Merge branch 'pr/765' into pr/756

wahln · wahln · commit 8c421da60f93 · 2024-10-15T15:57:04.000+02:00
# Conflicts:
#	examples/matRad_example12_simpleParticleMonteCarlo.m
diff --git a/examples/matRad_example12_simpleParticleMonteCarlo.m b/examples/matRad_example12_simpleParticleMonteCarlo.m
@@ -24,6 +24,7 @@
 % meta information for treatment plan
 pln.radiationMode   = 'protons';     % either photons / protons / carbon
 pln.machine         = 'Generic';
+
 %Biology
 pln.bioModel = 'none';
 %Scenario Model
@@ -69,8 +70,8 @@
 stf = matRad_generateStf(ct,cst,pln);
 
 %% analytical dose calculation
-pln.propDoseCalc.engine = 'MCsquare';
-pln.propDoseCalc.numHistoriesPerBeamlet = 1e4;
+pln.propDoseCalc.engine = 'HongPB';
+%pln.propDoseCalc.numHistoriesPerBeamlet = 1e6;
 
 dij = matRad_calcDoseInfluence(ct, cst,stf, pln); %Calculate particle dose influence matrix (dij) with analytical algorithm
 
@@ -84,7 +85,7 @@
 %pln.propDoseCalc.engine = 'TOPAS';
 
 % set number of histories lower than default for this example (default: 1e8)
-pln.propDoseCalc.numHistoriesDirect = 1e3;
+pln.propDoseCalc.numHistoriesDirect = 5e6;
 %pln.propDoseCalc.externalCalculation = 'write';
 resultGUI_MC = matRad_calcDoseForward(ct,cst,stf,pln,resultGUI.w);
 
diff --git a/examples/matRad_example13_fitAnalyticalParticleBaseData.m b/examples/matRad_example13_fitAnalyticalParticleBaseData.m
@@ -109,18 +109,18 @@
 pln.radiationMode   = 'protons'; 
 
 % create meta machine data
-machine.meta.machine = 'example'; %name of the machine
+machine.meta.name = 'example'; %name of the machine
 machine.meta.radiationMode = 'protons'; %modality
 machine.meta.dataType = 'singleGauss'; %singleGauss or doubleGauss
 machine.meta.created_on = date;
 machine.meta.created_by = 'matRad_example';
 machine.meta.SAD = (2218 + 1839) / 2; %This is the (virtual) source to axis distance
 machine.meta.BAMStoIsoDist = 420.0; %distance from beam nozzle ot isocenter
-machine.meta.LUT_bxWidthminFWHM = [0, Inf; 5 ,5]; %Specifies which minimum FWHM to use as spot sice for which ranges of lateral spot distance (here, each spot distance of 0 to to Inf gets at least 5mm wide spots
+machine.meta.LUTspotSize = [0, Inf; 5 ,5]; %Specifies which minimum FWHM to use as spot sice for which ranges of lateral spot distance (here, each spot distance of 0 to to Inf gets at least 5mm wide spots
 machine.meta.fitAirOffset = 420.0; %Tells matRad how much "air" was considered during fitting. Set this to 0 if the fit is obtained in vacuum and no air transport is simulated up to the phantom. matRad assumes that the phantom starts at the isocenter.
 
 % Now add the example machine to the pln and then save it
-pln.machine = machine.meta.machine;
+pln.machine = machine.meta.name;
 pln.radiationMode = machine.meta.radiationMode;
 fileName = [pln.radiationMode '_' pln.machine];
 filePath = fullfile(matRad_cfg.userfolders{1},'machines',[fileName '.mat']);
diff --git a/matRad/basedata/protons_Generic.mat b/matRad/basedata/protons_Generic.mat
diff --git a/matRad/basedata/protons_Generic_Legacy.mat b/matRad/basedata/protons_Generic_Legacy.mat
diff --git a/matRad/doseCalc/+DoseEngines/matRad_ParticleAnalyticalBortfeldEngine.m b/matRad/doseCalc/+DoseEngines/matRad_ParticleAnalyticalBortfeldEngine.m
@@ -372,7 +372,10 @@ function calcLateralParticleCutOff(this,cutOffLevel,~)
                 return;
             end
 
-            checkMeta = all(isfield(machine.meta,{'SAD','BAMStoIsoDist','LUT_bxWidthminFWHM','dataType'}));
+            checkMeta = all(isfield(machine.meta,{'SAD','BAMStoIsoDist','dataType'}));
+            
+            %Superseded names from older machine file versions
+            checkMeta = checkMeta && any(isfield(machine.meta,{'LUTspotSize','LUT_bxWidthminFWHM'}));
 
             dataType = machine.meta.dataType;
             if strcmp(dataType,'singleGauss')
diff --git a/matRad/doseCalc/+DoseEngines/matRad_ParticleFineSamplingPencilBeamEngine.m b/matRad/doseCalc/+DoseEngines/matRad_ParticleFineSamplingPencilBeamEngine.m
@@ -469,7 +469,10 @@ function setDefaults(this)
                 return;
             end
 
-            checkMeta = all(isfield(machine.meta,{'SAD','BAMStoIsoDist','LUT_bxWidthminFWHM','dataType'}));
+            checkMeta = all(isfield(machine.meta,{'SAD','BAMStoIsoDist','dataType'}));
+            
+            %Superseded names from older machine file versions
+            checkMeta = checkMeta && any(isfield(machine.meta,{'LUTspotSize','LUT_bxWidthminFWHM'}));
 
             dataType = machine.meta.dataType;
             if strcmp(dataType,'singleGauss')
diff --git a/matRad/doseCalc/+DoseEngines/matRad_ParticleHongPencilBeamEngine.m b/matRad/doseCalc/+DoseEngines/matRad_ParticleHongPencilBeamEngine.m
@@ -131,7 +131,10 @@
                 return;
             end
 
-            checkMeta = all(isfield(machine.meta,{'SAD','BAMStoIsoDist','LUT_bxWidthminFWHM','dataType'}));
+            checkMeta = all(isfield(machine.meta,{'SAD','BAMStoIsoDist','dataType'}));
+            
+            %Superseded names from older machine file versions
+            checkMeta = checkMeta && any(isfield(machine.meta,{'LUTspotSize','LUT_bxWidthminFWHM'}));
 
             dataType = machine.meta.dataType;
             if strcmp(dataType,'singleGauss')
diff --git a/matRad/doseCalc/+DoseEngines/matRad_ParticleMCsquareEngine.m b/matRad/doseCalc/+DoseEngines/matRad_ParticleMCsquareEngine.m
@@ -150,8 +150,14 @@ function setDefaults(this)
                 bdFile = this.forceBDL;
 
             else
+                % Newer machine files have "name" instead of "machine"
+                if ~isfield(this.machine.meta,'machine')
+                    machineName = this.machine.meta.name;                    
+                else
+                    machineName = this.machine.meta.machine;
+                end
                 % fit and create BDL file using selected machine file
-                bdFile = [this.machine.meta.machine '.txt'];
+                bdFile = [machineName '.txt'];
 
                 % Calculate MCsquare base data
                 % Argument stf is optional, if given, calculation only for energies given in stf
diff --git a/matRad/doseCalc/+DoseEngines/matRad_ParticlePencilBeamEngineAbstract.m b/matRad/doseCalc/+DoseEngines/matRad_ParticlePencilBeamEngineAbstract.m
@@ -24,7 +24,7 @@
         calcLET = true;                 % Boolean which defines if LET should be calculated
         calcBioDose = false;            % Boolean which defines if biological dose calculation shoudl be performed (alpha*dose and sqrt(beta)*dose)
         airOffsetCorrection  = true;    % Corrects WEPL for SSD difference to kernel database
-        lateralModel = 'auto';          % Lateral Model used. 'auto' uses the most accurate model available (i.e. multiple Gaussians). 'single','double','multi' try to force a singleGaussian or doubleGaussian model, if available
+        lateralModel = 'fast';          % Lateral Model used. 'auto' uses the most accurate model available (i.e. multiple Gaussians), 'fastest' uses the most simple model. 'single','double','multi' try to force a singleGaussian or doubleGaussian model, if available
 
         cutOffMethod = 'integral';      % or 'relative' - describes how to calculate the lateral dosimetric cutoff
 
@@ -69,23 +69,29 @@ function chooseLateralModel(this)
             
             matRad_cfg = MatRad_Config.instance();
 
+            singleAvailable = all(arrayfun(fValidateSingle,this.machine.data));
+            doubleAvailable = all(arrayfun(fValidateDouble,this.machine.data));
+            multiAvailable = all(arrayfun(fValidateMulti,this.machine.data));
+
+            matRad_cfg.dispInfo('''%s'' selected for lateral beam model, checking machine...\n',this.lateralModel);
+
             switch this.lateralModel
                 case 'single'
-                    if ~all(arrayfun(fValidateSingle,this.machine.data))
+                    if ~singleAvailable
                         matRad_cfg.dispWarning('Chosen Machine does not support a singleGaussian Pencil-Beam model!');
                         this.lateralModel = 'auto';
                     end
                 case 'double'
-                    if ~all(arrayfun(fValidateDouble,this.machine.data))
+                    if ~doubleAvailable
                         matRad_cfg.dispWarning('Chosen Machine does not support a doubleGaussian Pencil-Beam model!');
                         this.lateralModel = 'auto';
                     end
                 case 'multi'
-                    if ~all(arrayfun(fValidateMulti,this.machine.data))
+                    if ~multiAvailable
                         matRad_cfg.dispWarning('Chosen Machine does not support a multiGaussian Pencil-Beam model!');
                         this.lateralModel = 'auto';
                     end
-                case 'auto'
+                case {'auto','fast'}
                     %Do nothing, will be handled below
                 otherwise
                     matRad_cfg.dispError('Lateral model ''%s'' not known!',this.lateralModel);
@@ -94,12 +100,24 @@ function chooseLateralModel(this)
             %Now check if we need tho chose the lateral model because it
             %was set to auto
             if strcmp(this.lateralModel,'auto') 
-                if all(arrayfun(fValidateMulti,this.machine.data))
+                if multiAvailable
                     this.lateralModel = 'multi';
-                elseif all(arrayfun(fValidateDouble,this.machine.data))
+                elseif doubleAvailable
                     this.lateralModel = 'double';
-                elseif all(arrayfun(fValidateSingle,this.machine.data))
+                elseif singleAvailable
+                    this.lateralModel = 'single';
+                else
+                    matRad_cfg.dispError('Invalid kernel model!');
+                end
+            end
+
+            if strcmp(this.lateralModel,'fast')
+                if singleAvailable
                     this.lateralModel = 'single';
+                elseif doubleAvailable
+                    this.lateralModel = 'double';
+                elseif multiAvailable
+                    this.lateralModel = 'multi';
                 else
                     matRad_cfg.dispError('Invalid kernel model!');
                 end
@@ -566,7 +584,7 @@ function calcLateralParticleCutOff(this,cutOffLevel,stfElement)
                 sigmaIni_sq = sigmaIni^2;
 
                 % consider range shifter for protons if applicable
-                if  strcmp(this.machine.meta.radiationMode,'protons') && rangeShifterLUT(i).eqThickness > 0  && ~strcmp(this.machine.meta.machine,'Generic')
+                if  strcmp(this.machine.meta.radiationMode,'protons') && rangeShifterLUT(i).eqThickness > 0 
 
                     %get max range shift
                     sigmaRashi = matRad_calcSigmaRashi(this.machine.data(energyIx).energy, ...
diff --git a/matRad/doseCalc/MCsquare/matRad_MCsquareBaseData.m b/matRad/doseCalc/MCsquare/matRad_MCsquareBaseData.m
@@ -47,7 +47,6 @@
                 fileID = fopen(filepath,'w');
                 
                 %Header
-                %fprintf(fileID,'--matRad: Beam Model for machine %s (%s)--\n',machine.meta.machine,machine.meta.dataType);
                 fprintf(fileID,'--UPenn beam model (double gaussian)--\n');
                 fprintf(fileID,'# %s\n', obj.machine.meta.description);
                 fprintf(fileID,'# created by %s on %s\n\n', obj.machine.meta.created_by, obj.machine.meta.created_on);
diff --git a/matRad/gui/matRad_MainGUI.m b/matRad/gui/matRad_MainGUI.m
@@ -21,7 +21,7 @@
         lastStoragePath = []
     end
 
-    properties (Access = private)
+    properties (SetAccess = private)
         LogoWidget
         WorkflowWidget
         PlanWidget
diff --git a/matRad/steering/matRad_StfGeneratorExternalRayBixelAbstract.m b/matRad/steering/matRad_StfGeneratorExternalRayBixelAbstract.m
@@ -202,8 +202,16 @@ function initialize(this)
             beam.isoCenter       = this.isoCenter(beamIndex,:);
             beam.bixelWidth      = this.bixelWidth;
             beam.radiationMode   = this.radiationMode;
-            beam.machine         = this.machine.meta.machine;
-            beam.SAD             = this.machine.meta.SAD;
+
+            % Newer machine files have "name" instead of "machine"
+            if ~isfield(this.machine.meta,'machine')
+                machineName = this.machine.meta.name;                    
+            else
+                machineName = this.machine.meta.machine;
+            end
+            beam.machine = machineName;
+
+            beam.SAD = this.machine.meta.SAD;
         end
             
         
@@ -464,7 +472,7 @@ function initialize(this)
             %checkBasic
             available = isfield(machine,'meta') && isfield(machine,'data');
 
-            available = available && isfield(machine.meta,'machine');
+            available = available && any(isfield(machine.meta,{'machine','name'}));
 
             available = available && isfield(machine.meta,'SAD') && isscalar(machine.meta.SAD);
     
diff --git a/matRad/steering/matRad_StfGeneratorParticleIMPT.m b/matRad/steering/matRad_StfGeneratorParticleIMPT.m
@@ -47,6 +47,13 @@
 
             isoCenterInCubeCoords = matRad_world2cubeCoords(beam.isoCenter,this.ct);
 
+            if isfield(this.machine.meta,'LUT_bxWidthminFWHM')
+                LUTspotSize = this.machine.meta.LUT_bxWidthminFWHM;
+            else
+                LUTspotSize = this.machine.meta.LUTspotSize;
+            end
+            
+
             beam.numOfBixelsPerRay = zeros(1,beam.numOfRays);
 
             for j = beam.numOfRays:-1:1
@@ -173,10 +180,10 @@
 
                     % book keeping & calculate focus index
                     beam.numOfBixelsPerRay(j) = numel([beam.ray(j).energy]);
-                    currentMinimumFWHM = matRad_interp1(this.machine.meta.LUT_bxWidthminFWHM(1,:)',...
-                        this.machine.meta.LUT_bxWidthminFWHM(2,:)',...
+                    currentMinimumFWHM = matRad_interp1(LUTspotSize(1,:)',...
+                        LUTspotSize(2,:)',...
                         this.bixelWidth, ...
-                        this.machine.meta.LUT_bxWidthminFWHM(2,end));
+                        LUTspotSize(2,end));
                     focusIx  =  ones(beam.numOfBixelsPerRay(j),1);
                     [~, vEnergyIx] = min(abs(bsxfun(@minus,[this.machine.data.energy]',...
                         repmat(beam.ray(j).energy,length([this.machine.data]),1))));
diff --git a/matRad/steering/matRad_StfGeneratorParticleSingleBeamlet.m b/matRad/steering/matRad_StfGeneratorParticleSingleBeamlet.m
@@ -170,10 +170,18 @@ function createPatientGeometry(this)
 
             % get the focus index
             if isfield(this.machine.meta,'LUT_bxWidthminFWHM')
-                currentMinimumFWHM = matRad_interp1(this.machine.meta.LUT_bxWidthminFWHM(1,:)',...
-                    this.machine.meta.LUT_bxWidthminFWHM(2,:)',...
+                LUTspotSize = this.machine.meta.LUT_bxWidthminFWHM;
+            elseif isfield(this.machine.meta,'LUTspotSize')
+                LUTspotSize = this.machine.meta.LUTspotSize;
+            else
+                LUTspotSize = [];
+            end
+                    
+            if ~isempty(LUTspotSize)
+                currentMinimumFWHM = matRad_interp1(LUTspotSize(1,:)',...
+                    LUTspotSize(2,:)',...
                     beam.bixelWidth, ...
-                    this.machine.meta.LUT_bxWidthminFWHM(2,end));
+                    LUTspotSize(2,end));
                 
                 beam.ray.focusIx = find(this.machine.data(vEnergyIx).initFocus.SisFWHMAtIso > currentMinimumFWHM,1,'first');
             else
