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JenHardtJenHardt
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replace replace function as it causes porblems with octave
1 parent 42e31d2 commit ad938d3

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‎matRad/doseCalc/+DoseEngines/matRad_TopasMCEngine.m‎

Lines changed: 53 additions & 53 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
classdef matRad_TopasMCEngine < DoseEngines.matRad_MonteCarloEngineAbstract
2-
% matRad_TopasMCEngine
2+
% matRad_TopasMCEngine
33
% Implementation of the TOPAS interface for Monte Carlo dose
44
% calculation
55
%
@@ -18,7 +18,7 @@
1818
%
1919
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2020

21-
properties (Constant)
21+
properties (Constant)
2222
possibleRadiationModes = {'photons','protons','helium','carbon'};
2323
name = 'TOPAS';
2424
shortName = 'TOPAS';
@@ -38,7 +38,7 @@
3838
topasExecCommand; %Defaults will be set during construction according to TOPAS installation instructions and used system
3939

4040
parallelRuns = false; %Starts runs in parallel
41-
41+
4242
externalCalculation = 'off'; %Generates folder for external TOPAS calculation (e.g. on a server)
4343

4444
workingDir; %working directory for the simulation
@@ -157,7 +157,7 @@
157157
'Scorer_RBE_MCN','TOPAS_scorer_doseRBE_McNamara.txt.in', ...
158158
... %PhaseSpace Source
159159
'phaseSpaceSourcePhotons' ,'VarianClinaciX_6MV_20x20_aboveMLC_w2' );
160-
160+
161161

162162
end
163163

@@ -182,9 +182,9 @@
182182
function setDefaults(this)
183183
this.setDefaults@DoseEngines.matRad_MonteCarloEngineAbstract();
184184
matRad_cfg = MatRad_Config.instance(); %Instance of matRad configuration class
185-
185+
186186
this.useGivenEqDensityCube = matRad_cfg.defaults.propDoseCalc.useGivenEqDensityCube;
187-
187+
188188
% Default execution paths are set here
189189
this.topasFolder = [matRad_cfg.matRadSrcRoot filesep 'doseCalc' filesep 'topas' filesep];
190190
this.workingDir = [matRad_cfg.primaryUserFolder filesep 'TOPAS' filesep];
@@ -193,7 +193,7 @@ function setDefaults(this)
193193
mkdir(this.workingDir);
194194
matRad_cfg.dispInfo('Created TOPAS working directory in userfolder %s\n',this.workingDir);
195195
end
196-
196+
197197

198198
%Let's set some default commands taken from topas installation
199199
%instructions for mac & debain/ubuntu
@@ -465,7 +465,7 @@ function writeAllFiles(obj,ct,cst,stf,machine,w)
465465
return;
466466
else
467467
end
468-
468+
469469

470470
%% Initialize dose grid and dij
471471

@@ -496,12 +496,12 @@ function writeAllFiles(obj,ct,cst,stf,machine,w)
496496
end
497497
end
498498
end
499-
499+
500500
for i = 1:numel(stf)
501501
if strcmp(stf(i).radiationMode,'photons')
502502
stf(i).ray.energy = stf(i).ray.energy.*ones(size(w));
503503
end
504-
end
504+
end
505505

506506
% Get photon parameters for RBExDose calculation
507507
if this.calcBioDose
@@ -645,7 +645,7 @@ function writeAllFiles(obj,ct,cst,stf,machine,w)
645645
dij.beamNum = 1;
646646
dij.bixelNum = 1;
647647
dij.ctGrid = this.ctR.ctGrid;
648-
dij.doseGrid = this.doseGrid;
648+
dij.doseGrid = this.doseGrid;
649649
dij.numOfBeams = 1;
650650
dij.numOfRaysPerBeam = 1;
651651
dij.numOfScenarios = this.multScen.totNumScen;
@@ -671,7 +671,7 @@ function writeAllFiles(obj,ct,cst,stf,machine,w)
671671

672672
end
673673

674-
674+
675675
function dij = initDoseCalc(this,ct,cst,stf)
676676
dij = this.initDoseCalc@DoseEngines.matRad_MonteCarloEngineAbstract(ct,cst,stf);
677677
matRad_cfg = MatRad_Config.instance();
@@ -702,35 +702,35 @@ function writeAllFiles(obj,ct,cst,stf,machine,w)
702702
% Allpcate resampled cubes
703703
cubeHUresampled = cell(1,ct.numOfCtScen);
704704
cubeResampled = cell(1,ct.numOfCtScen);
705-
705+
706706
% Perform resampling to dose grid
707707
for s = 1:ct.numOfCtScen
708708
cubeHUresampled{s} = matRad_interp3(dij.ctGrid.x, dij.ctGrid.y', dij.ctGrid.z,ct.cubeHU{s}, ...
709709
dij.doseGrid.x,dij.doseGrid.y',dij.doseGrid.z,'linear');
710710
cubeResampled{s} = matRad_interp3(dij.ctGrid.x, dij.ctGrid.y', dij.ctGrid.z,ct.cube{s}, ...
711711
dij.doseGrid.x,dij.doseGrid.y',dij.doseGrid.z,'linear');
712712
end
713-
713+
714714
% Allocate temporary resampled CT
715715
this.ctR = ct;
716716
this.ctR.cube = cell(1);
717717
this.ctR.cubeHU = cell(1);
718-
718+
719719
% Set CT resolution to doseGrid resolution
720720
this.ctR.resolution = dij.doseGrid.resolution;
721721
this.ctR.cubeDim = dij.doseGrid.dimensions;
722722
this.ctR.x = dij.doseGrid.x;
723723
this.ctR.y = dij.doseGrid.y;
724724
this.ctR.z = dij.doseGrid.z;
725-
725+
726726
% Write resampled cubes
727727
this.ctR.cubeHU = cubeHUresampled;
728728
this.ctR.cube = cubeResampled;
729-
729+
730730
% Set flag for complete resampling
731731
this.ctR.resampled = 1;
732732
this.ctR.ctGrid = dij.doseGrid;
733-
733+
734734
% Save original grid
735735
this.ctR.originalGrid = dij.ctGrid;
736736
matRad_cfg.dispInfo('done!\n');
@@ -905,7 +905,7 @@ function writeAllFiles(obj,ct,cst,stf,machine,w)
905905
end
906906

907907
% Tally per field
908-
if isfield(topasSum,'Sum')
908+
if isfield(topasSum,'Sum')
909909
if obj.calc4DInterplay || obj.MCparam.numOfCtScen > 1
910910
if strcmp(tname, 'physicalDose')
911911
topasCube.(['phaseDose_beam' num2str(f)]){ctScen} = topasSum.Sum;
@@ -1071,7 +1071,7 @@ function writeAllFiles(obj,ct,cst,stf,machine,w)
10711071
% Allocate possible scored quantities
10721072
processedQuantities = {'','_std','_batchStd'};
10731073
topasCubesTallies = unique(erase(topasCubesTallies,processedQuantities(2:end)));
1074-
1074+
10751075

10761076
% Loop through 4D scenarios
10771077
for ctScen = 1:dij.numOfScenarios
@@ -1232,7 +1232,7 @@ function writeRunHeader(obj,fID,fieldIx,runIx,ctScen)
12321232
fprintf(fID,'\n');
12331233
fprintf(fID,['i:Ts/Seed = ',num2str(runIx),'\n']);
12341234

1235-
%TODO: remove or document
1235+
%TODO: remove or document
12361236
%fprintf(fID,'includeFile = %s/TOPAS_Simulation_Setup.txt\n',obj.thisFolder);
12371237
%fprintf(fID,'includeFile = %s/TOPAS_matRad_geometry.txt\n',obj.thisFolder);
12381238
%fprintf(fID,'includeFile = %s/TOPAS_scorer_surfaceIC.txt\n',obj.thisFolder);
@@ -1295,12 +1295,12 @@ function writeScorers(obj,fID,beamIx)
12951295
matRad_cfg.dispDebug('Reading doseToMedium scorer from %s\n',fname);
12961296
scorerName = fileread(fname);
12971297
fprintf(fID,'\n%s\n\n',scorerName);
1298-
1298+
12991299
if obj.calc4DInterplay
13001300
for PhaseNum = obj.MCparam.Phases{beamIx}'
13011301
scorerTxt = fileread(fname);
1302-
scorerTxt = replace(scorerTxt, '/Patient', ['/Patient' num2str(PhaseNum)]);
1303-
scorerTxt = replace(scorerTxt, '_physicalDose', ['_physicalDose-matRad_cube' num2str(PhaseNum)]);
1302+
scorerTxt = strrep(scorerTxt, '/Patient', ['/Patient' num2str(PhaseNum)]);
1303+
scorerTxt = strrep(scorerTxt, '_physicalDose', ['_physicalDose-matRad_cube' num2str(PhaseNum)]);
13041304
fprintf(fID,'\n%s\n\n',scorerTxt);
13051305
fprintf(fID, 'b:Sc/Patient%i/Tally_DoseToMedium/Active = Tf/Patient%i/Tally_DoseToMedium/Active/Value\n', PhaseNum, PhaseNum);
13061306
fprintf(fID,'s:Tf/Patient%i/Tally_DoseToMedium/Active/Function = "Step"\n', PhaseNum);
@@ -1354,33 +1354,33 @@ function writeScorers(obj,fID,beamIx)
13541354
fprintf(fID,'\n%s\n\n',scorerName);
13551355

13561356
if obj.calc4DInterplay
1357-
for PhaseNum = obj.MCparam.Phases{beamIx}'
1357+
for PhaseNum = obj.MCparam.Phases{beamIx}'
13581358
scorerTxt = fileread(fname);
1359-
scorerTxt = replace(scorerTxt, 'Alpha/', ['Alpha' num2str(PhaseNum) '/']);
1360-
scorerTxt = replace(scorerTxt, 'Beta/', ['Beta' num2str(PhaseNum) '/']);
1361-
scorerTxt = replace(scorerTxt, '/RBE', ['/RBE' num2str(PhaseNum)]);
1359+
scorerTxt = strrep(scorerTxt, 'Alpha/', ['Alpha' num2str(PhaseNum) '/']);
1360+
scorerTxt = strrep(scorerTxt, 'Beta/', ['Beta' num2str(PhaseNum) '/']);
1361+
scorerTxt = strrep(scorerTxt, '/RBE', ['/RBE' num2str(PhaseNum)]);
13621362
if contains(lower(obj.scorer.RBE_model{i}),'mcn')
1363-
scorerTxt = replace(scorerTxt, '_alpha_MCN', ['_alpha_MCN-matRad_cube' num2str(PhaseNum)]);
1364-
scorerTxt = replace(scorerTxt, '_beta_MCN', ['_beta_MCN-matRad_cube' num2str(PhaseNum)]);
1363+
scorerTxt = strrep(scorerTxt, '_alpha_MCN', ['_alpha_MCN-matRad_cube' num2str(PhaseNum)]);
1364+
scorerTxt = strrep(scorerTxt, '_beta_MCN', ['_beta_MCN-matRad_cube' num2str(PhaseNum)]);
13651365
elseif contains(lower(obj.scorer.RBE_model{i}),'wed')
1366-
scorerTxt = replace(scorerTxt, '_alpha_WED', ['_alpha_WED-matRad_cube' num2str(PhaseNum)]);
1367-
scorerTxt = replace(scorerTxt, '_beta_WED', ['_beta_WED-matRad_cube' num2str(PhaseNum)]);
1366+
scorerTxt = strrep(scorerTxt, '_alpha_WED', ['_alpha_WED-matRad_cube' num2str(PhaseNum)]);
1367+
scorerTxt = strrep(scorerTxt, '_beta_WED', ['_beta_WED-matRad_cube' num2str(PhaseNum)]);
13681368
elseif contains(lower(obj.scorer.RBE_model{i}),'lem')
1369-
scorerTxt = replace(scorerTxt, '_alpha_LEM', ['_alpha_LEM-matRad_cube' num2str(PhaseNum)]);
1370-
scorerTxt = replace(scorerTxt, '_beta_LEM', ['_beta_LEM-matRad_cube' num2str(PhaseNum)]);
1371-
scorerTxt = replace(scorerTxt, '_RBE_LEM', ['_RBE_LEM-matRad_cube' num2str(PhaseNum)]);
1369+
scorerTxt = strrep(scorerTxt, '_alpha_LEM', ['_alpha_LEM-matRad_cube' num2str(PhaseNum)]);
1370+
scorerTxt = strrep(scorerTxt, '_beta_LEM', ['_beta_LEM-matRad_cube' num2str(PhaseNum)]);
1371+
scorerTxt = strrep(scorerTxt, '_RBE_LEM', ['_RBE_LEM-matRad_cube' num2str(PhaseNum)]);
13721372
elseif contains(lower(obj.scorer.RBE_model{i}),'libamtrack')
1373-
scorerTxt = replace(scorerTxt, '_alpha_libamtrack', ['_alpha_libamtrack-matRad_cube' num2str(PhaseNum)]);
1374-
scorerTxt = replace(scorerTxt, '_beta_libamtrack', ['_beta_libamtrack-matRad_cube' num2str(PhaseNum)]);
1375-
scorerTxt = replace(scorerTxt, '_RBE_libamtrack', ['_RBE_libamtrack-matRad_cube' num2str(PhaseNum)]);
1373+
scorerTxt = strrep(scorerTxt, '_alpha_libamtrack', ['_alpha_libamtrack-matRad_cube' num2str(PhaseNum)]);
1374+
scorerTxt = strrep(scorerTxt, '_beta_libamtrack', ['_beta_libamtrack-matRad_cube' num2str(PhaseNum)]);
1375+
scorerTxt = strrep(scorerTxt, '_RBE_libamtrack', ['_RBE_libamtrack-matRad_cube' num2str(PhaseNum)]);
13761376
end
13771377
%dont allways write cell lines
13781378
if contains(scorerTxt,'### HCP Tabulated ###')
13791379
scorerTxt = extractBefore(scorerTxt, '### HCP Tabulated ###');
13801380
end
13811381
fprintf(fID,'\n%s\n\n',scorerTxt);
13821382
scorerInString = {'tabulatedAlpha', 'tabulatedBeta', 'RBE', 'McNamaraAlpha', 'McNamaraBeta', 'WedenbergAlpha', 'WedenbergBeta'};
1383-
for ixWrite = ixToWrite4DInterplay
1383+
for ixWrite = ixToWrite4DInterplay
13841384
fprintf(fID,'b:Sc/%s%i/Active = Tf/%s%i/Active/Value\n', scorerInString{ixWrite},PhaseNum,scorerInString{ixWrite},PhaseNum);
13851385
fprintf(fID,'s:Tf/%s%i/Active/Function = "Step"\n', scorerInString{ixWrite}, PhaseNum);
13861386
fprintf(fID,'dv:Tf/%s%i/Active/Times= %i ',scorerInString{ixWrite},PhaseNum, obj.MCparam.cutNumOfBixel(beamIx));
@@ -1450,7 +1450,7 @@ function writeScorers(obj,fID,beamIx)
14501450
end
14511451
fprintf(fID,'s:Sc/%s%s/ReferencedSubScorer_Dose = "Tally_DoseToWater"\n',scorerPrefix,scorerNames{s});
14521452
if obj.calc4DInterplay
1453-
for PhaseNum = obj.MCparam.Phases{beamIx}'
1453+
for PhaseNum = obj.MCparam.Phases{beamIx}'
14541454
if strcmp(obj.radiationMode,'protons')
14551455
fprintf(fID,'s:Sc/%s%s%i/ReferencedSubScorer_LET = "ProtonLET%i"\n',scorerPrefix,scorerNames{s},PhaseNum,PhaseNum);
14561456
end
@@ -1473,8 +1473,8 @@ function writeScorers(obj,fID,beamIx)
14731473
if obj.calc4DInterplay
14741474
for PhaseNum = obj.MCparam.Phases{beamIx}'
14751475
scorerTxt = fileread(fname);
1476-
scorerTxt = replace(scorerTxt, 'Tally_DoseToWater', ['Tally_DoseToWater' num2str(PhaseNum)]);
1477-
scorerTxt = replace(scorerTxt, '_doseToWater', ['_doseToWater-matRad_cube' num2str(PhaseNum)]);
1476+
scorerTxt = strrep(scorerTxt, 'Tally_DoseToWater', ['Tally_DoseToWater' num2str(PhaseNum)]);
1477+
scorerTxt = strrep(scorerTxt, '_doseToWater', ['_doseToWater-matRad_cube' num2str(PhaseNum)]);
14781478
fprintf(fID,'\n%s\n\n',scorerTxt);
14791479
fprintf(fID, 'b:Sc/Tally_DoseToWater%i/Active = Tf/Tally_DoseToWater%i/Active/Value\n', PhaseNum, PhaseNum);
14801480
fprintf(fID,'s:Tf/Tally_DoseToWater%i/Active/Function = "Step"\n', PhaseNum);
@@ -1502,8 +1502,8 @@ function writeScorers(obj,fID,beamIx)
15021502
if obj.calc4DInterplay
15031503
for PhaseNum = obj.MCparam.Phases{beamIx}'
15041504
scorerTxt = fileread(fname);
1505-
scorerTxt = replace(scorerTxt, '/ProtonLET', ['/ProtonLET' num2str(PhaseNum)]);
1506-
scorerTxt = replace(scorerTxt, '_LET', ['_LET-matRad_cube' num2str(PhaseNum)]);
1505+
scorerTxt = strrep(scorerTxt, '/ProtonLET', ['/ProtonLET' num2str(PhaseNum)]);
1506+
scorerTxt = strrep(scorerTxt, '_LET', ['_LET-matRad_cube' num2str(PhaseNum)]);
15071507
fprintf(fID,'\n%s\n\n',scorerTxt);
15081508
fprintf(fID, 'b:Sc/ProtonLET%i/Active = Tf/ProtonLET%i/Active/Value\n', PhaseNum, PhaseNum);
15091509
fprintf(fID,'s:Tf/ProtonLET%i/Active/Function = "Step"\n', PhaseNum);
@@ -1700,8 +1700,8 @@ function writeStfFields(obj,ct,stf,w,baseData)
17001700
selectedData = [];
17011701
focusIndex = baseData.selectedFocus(baseData.energyIndex);
17021702

1703-
scalarFields = {'NominalEnergy','EnergySpread','MeanEnergy'};
1704-
1703+
scalarFields = {'NominalEnergy','EnergySpread','MeanEnergy'};
1704+
17051705
for i = 1:numel(focusIndex)
17061706
for field = scalarFields
17071707
baseData.monteCarloData(i).(field{1}) = ones(1,max(focusIndex))*baseData.monteCarloData(i).(field{1});
@@ -1821,7 +1821,7 @@ function writeStfFields(obj,ct,stf,w,baseData)
18211821
nBeamParticlesTotal(beamIx) = nBeamParticlesTotal(beamIx) + nCurrentParticles;
18221822
currentBixel = currentBixel + 1;
18231823

1824-
1824+
18251825
end
18261826
end
18271827

@@ -1890,7 +1890,7 @@ function writeStfFields(obj,ct,stf,w,baseData)
18901890
end
18911891

18921892
% NozzleAxialDistance
1893-
if isPhoton
1893+
if isPhoton
18941894
fprintf(fileID,'d:Ge/Nozzle/TransZ = -%f mm\n', stf(beamIx).SCD+40); %Phasespace hardcorded infront of MLC at SSD 46 cm
18951895
else
18961896
fprintf(fileID,'d:Ge/Nozzle/TransZ = -%f mm\n', nozzleToAxisDistance);
@@ -2082,7 +2082,7 @@ function writeStfFields(obj,ct,stf,w,baseData)
20822082

20832083
fprintf(fileID,'d:Sim/GantryAngle = %f deg\n',stf(beamIx).gantryAngle); %just one beam angle for now
20842084
fprintf(fileID,'d:Sim/CouchAngle = %f deg\n',stf(beamIx).couchAngle);
2085-
% Here the phasespace file is loaded and referenced in the beamSetup file
2085+
% Here the phasespace file is loaded and referenced in the beamSetup file
20862086
if strcmp(obj.externalCalculation,'write')
20872087
matRad_cfg.dispWarning(['External calculation and phaseSpace selected, manually place ' obj.infilenames.phaseSpaceSourcePhotons '.header and ' obj.infilenames.phaseSpaceSourcePhotons '.phsp into your simulation directory.']);
20882088
else
@@ -2091,7 +2091,7 @@ function writeStfFields(obj,ct,stf,w,baseData)
20912091
end
20922092
end
20932093
%phasespaceStr = ['..' filesep 'beamSetup' filesep 'phasespace' filesep phaseSpaceFileName];
2094-
%&phasespaceStr = replace(phasespaceStr, '\', '/');
2094+
%&phasespaceStr = strrep(phasespaceStr, '\', '/');
20952095
fprintf(fileID,'s:So/Phasespace/PhaseSpaceFileName = "%s"\n', obj.infilenames.phaseSpaceSourcePhotons );
20962096

20972097
end
@@ -2238,7 +2238,7 @@ function writeStfFields(obj,ct,stf,w,baseData)
22382238
if isempty(obj.calcTimeSequence)
22392239
matRad_cfg.dispError('Time Sequence Data required for 4D calculation \n');
22402240
end
2241-
2241+
22422242
% Write changing CT phases in matRad_cube file
22432243
outfilePatient = obj.outfilenames.patientParam;
22442244
outfilePatient = strsplit(outfilePatient,'.');
@@ -2261,7 +2261,7 @@ function writeStfFields(obj,ct,stf,w,baseData)
22612261
fprintf(fIDPatient,'sv:Tf/InputFile/Values = %d %s \n ', numel(fileNamesPhases),strjoin(fileNamesPhases,' '));
22622262
fprintf(fIDPatient, '\n');
22632263
fclose(fIDPatient);
2264-
2264+
22652265
%write On of Feature into MCparam to create scorers
22662266
%later
22672267
uniquePhaseNum = unique(PhaseNum);
@@ -2714,7 +2714,7 @@ function writeMCparam(obj)
27142714
%Used to check against a machine file if a specific quantity can be
27152715
%computed.
27162716
function q = providedQuantities(machine)
2717-
q = {'physicalDose','LET','alpha','beta'};
2717+
q = {'physicalDose','LET','alpha','beta'};
27182718
end
27192719
end
27202720
end

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