diff --git a/apps/VoxelizerTool/VoxelizerToolCmdLineParser.cpp b/apps/VoxelizerTool/VoxelizerToolCmdLineParser.cpp index 3e4775e..94c0c79 100644 --- a/apps/VoxelizerTool/VoxelizerToolCmdLineParser.cpp +++ b/apps/VoxelizerTool/VoxelizerToolCmdLineParser.cpp @@ -1,122 +1,124 @@ // ----------------------------------------------------------------------- // RTToolbox - DKFZ radiotherapy quantitative evaluation library // // Copyright (c) German Cancer Research Center (DKFZ), // Software development for Integrated Diagnostics and Therapy (SIDT). // ALL RIGHTS RESERVED. // See rttbCopyright.txt or // http://www.dkfz.de/en/sidt/projects/rttb/copyright.html // // This software is distributed WITHOUT ANY WARRANTY; without even // the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR // PURPOSE. See the above copyright notices for more information. // //------------------------------------------------------------------------ /*! // @file // @version $Revision: 1221 $ (last changed revision) // @date $Date: 2015-12-01 13:43:31 +0100 (Di, 01 Dez 2015) $ (last change date) // @author $Author: strubel $ (last changed by) */ #include "VoxelizerToolCmdLineParser.h" namespace rttb { namespace apps { namespace voxelizerTool { VoxelizerCmdLineParser::VoxelizerCmdLineParser(int argc, const char** argv, const std::string& name, const std::string& version, const std::string& description, const std::string& contributor, const std::string& category) : CmdLineParserBase(name, version, description, contributor, category) { //REQUIRED addOption(OPTION_STRUCT_FILE, OPTION_GROUP_REQUIRED, "Filename of the structfile (*.dcm)", 's', true); addInformationForXML(OPTION_STRUCT_FILE, cmdlineparsing::XMLGenerator::paramType::INPUT, {"dcm"}); addOption(OPTION_REFERENCE_FILE, OPTION_GROUP_REQUIRED, "Filename of the reference image (*.dcm)", 'r', true); addInformationForXML(OPTION_REFERENCE_FILE, cmdlineparsing::XMLGenerator::paramType::INPUT, { "dcm" }); addOptionWithDefaultValue(OPTION_OUTPUT_FILE_NAME, OPTION_GROUP_REQUIRED, - "set output file name","out.hdr","out.hdr", 'o', true); + "Set output file name. Remark: if it used in conjunction with flag -m, it is only regarded as " + "hint for the file name pattern. VoxelizerTool will add a suffix indicating the voxelized " + "structure to each filename.","out.hdr","out.hdr", 'o', true); addInformationForXML(OPTION_OUTPUT_FILE_NAME, cmdlineparsing::XMLGenerator::paramType::OUTPUT, { "nrrd", "hdr" }); addPositionalOption(OPTION_STRUCT_FILE,1); addPositionalOption(OPTION_REFERENCE_FILE, 1); addPositionalOption(OPTION_OUTPUT_FILE_NAME, 1); std::vector defaultLoadingStyle; defaultLoadingStyle.push_back("dicom"); addOptionWithDefaultValue(OPTION_REGEX, OPTION_GROUP_REQUIRED, "set a regular expression describing the structs of interest", "", "",'e', true); addInformationForXML(OPTION_REGEX, cmdlineparsing::XMLGenerator::paramType::STRING); addOptionWithDefaultValue>(OPTION_REFERENCE_FILE_LOAD_STYLE, OPTION_GROUP_REQUIRED, "set the load style for the reference file. Available styles are: " "dicom: normal dicom dose" "itk: use itk image loading.", defaultLoadingStyle, defaultLoadingStyle.at(0), 'y', true); addInformationForXML(OPTION_REFERENCE_FILE_LOAD_STYLE, cmdlineparsing::XMLGenerator::paramType::STRINGENUMERATION, { "dicom", "itk" }); //OPTIONAL addOption(OPTION_MULTIPLE_STRUCTS, OPTION_GROUP_OPTIONAL, "if multiple structs match the regular expression" + OPTION_STRUCT_FILE + ", save all in files\n" "If structures 'Kidney_left' and 'Kidney_right' are defined,\n" "both are written under the names outputFile_Kidney_left.mhd and outputFile_Kidney_right.mhd",'m'); addInformationForXML(OPTION_MULTIPLE_STRUCTS, cmdlineparsing::XMLGenerator::paramType::BOOLEAN); addOption(OPTION_BOOLEAN_VOXELIZATION, OPTION_GROUP_OPTIONAL, "Determines if the voxelization should be binarized (only values 0 or 1), the threshold value is by 0.5",'z'); addInformationForXML(OPTION_BOOLEAN_VOXELIZATION, cmdlineparsing::XMLGenerator::paramType::BOOLEAN); addOption(OPTION_ADDSTRUCTURES, OPTION_GROUP_OPTIONAL, "Voxelizes multiple structs in one result file.",'a'); addInformationForXML(OPTION_ADDSTRUCTURES, cmdlineparsing::XMLGenerator::paramType::BOOLEAN); addOption(OPTION_ALLOW_SELF_INTERSECTIONS, OPTION_GROUP_OPTIONAL, "If self intersections of polygons should be tolerated.",'i'); addInformationForXML(OPTION_ALLOW_SELF_INTERSECTIONS, cmdlineparsing::XMLGenerator::paramType::BOOLEAN); parse(argc, argv); } void VoxelizerCmdLineParser::validateInput() const { std::vector referenceLoadStyle = get >(OPTION_REFERENCE_FILE_LOAD_STYLE); std::string referenceLoadStyleString = referenceLoadStyle.at(0); if (referenceLoadStyleString != "dicom" && referenceLoadStyleString != "itk") { throw cmdlineparsing::InvalidConstraintException("Unknown load style for reference file:" + referenceLoadStyleString+ ".\nPlease refer to the help for valid loading style settings."); } if (get(OPTION_OUTPUT_FILE_NAME).find('.') == std::string::npos) { throw cmdlineparsing::InvalidConstraintException(OPTION_OUTPUT_FILE_NAME + " has to specify a file format (e.g. output.hdr). None is given: " + get(OPTION_OUTPUT_FILE_NAME) ); } } void VoxelizerCmdLineParser::printHelp() const { cmdlineparsing::CmdLineParserBase::printHelp(); std::cout << "Example: VoxelizerTool -s structFile.dcm -r referenceFile.dcm -e Kidney -o outputFile.mhd -m" << std::endl; std::cout << "Computes a voxelization file outputFile.mhd based on the DICOMRT-STRUCT structFile.dcm " "in the geometry of referenceFile.dcm where "; std::cout << "the name of the struct matches the regular expression 'Kidney'.\n"; std::cout << "If structures 'Kidney_left' and 'Kidney_right' are defined, "; std::cout << "both are written under the names outputFile_Kidney_left.mhd and outputFile_Kidney_right.mhd (parameter -m)." << std::endl; } } } } \ No newline at end of file diff --git a/testing/apps/VoxelizerTool/VoxelizerToolDifferentCommandsTest.cpp b/testing/apps/VoxelizerTool/VoxelizerToolDifferentCommandsTest.cpp index cfae715..d597486 100644 --- a/testing/apps/VoxelizerTool/VoxelizerToolDifferentCommandsTest.cpp +++ b/testing/apps/VoxelizerTool/VoxelizerToolDifferentCommandsTest.cpp @@ -1,104 +1,104 @@ // ----------------------------------------------------------------------- // RTToolbox - DKFZ radiotherapy quantitative evaluation library // // Copyright (c) German Cancer Research Center (DKFZ), // Software development for Integrated Diagnostics and Therapy (SIDT). // ALL RIGHTS RESERVED. // See rttbCopyright.txt or // http://www.dkfz.de/en/sidt/projects/rttb/copyright.html // // This software is distributed WITHOUT ANY WARRANTY; without even // the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR // PURPOSE. See the above copyright notices for more information. // //------------------------------------------------------------------------ /*! // @file // @version $Revision: 1333 $ (last changed revision) // @date $Date: 2016-04-22 11:12:14 +0200 (Fr, 22 Apr 2016) $ (last change date) // @author $Author: hentsch $ (last changed by) */ #include "litCheckMacros.h" #include #include #include /*! @brief VoxelizerToolTest3. Test the output, multipleStructs and the booleanVoxelization parameter. */ namespace rttb { namespace testing { //path to the current running directory. VoxelizerTool is in the same directory (Debug/Release) extern const char* _callingAppPath; int VoxelizerToolDifferentCommandsTest(int argc, char* argv[]) { PREPARE_DEFAULT_TEST_REPORTING; std::string voxelizerToolExe; std::string tempDirectory; std::string structFile; std::string referenceFile; if (argc > 4) { voxelizerToolExe = argv[1]; tempDirectory = argv[2]; structFile = argv[3]; referenceFile = argv[4]; } std::vector commands; commands.push_back("\"Niere.*\" -m -o Test.hdr"); commands.push_back("\"Rueckenmark\" -o Boolean.hdr -z"); std::vector filenames; filenames.push_back("Test_Niere li"); filenames.push_back("Test_Niere re"); - filenames.push_back("Boolean_Rueckenmark"); + filenames.push_back("Boolean"); boost::filesystem::path callingPath(_callingAppPath); std::string voxelizerToolExeWithPath = callingPath.parent_path().string() + "/" + voxelizerToolExe; std::string baseCommand = voxelizerToolExeWithPath; baseCommand += " -s " + structFile; baseCommand += " -r " + referenceFile; baseCommand += " -e "; for (size_t i = 0; i < commands.size(); i++) { std::string command = baseCommand + commands.at(i); int returnValue = system(command.c_str()); std::cout << "Command line call: " + command << std::endl; CHECK_EQUAL(returnValue, 0); } for (size_t i = 0; i < filenames.size(); i++) { const std::string HDRfileName = tempDirectory + "/" + filenames.at(i) + ".hdr"; boost::filesystem::path HDRFile(HDRfileName); const std::string IMGfileName = tempDirectory + "/" + filenames.at(i) + ".img"; boost::filesystem::path IMGFile(IMGfileName); CHECK_EQUAL(boost::filesystem::exists(HDRFile), true); CHECK_EQUAL(boost::filesystem::exists(IMGFile), true); if (boost::filesystem::exists(IMGFile)) { boost::filesystem::remove(IMGFile); } if (boost::filesystem::exists(HDRFile)) { boost::filesystem::remove(HDRFile); } } RETURN_AND_REPORT_TEST_SUCCESS; } } } diff --git a/testing/apps/VoxelizerTool/VoxelizerToolVoxelValueTest.cpp b/testing/apps/VoxelizerTool/VoxelizerToolVoxelValueTest.cpp index 272bfb1..67552d2 100644 --- a/testing/apps/VoxelizerTool/VoxelizerToolVoxelValueTest.cpp +++ b/testing/apps/VoxelizerTool/VoxelizerToolVoxelValueTest.cpp @@ -1,134 +1,134 @@ // ----------------------------------------------------------------------- // RTToolbox - DKFZ radiotherapy quantitative evaluation library // // Copyright (c) German Cancer Research Center (DKFZ), // Software development for Integrated Diagnostics and Therapy (SIDT). // ALL RIGHTS RESERVED. // See rttbCopyright.txt or // http://www.dkfz.de/en/sidt/projects/rttb/copyright.html // // This software is distributed WITHOUT ANY WARRANTY; without even // the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR // PURPOSE. See the above copyright notices for more information. // //------------------------------------------------------------------------ /*! // @file // @version $Revision: 1333 $ (last changed revision) // @date $Date: 2016-04-22 11:12:14 +0200 (Fr, 22 Apr 2016) $ (last change date) // @author $Author: hentsch $ (last changed by) */ #include "litCheckMacros.h" #include #include "itkImage.h" #include "itkImageFileReader.h" #include #include /*! @brief VoxelizerToolTest5. Search the coordinate at the Image and return the Voxel(Pixel) value. */ namespace rttb { namespace testing { //path to the current running directory. VoxelizerTool is in the same directory (Debug/Release) extern const char* _callingAppPath; int VoxelizerToolVoxelValue(int argc, char* argv[]) { PREPARE_DEFAULT_TEST_REPORTING; typedef itk::Image< double, 3 > ImageType; typedef itk::ImageFileReader ReaderType; std::string voxelizerToolExe; std::string tempDirectory; std::string structFile; std::string referenceFile; std::string structName; if (argc > 5) { voxelizerToolExe = argv[1]; tempDirectory = argv[2]; structFile = argv[3]; referenceFile = argv[4]; structName = argv[5]; } boost::filesystem::path callingPath(_callingAppPath); std::string voxelizerToolExeWithPath = callingPath.parent_path().string() + "/" + voxelizerToolExe; std::string command = voxelizerToolExeWithPath; command += " -s " + structFile; command += " -r " + referenceFile; command += " -e " + structName; int returnValue = system(command.c_str()); CHECK_EQUAL(returnValue, 0); //image values taken in Mevislab //Index inside ImageType::IndexType voxelInside1 = {{20, 30, 30}}; ImageType::IndexType voxelInside2 = {{30, 10, 40}}; //Outside index ImageType::IndexType voxelOutside1 = {{40, 30, 30}}; ImageType::IndexType voxelOutside2 = {{10, 40, 30}}; //Border index ImageType::IndexType voxelBorder1 = {{12, 23, 27}}; ImageType::IndexType voxelBorder2 = {{34, 21, 31}}; std::vector voxelIndices = boost::assign::list_of(voxelInside1)(voxelInside2)( voxelOutside1)( voxelOutside2)(voxelBorder1)(voxelBorder2); std::vector expectedVoxelValues = boost::assign::list_of(1.0)(1.0)(0.0)(0.0)( 0.265865)(0.819613); - std::string filenameHDRWithVoxelization = tempDirectory + "/out_" + structName + ".hdr"; - std::string filenameIMGWithVoxelization = tempDirectory + "/out_" + structName + ".img"; + std::string filenameHDRWithVoxelization = tempDirectory + "/out.hdr"; + std::string filenameIMGWithVoxelization = tempDirectory + "/out.img"; CHECK(boost::filesystem::exists(filenameHDRWithVoxelization)); CHECK(boost::filesystem::exists(filenameIMGWithVoxelization)); if (boost::filesystem::exists(filenameHDRWithVoxelization)) { ReaderType::Pointer reader = ReaderType::New(); reader->SetFileName(filenameHDRWithVoxelization); reader->Update(); ReaderType::OutputImageType::ConstPointer image = reader->GetOutput(); for (size_t i = 0; i < voxelIndices.size(); i++) { ImageType::PixelType voxelValue = image->GetPixel(voxelIndices.at(i)); ImageType::PixelType expectedVoxelValue = expectedVoxelValues.at(i); if (expectedVoxelValue == 0.0 || expectedVoxelValue == 1.0) { CHECK_EQUAL(voxelValue, expectedVoxelValue); } else { CHECK_CLOSE(voxelValue, expectedVoxelValue, 1e-4); } } if (boost::filesystem::exists(filenameHDRWithVoxelization)) { boost::filesystem::remove(filenameHDRWithVoxelization); } if (boost::filesystem::exists(filenameIMGWithVoxelization)) { boost::filesystem::remove(filenameIMGWithVoxelization); } } RETURN_AND_REPORT_TEST_SUCCESS; } } } diff --git a/testing/apps/VoxelizerTool/VoxelizerToolVoxelizerAllStructsTest.cpp b/testing/apps/VoxelizerTool/VoxelizerToolVoxelizerAllStructsTest.cpp index 6e87e64..30d5690 100644 --- a/testing/apps/VoxelizerTool/VoxelizerToolVoxelizerAllStructsTest.cpp +++ b/testing/apps/VoxelizerTool/VoxelizerToolVoxelizerAllStructsTest.cpp @@ -1,109 +1,103 @@ // ----------------------------------------------------------------------- // RTToolbox - DKFZ radiotherapy quantitative evaluation library // // Copyright (c) German Cancer Research Center (DKFZ), // Software development for Integrated Diagnostics and Therapy (SIDT). // ALL RIGHTS RESERVED. // See rttbCopyright.txt or // http://www.dkfz.de/en/sidt/projects/rttb/copyright.html // // This software is distributed WITHOUT ANY WARRANTY; without even // the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR // PURPOSE. See the above copyright notices for more information. // //------------------------------------------------------------------------ /*! // @file // @version $Revision: 1333 $ (last changed revision) // @date $Date: 2016-04-22 11:12:14 +0200 (Fr, 22 Apr 2016) $ (last change date) // @author $Author: hentsch $ (last changed by) */ #include #include "litCheckMacros.h" #include #include /*! @brief VoxelizerToolTest. Tests a selection of structs. */ namespace rttb { namespace testing { //path to the current running directory. VoxelizerTool is in the same directory (Debug/Release) extern const char* _callingAppPath; int VoxelizerToolVoxelizerAllStructsTest(int argc, char* argv[]) { PREPARE_DEFAULT_TEST_REPORTING; std::string voxelizerToolExe; std::string tempDirectory; std::string structFile; std::string referenceFile; if (argc > 4) { voxelizerToolExe = argv[1]; tempDirectory = argv[2]; structFile = argv[3]; referenceFile = argv[4]; } boost::filesystem::path callingPath(_callingAppPath); std::string voxelizerToolExeWithPath = callingPath.parent_path().string() + "/" + voxelizerToolExe; std::vector structNames; structNames.push_back("Niere.*"); structNames.push_back("Magen/DD"); structNames.push_back("PTV"); - //structure names will be used for file naming, BUT '.' in the end will be cropped and '/' will be replaced by '_'. Thus, the different filenames. - std::vector filenames; - filenames.push_back("Niere re"); - filenames.push_back("Magen_DD"); - filenames.push_back("PTV"); - std::string baseCommand = voxelizerToolExeWithPath; baseCommand += " -s " + structFile; baseCommand += " -r " + referenceFile; baseCommand += " -e \""; for (size_t i = 0; i < structNames.size(); i++) { std::string command = baseCommand + structNames.at(i) + "\""; std::cout << "Command line call: " + command << std::endl; int returnValue = system(command.c_str()); CHECK_EQUAL(returnValue, 0); boost::filesystem::path HDRFile(tempDirectory); - HDRFile /= "out_" + filenames.at(i) + ".hdr"; + HDRFile /= "out.hdr"; boost::filesystem::path IMGFile(tempDirectory); - IMGFile /= "out_" + filenames.at(i) + ".img"; + IMGFile /= "out.img"; CHECK_EQUAL( boost::filesystem::exists(HDRFile), true); CHECK_EQUAL( boost::filesystem::exists(IMGFile), true); if (boost::filesystem::exists(IMGFile)) { boost::filesystem::remove(IMGFile); } if (boost::filesystem::exists(HDRFile)) { boost::filesystem::remove(HDRFile); } } RETURN_AND_REPORT_TEST_SUCCESS; } } }