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remove useWSL and use static information for calls & version
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@wahln
wahln committed Dec 3, 2024
1 parent 4a61b08 commit e46442f
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Showing 4 changed files with 82 additions and 119 deletions.
1 change: 1 addition & 0 deletions examples/matRad_example18_FREDMC.m
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Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,7 @@

%% Let's now re-compute the dose distribution with FRED MC
pln.propDoseCalc.engine = 'FRED';
pln.propDoseCalc.useGPU = false;

% For illustraton, let's compute a dose influence matrix.
dij_FRED = matRad_calcDoseInfluence(ct,cst,stf,pln);
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13 changes: 6 additions & 7 deletions matRad/doseCalc/+DoseEngines/@matRad_ParticleFREDEngine/calcDose.m
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Expand Up @@ -306,23 +306,22 @@
if ~this.exportCalculation

% Check consistency of installation
if this.checkSystemAvailability()
if this.isAvailable(struct('radiationMode',this.radiationMode),this.machine)

matRad_cfg.dispInfo('calling FRED');

cd(this.MCrunFolder);


systemCall = [this.cmdCall, '-f fred.inp'];
if ~this.useGPU
cmdCall = [this.cmdCall, 'fred -f fred.inp -nogpu'];
else
cmdCall = [this.cmdCall, 'fred -f fred.inp'];
systemCall = [this.cmdCall, ' -nogpu'];
end

% printOutput to matLab console
if this.printOutput
[status,~] = system(cmdCall,'-echo');
[status,~] = system(systemCall,'-echo');
else
[status,~] = system(cmdCall);
[status,~] = system(systemCall);
end
cd(this.FREDrootFolder);
else
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186 changes: 75 additions & 111 deletions matRad/doseCalc/+DoseEngines/@matRad_ParticleFREDEngine/matRad_ParticleFREDEngine.m
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,6 @@
% exportCalculation [b] t: Only write simulation paramter files
% f: run FRED
% sourceModel [s] see AvailableSourceModels, {'gaussian', 'emittance', 'sigmaSqrModel'}
% useWSL [b] for Windows user: use WSL
% useGPU [b] trigger use of GPU (if available)
% roomMaterial [s] material of the patient surroundings. Example:
% 'vacuum', 'Air'
Expand Down Expand Up @@ -63,20 +62,19 @@

properties
exportCalculation;
useGPU;
calcLET;
constantRBE;
HUclamping;
scorers;
HUtable;
sourceModel;
roomMaterial;
useWSL;
useGPU;
printOutput;
primaryMass;
numOfNucleons;
ignoreOutsideDensities;
end
end


properties (SetAccess = private, Hidden)
Expand All @@ -100,12 +98,9 @@
inputFolder;
regionsFolder;
planFolder;

cmdCall;
end

methods

function this = matRad_ParticleFREDEngine(pln)
% Constructor
%
Expand Down Expand Up @@ -309,9 +304,8 @@ function setDefaults(this)
this.HUclamping = false;
this.HUtable = this.defaultHUtable;
this.exportCalculation = false;
this.useGPU = false;
this.sourceModel = this.AvailableSourceModels{1};
this.useWSL = false;
this.useGPU = true;
this.roomMaterial = 'Air';
this.printOutput = true;
this.numHistoriesDirect = matRad_cfg.defaults.propDoseCalc.numHistoriesDirect;
Expand All @@ -335,13 +329,6 @@ function writeHlut(this,hLutFile)
fredDefinedFolder = fullfile(matRad_cfg.matRadSrcRoot, 'doseCalc', 'FRED', 'hluts');

% Collect all the subfolders
% if ispc
% folderDelimiter = ';';
% elseif isunix
% folderDelimiter = ':';
% else
% folderDelimiter = ';';
% end

searchPath = [strsplit(genpath(mainFolder), pathsep)';...
strsplit(genpath(userDefinedFolder), pathsep)';...
Expand Down Expand Up @@ -380,6 +367,46 @@ function writeHlut(this,hLutFile)
end

methods (Static)
function cmdString = cmdCall(newCmdString)
persistent fredCmdCall;
if nargin > 0
fredCmdCall = newCmdString;
elseif isempty(fredCmdCall)
if ispc
fredCmdCall = 'wsl if [ -f ~/.fredenv.sh ] ; then source ~/.fredenv.sh ; fi; fred';
elseif isunix
fredCmdCall = 'if [ -f ~/.fredenv.sh ] ; then source ~/.fredenv.sh ; fi; fred';
else
matRad_cfg = MatRad_Config.instance();
matRad_cfg.dispError('OS not supported for FRED!');
end
end
cmdString = fredCmdCall;
end

function availableVersions = getAvailableVersions()
% Function to get available FRED version

matRad_cfg = MatRad_Config.instance();

currCmdCall = DoseEngines.matRad_ParticleFREDEngine.cmdCall;

availableVersions = [];

[status, cmdOut] = system([currCmdCall, ' -listVers']);

if status == 0
nLidx = regexp(cmdOut, '\n')+6; %6 because of tab
nVersions = numel(nLidx)-1;

for versIdx=1:nVersions
availableVersions = [availableVersions,{cmdOut(nLidx(versIdx):nLidx(versIdx)+5)}];
end

else
matRad_cfg.dispError('Something wrong occured in checking FRED available version. Please check correct FRED installation');
end
end

function [available,msg] = isAvailable(pln,machine)
% see superclass for information
Expand Down Expand Up @@ -408,7 +435,38 @@ function writeHlut(this,hLutFile)
return;
end

available = preCheck;
%Check if I can obtain FRED version
try
ver = DoseEngines.matRad_ParticleFREDEngine.getVersion();
if ~isempty(ver)
execCheck = true;
else
execCheck = false;
msg = sprintf('Couldn''t call FRED executable. Please set the correct system call with DoseEngines.matRad_ParticleFREDEngine.cmdCall(''path/to/executable''). Current value is ''%s''',DoseEngines.matRad_ParticleFREDEngine.cmdCall);
end
catch
msg = 'Your machine file is invalid and does not contain the basic field (meta/data/radiationMode)!';
return;
end

available = preCheck & execCheck;
end

function version = getVersion()
% Function to get current default FRED version
matRad_cfg = MatRad_Config.instance();

try
[status, cmdOut] = system([DoseEngines.matRad_ParticleFREDEngine.cmdCall,' -vn']);

if status == 0
version = cmdOut(1:end-1);
else
matRad_cfg.dispError('Something wrong occured in checking FRED installation. Please check correct FRED installation');
end
catch
matRad_cfg.dispWarning('Something wrong occured in checking FRED installation. Please check correct FRED installation');
end
end

% end
Expand Down Expand Up @@ -503,89 +561,6 @@ function updatePaths(obj)
obj.planFolder = fullfile(obj.inputFolder, 'plan');
end


function calculationAvailable = checkSystemAvailability(this)
matRad_cfg = MatRad_Config.instance();

calculationAvailable = true;

% Disabling GPU for WSL
if this.useWSL
matRad_cfg.dispInfo('Calling FRED from WSL');

if this.useGPU
matRad_cfg.dispWarning('GPU not available in WSL');
end
this.useGPU = false;
end

switch this.machine.meta.radiationMode
case 'protons'

otherwise
matRad_cfg.dispError('Only proton dose calculation available with this version of FRED');
calculationAvailable = false;

end

this.availableVersions = this.getAvailableVersions;

end


function version = getVersion(this)
% Function to get current default FRED version
matRad_cfg = MatRad_Config.instance();

try
[status, cmdOut] = system([this.cmdCall,'fred -vn']);

if status == 0
version = cmdOut(1:end-1);
else
matRad_cfg.dispError('Something wrong occured in checking FRED installation. Please check correct FRED installation');
end
catch
matRad_cfg.dispWarning('Something wrong occured in checking FRED installation. Please check correct FRED installation');
end
end

function availableVersions = getAvailableVersions(this, sist)
% Function to get available FRED version

matRad_cfg = MatRad_Config.instance();

if ~exist('sist', 'var') || isempty(sist)
if this.useWSL
sist = 'wsl';
else
sist = 'win';
end
end

if strcmp(sist, 'win')
currCmdCall = '';
else
currCmdCall = 'wsl if [ -f ~/.fredenv.sh ] ; then source ~/.fredenv.sh ; fi;';
end

availableVersions = [];

[status, cmdOut] = system([currCmdCall, 'fred -listVers']);

if status == 0
nLidx = regexp(cmdOut, '\n')+6; %6 because of tab
nVersions = numel(nLidx)-1;

for versIdx=1:nVersions
availableVersions = [availableVersions,{cmdOut(nLidx(versIdx):nLidx(versIdx)+5)}];
end

else
matRad_cfg.dispError('Something wrong occured in checking FRED available version. Please check correct FRED installation');
end
end

function [radiationMode] = updateRadiationMode(this,value)
% This function also resets the values for primary mass and numebr
% of nucleons. Used for possible future extension to multiple
Expand Down Expand Up @@ -641,17 +616,6 @@ function updatePaths(obj)

end

function set.useWSL(this,value)

this.useWSL = value;

if value
this.cmdCall = 'wsl if [ -f ~/.fredenv.sh ] ; then source ~/.fredenv.sh ; fi;';
else
this.cmdCall = '';
end
end

function set.radiationMode(this,value)
if ischar(value)
if ~isempty(this.radiationMode) && ~strcmp(this.radiationMode, value)
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1 change: 0 additions & 1 deletion test/doseCalc/test_FREDEngine.m
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,6 @@
pln.propDoseCalc.HUtable = 'matRad_default_FredMaterialConverter';
pln.propDoseCalc.exportCalculation = true;
pln.propDoseCalc.sourceModel = 'gaussian';
pln.propDoseCalc.useWSL = true;
pln.propDoseCalc.useGPU = false;
pln.propDoseCalc.roomMaterial = 'Vacuum';
pln.propDoseCalc.printOutput = false;
Expand Down

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