void addPath(std::string dir) { namespace bp = ::boost::python; SLM_ERROR_IF("Python must be initialized before adding a new dir", Py_IsInitialized()); bp::object sys = bp::import("sys"); sys.attr("path").attr("insert")(0, dir); OSLM_INFO(dir << " appended to Python Path"); }
void Video::doUpdate() throw(fwTools::Failed) { ::fwData::Video::sptr video = this->getObject< ::fwData::Video >(); if (!video->dataAvailable()) return; const ::boost::uint8_t * _pImageBuffer = video->getImageBuffer(); int size[3]; size[0] = video->getXSize() ; size[1] = video->getYSize(); size[2] = 1; m_array->SetNumberOfComponents(video->m_ui8BPP ); m_array->SetVoidArray( (unsigned char*)_pImageBuffer, video->getXSize() * video->getYSize() ,1); m_imageData->AllocateScalars(VTK_UNSIGNED_CHAR, video->m_ui8BPP); m_imageData->GetPointData()->SetScalars(m_array) ; m_imageData->SetDimensions(size) ; m_imageData->SetSpacing(1.0, 1.0, 1.0 ); m_imageData->SetOrigin(0.0, 0.0, 0.0 ); if(!bText_init) { m_texture->SetInputData(m_imageData ) ; this->getActor()->SetScale(size[0], size[1], 1.0); this->getRenderer()->InteractiveOff(); this->getRenderer()->GetActiveCamera()->ParallelProjectionOn(); this->getRenderer()->ResetCamera(); //fit the image to the render window this->getRenderer()->GetActiveCamera()->SetParallelScale(size[1] / 2.0); this->addToRenderer(this->getActor()); bText_init = true; ::boost::filesystem::path pathShaderVP ( "Bundles/visuVTKAdaptor_" + std::string(VISUVTKADAPTOR_VER) + "/vp.glsl" ); ::boost::filesystem::path pathShaderFP ( "Bundles/visuVTKAdaptor_" + std::string(VISUVTKADAPTOR_VER) + "/fp.glsl" ); vtkSmartPointer<vtkShaderProgram2> pProgram; pProgram = ::fwRenderVTK::vtk::buildShaderFromFile(this->getRenderer()->GetRenderWindow(), pathShaderVP.string().c_str(), pathShaderFP.string().c_str()); SLM_ERROR_IF("Failed to build shader program", !pProgram); vtkProperty *property = this->getActor()->GetProperty(); vtkOpenGLProperty *pOpenGLProperty = vtkOpenGLProperty::SafeDownCast(property); SLM_ASSERT("Shader program not supported", pOpenGLProperty); pOpenGLProperty->SetPropProgram(pProgram); } m_imageData->Modified(); this->setVtkPipelineModified(); }
void setHome(std::string dir) { if(!Py_IsInitialized()) { if (::fwPython::Config::home) { delete [] ::fwPython::Config::home; } ::fwPython::Config::home = charFromString(dir); Py_SetPythonHome( ::fwPython::Config::home ); OSLM_INFO("Python Home set to " << dir); } SLM_ERROR_IF("Python home must be set before python initialisation", Py_IsInitialized()); }
void SSliceIndexDicomPullerEditor::readImage(std::size_t selectedSliceIndex) { // DicomSeries ::fwMedData::DicomSeries::csptr dicomSeries = this->getInOut< ::fwMedData::DicomSeries >("series"); SLM_ASSERT("DicomSeries should not be null !", dicomSeries); if( dicomSeries->getModality() != "CT" && dicomSeries->getModality() != "MR" && dicomSeries->getModality() != "XA") { return; } // Clear temporary seriesDB ::fwMedDataTools::helper::SeriesDB sDBTempohelper(m_tempSeriesDB); sDBTempohelper.clear(); // Creates unique temporary folder, no need to check if exists before (see ::fwTools::System::getTemporaryFolder) ::boost::filesystem::path path = ::fwTools::System::getTemporaryFolder("dicom"); ::boost::filesystem::path tmpPath = path / "tmp"; SLM_INFO("Create " + tmpPath.string()); ::boost::filesystem::create_directories(tmpPath); const auto& binaries = dicomSeries->getDicomContainer(); auto iter = binaries.find(selectedSliceIndex); OSLM_ASSERT("Index '"<<selectedSliceIndex<<"' is not found in DicomSeries", iter != binaries.end()); const ::fwMemory::BufferObject::sptr bufferObj = iter->second; const ::fwMemory::BufferObject::Lock lockerDest(bufferObj); const char* buffer = static_cast<char*>(lockerDest.getBuffer()); const size_t size = bufferObj->getSize(); ::boost::filesystem::path dest = tmpPath / std::to_string(selectedSliceIndex); ::boost::filesystem::ofstream fs(dest, std::ios::binary|std::ios::trunc); FW_RAISE_IF("Can't open '" << tmpPath << "' for write.", !fs.good()); fs.write(buffer, size); fs.close(); // Read image m_dicomReader.lock()->setFolder(tmpPath); if(!m_dicomReader.expired()) { m_dicomReader.lock()->update(); if(m_dicomReader.expired() || m_dicomReader.lock()->isStopped()) { return; } } else { return; } //Copy image ::fwMedData::ImageSeries::sptr imageSeries; if(m_tempSeriesDB->getContainer().size() > 0) { imageSeries = ::fwMedData::ImageSeries::dynamicCast(*(m_tempSeriesDB->getContainer().begin())); } if(imageSeries) { ::fwData::Image::sptr newImage = imageSeries->getImage(); ::fwData::Image::SizeType newSize = newImage->getSize(); newImage->setField(::fwDataTools::fieldHelper::Image::m_axialSliceIndexId, m_axialIndex); m_frontalIndex->setValue(static_cast<int>(newSize[0]/2)); newImage->setField(::fwDataTools::fieldHelper::Image::m_frontalSliceIndexId, m_frontalIndex); m_sagittalIndex->setValue(static_cast<int>(newSize[1]/2)); newImage->setField(::fwDataTools::fieldHelper::Image::m_sagittalSliceIndexId, m_sagittalIndex); this->setOutput("image", newImage); } ::boost::system::error_code ec; ::boost::filesystem::remove_all(path, ec); SLM_ERROR_IF("remove_all error for path " + path.string() + ": " + ec.message(), ec.value()); }
void SeriesDBReader::addSeries( const ::fwMedData::SeriesDB::sptr& seriesDB, const std::vector< std::string >& filenames) { //gdcm::Trace::SetDebug( 1 ); //gdcm::Trace::SetWarning( 1 ); //gdcm::Trace::SetError( 1 ); ::gdcm::Scanner scanner; const ::gdcm::Tag seriesUIDTag(0x0020, 0x000e); const ::gdcm::Tag seriesDateTag(0x0008, 0x0021); const ::gdcm::Tag seriesTimeTag(0x0008, 0x0031); const ::gdcm::Tag seriesTypeTag(0x0008, 0x0060); const ::gdcm::Tag seriesDescriptionTag(0x0008, 0x103e); const ::gdcm::Tag seriesPhysicianNamesTag(0x0008, 0x1050); const ::gdcm::Tag equipmentInstitutionNameTag(0x0008, 0x0080); const ::gdcm::Tag patientNameTag(0x0010, 0x0010); const ::gdcm::Tag patientIDTag(0x0010, 0x0020); const ::gdcm::Tag patientBirthdateTag(0x0010, 0x0030); const ::gdcm::Tag patientSexTag(0x0010, 0x0040); const ::gdcm::Tag studyUIDTag(0x0020, 0x000d); const ::gdcm::Tag studyDateTag(0x0008, 0x0020); const ::gdcm::Tag studyTimeTag(0x0008, 0x0030); const ::gdcm::Tag studyReferingPhysicianNameTag(0x0008, 0x0090); const ::gdcm::Tag studyDescriptionTag(0x0008, 0x1030); const ::gdcm::Tag studyPatientAgeTag(0x0010, 0x1010); const ::gdcm::Tag imageTypeTag(0x0008, 0x0008); const ::gdcm::Tag acquisitionDateTag(0x0008, 0x0022); const ::gdcm::Tag acquisitionTimeTag(0x0008, 0x0032); scanner.AddTag( seriesUIDTag ); scanner.AddTag( seriesDateTag ); scanner.AddTag( seriesTimeTag ); scanner.AddTag( seriesTypeTag ); scanner.AddTag( seriesDescriptionTag ); scanner.AddTag( seriesPhysicianNamesTag ); scanner.AddTag( equipmentInstitutionNameTag ); scanner.AddTag( studyUIDTag ); scanner.AddTag( patientNameTag ); scanner.AddTag( patientIDTag ); scanner.AddTag( patientBirthdateTag ); scanner.AddTag( patientSexTag ); scanner.AddTag( studyUIDTag ); scanner.AddTag( studyDateTag ); scanner.AddTag( studyTimeTag ); scanner.AddTag( studyReferingPhysicianNameTag ); scanner.AddTag( studyDescriptionTag ); scanner.AddTag( studyPatientAgeTag ); scanner.AddTag( imageTypeTag ); scanner.AddTag( acquisitionDateTag ); scanner.AddTag( acquisitionTimeTag ); try { const bool isScanned = scanner.Scan( filenames ); if( !isScanned ) { SLM_ERROR("Scanner failed"); return; } const ::gdcm::Directory::FilenamesType keys = scanner.GetKeys(); typedef std::map< std::string, std::vector< std::string > > MapSeriesType; MapSeriesType mapSeries; for(const std::string& filename : keys) { SLM_ASSERT("'"+filename+"' is not a key in the mapping table", scanner.IsKey(filename.c_str())); const char* seriesUID = scanner.GetValue( filename.c_str(), seriesUIDTag ); const char* acqDate = scanner.GetValue( filename.c_str(), acquisitionDateTag ); if (seriesUID) { std::string fileSetId = seriesUID; if (acqDate) { fileSetId += "_"; fileSetId += acqDate; } const char* imageType = scanner.GetValue(filename.c_str(), imageTypeTag); if(imageType) { // Treatment of secondary capture dicom file. SLM_TRACE("Image Type : " + std::string(imageType)); fileSetId += "_"; fileSetId += imageType; } mapSeries[fileSetId].push_back(filename); } else { SLM_ERROR("No series name found in : " + filename ); } } for(const auto& elt : mapSeries) { ::fwMedData::ImageSeries::sptr series = ::fwMedData::ImageSeries::New(); ::fwMedData::Patient::sptr patient = series->getPatient(); ::fwMedData::Study::sptr study = series->getStudy(); ::fwMedData::Equipment::sptr equipment = series->getEquipment(); seriesDB->getContainer().push_back(series); SLM_TRACE( "Processing: '" + elt.first + "' file set."); const MapSeriesType::mapped_type& files = elt.second; if ( !files.empty() ) { vtkSmartPointer< vtkStringArray > fileArray = vtkSmartPointer< vtkStringArray >::New(); vtkSmartPointer< vtkGDCMImageReader > reader = vtkSmartPointer< vtkGDCMImageReader >::New(); reader->FileLowerLeftOn(); ::gdcm::IPPSorter ippSorter; ippSorter.SetComputeZSpacing( true ); ippSorter.SetZSpacingTolerance( 1e-3 ); bool isSorted = ippSorter.Sort( files ); std::vector<std::string> sorted; double zspacing = 0.; if(isSorted) { sorted = ippSorter.GetFilenames(); zspacing = ippSorter.GetZSpacing(); OSLM_TRACE("Found z-spacing:" << ippSorter.GetZSpacing()); } else { // Else an error has been encountered. // We fall back to a more trivial sorting based on the InstanceNumber DICOM tag. SLM_WARN("IPP Sorting failed. Falling back to Instance Number sorting."); ::gdcm::Sorter sorter; sorter.SetSortFunction(sortByInstanceNumber); isSorted = sorter.StableSort( filenames); if(isSorted) { // If the custom sorted returns true, it worked // and the filenames are sorted by InstanceNumber (ASC). sorted = sorter.GetFilenames(); } else { // There is nothing more we can do to sort DICOM files. SLM_ERROR("Failed to sort '"+elt.first+"'"); } } fileArray->Initialize(); if(isSorted) { SLM_TRACE("Success to sort '" + elt.first+"'"); if (!zspacing && sorted.size() > 1) { SLM_TRACE( "Guessing zspacing ..." ); if (!sorted.empty()) { ::gdcm::Reader localReader1; ::gdcm::Reader localReader2; const std::string& f1 = *(sorted.begin()); const std::string& f2 = *(sorted.begin() + 1); SLM_TRACE( "Search spacing in: '" + f1 +"'"); SLM_TRACE( "Search spacing in: '" + f2 +"'"); localReader1.SetFileName( f1.c_str() ); localReader2.SetFileName( f2.c_str() ); const bool canRead = localReader1.Read() && localReader2.Read(); if(canRead) { const std::vector<double> vOrigin1 = ::gdcm::ImageHelper::GetOriginValue(localReader1.GetFile()); const std::vector<double> vOrigin2 = ::gdcm::ImageHelper::GetOriginValue(localReader2.GetFile()); zspacing = vOrigin2[2] - vOrigin1[2]; OSLM_TRACE( "Found z-spacing:" << zspacing << " from : << " << vOrigin2[2] << " | " << vOrigin1[2]); } SLM_ERROR_IF("Cannot read: '" + f1 + "' or: '" + f2 +"'", !canRead); } } } for(const std::string& file : sorted) { SLM_TRACE("Add '" + file + "' to vtkGdcmReader"); fileArray->InsertNextValue(file.c_str()); } ::fwData::Image::sptr pDataImage = ::fwData::Image::New(); bool res = false; if (fileArray->GetNumberOfValues() > 0) { reader->SetFileNames( fileArray ); try { SLM_TRACE("Read Series: '" + elt.first + "'"); //add progress observation vtkSmartPointer< ::fwVtkIO::helper::vtkLambdaCommand > progressCallback = vtkSmartPointer< ::fwVtkIO::helper::vtkLambdaCommand >::New(); progressCallback->SetCallback([this](vtkObject* caller, long unsigned int, void* ) { auto filter = static_cast<vtkGDCMImageReader*>(caller); m_job->doneWork( filter->GetProgress()*100 ); }); reader->AddObserver(vtkCommand::ProgressEvent, progressCallback); m_job->addSimpleCancelHook( [&]() { reader->AbortExecuteOn(); } ); reader->Update(); reader->UpdateInformation(); reader->PropagateUpdateExtent(); try { ::fwVtkIO::fromVTKImage(reader->GetOutput(), pDataImage); res = true; } catch(std::exception& e) { OSLM_ERROR("VTKImage to fwData::Image failed : "<<e.what()); } } catch (std::exception& e) { OSLM_ERROR( "Error during conversion : " << e.what() ); } catch (...) { SLM_ERROR( "Unexpected error during conversion" ); } m_job->finish(); } if (res) { SLM_ASSERT("No file to read", !files.empty()); // Read medical info vtkMedicalImageProperties* medprop = reader->GetMedicalImageProperties(); const std::string patientName = medprop->GetPatientName(); //"0010|0010" const std::string patientId = medprop->GetPatientID(); const std::string patientBirthdate = medprop->GetPatientBirthDate(); //"0010|0030" const std::string patientSex = medprop->GetPatientSex(); //"0010|0040" const ::gdcm::Scanner::ValuesType gdcmPhysicianNames = scanner.GetValues( seriesPhysicianNamesTag ); const char* seriesUIDStr = scanner.GetValue( files[0].c_str(), seriesUIDTag ); const char* seriesTimeStr = scanner.GetValue( files[0].c_str(), seriesTimeTag ); const char* seriesDateStr = scanner.GetValue( files[0].c_str(), seriesDateTag ); const std::string seriesModality = medprop->GetModality(); //"0008|0060" const std::string seriesDescription = medprop->GetSeriesDescription(); const std::string seriesDate = ( seriesDateStr ? seriesDateStr : "" ); const std::string seriesTime = ( seriesTimeStr ? seriesTimeStr : "" ); ::fwMedData::DicomValuesType seriesPhysicianNames; for(const std::string& name : gdcmPhysicianNames) { ::fwMedData::DicomValuesType result; ::boost::split( result, name, ::boost::is_any_of("\\")); seriesPhysicianNames.reserve(seriesPhysicianNames.size() + result.size()); seriesPhysicianNames.insert(seriesPhysicianNames.end(), result.begin(), result.end()); } const char* studyUIDStr = scanner.GetValue( files[0].c_str(), studyUIDTag ); const char* studyReferingPhysicianNameStr = scanner.GetValue( files[0].c_str(), studyReferingPhysicianNameTag ); const std::string studyDate = medprop->GetStudyDate(); const std::string studyTime = medprop->GetStudyTime(); const std::string studyDescription = medprop->GetStudyDescription(); //"0008|1030" const std::string studyPatientAge = medprop->GetPatientAge(); const std::string equipementInstitution = medprop->GetInstitutionName(); //"0008|0080" const std::string studyReferingPhysicianName = ( studyReferingPhysicianNameStr ? studyReferingPhysicianNameStr : "" ); const double thickness = medprop->GetSliceThicknessAsDouble();//"0018|0050" double center = 0.0; double width = 0.0; if (medprop->GetNumberOfWindowLevelPresets())//FIXME : Multiple preset !!! { medprop->GetNthWindowLevelPreset(0, &width, ¢er); //0028|1050,1051 } // Image must have 3 dimensions if(pDataImage->getNumberOfDimensions() == 2) { ::fwData::Image::SizeType imgSize = pDataImage->getSize(); imgSize.resize(3); imgSize[2] = 1; pDataImage->setSize(imgSize); ::fwData::Image::OriginType imgOrigin = pDataImage->getOrigin(); imgOrigin.resize(3); imgOrigin[2] = 0.; pDataImage->setOrigin(imgOrigin); } ::fwData::Image::SpacingType vPixelSpacing = pDataImage->getSpacing(); vPixelSpacing.resize(3); // assume z-spacing = 1 if not guessed vPixelSpacing[2] = zspacing ? zspacing : (thickness ? thickness : 1.); pDataImage->setSpacing(vPixelSpacing); pDataImage->setWindowCenter(center); pDataImage->setWindowWidth(width); // Get the series instance UID. SLM_ASSERT("No series UID", seriesUIDStr); series->setInstanceUID(( seriesUIDStr ? seriesUIDStr : "UNKNOWN-UID" )); series->setModality( seriesModality ); series->setDescription( seriesDescription ); series->setDate( seriesDate ); series->setTime( seriesTime ); series->setPerformingPhysiciansName( seriesPhysicianNames ); series->setImage(pDataImage); SLM_ASSERT("No study UID", studyUIDStr); study->setInstanceUID(( studyUIDStr ? studyUIDStr : "UNKNOWN-UID" )); study->setDate(studyDate); study->setTime(studyTime); study->setDescription(studyDescription); study->setPatientAge(studyPatientAge); study->setReferringPhysicianName(studyReferingPhysicianName); patient->setName(patientName); patient->setPatientId(patientId); patient->setBirthdate(patientBirthdate); patient->setSex(patientSex); equipment->setInstitutionName(equipementInstitution); } // if res } // if !files.empty() } } // try catch (std::exception& e) { OSLM_ERROR( "Try with another reader or retry with this reader on a specific subfolder : " << e.what() ); for(const auto filename : filenames) { SLM_ERROR("file error : " + filename ); } } }