRad?branchName=dev_varRBErobOpt)](https://dev.azure.com/e0404/matRad)
 
+DOIs:
+- General DOI: [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.3879615.svg)](https://doi.org/10.5281/zenodo.3879615)
+- Latest Release: [![DOI](https://zenodo.org/badge/29671667.svg)](https://zenodo.org/badge/latestdoi/29671667)
 
 # General information
 
@@ -68,9 +71,13 @@ Still having problems? Then create an issue, provide a **minimum example** of yo
 
 # Citing matRad
 
+### Scientific papers
+
 If you use matRad in a scientific publication, consider citing the following paper:
 
-Wieser, Hans-Peter, et al. "Development of the open-source dose calculation and optimization toolkit matRad." Medical Physics 44.6 (2017): 2556-2568.
+Wieser, Hans-Peter, et al. "Development of the open-source dose calculation and optimization toolkit matRad." Medical Physics 44.6 (2017): 2556-2568. 
+
+[![DOI](https://img.shields.io/badge/DOI-10.1002%2Fmp.12251-blue)](https://doi.org/10.1002/mp.12251) 
 
 BibTex entry:
 ```
@@ -82,10 +89,21 @@ BibTex entry:
   number={6},
   pages={2556--2568},
   year={2017},
-  publisher={Wiley Online Library}
+  publisher={Wiley Online Library},
+  doi={10.1002/mp.12251}
 }
 ```
 
+### Citing as Software
+
+matRad's code also has its own general DOI with Zenodo: 
+
+[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.3879615.svg)](https://doi.org/10.5281/zenodo.3879615)
+
+You can cite specific versions of matRad in your work! For example, Here is the badge that lead's to the latest release of matRad:
+
+[![DOI](https://zenodo.org/badge/29671667.svg)](https://zenodo.org/badge/latestdoi/29671667)
+
 ---
 
 Copyright 2020 the matRad development team. 

diff --git a/matRad.prj b/matRad.prj
@@ -39,8 +39,8 @@
       <param.web.mcr>true</param.web.mcr>
       <param.package.mcr>false</param.package.mcr>
       <param.no.mcr>false</param.no.mcr>
-      <param.web.mcr.name>matRad_installerWin64_v2.10.0_prepareBlaise-ef7488df</param.web.mcr.name>
-      <param.package.mcr.name>matRad_installerWin64_wRT_v2.10.0_prepareBlaise-ef7488df</param.package.mcr.name>
+      <param.web.mcr.name>matRad_installerWin64_v2.10.1</param.web.mcr.name>
+      <param.package.mcr.name>matRad_installerWin64_wRT_v2.10.1</param.package.mcr.name>
       <param.no.mcr.name>MyAppInstaller_app</param.no.mcr.name>
       <param.windows.command.prompt>true</param.windows.command.prompt>
       <param.create.log>true</param.create.log>
@@ -78,44 +78,10 @@
       </fileset.main>
       <fileset.resources>
          <file>${PROJECT_ROOT}\basedata\photons_Generic.mat</file>
-		       <file>${PROJECT_ROOT}\basedata\protons_Generic.mat</file>
-		       <file>${PROJECT_ROOT}\basedata\carbon_Generic.mat</file>
+		 <file>${PROJECT_ROOT}\basedata\protons_Generic.mat</file>
+		 <file>${PROJECT_ROOT}\basedata\carbon_Generic.mat</file>
          <file>${PROJECT_ROOT}\dicom</file>
-         <file>${PROJECT_ROOT}\dicom\DKFZ_Logo.png</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_calcHU.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_calcWaterEqD.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_convRtssContours2Indices.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_createCst.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_dummyCst.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_importDicom.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_importDicomCt.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_importDicomGUI.fig</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_importDicomGUI.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_importDicomRTDose.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_importDicomRTPlan.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_importDicomRtss.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_importDicomSteeringParticles.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_importDicomSteeringPhotons.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_importFieldShapes.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_interpDicomCtCube.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_interpDicomDoseCube.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_listAllFiles.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_loadHLUT.m</file>
-         <file>${PROJECT_ROOT}\dicom\matrad_logo.png</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_progress.m</file>
-         <file>${PROJECT_ROOT}\dicom\matRad_scanDicomImportFolder.m</file>
          <file>${PROJECT_ROOT}\IO</file>
-         <file>${PROJECT_ROOT}\IO\matRad_exportGUI.fig</file>
-         <file>${PROJECT_ROOT}\IO\matRad_exportGUI.m</file>
-         <file>${PROJECT_ROOT}\IO\matRad_importGUI.fig</file>
-         <file>${PROJECT_ROOT}\IO\matRad_importGUI.m</file>
-         <file>${PROJECT_ROOT}\IO\matRad_importPatient.m</file>
-         <file>${PROJECT_ROOT}\IO\matRad_readCube.m</file>
-         <file>${PROJECT_ROOT}\IO\matRad_readNRRD.m</file>
-         <file>${PROJECT_ROOT}\IO\matRad_writeCube.m</file>
-         <file>${PROJECT_ROOT}\IO\matRad_writeMHA.m</file>
-         <file>${PROJECT_ROOT}\IO\matRad_writeNRRD.m</file>
-         <file>${PROJECT_ROOT}\IO\matRad_writeVTK.m</file>
          <file>${PROJECT_ROOT}\matRad.m</file>
          <file>${PROJECT_ROOT}\matRad_addMargin.m</file>
          <file>${PROJECT_ROOT}\matRad_calcCubes.m</file>
@@ -168,30 +134,8 @@
          <file>${PROJECT_ROOT}\matRadGUI.fig</file>
          <file>${PROJECT_ROOT}\matRadGUI.m</file>
          <file>${PROJECT_ROOT}\optimization</file>
-         <file>${PROJECT_ROOT}\optimization\matRad_backProjection.m</file>
-         <file>${PROJECT_ROOT}\optimization\matRad_calcInversDVH.m</file>
-         <file>${PROJECT_ROOT}\optimization\matRad_collapseDij.m</file>
          <file>${PROJECT_ROOT}\plotting</file>
-         <file>${PROJECT_ROOT}\plotting\colormaps\colormapTemplate.txt</file>
-         <file>${PROJECT_ROOT}\plotting\matRad_computeAllVoiSurfaces.m</file>
-         <file>${PROJECT_ROOT}\plotting\matRad_computeIsoDoseContours.m</file>
-         <file>${PROJECT_ROOT}\plotting\matRad_computeVoiContours.m</file>
-         <file>${PROJECT_ROOT}\plotting\matRad_computeVoiContoursWrapper.m</file>
-         <file>${PROJECT_ROOT}\plotting\matRad_getColormap.m</file>
-         <file>${PROJECT_ROOT}\plotting\matRad_plotAxisLabels.m</file>
-         <file>${PROJECT_ROOT}\plotting\matRad_plotColorbar.m</file>
-         <file>${PROJECT_ROOT}\plotting\matRad_plotCtSlice.m</file>
-         <file>${PROJECT_ROOT}\plotting\matRad_plotCtSlice3D.m</file>
-         <file>${PROJECT_ROOT}\plotting\matRad_plotDoseSlice.m</file>
-         <file>${PROJECT_ROOT}\plotting\matRad_plotDoseSlice3D.m</file>
-         <file>${PROJECT_ROOT}\plotting\matRad_plotIsoCenterMarker.m</file>
-         <file>${PROJECT_ROOT}\plotting\matRad_plotIsoDoseLines.m</file>
-         <file>${PROJECT_ROOT}\plotting\matRad_plotIsoDoseLines3D.m</file>
-         <file>${PROJECT_ROOT}\plotting\matRad_plotPlan3D.m</file>
-         <file>${PROJECT_ROOT}\plotting\matRad_plotVoiContourSlice.m</file>
-         <file>${PROJECT_ROOT}\plotting\matRad_plotVois3D.m</file>
          <file>${PROJECT_ROOT}\tools</file>
-         <file>${PROJECT_ROOT}\tools\matRad_getEnvironment.m</file>
       </fileset.resources>
       <fileset.package>
          <file>${PROJECT_ROOT}\phantoms</file>
@@ -212,7 +156,7 @@
       </build-deliverables>
       <workflow/>
       <matlab>
-        <root>C:\Program Files\MATLAB\R2018b</root>
+        <root>C:\Program Files\MATLAB\R2019a</root>
       </matlab>
       <platform>
          <unix>false</unix>

diff --git a/matRadGUI.m b/matRadGUI.m
@@ -1993,14 +1993,27 @@ function UpdateState(handles)
 
 % fill GUI elements with plan information
 function setPln(handles)
+
+matRad_cfg = MatRad_Config.instance();
+
 pln = evalin('base','pln');
 % sanity check of isoCenter
 if size(pln.propStf.isoCenter,1) ~= pln.propStf.numOfBeams && size(pln.propStf.isoCenter,1) == 1
   pln.propStf.isoCenter = ones(pln.propStf.numOfBeams,1) * pln.propStf.isoCenter(1,:);
 elseif size(pln.propStf.isoCenter,1) ~= pln.propStf.numOfBeams && size(pln.propStf.isoCenter,1) ~= 1
-  error('Isocenter in plan file are incosistent.');
+  matRad_cfg.dispError('Isocenter in plan file are incosistent.');
 end
-set(handles.editBixelWidth,'String',num2str(pln.propStf.bixelWidth));
+
+%Sanity check for the bixelWidth field
+bixelWidth = pln.propStf.bixelWidth;
+
+if isnumeric(bixelWidth) && isscalar(bixelWidth)
+    bixelWidth = num2str(pln.propStf.bixelWidth);
+elseif ~isnumeric(bixelWidth) && ~strcmp(bixelWidth,'field')
+    matRad_cfg.dispError('Invalid bixel width! Must be a scalar number or ''field'' for field-based dose calculation with shapes stored in stf!');
+end   
+
+set(handles.editBixelWidth,'String',bixelWidth);
 set(handles.editFraction,'String',num2str(pln.numOfFractions));
 
 if isfield(pln.propStf,'isoCenter')
@@ -2135,7 +2148,20 @@ function getPlnFromGUI(handles)
     pln = evalin('base','pln');
 end
 
-pln.propStf.bixelWidth      = parseStringAsNum(get(handles.editBixelWidth,'String'),false); % [mm] / also corresponds to lateral spot spacing for particles
+% Special parsing of bixelWidth (since it can also be "field") for imported
+% shapes
+bixelWidth = get(handles.editBixelWidth,'String'); % [mm] / also corresponds to lateral spot spacing for particles
+if strcmp(bixelWidth,'field')
+    pln.propStf.bixelWidth = bixelWidth; 
+else
+    pln.propStf.bixelWidth = parseStringAsNum(bixelWidth,false);
+    if isnan(pln.propStf.bixelWidth)
+        warndlg('Invalid bixel width! Use standard bixel width of 5mm!');
+        pln.propStf.bixelWidth = 5;
+        set(handles.editBixelWidth,'String','5');
+    end
+end
+
 pln.propStf.gantryAngles    = parseStringAsNum(get(handles.editGantryAngle,'String'),true); % [???]
 
 if handles.eduMode
@@ -2591,9 +2617,22 @@ function pushbutton_recalc_Callback(hObject, ~, handles)
         Suffix = '';
     end
 
-    if sum([stf.totalNumOfBixels]) ~= length(resultGUI.(['w' Suffix]))
-        warndlg('weight vector does not corresponding to current steering file');
-        return
+    wField = ['w' Suffix];
+
+    if ~isfield(resultGUI,wField) 
+        warndlg(['No exact match found for weight vector ''' wField ''' with selected dose insance. Trying common weight vector ''w'' instead!']);
+        wField = 'w';
+    end
+
+    %Second sanity check to exclude case with no 'w' present
+    if ~isfield(resultGUI,wField)
+        errordlg('No weight vector found for forward dose recalculation!');
+        return;
+    end
+
+    if sum([stf.totalNumOfBixels]) ~= length(resultGUI.(wField))
+        errordlg('Selected weight vector does not correspond to current steering file (wrong number of entries/bixels!)!');
+        return;
     end
 
     % change isocenter if that was changed and do _not_ recreate steering
@@ -2610,7 +2649,7 @@ function pushbutton_recalc_Callback(hObject, ~, handles)
     end
 
     % recalculate cubes in resultGUI
-    resultGUIreCalc = matRad_calcCubes(resultGUI.(['w' Suffix]),dij,cst);
+    resultGUIreCalc = matRad_calcCubes(resultGUI.(wField),dij);
 
     % delete old variables to avoid confusion
     if isfield(resultGUI,'effect')