incorrect merge revert and code cleanup

e0404 · Feb 26, 2025 · f07b82b · f07b82b
1 parent 5600b1f
commit f07b82b
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Showing 39 changed files with 2,239 additions and 273 deletions.
diff --git a/matRad/IO/matRad_writeNifTI.m b/matRad/IO/matRad_writeNifTI.m
@@ -63,6 +63,9 @@
 info.Datatype = metadata.datatype;
 info.ImageSize = size(cube);
 info.Description = sprintf('Exported from matRad %s',matRad_version());
+if length(info.Description) >= 80
+    info.Description = info.Description(1:79);
+end
 
 if max(info.ImageSize) > 32767
     info.Version = 'NIfTI2';

diff --git a/matRad/basedata/matRad_MCemittanceBaseData.m b/matRad/basedata/matRad_MCemittanceBaseData.m
@@ -541,6 +541,21 @@
             mcDataOptics.Divergence2y  = 0;
             mcDataOptics.Correlation2y = 0;
             mcDataOptics.FWHMatIso = 2.355 * sigmaSqIso;
+
+            % Parameters for parametrization of sigma squared model.
+            % sigma^2 = a + b*z + c*z^2;
+            mcDataOptics.sSQ_a = (sigmaSqIso/10)^2;
+            mcDataOptics.sSQ_b = (2*rho*sigmaT*sigmaSqIso)/10;
+            mcDataOptics.sSQ_c = sigmaT^2;
+
+            % Parameters for emittance model
+            mcDataOptics.twissEpsilonX =  sqrt(mcDataOptics.sSQ_a*mcDataOptics.sSQ_c - (mcDataOptics.sSQ_b^2)/4);
+            mcDataOptics.twissAlphaX   = - mcDataOptics.sSQ_b/(2*mcDataOptics.twissEpsilonX);
+            mcDataOptics.twissBetaX    =  mcDataOptics.sSQ_a/mcDataOptics.twissEpsilonX;
+
+            mcDataOptics.twissEpsilonY = mcDataOptics.twissEpsilonX;
+            mcDataOptics.twissAlphaY   = mcDataOptics.twissAlphaX;
+            mcDataOptics.twissBetaY    = mcDataOptics.twissBetaX;
         end
 
 

diff --git a/matRad/bioModels/matRad_BiologicalModel.m b/matRad/bioModels/matRad_BiologicalModel.m
@@ -126,7 +126,13 @@
             %Use the root folder and the biomodel folder only
             folders = {fileparts(mfilename('fullpath'))};
             folders = [folders matRad_cfg.userfolders];
-            metaBioModels = matRad_findSubclasses(meta.class.fromName(mfilename('class')),'folders',folders,'includeSubfolders',true);
+
+            persistent metaBioModels lastOptionalPaths
+            if isempty(metaBioModels) || (~isempty(lastOptionalPaths) && ~isequal(lastOptionalPaths, folders))
+                lastOptionalPaths = folders;
+                metaBioModels = matRad_findSubclasses(meta.class.fromName(mfilename('class')),'folders',folders,'includeSubfolders',true);
+            end
+
             classList = matRad_identifyClassesByConstantProperties(metaBioModels,'model','defaults',{'none'});
 
             if nargin > 0 

diff --git a/matRad/dicom/@matRad_DicomExporter/matRad_exportDicomRTDoses.m b/matRad/dicom/@matRad_DicomExporter/matRad_exportDicomRTDoses.m
@@ -44,15 +44,12 @@
 
 meta.Modality = 'RTDOSE';
 meta.Manufacturer = '';
-meta.DoseUnits = 'GY';
 
 %Reference
 %ID of the CT
 meta.StudyInstanceUID = obj.StudyInstanceUID;
 meta.StudyID = obj.StudyID; 
 
-
-
 %Dates & Times
 currDate = now;
 currDateStr = datestr(currDate,'yyyymmdd');
@@ -99,10 +96,11 @@
 meta.GridFrameOffsetVector = transpose(ct.z - ct.z(1));
 
 %Referenced Plan
-%This does currently not work due to how Matlab creates UIDs by itself,
-%we can not know the reference before it is written by the RTPlanExport,
-%which itself needs the RTDose UIDs
-%{
+%This does currently not work well due to how Matlab creates UIDs by
+%itself, we can not know the reference before it is written by the 
+%RTPlanExport, which itself needs the RTDose UIDs.
+%However, we need to set the ReferencedRTPlanSequence, because it is a
+%conditionally required field according to the DICOM standard
 try
     rtPlanUID = obj.rtPlanMeta.SOPInstanceUID;   
 catch
@@ -111,38 +109,34 @@
     obj.rtPlanMeta.SOPClassUID = obj.rtPlanClassUID;
     rtPlanUID = obj.rtPlanMeta.SOPInstanceUID;
 end
-%}
-
-
-%meta.ReferencedRTPlanSequence.Item_1.ReferencedSOPClassUID = obj.rtPlanClassUID;
-%meta.ReferencedRTPlanSequence.Item_1.ReferencedSOPInstanceUID = rtPlanUID;
-
-if nargin < 4 || isempty(doseFieldNames)
-    doseFieldNames = cell(0);
-    fn = fieldnames(obj.resultGUI);
-    for i = 1:numel(fn)
-        if numel(size(obj.resultGUI.(fn{i}))) == 3
-            doseFieldNames{end+1} = fn{i};
-        end
+
+meta.ReferencedRTPlanSequence.Item_1.ReferencedSOPClassUID = obj.rtPlanClassUID;
+meta.ReferencedRTPlanSequence.Item_1.ReferencedSOPInstanceUID = rtPlanUID;
+
+doseFieldNames = cell(0);
+fn = fieldnames(obj.resultGUI);
+for i = 1:numel(fn)
+    if numel(size(obj.resultGUI.(fn{i}))) == 3
+        doseFieldNames{end+1} = fn{i};
     end
 end
 
-
-
-
-
 obj.rtDoseMetas = struct([]);
 obj.rtDoseExportStatus = struct([]);
 
 for i = 1:numel(doseFieldNames)
-    doseName = doseFieldNames{i};
+    doseName = doseFieldNames{i};    
+    doseUnits = 'GY';
 
     %Now check if we export physical or RBE weighted dose, they are known
     %to dicom
-    if strncmp(doseName,'physicalDose',12)
+    if strncmp(doseName,'physicalDose',12) || strncmp(doseName,'LET',3)
         doseType = 'PHYSICAL';
-    elseif strncmp(doseName,'RBExDose',8)
+    elseif strncmp(doseName,'RBExDose',8) || strncmp(doseName,'BED',3) || strncmp(doseName,'alpha',3) || strncmp(doseName,'beta',3) || strncmp(doseName,'effect',6) || strncmp(doseName,'RBE',3)
         doseType = 'EFFECTIVE';
+        if strncmp(doseName,'RBE',3)
+            doseUnits = 'RELATIVE';
+        end
     else
         matRad_cfg.dispInfo('Dose Cube ''%s'' of unknown type for DICOM. Not exported!\n',doseName);
         continue;
@@ -174,6 +168,8 @@
     metaCube = meta;
     metaCube.DoseType = doseType;
     metaCube.DoseSummationType = deliveryType;
+    metaCube.DoseComment = doseName;
+    metaCube.DoseUnits = doseUnits;
 
     %ID of the RTDose
     metaCube.SeriesInstanceUID = dicomuid;    

diff --git a/matRad/dicom/@matRad_DicomImporter/matRad_importDicomRTDose.m b/matRad/dicom/@matRad_DicomImporter/matRad_importDicomRTDose.m
@@ -62,11 +62,24 @@
     else
         doseInstanceHelper = [];
     end
-
+
+    doseComment = '';
+    if isfield(dose.(itemName).dicomInfo,'DoseComment')
+        doseComment = dose.(itemName).dicomInfo.DoseComment;
+    end
+
     if strncmpi(doseTypeHelper,'PHYSICAL',6)
-        doseTypeHelper = 'physicalDose';
+        if any(strcmp(doseComment,{'physicalDose','LET'}))
+            doseTypeHelper = doseComment;
+        else
+            doseTypeHelper = 'physicalDose';
+        end
     elseif strncmpi(doseTypeHelper,'EFFECTIVE',6)
-        doseTypeHelper = 'RBExDose';
+        if any(strcmp(doseComment,{'RBExDose','BED','alpha','beta','effect','RBE'}))
+            doseTypeHelper = doseComment;
+        else
+            doseTypeHelper = 'RBExDose';
+        end
     end
 
     %If given as plan and not per fraction

diff --git a/matRad/dicom/@matRad_DicomImporter/matRad_interpDicomDoseCube.m b/matRad/dicom/@matRad_DicomImporter/matRad_interpDicomDoseCube.m
@@ -102,7 +102,9 @@
 %always given
 obj.importRTDose.dose.dicomInfo.SOPClassUID             = doseInfo.SOPClassUID;
 obj.importRTDose.dose.dicomInfo.SOPInstanceUID          = doseInfo.SOPInstanceUID;
-obj.importRTDose.dose.dicomInfo.ReferencedRTPlanSequence = doseInfo.ReferencedRTPlanSequence;
+if isfield(doseInfo,'ReferencedRTPlanSequence')
+    obj.importRTDose.dose.dicomInfo.ReferencedRTPlanSequence = doseInfo.ReferencedRTPlanSequence;
+end
 
 end
 
diff --git a/matRad/dicom/@matRad_DicomImporter/matRad_scanDicomImportFolder.m b/matRad/dicom/@matRad_DicomImporter/matRad_scanDicomImportFolder.m
@@ -246,9 +246,9 @@
     close(h)
 
     if ~isempty(obj.allfiles)
-        obj.patient = unique(obj.allfiles(:,3));
+        obj.patients = unique(obj.allfiles(:,3));
 
-        if isempty(obj.patient)
+        if isempty(obj.patients)
              matRad_cfg.dispError('No patient found with DICOM CT _and_ RT structure set in patient directory!');
         end
     else

diff --git a/matRad/doseCalc/+DoseEngines/@matRad_DoseEngineBase/getAvailableEngines.m b/matRad/doseCalc/+DoseEngines/@matRad_DoseEngineBase/getAvailableEngines.m
@@ -36,7 +36,13 @@
 
 %Get available, valid classes through call to matRad helper function
 %for finding subclasses
-availableDoseEngines = matRad_findSubclasses('DoseEngines.matRad_DoseEngineBase','packages',{'DoseEngines'},'folders',optionalPaths,'includeAbstract',false);
+persistent allAvailableDoseEngines lastOptionalPaths
+if isempty(allAvailableDoseEngines) || (~isempty(lastOptionalPaths) && ~isequal(lastOptionalPaths, optionalPaths))
+    lastOptionalPaths = optionalPaths;
+    allAvailableDoseEngines = matRad_findSubclasses('DoseEngines.matRad_DoseEngineBase','packages',{'DoseEngines'},'folders',optionalPaths,'includeAbstract',false);
+end
+
+availableDoseEngines = allAvailableDoseEngines;
 
 %Now filter for pln
 ix = [];

diff --git a/matRad/doseCalc/+DoseEngines/@matRad_DoseEngineBase/matRad_DoseEngineBase.m b/matRad/doseCalc/+DoseEngines/@matRad_DoseEngineBase/matRad_DoseEngineBase.m
@@ -114,6 +114,11 @@ function warnDeprecatedEngineProperty(this,oldProp,msg,newProp)
         function assignPropertiesFromPln(this,pln,warnWhenPropertyChanged)
             matRad_cfg = MatRad_Config.instance();
 
+            %Check radiation mode
+            if ~isfield(pln,'radiationMode') || ~any(strcmp(pln.radiationMode,this.possibleRadiationModes))
+                matRad_cfg.dispError('Invalid radiation mode for engine ''%s''!',this.name);
+            end
+
             %Set Scenario Model
             if isfield(pln,'multScen')
                 this.multScen = pln.multScen;