Merge branch 'dev' of https://github.com/JenHardt/matRad into dev

HomolkaN · Feb 7, 2023 · aab03e9 · aab03e9
2 parents 9f4af93 + 27ad9ff
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -1,5 +1,5 @@
 # This is a basic workflow to help you get started with Actions
-name: Testing
+name: Tests
 # Controls when the action will run. 
 on: [push, pull_request, workflow_dispatch]  
 jobs:

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,123 @@
+cff-version: 1.2.0
+message: "If you use matRad, consider citing it and the corresponding research paper"
+authors:
+- family-names: "Ackermann"
+  given-names: "Benjamin"
+- family-names: "Bangert"
+  given-names: "Mark"
+- family-names: "Bennan"
+  given-names: "Amit Ben Antony"
+- family-names: "Burigo"
+  given-names: "Lucas"
+- family-names: "Cabal"
+  given-names: "Gonzalo"
+- family-names: "Cisternas"
+  given-names: "Eduardo"
+- family-names: "Charton"
+  given-names: "Louis"
+- family-names: "Christiansen"
+  given-names: "Eric"
+- family-names: "Ecker"
+  given-names: "Swantje"
+- family-names: "Ellerbrock"
+  given-names: "Malte"
+- family-names: "Gabryś"
+  given-names: "Hubert"
+- family-names: "Handrack"
+  given-names: "Josefine"
+- family-names: "Heath"
+  given-names: "Emily"
+- family-names: "Hermann"
+  given-names: "Cindy"
+- family-names: "Homolka"
+  given-names: "Noa"
+- family-names: "Jäkel"
+  given-names: "Oliver"
+- family-names: "Klinge"
+  given-names: "Thomas"
+- family-names: "Mairani"
+  given-names: "Andrea"
+- family-names: "Mescher"
+  given-names: "Hennig"
+- family-names: "Müller"
+  given-names: "Lucas-Raphael"
+- family-names: "Neishabouri"
+  given-names: "Ahmad"
+- family-names: "Palkowitsch"
+  given-names: "Martina"
+- family-names: "Parodi"
+  given-names: "Katia"
+- family-names: "Pezzano"
+  given-names: "Giuseppe"
+- family-names: "Ramirez"
+  given-names: "Daniel"
+- family-names: "Stadler"
+  given-names: "Alexander"
+- family-names: "Ulrich"
+  given-names: "Silke"
+- family-names: "Wahl"
+  given-names: "Niklas"
+  orcid: "https://orcid.org/0000-0002-1451-223X"
+- family-names: "Welsch"
+  given-names: "Jona"
+- family-names: "Wieser"
+  given-names: "Hans-Peter"
+- family-names: "Winter"
+  given-names: "Johanna"
+- family-names: "Xu"
+  given-names: "Tong" 
+
+title: "matRad"
+version: 2.10.1
+doi: 10.5281/zenodo.3879616
+date-released: 2020-06-05
+url: "http://www.matRad.org"
+location: "Heidelberg"
+organization: "Deutsches Krebsforschungszentrum"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Wieser"
+    given-names: "Hans-Peter"
+  - family-names: "Cisternas"
+    given-names: "Eduardo"
+  - family-names: "Wahl"
+    given-names: "Niklas"
+    orcid: "https://orcid.org/0000-0002-1451-223X"
+  - family-names: "Ulrich"
+    given-names: "Silke"
+  - family-names: "Stadler"
+    given-names: "Alexander"
+  - family-names: "Mescher"
+    given-names: "Hennig"
+  - family-names: "Müller"
+    given-names: "Lucas-Raphael"
+  - family-names: "Klinge"
+    given-names: "Thomas"
+  - family-names: "Gabryś"
+    given-names: "Hubert"
+  - family-names: "Burigo"
+    given-names: "Lucas"
+  - family-names: "Mairani"
+    given-names: "Andrea"
+  - family-names: "Ecker"
+    given-names: "Swantje"
+  - family-names: "Ackermann"
+    given-names: "Benjamin"
+  - family-names: "Ellerbrock"
+    given-names: "Malte"
+  - family-names: "Parodi"
+    given-names: "Katia"
+  - family-names: "Jäkel"
+    given-names: "Oliver"
+  - family-names: "Bangert"
+    given-names: "Mark"
+
+  doi: 10.1002/mp.12251
+  journal: "Medical Physics"
+  start: 2556 
+  end: 2568
+  title: "Development of the open-source dose calculation and optimization toolkit matRad"
+  issue: 6
+  volume: 46
+  year: 2017
diff --git a/MatRad_Config.m b/MatRad_Config.m
@@ -59,11 +59,15 @@
             %  Therefore its constructor is private
             %  For instantiation, use the static MatRad_Config.instance();
 
+            obj.matRadRoot = fileparts(mfilename('fullpath'));
+            addpath(genpath(obj.matRadRoot));
+
             %Set Version
             obj.getEnvironment();
             obj.matRad_version = matRad_version();
-
-            obj.matRadRoot = fileparts(mfilename('fullpath'));
+
+            %Configure Environment
+            obj.configureEnvironment();
 
             %Just to catch people messing with the properties in the file
             if ~isempty(obj.writeLog) && obj.writeLog
@@ -74,6 +78,11 @@
             %Call the reset function for remaining inatialization
             obj.reset();
         end
+
+        function delete(~)
+            %might not be desired by users
+            %rmpath(genpath(matRad_cfg.matRadRoot));
+        end
 
         function displayToConsole(obj,type,formatSpec,varargin)
             %displayToConsole lowest-level logging function for matRad.
@@ -299,6 +308,13 @@ function getEnvironment(obj)
 
             end
         end
+
+        function configureEnvironment(obj)
+            if obj.isOctave
+                struct_levels_to_print(0);                  %Disables full printing of struct array fields
+                warning("off","Octave:data-file-in-path");  %Disables warning of loading patients from the data folder
+            end
+        end
     end
 
     methods(Static)

diff --git a/README.md b/README.md
@@ -3,8 +3,8 @@
 [![Contributors](https://img.shields.io/github/contributors/e0404/matRad)](https://github.com/e0404/matRad/graphs/contributors)
 [![GitPitch](https://gitpitch.com/assets/badge.svg)](https://gitpitch.com/e0404/matRad/master) 
 
-[![TravisCI Build Status](https://travis-ci.org/e0404/matRad.svg?branch=dev)](https://travis-ci.org/e0404/matRad)
-[![Azure Pipelines Build Status](https://dev.azure.com/e0404/matRad/_apis/build/status/e0404.matRad?branchName=dev)](https://dev.azure.com/e0404/matRad)
+[![GitHub Build Status](https://github.com/e0404/matRad/actions/workflows/tests.yml/badge.svg)](https://github.com/e0404/matRad/actions/workflows/tests.yml)
+[![Azure Pipelines Build Status](https://dev.azure.com/e0404/matRad/_apis/build/status/e0404.matRad)](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)
@@ -104,9 +104,16 @@ You can cite specific versions of matRad in your work! For example, Here is the
 
 [![DOI](https://zenodo.org/badge/29671667.svg)](https://zenodo.org/badge/latestdoi/29671667)
 
+# Funding Sources
+matRad developments (on this branch) were (in parts) funded by:
+- Grant  No. BA 2279/3-1 (Project No. 265744405) from the German Research Foundation (DFG)
+- Grant No. 70113094 from the German Cancer Aid
+- Grant No. WA 4707/1-1 (Project No. 443188743) from the German Research Foundation (DFG)
+- Mathworks Academic Research Support
+
 ---
 
-Copyright 2020 the matRad development team. 
+Copyright 2022 the matRad development team. 
 
 [email protected]
 

diff --git a/dicom/matRad_convRtssContours2Indices.m b/dicom/matRad_convRtssContours2Indices.m
@@ -39,20 +39,26 @@
 
         dicomCtSlicePos = unique(structure.item(i).points(:,3));
 
-        if numel(dicomCtSlicePos) > 1
-            error('Contour defined over multiple planes\n');
+        if numel(dicomCtSlicePos) > 1 || isempty(dicomCtSlicePos)
+            error('Contour defined over multiple planes!');
         end
 
         round2 = @(a,b) round(a*10^b)/10^b;
         dicomCtSliceThickness = ct.dicomInfo.SliceThickness(round2(ct.dicomInfo.SlicePositions,1)==round2(dicomCtSlicePos,1));
 
+        %Sanity check
+        msg = checkSliceThickness(dicomCtSliceThickness);
+        if ~isempty(msg)
+            error('Slice Thickness of slice at %f could not be identified: %s',dicomCtSlicePos,msg);
+        end
+
+        slicesInMatradCt = find(dicomCtSlicePos+dicomCtSliceThickness/2 > ct.z & dicomCtSlicePos-dicomCtSliceThickness/2 <= ct.z);
+
         coords1 = interp1(ct.x,1:ct.cubeDim(2),structure.item(i).points(:,1),'linear','extrap');
         coords2 = interp1(ct.y,1:ct.cubeDim(1),structure.item(i).points(:,2),'linear','extrap');
 
         binIn = poly2mask(coords1,coords2,ct.cubeDim(1),ct.cubeDim(2));
 
-        slicesInMatradCt = find(dicomCtSlicePos+dicomCtSliceThickness/2 > ct.z & dicomCtSlicePos-dicomCtSliceThickness/2 <= ct.z);
-
         % loop over all slices in matRad ct
         for j = 1:numel(slicesInMatradCt)
             voiCube(:,:,slicesInMatradCt(j)) = voiCube(:,:,slicesInMatradCt(j)) | binIn;
@@ -63,3 +69,17 @@
 end
 
 indices = find(voiCube(:));
+
+end
+
+function msg = checkSliceThickness(dicomCtSliceThickness)
+    if isempty(dicomCtSliceThickness)
+        msg = 'Slice could not be identified (empty)';
+    elseif ~isscalar(dicomCtSliceThickness)
+        msg = 'Slice thickness not unique';
+    elseif ~isnumeric(dicomCtSliceThickness)
+        msg = 'unexpected value';
+    else
+        msg = '';
+    end
+end
diff --git a/dicom/matRad_importDicom.m b/dicom/matRad_importDicom.m
@@ -1,10 +1,10 @@
-function [ct, cst, pln, resultGUI] = matRad_importDicom( files, dicomMetaBool )
+function [ct,cst,pln,stf,resultGUI] = matRad_importDicom( files, dicomMetaBool )
 % matRad wrapper function to import a predefined set of dicom files 
 % into matRad's native data formats
 % 
 % call
-% [ct, cst, pln, resultGUI] = matRad_importDicom( files )  
-% [ct, cst, pln, resultGUI] = matRad_importDicom( files, dicomMetaBool )
+% [ct, cst, pln, stf, resultGUI] = matRad_importDicom( files )  
+% [ct, cst, pln, stf, resultGUI] = matRad_importDicom( files, dicomMetaBool )
 %
 % input
 %   files:          list of files to be imported (will contain cts and rt
@@ -16,6 +16,7 @@
 %   ct:        matRad ct struct
 %   cst:       matRad cst struct
 %   pln:       matRad plan struct
+%   stf:       matRad stf struct
 %   resultGUI: matRad result struct holding data for visualization in GUI
 %
 % References
@@ -34,7 +35,7 @@
 %
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-[env, ~] = matRad_getEnvironment();
+%[env, ~] = matRad_getEnvironment();
 
 %%
 if ~exist('dicomMetaBool','var')
@@ -85,8 +86,14 @@
     for i = 1:numel(structures)
         % computations take place here
         waitbar(i / steps)
-        fprintf('creating cube for %s volume...\n', structures(i).structName);
-        structures(i).indices = matRad_convRtssContours2Indices(structures(i),ct);
+        fprintf('creating cube for %s volume... ', structures(i).structName);
+        try
+            structures(i).indices = matRad_convRtssContours2Indices(structures(i),ct);
+            fprintf('\n');
+        catch ME
+            warning('matRad:dicomImport','could not be imported: %s',ME.message);
+            structures(i).indices = [];
+        end      
     end
     fprintf('finished!\n');
     close(h)
@@ -105,6 +112,8 @@
     if ~(cellfun(@isempty,files.rtplan(1,:)))
         pln = matRad_importDicomRTPlan(ct, files.rtplan, dicomMetaBool);
     end
+else
+    pln = struct([]);
 end
 
 %% import stf
@@ -121,6 +130,8 @@
             warning('No support for DICOM import of steering information for this modality.');
         end
     end
+else
+    stf = struct([]);
 end
 
 %% import dose cube
@@ -130,38 +141,23 @@
     if ~(cellfun(@isempty,files.rtdose(1,1:2))) 
         fprintf('loading Dose files \n', structures(i).structName);
         % parse plan in order to scale dose cubes to a fraction based dose
-        if exist('pln','var')
-            if isfield(pln,'numOfFractions')
-                resultGUI = matRad_importDicomRTDose(ct, files.rtdose, pln);
-            end
+        if exist('pln','var') && ~isempty(pln) && isfield(pln,'numOfFractions')
+            resultGUI = matRad_importDicomRTDose(ct, files.rtdose, pln);
         else
             resultGUI = matRad_importDicomRTDose(ct, files.rtdose);
         end
         if size(resultGUI) == 0
-           clear resultGUI;
+           resultGUI = struct([]);
         end
     end
+else
+    resultGUI = struct([]);
 end
 
 %% put weight also into resultGUI
-if exist('stf','var') && exist('resultGUI','var')
+if ~isempty(stf) && ~isempty(resultGUI)
     resultGUI.w = [];
     for i = 1:size(stf,2)
         resultGUI.w = [resultGUI.w; [stf(i).ray.weight]'];
     end
 end
-
-%% save ct, cst, pln, dose
-matRadFileName = [files.ct{1,3} '.mat']; % use default from dicom
-[FileName,PathName] = uiputfile('*','Save as...',matRadFileName);
-if ischar(FileName)
-    % delete unnecessary variables
-    switch env
-    case 'MATLAB'
-        clearvars -except ct cst pln stf resultGUI FileName PathName;
-    case 'OCTAVE' 
-        clear -x ct cst pln stf resultGUI FileName PathName;
-    end
-    % save all except FileName and PathName
-    save([PathName, FileName], '-regexp', '^(?!(FileName|PathName)$).','-v7.3');
-end
diff --git a/dicom/matRad_importDicomGUI.m b/dicom/matRad_importDicomGUI.m
@@ -327,7 +327,23 @@ function import_button_Callback(hObject, eventdata, handles)
 
 % dicomMetaBool: store complete DICOM information and patientName or not
 dicomMetaBool = logical(get(handles.checkPatientName,'Value'));
-matRad_importDicom(files, dicomMetaBool);
+[ct,cst,pln,stf,resultGUI] = matRad_importDicom(files, dicomMetaBool);
+
+
+% Save file
+matRadFileName = [files.ct{1,3} '.mat']; % use default from dicom
+[FileName,PathName] = uiputfile('*','Save as...',matRadFileName);
+if ischar(FileName)
+    %Hack to get non-empty variables
+    varNames = {'ct','cst','pln','stf','resultGUI'};
+    ix = cellfun(@(s) ~isempty(evalin('caller',s)),varNames);
+    varNames = varNames(ix);
+
+    FileName = fullfile(PathName,FileName);
+
+    % save all non-empty variables imported
+    save(FileName,'-v7.3',varNames{:});
+end
 
 
 % --- Executes on button press in cancel_button.

diff --git a/matRad_calcCubes.m b/matRad_calcCubes.m
@@ -36,6 +36,10 @@
 
 resultGUI.w = w;
 
+if isfield(dij,'numParticlesPerMU')
+    resultGUI.MU = (w.*1e6) ./ dij.numParticlesPerMU;
+end
+
 % get bixel - beam correspondence  
 for i = 1:dij.numOfBeams
     beamInfo(i).suffix = ['_beam', num2str(i)];