diff --git a/Modules/PhotoacousticsLib/MitkPAPhantomGenerator/PAPhantomGenerator.cpp b/Modules/PhotoacousticsLib/MitkPAPhantomGenerator/PAPhantomGenerator.cpp index 4f54fefac4..cb83119f46 100644 --- a/Modules/PhotoacousticsLib/MitkPAPhantomGenerator/PAPhantomGenerator.cpp +++ b/Modules/PhotoacousticsLib/MitkPAPhantomGenerator/PAPhantomGenerator.cpp @@ -1,218 +1,230 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include #include #include using namespace mitk::pa; TissueGeneratorParameters::Pointer CreatePhantom_04_04_18_Parameters() { auto returnParameters = TissueGeneratorParameters::New(); returnParameters->SetAirThicknessInMillimeters(12); returnParameters->SetMinBackgroundAbsorption(0.1); returnParameters->SetMaxBackgroundAbsorption(0.1); returnParameters->SetBackgroundAnisotropy(0.9); returnParameters->SetBackgroundScattering(15); returnParameters->SetCalculateNewVesselPositionCallback(&VesselMeanderStrategy::CalculateNewPositionInStraightLine); returnParameters->SetDoPartialVolume(true); returnParameters->SetMinNumberOfVessels(1); returnParameters->SetMaxNumberOfVessels(8); returnParameters->SetMinVesselAbsorption(1); returnParameters->SetMaxVesselAbsorption(10); returnParameters->SetMinVesselAnisotropy(0.9); returnParameters->SetMaxVesselAnisotropy(0.9); returnParameters->SetMinVesselBending(0.1); returnParameters->SetMaxVesselBending(0.3); returnParameters->SetMinVesselRadiusInMillimeters(0.25); returnParameters->SetMaxVesselRadiusInMillimeters(4); returnParameters->SetMinVesselScattering(15); returnParameters->SetMaxVesselScattering(15); returnParameters->SetMinVesselZOrigin(1.6); returnParameters->SetMaxVesselZOrigin(4); returnParameters->SetVesselBifurcationFrequency(5000); returnParameters->SetRandomizePhysicalProperties(false); returnParameters->SetSkinThicknessInMillimeters(0); returnParameters->SetUseRngSeed(false); returnParameters->SetVoxelSpacingInCentimeters(0.03); returnParameters->SetXDim(140); returnParameters->SetYDim(100); returnParameters->SetZDim(180); //returnParameters->SetVoxelSpacingInCentimeters(0.015); //returnParameters->SetXDim(280); //returnParameters->SetYDim(200); //returnParameters->SetZDim(360); returnParameters->SetForceVesselsMoveAlongYDirection(true); //returnParameters->SetVoxelSpacingInCentimeters(0.0075); //returnParameters->SetXDim(560); //returnParameters->SetYDim(400); //returnParameters->SetZDim(720); return returnParameters; } struct InputParameters { std::string saveFolderPath; std::string identifyer; std::string exePath; std::string probePath; + bool empty; bool verbose; }; InputParameters parseInput(int argc, char* argv[]) { - MITK_INFO << "Paring arguments..."; + MITK_INFO << "Parsing arguments..."; mitkCommandLineParser parser; - // set general information + parser.setCategory("MITK-Photoacoustics"); parser.setTitle("Mitk Tissue Batch Generator"); parser.setDescription("Creates in silico tissue in batch processing and automatically calculates fluence values for the central slice of the volume."); parser.setContributor("Computer Assisted Medical Interventions, DKFZ"); - // how should arguments be prefixed parser.setArgumentPrefix("--", "-"); - // add each argument, unless specified otherwise each argument is optional - // see mitkCommandLineParser::addArgument for more information + parser.beginGroup("Required parameters"); parser.addArgument( "savePath", "s", mitkCommandLineParser::InputDirectory, "Input save folder (directory)", "input save folder", us::Any(), false); parser.addArgument( "mitkMcxyz", "m", mitkCommandLineParser::OutputFile, "MitkMcxyz binary (file)", "path to the MitkMcxyz binary", us::Any(), false); parser.endGroup(); + parser.beginGroup("Optional parameters"); parser.addArgument( "probe", "p", mitkCommandLineParser::OutputFile, "xml probe file (file)", "file to the definition of the used probe (*.xml)", us::Any()); parser.addArgument( "verbose", "v", mitkCommandLineParser::Bool, "Verbose Output", "Whether to produce verbose, or rather debug output"); parser.addArgument( "identifyer", "i", mitkCommandLineParser::String, "Generator identifyer (string)", "A unique identifyer for the calculation instance"); + parser.addArgument( + "empty-volume", "e", mitkCommandLineParser::Bool, + "omit vessel structures (boolean flag)", "Whether to create an empty volume with no structures inside."); + parser.endGroup(); InputParameters input; std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size() == 0) exit(-1); + if (parsedArgs.count("empty-volume")) + { + input.empty = us::any_cast(parsedArgs["empty-volume"]); + } + else + { + input.empty = false; + } + if (parsedArgs.count("verbose")) { - MITK_INFO << "verbose"; input.verbose = us::any_cast(parsedArgs["verbose"]); } else { input.verbose = false; } if (parsedArgs.count("savePath")) { - MITK_INFO << "savePath"; input.saveFolderPath = us::any_cast(parsedArgs["savePath"]); } if (parsedArgs.count("mitkMcxyz")) { - MITK_INFO << "mitkMcxyz"; input.exePath = us::any_cast(parsedArgs["mitkMcxyz"]); } if (parsedArgs.count("probe")) { - MITK_INFO << "probe"; input.probePath = us::any_cast(parsedArgs["probe"]); } if (parsedArgs.count("identifyer")) { - MITK_INFO << "identifyer"; input.identifyer = us::any_cast(parsedArgs["identifyer"]); } else { - MITK_INFO << "generating identifyer"; auto uid = mitk::UIDGenerator("", 8); input.identifyer = uid.GetUID(); } - MITK_INFO << "Paring arguments...[Done]"; + MITK_INFO << "Parsing arguments...[Done]"; return input; } int main(int argc, char * argv[]) { auto input = parseInput(argc, argv); auto parameters = CreatePhantom_04_04_18_Parameters(); + if (input.empty) + { + parameters->SetMaxNumberOfVessels(0); + parameters->SetMinNumberOfVessels(0); + } MITK_INFO(input.verbose) << "Generating tissue.."; auto resultTissue = InSilicoTissueGenerator::GenerateInSilicoData(parameters); MITK_INFO(input.verbose) << "Generating tissue..[Done]"; auto inputfolder = std::string(input.saveFolderPath + "input/"); auto outputfolder = std::string(input.saveFolderPath + "output/"); if (!itksys::SystemTools::FileIsDirectory(inputfolder)) { itksys::SystemTools::MakeDirectory(inputfolder); } if (!itksys::SystemTools::FileIsDirectory(outputfolder)) { itksys::SystemTools::MakeDirectory(outputfolder); } std::string savePath = input.saveFolderPath + "input/Phantom_" + input.identifyer + ".nrrd"; mitk::IOUtil::Save(resultTissue->ConvertToMitkImage(), savePath); std::string outputPath = input.saveFolderPath + "output/Phantom_" + input.identifyer + "/"; resultTissue = nullptr; if (!itksys::SystemTools::FileIsDirectory(outputPath)) { itksys::SystemTools::MakeDirectory(outputPath); } outputPath = outputPath + "Fluence_Phantom_" + input.identifyer; MITK_INFO(input.verbose) << "Simulating fluence.."; int result = -4; std::string cmdString = std::string(input.exePath + " -i " + savePath + " -o " + (outputPath + ".nrrd") + " -yo " + "0" + " -p " + input.probePath + " -n 10000000"); MITK_INFO << "Executing: " << cmdString; result = std::system(cmdString.c_str()); MITK_INFO << result; MITK_INFO(input.verbose) << "Simulating fluence..[Done]"; }