diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleDicomWriter.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleDicomWriter.cpp index a289cc11ef..63e5e28543 100644 --- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleDicomWriter.cpp +++ b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleDicomWriter.cpp @@ -1,184 +1,187 @@ /*=================================================================== 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 "mitkFiberBundleDicomWriter.h" #include #include #include #include #include #include #include #include #include "mitkDiffusionIOMimeTypes.h" #include "dcmtk/config/osconfig.h" /* make sure OS specific configuration is included first */ #include "dcmtk/dcmtract/trctractographyresults.h" mitk::FiberBundleDicomWriter::FiberBundleDicomWriter() : mitk::AbstractFileWriter(mitk::FiberBundle::GetStaticNameOfClass(), mitk::DiffusionIOMimeTypes::FIBERBUNDLE_DICOM_MIMETYPE_NAME(), "DICOM Fiber Bundle Writer") { RegisterService(); } mitk::FiberBundleDicomWriter::FiberBundleDicomWriter(const mitk::FiberBundleDicomWriter & other) :mitk::AbstractFileWriter(other) {} mitk::FiberBundleDicomWriter::~FiberBundleDicomWriter() {} mitk::FiberBundleDicomWriter * mitk::FiberBundleDicomWriter::Clone() const { return new mitk::FiberBundleDicomWriter(*this); } void mitk::FiberBundleDicomWriter::Write() { try { mitk::FiberBundle::ConstPointer fib = dynamic_cast(this->GetInput()); vtkPolyData* poly = fib->GetFiberPolyData(); mitk::PropertyList* p_list = fib->GetPropertyList(); std::string patient_id = ""; if (!p_list->GetStringProperty("DICOM.patient_id", patient_id)) patient_id = "-"; std::string patient_name = ""; if (!p_list->GetStringProperty("DICOM.patient_name", patient_name)) patient_name = "-"; std::string study_instance_uid = ""; if (!p_list->GetStringProperty("DICOM.study_instance_uid", study_instance_uid)) study_instance_uid = "-"; std::string series_instance_uid = ""; if (!p_list->GetStringProperty("DICOM.series_instance_uid", series_instance_uid)) series_instance_uid = "-"; std::string sop_instance_uid = ""; if (!p_list->GetStringProperty("DICOM.sop_instance_uid", sop_instance_uid)) sop_instance_uid = "-"; std::string frame_of_reference_uid = ""; if (!p_list->GetStringProperty("DICOM.frame_of_reference_uid", frame_of_reference_uid)) frame_of_reference_uid = "-"; std::string algo_code_value = ""; if (!p_list->GetStringProperty("DICOM.algo_code.value", algo_code_value)) algo_code_value = "-"; std::string algo_code_meaning = ""; if (!p_list->GetStringProperty("DICOM.algo_code.meaning", algo_code_meaning)) algo_code_meaning = "-"; std::string model_code_value = ""; if (!p_list->GetStringProperty("DICOM.model_code.value", model_code_value)) model_code_value = "-"; std::string model_code_meaning = ""; if (!p_list->GetStringProperty("DICOM.model_code.meaning", model_code_meaning)) model_code_meaning = "-"; std::string anatomy_value = ""; if (!p_list->GetStringProperty("DICOM.anatomy.value", anatomy_value)) anatomy_value = "-"; std::string anatomy_meaning = ""; if (!p_list->GetStringProperty("DICOM.anatomy.meaning", anatomy_meaning)) anatomy_meaning = "-"; const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, nullptr ); setlocale(LC_ALL, locale.c_str()); // Instance Number, Label, Description, Creator's Name ContentIdentificationMacro id("1", "TRACTOGRAM", "Tractogram processed with MITK Diffusion", "MIC@DKFZ"); // Manufacturer, model name, serial number, software version(s) IODEnhGeneralEquipmentModule::EquipmentInfo equipment("MIC@DKFZ", "dcmtract library", "0815", OFFIS_DCMTK_VERSION_STRING); IODReferences refs; // We need at least one image reference this Tractography Results object is based on. // We provide: Patient ID, Study Instance UID, Series Instance UID, SOP Instance UID, SOP Class UID IODImageReference* ref = new IODImageReference(patient_id.c_str(), study_instance_uid.c_str(), series_instance_uid.c_str(), sop_instance_uid.c_str(), UID_MRImageStorage); refs.add(ref); std::time_t t = std::time(NULL); char date_buffer[20]; std::strftime(date_buffer, sizeof(date_buffer), "%Y%m%d", std::gmtime(&t)); char time_buffer[20]; std::strftime(time_buffer, sizeof(time_buffer), "%H%M%S", std::gmtime(&t)); OFString contentDate(date_buffer); OFString contentTime(time_buffer); + OFString val = "-"; TrcTractographyResults *trc = NULL; TrcTractographyResults::create(id, contentDate, contentTime, equipment, refs, trc); - OFString val = "-"; trc->getStudy().getStudyInstanceUID(val); - MITK_INFO << "getStudyInstanceUID " << val; + trc->getStudy().setStudyInstanceUID(study_instance_uid.c_str()); + trc->getSeries().setSeriesInstanceUID(series_instance_uid.c_str()); + trc->getSOPCommon().setSOPInstanceUID(sop_instance_uid.c_str()); + trc->getSeries().getSeriesInstanceUID(val); // Create track set CodeWithModifiers anatomy(""); anatomy.set(anatomy_value.c_str(), "SRT", anatomy_meaning.c_str()); // Every CodeSequenceMacro has: Code Value, Coding Scheme Designator, Code Meaning CodeSequenceMacro diffusionModel(model_code_value.c_str(), "DCM", model_code_meaning.c_str()); CodeSequenceMacro algorithmId(algo_code_value.c_str(), "DCM", algo_code_meaning.c_str()); TrcTrackSet *set = NULL; trc->addTrackSet("TRACTOGRAM", "Tractogram processed with MITK Diffusion", anatomy, diffusionModel, algorithmId, set); // Create trackset Uint16 cieLabColor[3]; // color the whole track with this color; we use some blue cieLabColor[0] = 30000; // L cieLabColor[1] = 0 ; // a cieLabColor[2] = 0 ; // b std::vector< Float32* > tracts; for (int i=0; iGetNumFibers(); i++) { vtkCell* cell = poly->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); Float32* pointData = new Float32[numPoints*3]; for(int i=0; iGetPoint(i); pointData[i*3] = p[0]; pointData[i*3+1] = p[1]; pointData[i*3+2] = p[2]; } tracts.push_back(pointData); TrcTrack* track = NULL; set->addTrack(pointData, numPoints, cieLabColor, 1 /* numColors */, track); } // Frame of Reference is required; could be the same as from related MR series trc->getFrameOfReference().setFrameOfReferenceUID(frame_of_reference_uid.c_str()); // Set some optional data trc->getPatient().setPatientID(patient_id.c_str()); trc->getPatient().setPatientName(patient_name.c_str()); trc->getSeries().setSeriesDescription("Tractogram processed with MITK Diffusion"); // Save file OFCondition result = trc->saveFile(this->GetOutputLocation().c_str()); delete trc; if (result.bad()) mitkThrow() << "Unable to save tractography as DICOM file: " << result.text(); for (Float32* tract : tracts) delete [] tract; setlocale(LC_ALL, currLocale.c_str()); MITK_INFO << "DICOM Fiber bundle written to " << this->GetOutputLocation(); } catch(...) { throw; } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/plugin.xml index 70d4ac3382..cc8c81d085 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/plugin.xml +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/plugin.xml @@ -1,24 +1,24 @@ - + - + - - - + + +