Merge pull request e0404#625 from amitantony/dev_classGUI_a_DicomImpo…

…rtBug

Dev class GUI a dicom import bug

MatRad_Config.m

@@ -259,6 +259,7 @@ function setDefaultPropertiesForEduMode(obj)
 
             obj.devMode = false;
             obj.eduMode = true;
+
         end
 
         function setDefaultGUIProperties(obj)

dicom/matRad_importDicom.m

@@ -35,7 +35,8 @@
 %
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-%[env, ~] = matRad_getEnvironment();
+[env, ~] = matRad_getEnvironment();
+
 
 %%
 if ~exist('dicomMetaBool','var')
@@ -54,7 +55,7 @@
 resolution.z = files.resz; % [mm] / lps coordinate system
 if files.useDoseGrid && isfield(files,'rtdose')
     % get grid from dose cube
-    if verLessThan('matlab','9')
+    if isOctave || verLessThan('matlab','9')
         doseInfo = dicominfo(files.rtdose{1,1});
     else
         doseInfo = dicominfo(files.rtdose{1,1},'UseDictionaryVR',true);
@@ -161,3 +162,21 @@
         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;
+        save([PathName, FileName], '-regexp', '^(?!(FileName|PathName)$).','-v7');
+    case 'OCTAVE' 
+        clear -x ct cst pln stf resultGUI FileName PathName;
+        save([PathName, FileName],'-v6');
+    end
+    % save all except FileName and PathName
+
+end

dicom/matRad_importDicomRtss.m

@@ -37,7 +37,7 @@
 if nargin < 3
     visBool = 0;
 end
-
+matRad_cfg = MatRad_Config.instance();
 env = matRad_getEnvironment();
 matRad_checkEnvDicomRequirements(env);
 isOctave = strcmp(env,'OCTAVE');
@@ -52,9 +52,17 @@
 end
 
 % list the defined structures
-listOfDefStructs = fieldnames(structInfo.StructureSetROISequence);
+try
+    listOfDefStructs = fieldnames(structInfo.StructureSetROISequence);
+catch
+    matRad_cfg.dispError('StructureSetROISequence not defined ')
+end
 % list of contoured structures
-listOfContStructs = fieldnames(structInfo.ROIContourSequence);
+try
+    listOfContStructs = fieldnames(structInfo.ROIContourSequence);
+catch
+    matRad_cfg.dispError('ROIContourSequence not defined ')
+end 
 
 %% process structure data
 numOfDefStructs  = numel(listOfDefStructs);
@@ -86,11 +94,11 @@
                     listOfSlices = fieldnames(structInfo.ROIContourSequence.(...
                                                 listOfContStructs{i}).ContourSequence);
                 else
-                    warning(['Contour ' structures(i).structName ' is empty'])
+                    matRad_cfg.dispWarning(['Contour ' structures(i).structName ' is empty'])
                     continue;
                 end
     else
-        warning(['Contour ' structures(i).structName ' is empty'])
+        matRad_cfg.dispWarning(['Contour ' structures(i).structName ' is empty'])
         continue;
     end
 
@@ -113,12 +121,12 @@
 
         % sanity check 1
         if numel(unique(structZ)) > 1
-            error('Detected contour points outside of single slice\n');
+            matRad_cfg.dispError('Detected contour points outside of single slice\n');
         end
 
         % sanity check 2
         if unique(structZ) > max(dicomInfo.SlicePositions) || unique(structZ) < min(dicomInfo.SlicePositions)
-            warning(['Omitting contour data for ' structures(i).structName ' at slice position ' num2str(unique(structZ)) 'mm - no ct data available.\n']);
+            matRad_cfg.dispWarning(['Omitting contour data for ' structures(i).structName ' at slice position ' num2str(unique(structZ)) 'mm - no ct data available.\n']);
         else
             structures(i).item(j).points = [structX, structY, structZ];
         end

dicom/matRad_scanDicomImportFolder.m

@@ -41,6 +41,7 @@
 
 % dicom import needs image processing toolbox -> check if available
 available = matRad_checkEnvDicomRequirements();
+isOctave = strcmp(matRad_cfg.env,'OCTAVE');
 
 if ~available
     matRad_cfg.dispError('Image processing toolbox / packages not available!');

examples/matRad_example2_photons.m

@@ -126,7 +126,7 @@
 %%
 % Enable sequencing and disable direct aperture optimization (DAO) for now.
 % A DAO optimization is shown in a seperate example.
-pln.propOpt.runSequencing = 1;
+pln.propSeq.runSequencing = 1;
 pln.propOpt.runDAO        = 0;
 
 %%

examples/matRad_example3_photonsDAO.m

@@ -64,8 +64,8 @@
 
 %%
 % Enable sequencing and direct aperture optimization (DAO).
-pln.propOpt.runSequencing = 1;
-pln.propOpt.runDAO        = 1;
+pln.propSeq.runSequencing = true;
+pln.propOpt.runDAO        = true;
 
 %% Generate Beam Geometry STF
 stf = matRad_generateStf(ct,cst,pln);
@@ -90,7 +90,7 @@
 % order to modulate the intensity of the beams with multiple static 
 % segments, so that translates each intensity map into a set of deliverable 
 % aperture shapes.
-resultGUI = matRad_siochiLeafSequencing(resultGUI,stf,dij,5);
+resultGUI = matRad_sequencing(resultGUI,stf,dij,pln);
 
 %% DAO - Direct Aperture Optimization
 % The Direct Aperture Optimization is an optimization approach where we 

examples/matRad_example4_photonsMC.m

@@ -42,7 +42,7 @@
 pln.propStf.bixelWidth      = 10;
 pln.propStf.numOfBeams      = numel(pln.propStf.gantryAngles);
 pln.propStf.isoCenter       = ones(pln.propStf.numOfBeams,1) * matRad_getIsoCenter(cst,ct,0);
-pln.propOpt.runSequencing   = 0;
+pln.propSeq.runSequencing   = 0;
 pln.propOpt.runDAO          = 0;
 
 % dose calculation settings

examples/matRad_example5_protons.m

@@ -70,7 +70,7 @@
 pln.propStf.numOfBeams    = numel(pln.propStf.gantryAngles);
 pln.propStf.isoCenter     = ones(pln.propStf.numOfBeams,1) * matRad_getIsoCenter(cst,ct,0);
 pln.propOpt.runDAO        = 0;
-pln.propOpt.runSequencing = 0;
+pln.propSeq.runSequencing = 0;
 
 % dose calculation settings
 pln.propDoseCalc.doseGrid.resolution.x = 3; % [mm]

examples/matRad_example6_protonsNoise.m

@@ -47,7 +47,7 @@
 pln.propStf.numOfBeams      = numel(pln.propStf.gantryAngles);
 pln.propStf.isoCenter       = ones(pln.propStf.numOfBeams,1) * matRad_getIsoCenter(cst,ct,0);
 pln.propOpt.runDAO          = 0;
-pln.propOpt.runSequencing   = 0;
+pln.propSeq.runSequencing   = 0;
 
 % dose calculation settings
 pln.propDoseCalc.doseGrid.resolution.x = 3; % [mm]

examples/matRad_example7_carbon.m

@@ -66,7 +66,7 @@
 pln.propStf.numOfBeams    = numel(pln.propStf.gantryAngles);
 pln.propStf.isoCenter     = ones(pln.propStf.numOfBeams,1) * matRad_getIsoCenter(cst,ct,0);
 pln.propOpt.runDAO        = 0;
-pln.propOpt.runSequencing = 0;
+pln.propSeq.runSequencing = 0;
 
 % dose calculation settings
 pln.propDoseCalc.doseGrid.resolution.x = 3; % [mm]

gui/matRad_MainGUI.m

@@ -16,6 +16,7 @@
         StructureVisibilityWidget
         InfoWidget
         ViewingWidget
+        DVHStatsWidget
         eventListeners
 
         matRad_cfg = MatRad_Config.instance();

gui/matRad_Widget.m

@@ -1,4 +1,27 @@
 classdef matRad_Widget <  handle 
+
+    % matRad_Widget Main Class for GUI widget generation 
+    % Describes a standard fluence optimization problem by providing the 
+    % implementation of the objective & constraint function/gradient wrappers
+    % and managing the mapping and backprojection of the respective dose-
+    % related quantity
+    %
+    % References
+    %   -
+    %
+    % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    %
+    % Copyright 2020 the matRad development team. 
+    % 
+    % This file is part of the matRad project. It is subject to the license 
+    % terms in the LICENSE file found in the top-level directory of this 
+    % distribution and at https://github.com/e0404/matRad/LICENSES.txt. No part 
+    % of the matRad project, including this file, may be copied, modified, 
+    % propagated, or distributed except according to the terms contained in the 
+    % LICENSE file.
+    %
+    % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
 
     properties (GetAccess = public , SetAccess = protected)
         widgetHandle            %Holds parent widget handle

gui/widgets/matRad_3DWidget.m

@@ -1,5 +1,27 @@
 classdef matRad_3DWidget < matRad_ViewingWidget
-
+
+    % matRad_3DWidget class to generate GUI widget for 3D plan visualization 
+    % Describes a standard fluence optimization problem by providing the 
+    % implementation of the objective & constraint function/gradient wrappers
+    % and managing the mapping and backprojection of the respective dose-
+    % related quantity
+    %
+    % References
+    %   -
+    %
+    % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    %
+    % Copyright 2020 the matRad development team. 
+    % 
+    % This file is part of the matRad project. It is subject to the license 
+    % terms in the LICENSE file found in the top-level directory of this 
+    % distribution and at https://github.com/e0404/matRad/LICENSES.txt. No part 
+    % of the matRad project, including this file, may be copied, modified, 
+    % propagated, or distributed except according to the terms contained in the 
+    % LICENSE file.
+    %
+    % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
     properties
         viewingWidgetHandle;
     end