diff --git a/Core/Code/Common/mitkCoreObjectFactory.cpp b/Core/Code/Common/mitkCoreObjectFactory.cpp index 3b4cbe8a99..a909c77dfa 100644 --- a/Core/Code/Common/mitkCoreObjectFactory.cpp +++ b/Core/Code/Common/mitkCoreObjectFactory.cpp @@ -1,403 +1,405 @@ /*=================================================================== 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 "mitkConfig.h" #include "mitkCoreObjectFactory.h" #include "mitkAffineInteractor.h" #include "mitkColorProperty.h" #include "mitkDataNode.h" #include "mitkEnumerationProperty.h" #include "mitkGeometry2DData.h" #include "mitkGeometry2DDataMapper2D.h" #include "mitkGeometry2DDataVtkMapper3D.h" #include "mitkGeometry3D.h" #include "mitkGeometryData.h" #include "mitkImage.h" #include #include "mitkLevelWindowProperty.h" #include "mitkLookupTable.h" #include "mitkLookupTableProperty.h" #include "mitkPlaneGeometry.h" #include "mitkPointSet.h" #include "mitkPointSetVtkMapper2D.h" #include "mitkPointSetVtkMapper3D.h" #include "mitkPolyDataGLMapper2D.h" #include "mitkProperties.h" #include "mitkPropertyList.h" #include "mitkSlicedGeometry3D.h" #include "mitkSmartPointerProperty.h" #include "mitkStringProperty.h" #include "mitkSurface.h" #include "mitkSurface.h" #include "mitkSurfaceGLMapper2D.h" #include "mitkSurfaceVtkMapper3D.h" #include "mitkTimeSlicedGeometry.h" #include "mitkTransferFunctionProperty.h" #include "mitkVolumeDataVtkMapper3D.h" #include "mitkVtkInterpolationProperty.h" #include "mitkVtkRepresentationProperty.h" #include "mitkVtkResliceInterpolationProperty.h" //#include "mitkPicFileIOFactory.h" #include "mitkPointSetIOFactory.h" #include "mitkItkImageFileIOFactory.h" #include "mitkSTLFileIOFactory.h" #include "mitkVtkSurfaceIOFactory.h" #include "mitkVtkImageIOFactory.h" #include "mitkVtiFileIOFactory.h" //#include "mitkPicVolumeTimeSeriesIOFactory.h" #include "mitkImageWriterFactory.h" +#include "mitkImageWriter.h" #include "mitkPointSetWriterFactory.h" #include "mitkSurfaceVtkWriterFactory.h" mitk::CoreObjectFactory::FileWriterList mitk::CoreObjectFactory::m_FileWriters; void mitk::CoreObjectFactory::RegisterExtraFactory(CoreObjectFactoryBase* factory) { MITK_DEBUG << "CoreObjectFactory: registering extra factory of type " << factory->GetNameOfClass(); m_ExtraFactories.insert(CoreObjectFactoryBase::Pointer(factory)); } void mitk::CoreObjectFactory::UnRegisterExtraFactory(CoreObjectFactoryBase *factory) { MITK_DEBUG << "CoreObjectFactory: un-registering extra factory of type " << factory->GetNameOfClass(); try { m_ExtraFactories.erase(factory); } catch( std::exception const& e) { MITK_ERROR << "Caugt exception while unregistering: " << e.what(); } } mitk::CoreObjectFactory::Pointer mitk::CoreObjectFactory::GetInstance() { static mitk::CoreObjectFactory::Pointer instance; if (instance.IsNull()) { instance = mitk::CoreObjectFactory::New(); } return instance; } #include void mitk::CoreObjectFactory::SetDefaultProperties(mitk::DataNode* node) { if(node==NULL) return; mitk::DataNode::Pointer nodePointer = node; mitk::Image::Pointer image = dynamic_cast(node->GetData()); if(image.IsNotNull() && image->IsInitialized()) { mitk::ImageVtkMapper2D::SetDefaultProperties(node); mitk::VolumeDataVtkMapper3D::SetDefaultProperties(node); } mitk::Surface::Pointer surface = dynamic_cast(node->GetData()); if(surface.IsNotNull()) { mitk::SurfaceGLMapper2D::SetDefaultProperties(node); mitk::SurfaceVtkMapper3D::SetDefaultProperties(node); } mitk::PointSet::Pointer pointSet = dynamic_cast(node->GetData()); if(pointSet.IsNotNull()) { mitk::PointSetVtkMapper2D::SetDefaultProperties(node); mitk::PointSetVtkMapper3D::SetDefaultProperties(node); } for (ExtraFactoriesContainer::iterator it = m_ExtraFactories.begin(); it != m_ExtraFactories.end() ; it++ ) { (*it)->SetDefaultProperties(node); } } mitk::CoreObjectFactory::CoreObjectFactory() { static bool alreadyDone = false; if (!alreadyDone) { MITK_DEBUG << "CoreObjectFactory c'tor" << std::endl; // FIXME itk::ObjectFactoryBase::RegisterFactory( PicFileIOFactory::New() ); itk::ObjectFactoryBase::RegisterFactory( PointSetIOFactory::New() ); itk::ObjectFactoryBase::RegisterFactory( STLFileIOFactory::New() ); itk::ObjectFactoryBase::RegisterFactory( VtkSurfaceIOFactory::New() ); itk::ObjectFactoryBase::RegisterFactory( VtkImageIOFactory::New() ); itk::ObjectFactoryBase::RegisterFactory( VtiFileIOFactory::New() ); itk::ObjectFactoryBase::RegisterFactory( ItkImageFileIOFactory::New() ); // FIXME itk::ObjectFactoryBase::RegisterFactory( PicVolumeTimeSeriesIOFactory::New() ); mitk::SurfaceVtkWriterFactory::RegisterOneFactory(); mitk::PointSetWriterFactory::RegisterOneFactory(); mitk::ImageWriterFactory::RegisterOneFactory(); + m_FileWriters.push_back(mitk::ImageWriter::New().GetPointer()); CreateFileExtensionsMap(); alreadyDone = true; } } mitk::Mapper::Pointer mitk::CoreObjectFactory::CreateMapper(mitk::DataNode* node, MapperSlotId id) { mitk::Mapper::Pointer newMapper = NULL; mitk::Mapper::Pointer tmpMapper = NULL; // check whether extra factories provide mapper for (ExtraFactoriesContainer::iterator it = m_ExtraFactories.begin(); it != m_ExtraFactories.end() ; it++ ) { tmpMapper = (*it)->CreateMapper(node,id); if(tmpMapper.IsNotNull()) newMapper = tmpMapper; } if (newMapper.IsNull()) { mitk::BaseData *data = node->GetData(); if ( id == mitk::BaseRenderer::Standard2D ) { if((dynamic_cast(data)!=NULL)) { newMapper = mitk::ImageVtkMapper2D::New(); newMapper->SetDataNode(node); } else if((dynamic_cast(data)!=NULL)) { newMapper = mitk::Geometry2DDataMapper2D::New(); newMapper->SetDataNode(node); } else if((dynamic_cast(data)!=NULL)) { newMapper = mitk::SurfaceGLMapper2D::New(); // cast because SetDataNode is not virtual mitk::SurfaceGLMapper2D *castedMapper = dynamic_cast(newMapper.GetPointer()); castedMapper->SetDataNode(node); } else if((dynamic_cast(data)!=NULL)) { newMapper = mitk::PointSetVtkMapper2D::New(); newMapper->SetDataNode(node); } } else if ( id == mitk::BaseRenderer::Standard3D ) { if((dynamic_cast(data) != NULL)) { newMapper = mitk::VolumeDataVtkMapper3D::New(); newMapper->SetDataNode(node); } else if((dynamic_cast(data)!=NULL)) { newMapper = mitk::Geometry2DDataVtkMapper3D::New(); newMapper->SetDataNode(node); } else if((dynamic_cast(data)!=NULL)) { newMapper = mitk::SurfaceVtkMapper3D::New(); newMapper->SetDataNode(node); } else if((dynamic_cast(data)!=NULL)) { newMapper = mitk::PointSetVtkMapper3D::New(); newMapper->SetDataNode(node); } } } return newMapper; } /* // @deprecated // #define EXTERNAL_FILE_EXTENSIONS \ "All known formats(*.dcm *.DCM *.dc3 *.DC3 *.gdcm *.ima *.mhd *.mps *.nii *.pic *.pic.gz *.bmp *.png *.jpg *.tiff *.pvtk *.stl *.vtk *.vtp *.vtu *.obj *.vti *.hdr *.nrrd *.nhdr );;" \ "DICOM files(*.dcm *.DCM *.dc3 *.DC3 *.gdcm);;" \ "DKFZ Pic (*.seq *.pic *.pic.gz *.seq.gz);;" \ "NRRD Vector Images (*.nrrd *.nhdr);;" \ "Point sets (*.mps);;" \ "Sets of 2D slices (*.pic *.pic.gz *.bmp *.png *.dcm *.gdcm *.ima *.tiff);;" \ "Surface files (*.stl *.vtk *.vtp *.obj);;" \ "NIfTI format (*.nii)" #define SAVE_FILE_EXTENSIONS "all (*.pic *.mhd *.vtk *.vti *.hdr *.png *.tiff *.jpg *.hdr *.bmp *.dcm *.gipl *.nii *.nrrd *.nhdr *.spr *.lsm *.dwi *.hdwi *.qbi *.hqbi)" */ /** * @brief This method gets the supported (open) file extensions as string. This string is can then used by the QT QFileDialog widget. * @return The c-string that contains the file extensions * */ const char* mitk::CoreObjectFactory::GetFileExtensions() { MultimapType aMap; for (ExtraFactoriesContainer::iterator it = m_ExtraFactories.begin(); it != m_ExtraFactories.end() ; it++ ) { aMap = (*it)->GetFileExtensionsMap(); this->MergeFileExtensions(m_FileExtensionsMap, aMap); } this->CreateFileExtensions(m_FileExtensionsMap, m_FileExtensions); return m_FileExtensions.c_str(); } /** * @brief Merge the input map into the fileExtensionsMap. Duplicate entries are removed * @param fileExtensionsMap the existing map, it contains value pairs like ("*.dcm", "DICOM files"),("*.dc3", "DICOM files"). * This map is extented/merged with the values from the input map. * @param inputMap the input map, it contains value pairs like ("*.dcm", "DICOM files"),("*.dc3", "DICOM files") returned by * the extra factories. * */ void mitk::CoreObjectFactory::MergeFileExtensions(MultimapType& fileExtensionsMap, MultimapType inputMap) { bool duplicateFound = false; std::pair pairOfIter; for (MultimapType::iterator it = inputMap.begin(); it != inputMap.end(); ++it) { duplicateFound = false; pairOfIter = fileExtensionsMap.equal_range((*it).first); for (MultimapType::iterator it2 = pairOfIter.first; it2 != pairOfIter.second; ++it2) { //cout << " [" << (*it).first << ", " << (*it).second << "]" << endl; std::string aString = (*it2).second; if (aString.compare((*it).second) == 0) { //cout << " DUP!! [" << (*it).first << ", " << (*it).second << "]" << endl; duplicateFound = true; break; } } if (!duplicateFound) { fileExtensionsMap.insert(std::pair((*it).first, (*it).second)); } } } /** * @brief get the defined (open) file extension map * @return the defined (open) file extension map */ mitk::CoreObjectFactoryBase::MultimapType mitk::CoreObjectFactory::GetFileExtensionsMap() { return m_FileExtensionsMap; } /** * @brief initialize the file extension entries for open and save */ void mitk::CoreObjectFactory::CreateFileExtensionsMap() { m_FileExtensionsMap.insert(std::pair("*.dcm", "DICOM files")); m_FileExtensionsMap.insert(std::pair("*.DCM", "DICOM files")); m_FileExtensionsMap.insert(std::pair("*.dc3", "DICOM files")); m_FileExtensionsMap.insert(std::pair("*.DC3", "DICOM files")); m_FileExtensionsMap.insert(std::pair("*.gdcm", "DICOM files")); m_FileExtensionsMap.insert(std::pair("*.seq", "DKFZ Pic")); m_FileExtensionsMap.insert(std::pair("*.pic", "DKFZ Pic")); m_FileExtensionsMap.insert(std::pair("*.pic.gz", "DKFZ Pic")); m_FileExtensionsMap.insert(std::pair("*.mhd", "MetaImage")); m_FileExtensionsMap.insert(std::pair("*.seq.gz", "DKFZ Pic")); m_FileExtensionsMap.insert(std::pair("*.hdr", "Analyze Format")); m_FileExtensionsMap.insert(std::pair("*.img", "Analyze Format")); m_FileExtensionsMap.insert(std::pair("*.img.gz", "Analyze Format")); m_FileExtensionsMap.insert(std::pair("*.nrrd", "Nearly Raw Raster Data")); m_FileExtensionsMap.insert(std::pair("*.nhdr", "NRRD with detached header")); m_FileExtensionsMap.insert(std::pair("*.mps", "Point sets")); m_FileExtensionsMap.insert(std::pair("*.pic", "Sets of 2D slices")); m_FileExtensionsMap.insert(std::pair("*.pic.gz", "Sets of 2D slices")); m_FileExtensionsMap.insert(std::pair("*.bmp", "Sets of 2D slices")); m_FileExtensionsMap.insert(std::pair("*.png", "Sets of 2D slices")); m_FileExtensionsMap.insert(std::pair("*.jpg", "Sets of 2D slices")); m_FileExtensionsMap.insert(std::pair("*.jpeg", "Sets of 2D slices")); m_FileExtensionsMap.insert(std::pair("*.dcm", "Sets of 2D slices")); m_FileExtensionsMap.insert(std::pair("*.gdcm", "Sets of 2D slices")); m_FileExtensionsMap.insert(std::pair("*.ima", "Sets of 2D slices")); m_FileExtensionsMap.insert(std::pair("*.tiff", "Sets of 2D slices")); m_FileExtensionsMap.insert(std::pair("*.tif", "Sets of 2D slices")); m_FileExtensionsMap.insert(std::pair("*.stl", "Surface files")); m_FileExtensionsMap.insert(std::pair("*.vtk", "Surface files")); m_FileExtensionsMap.insert(std::pair("*.vtp", "Surface files")); m_FileExtensionsMap.insert(std::pair("*.obj", "Surface files")); m_FileExtensionsMap.insert(std::pair("*.nii", "NIfTI format")); m_FileExtensionsMap.insert(std::pair("*.nii.gz", "NIfTI format")); //m_SaveFileExtensionsMap.insert(std::pair("*.pic", "DKFZ Pic")); m_SaveFileExtensionsMap.insert(std::pair("*.mhd", "MetaImage")); m_SaveFileExtensionsMap.insert(std::pair("*.vtk", "Surface Files")); m_SaveFileExtensionsMap.insert(std::pair("*.vti", "VTK Image Data Files")); m_SaveFileExtensionsMap.insert(std::pair("*.hdr", "Analyze Format")); m_SaveFileExtensionsMap.insert(std::pair("*.png", "Sets of 2D slices")); m_SaveFileExtensionsMap.insert(std::pair("*.tiff", "Sets of 2D slices")); m_SaveFileExtensionsMap.insert(std::pair("*.tif", "Sets of 2D slices")); m_SaveFileExtensionsMap.insert(std::pair("*.jpg", "Sets of 2D slices")); m_SaveFileExtensionsMap.insert(std::pair("*.jpeg", "Sets of 2D slices")); m_SaveFileExtensionsMap.insert(std::pair("*.bmp", "Sets of 2D slices")); m_SaveFileExtensionsMap.insert(std::pair("*.dcm", "Sets of 2D slices")); m_SaveFileExtensionsMap.insert(std::pair("*.gipl", "UMDS GIPL Format Files")); m_SaveFileExtensionsMap.insert(std::pair("*.nii", "NIfTI format")); m_SaveFileExtensionsMap.insert(std::pair("*.nrrd", "Nearly Raw Raster Data")); m_SaveFileExtensionsMap.insert(std::pair("*.nhdr", "NRRD with detached header")); m_SaveFileExtensionsMap.insert(std::pair("*.lsm", "Microscope Images")); m_SaveFileExtensionsMap.insert(std::pair("*.dwi", "Diffusion Weighted Images")); m_SaveFileExtensionsMap.insert(std::pair("*.hdwi", "Diffusion Weighted Images")); m_SaveFileExtensionsMap.insert(std::pair("*.qbi", "Q-Ball Images")); m_SaveFileExtensionsMap.insert(std::pair("*.hqbi", "Q-Ball Images")); } /** * @brief This method gets the supported (save) file extensions as string. This string is can then used by the QT QFileDialog widget. * @return The c-string that contains the (save) file extensions * */ const char* mitk::CoreObjectFactory::GetSaveFileExtensions() { MultimapType aMap; for (ExtraFactoriesContainer::iterator it = m_ExtraFactories.begin(); it != m_ExtraFactories.end() ; it++ ) { aMap = (*it)->GetSaveFileExtensionsMap(); this->MergeFileExtensions(m_SaveFileExtensionsMap, aMap); } this->CreateFileExtensions(m_SaveFileExtensionsMap, m_SaveFileExtensions); return m_SaveFileExtensions.c_str(); }; /** * @brief get the defined (save) file extension map * @return the defined (save) file extension map */ mitk::CoreObjectFactoryBase::MultimapType mitk::CoreObjectFactory::GetSaveFileExtensionsMap() { return m_SaveFileExtensionsMap; } mitk::CoreObjectFactory::FileWriterList mitk::CoreObjectFactory::GetFileWriters() { FileWriterList allWriters = m_FileWriters; for (ExtraFactoriesContainer::iterator it = m_ExtraFactories.begin(); it != m_ExtraFactories.end() ; it++ ) { FileWriterList list2 = (*it)->GetFileWriters(); allWriters.merge(list2); } return allWriters; } void mitk::CoreObjectFactory::MapEvent(const mitk::Event*, const int) { } diff --git a/Core/Code/IO/mitkIOUtil.cpp b/Core/Code/IO/mitkIOUtil.cpp index d671110b0a..d14ad43a05 100644 --- a/Core/Code/IO/mitkIOUtil.cpp +++ b/Core/Code/IO/mitkIOUtil.cpp @@ -1,317 +1,373 @@ /*=================================================================== 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 "mitkIOUtil.h" #include "mitkDataNodeFactory.h" #include "mitkImageWriter.h" #include "mitkPointSetWriter.h" #include "mitkSurfaceVtkWriter.h" #include #include #include #include #include +#include + //ITK #include //VTK #include #include #include namespace mitk { const std::string IOUtil::DEFAULTIMAGEEXTENSION = ".nrrd"; const std::string IOUtil::DEFAULTSURFACEEXTENSION = ".stl"; const std::string IOUtil::DEFAULTPOINTSETEXTENSION = ".mps"; int IOUtil::LoadFiles(const std::vector &fileNames, DataStorage &ds) { // Get the set of registered mitk::IDataNodeReader services ModuleContext* context = mitk::GetModuleContext(); const std::list refs = context->GetServiceReferences(); std::vector services; services.reserve(refs.size()); for (std::list::const_iterator i = refs.begin(); i != refs.end(); ++i) { IDataNodeReader* s = context->GetService(*i); if (s != 0) { services.push_back(s); } } mitk::ProgressBar::GetInstance()->AddStepsToDo(2*fileNames.size()); // Iterate over all file names and use the IDataNodeReader services // to load them. int nodesRead = 0; for (std::vector::const_iterator i = fileNames.begin(); i != fileNames.end(); ++i) { for (std::vector::const_iterator readerIt = services.begin(); readerIt != services.end(); ++readerIt) { try { int n = (*readerIt)->Read(*i, ds); nodesRead += n; if (n > 0) break; } catch (const std::exception& e) { MITK_WARN << e.what(); } } mitk::ProgressBar::GetInstance()->Progress(2); } for (std::list::const_iterator i = refs.begin(); i != refs.end(); ++i) { context->UngetService(*i); } return nodesRead; } DataStorage::Pointer IOUtil::LoadFiles(const std::vector& fileNames) { mitk::StandaloneDataStorage::Pointer ds = mitk::StandaloneDataStorage::New(); LoadFiles(fileNames, *ds); return ds.GetPointer(); } DataNode::Pointer IOUtil::LoadDataNode(const std::string path) { mitk::DataNodeFactory::Pointer reader = mitk::DataNodeFactory::New(); try { reader->SetFileName( path ); reader->Update(); if((reader->GetNumberOfOutputs()<1)) { MITK_ERROR << "Could not find data '" << path << "'"; mitkThrow() << "An exception occured during loading the file " << path << ". Exception says could not find data."; } mitk::DataNode::Pointer node = reader->GetOutput(); if(node.IsNull()) { MITK_ERROR << "Could not find path: '" << path << "'" << " datanode is NULL" ; mitkThrow() << "An exception occured during loading the file " << path << ". Exception says datanode is NULL."; } return reader->GetOutput( 0 ); } catch ( itk::ExceptionObject & e ) { MITK_ERROR << "Exception occured during load data of '" << path << "': Exception: " << e.what(); mitkThrow() << "An exception occured during loading the file " << path << ". Exception says: " << e.what(); } } Image::Pointer IOUtil::LoadImage(const std::string path) { mitk::DataNode::Pointer node = LoadDataNode(path); mitk::Image::Pointer image = dynamic_cast(node->GetData()); if(image.IsNull()) { MITK_ERROR << "Image is NULL '" << path << "'"; mitkThrow() << "An exception occured during loading the image " << path << ". Exception says: Image is NULL."; } return image; } Surface::Pointer IOUtil::LoadSurface(const std::string path) { mitk::DataNode::Pointer node = LoadDataNode(path); mitk::Surface::Pointer surface = dynamic_cast(node->GetData()); if(surface.IsNull()) { MITK_ERROR << "Surface is NULL '" << path << "'"; mitkThrow() << "An exception occured during loading the file " << path << ". Exception says: Surface is NULL."; } return surface; } PointSet::Pointer IOUtil::LoadPointSet(const std::string path) { mitk::DataNode::Pointer node = LoadDataNode(path); mitk::PointSet::Pointer pointset = dynamic_cast(node->GetData()); if(pointset.IsNull()) { MITK_ERROR << "PointSet is NULL '" << path << "'"; mitkThrow() << "An exception occured during loading the file " << path << ". Exception says: Pointset is NULL."; } return pointset; } bool IOUtil::SaveImage(mitk::Image::Pointer image, const std::string path) { std::string dir = itksys::SystemTools::GetFilenamePath( path ); - std::string baseFilename = itksys::SystemTools::GetFilenameWithoutLastExtension( path ); - std::string extension = itksys::SystemTools::GetFilenameLastExtension( path ); + std::string baseFilename = itksys::SystemTools::GetFilenameWithoutExtension( path ); + std::string extension = itksys::SystemTools::GetFilenameExtension( path ); std::string finalFileName = dir + "/" + baseFilename; mitk::ImageWriter::Pointer imageWriter = mitk::ImageWriter::New(); //check if an extension is given, else use the defaul extension if( extension == "" ) { MITK_WARN << extension << " extension is not set. Extension set to default: " << finalFileName << DEFAULTIMAGEEXTENSION; extension = DEFAULTIMAGEEXTENSION; } // check if extension is suitable for writing image data if (!imageWriter->IsExtensionValid(extension)) { MITK_WARN << extension << " extension is unknown. Extension set to default: " << finalFileName << DEFAULTIMAGEEXTENSION; extension = DEFAULTIMAGEEXTENSION; } try { //write the data imageWriter->SetInput(image); imageWriter->SetFileName(finalFileName.c_str()); imageWriter->SetExtension(extension.c_str()); imageWriter->Write(); } catch ( std::exception& e ) { MITK_ERROR << " during attempt to write '" << finalFileName + extension << "' Exception says:"; MITK_ERROR << e.what(); mitkThrow() << "An exception occured during writing the file " << finalFileName << ". Exception says " << e.what(); } return true; } bool IOUtil::SaveSurface(Surface::Pointer surface, const std::string path) { std::string dir = itksys::SystemTools::GetFilenamePath( path ); std::string baseFilename = itksys::SystemTools::GetFilenameWithoutLastExtension( path ); std::string extension = itksys::SystemTools::GetFilenameLastExtension( path ); std::string finalFileName = dir + "/" + baseFilename; if (extension == "") // if no extension has been set we use the default extension { MITK_WARN << extension << " extension is not set. Extension set to default: " << finalFileName << DEFAULTSURFACEEXTENSION; extension = DEFAULTSURFACEEXTENSION; } try { finalFileName += extension; if(extension == ".stl" ) { mitk::SurfaceVtkWriter::Pointer surfaceWriter = mitk::SurfaceVtkWriter::New(); // check if surface actually consists of triangles; if not, the writer will not do anything; so, convert to triangles... vtkPolyData* polys = surface->GetVtkPolyData(); if( polys->GetNumberOfStrips() > 0 ) { vtkSmartPointer triangleFilter = vtkSmartPointer::New(); triangleFilter->SetInput(polys); triangleFilter->Update(); polys = triangleFilter->GetOutput(); polys->Register(NULL); surface->SetVtkPolyData(polys); } surfaceWriter->SetInput( surface ); surfaceWriter->SetFileName( finalFileName.c_str() ); surfaceWriter->GetVtkWriter()->SetFileTypeToBinary(); surfaceWriter->Write(); } else if(extension == ".vtp") { mitk::SurfaceVtkWriter::Pointer surfaceWriter = mitk::SurfaceVtkWriter::New(); surfaceWriter->SetInput( surface ); surfaceWriter->SetFileName( finalFileName.c_str() ); surfaceWriter->GetVtkWriter()->SetDataModeToBinary(); surfaceWriter->Write(); } else if(extension == ".vtk") { mitk::SurfaceVtkWriter::Pointer surfaceWriter = mitk::SurfaceVtkWriter::New(); surfaceWriter->SetInput( surface ); surfaceWriter->SetFileName( finalFileName.c_str() ); surfaceWriter->Write(); } else { // file extension not suitable for writing specified data type MITK_ERROR << "File extension is not suitable for writing'" << finalFileName; mitkThrow() << "An exception occured during writing the file " << finalFileName << ". File extension " << extension << " is not suitable for writing."; } } catch(std::exception& e) { MITK_ERROR << " during attempt to write '" << finalFileName << "' Exception says:"; MITK_ERROR << e.what(); mitkThrow() << "An exception occured during writing the file " << finalFileName << ". Exception says " << e.what(); } return true; } bool IOUtil::SavePointSet(PointSet::Pointer pointset, const std::string path) { mitk::PointSetWriter::Pointer pointSetWriter = mitk::PointSetWriter::New(); std::string dir = itksys::SystemTools::GetFilenamePath( path ); std::string baseFilename = itksys::SystemTools::GetFilenameWithoutLastExtension( path ); std::string extension = itksys::SystemTools::GetFilenameLastExtension( path ); std::string finalFileName = dir + "/" + baseFilename; if (extension == "") // if no extension has been entered manually into the filename { MITK_WARN << extension << " extension is not set. Extension set to default: " << finalFileName << DEFAULTPOINTSETEXTENSION; extension = DEFAULTPOINTSETEXTENSION; } // check if extension is valid if (!pointSetWriter->IsExtensionValid(extension)) { MITK_WARN << extension << " extension is unknown. Extension set to default: " << finalFileName << DEFAULTPOINTSETEXTENSION; extension = DEFAULTPOINTSETEXTENSION; } try { pointSetWriter->SetInput( pointset ); finalFileName += extension; pointSetWriter->SetFileName( finalFileName.c_str() ); pointSetWriter->Update(); } catch( std::exception& e ) { MITK_ERROR << " during attempt to write '" << finalFileName << "' Exception says:"; MITK_ERROR << e.what(); mitkThrow() << "An exception occured during writing the file " << finalFileName << ". Exception says " << e.what(); } return true; } + +bool IOUtil::SaveBaseData( mitk::BaseData* data, const std::string& path ) +{ + if (data == NULL || path.empty()) return false; + + std::string dir = itksys::SystemTools::GetFilenamePath( path ); + std::string baseFilename = itksys::SystemTools::GetFilenameWithoutExtension( path ); + std::string extension = itksys::SystemTools::GetFilenameExtension( path ); + std::string fileNameWithoutExtension = dir + "/" + baseFilename; + + mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); + + for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) + { + if ( (*it)->CanWriteBaseDataType(data) ) + { + // Ensure a valid filename + if(baseFilename=="") + { + baseFilename = (*it)->GetDefaultFilename(); + } + // Check if an extension exists already and if not, append the default extension + if (extension=="" ) + { + extension=(*it)->GetDefaultExtension(); + } + else + { + if (!(*it)->IsExtensionValid(extension)) + { + MITK_WARN << extension << " extension is unknown"; + continue; + } + } + + std::string finalFileName = fileNameWithoutExtension + extension; + try + { + (*it)->SetFileName( finalFileName.c_str() ); + (*it)->DoWrite( data ); + return true; + } + catch( const std::exception& e ) + { + MITK_ERROR << " during attempt to write '" << finalFileName << "' Exception says:"; + MITK_ERROR << e.what(); + mitkThrow() << "An exception occured during writing the file " << finalFileName << ". Exception says " << e.what(); + } + } + } + + return false; +} + } diff --git a/Core/Code/IO/mitkIOUtil.h b/Core/Code/IO/mitkIOUtil.h index af9d8c8593..d59a58176d 100644 --- a/Core/Code/IO/mitkIOUtil.h +++ b/Core/Code/IO/mitkIOUtil.h @@ -1,144 +1,154 @@ /*=================================================================== 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. ===================================================================*/ #ifndef MITKIOUTIL_H #define MITKIOUTIL_H #include #include #include #include #include namespace mitk { /** * \ingroup IO * * \brief A utility class to load and save data from/to the local file system. * * This method LoadFiles queries the MITK Micro Services registry for registered mitk::IDataNodeReader service * instances. The service instance with the highest ranking will be asked first to load the * given file. On error (exception thrown) or if no mitk::DataNode was constructed, the next * service instance is used. * * The methods LoadImage, LoadSurface, and LoadPointSet are convenience methods for general loading of * the three main data types in MITK. They all use the more generic method LoadDataNode. * * The methods SaveImage, SaveSurface, and SurfacePointSet are also meant for convenience (e.g. during testing). * Currently, there is no generic way to save a generic DataNode with an appropriate format. Thus, every method * initializes the corresponding instance of the special writer for the data type. * * \see mitk::IDataNodeReader */ class MITK_CORE_EXPORT IOUtil { public: /** * Load a files in fileNames and add the constructed mitk::DataNode instances * to the mitk::DataStorage storage * * \param fileNames A list (vector) of absolute file name paths. * \param storage The data storage to which the constructed data nodes are added. * \return The number of added mitk::DataNode instances. */ static int LoadFiles(const std::vector&fileNames, DataStorage& storage); /** * This method will create a new mitk::DataStorage instance and pass it to * LoadFiles(std::vector,DataStorage). * * \param fileNames A list (vector) of absolute file name paths. * \return The new mitk::DataStorage containing the constructed data nodes. * * \see LoadFiles(std::vector,DataStorage) */ static DataStorage::Pointer LoadFiles(const std::vector& fileNames); /** * @brief LoadDataNode Method to load an arbitrary DataNode. * @param path The path to the file including file name and file extension. * @throws mitk::Exception This exception is thrown when the DataNodeFactory is not able to read/find the file * or the DataNode is NULL. * @return Returns the DataNode. */ static mitk::DataNode::Pointer LoadDataNode(const std::string path); /** * @brief LoadImage Convenience method to load an arbitrary mitkImage. * @param path The path to the image including file name and file extension. * @throws mitk::Exception This exception is thrown when the Image is NULL. * @return Returns the mitkImage. */ static mitk::Image::Pointer LoadImage(const std::string path); /** * @brief LoadSurface Convenience method to load an arbitrary mitkSurface. * @param path The path to the surface including file name and file extension. * @throws mitk::Exception This exception is thrown when the Surface is NULL. * @return Returns the mitkSurface. */ static mitk::Surface::Pointer LoadSurface(const std::string path); /** * @brief LoadPointSet Convenience method to load an arbitrary mitkPointSet. * @param path The path to the pointset including file name and file extension (currently, only .mps is supported). * @throws mitk::Exception This exception is thrown when the PointSet is NULL. * @return Returns the mitkPointSet. */ static mitk::PointSet::Pointer LoadPointSet(const std::string path); /** * @brief SaveImage Convenience method to save an arbitrary mitkImage. * @param path The path to the image including file name and file extension. * If not extention is set, the default value (defined in DEFAULTIMAGEEXTENSION) is used. * @param image The image to save. * @throws mitk::Exception This exception is thrown when the writer is not able to write the image. * @return Returns true for success else false. */ static bool SaveImage(mitk::Image::Pointer image, const std::string path); + /** + * @brief SaveBaseData Convenience method to save arbitrary baseData. + * @param path The path to the image including file name and file extension. + * If not extention is set, the default value (defined in DEFAULTIMAGEEXTENSION) is used. + * @param data The data to save. + * @throws mitk::Exception This exception is thrown when the writer is not able to write the image. + * @return Returns true for success else false. + */ + static bool SaveBaseData(mitk::BaseData* data, const std::string& path); + /** * @brief SaveSurface Convenience method to save an arbitrary mitkSurface. * @param path The path to the surface including file name and file extension. * If not extention is set, the default value (defined in DEFAULTSURFACEEXTENSION) is used. * @throws mitk::Exception This exception is thrown when the writer is not able to write the surface. * or if the fileextension is not suitable for writing. * @return Returns true for success else false. */ static bool SaveSurface(mitk::Surface::Pointer surface, const std::string path); /** * @brief SavePointSet Convenience method to save an mitkPointSet. * @param path The path to the pointset including file name and file extension (currently, only .mps is supported). * If not extention is set, the default value (defined in DEFAULTPOINTSETEXTENSION) is used. * @throws mitk::Exception This exception is thrown when the writer is not able to write the pointset. * @return Returns true for success else false. */ static bool SavePointSet(mitk::PointSet::Pointer pointset, const std::string path); static const std::string DEFAULTIMAGEEXTENSION; static const std::string DEFAULTSURFACEEXTENSION; static const std::string DEFAULTPOINTSETEXTENSION; }; } #endif // MITKIOUTIL_H diff --git a/Core/Code/IO/mitkImageWriter.cpp b/Core/Code/IO/mitkImageWriter.cpp index b915f30859..5afaebd0bf 100644 --- a/Core/Code/IO/mitkImageWriter.cpp +++ b/Core/Code/IO/mitkImageWriter.cpp @@ -1,377 +1,457 @@ /*=================================================================== 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 "mitkImageWriter.h" #include "mitkItkPictureWrite.h" #include "mitkImage.h" #include "mitkImageTimeSelector.h" #include "mitkImageAccessByItk.h" #include "mitkImageReadAccessor.h" #include #include mitk::ImageWriter::ImageWriter() { this->SetNumberOfRequiredInputs( 1 ); m_MimeType = ""; SetDefaultExtension(); } mitk::ImageWriter::~ImageWriter() { } +void mitk::ImageWriter::SetFileName(const char* fileName) +{ + if ( fileName && ( fileName == this->m_FileName ) ) + { + return; + } + if ( fileName ) + { + this->m_FileName = fileName; + this->m_FileNameWithoutExtension = this->m_FileName; + this->m_Extension.clear(); + std::size_t pos = this->m_FileName.find_last_of("/\\"); + if (pos != std::string::npos) + { + std::size_t ppos = this->m_FileName.find_first_of('.', pos); + if (ppos != std::string::npos) + { + this->m_FileNameWithoutExtension = this->m_FileName.substr(0, ppos); + this->m_Extension = this->m_FileName.substr(ppos); + } + } + } + else + { + this->m_FileName.clear(); + this->m_FileNameWithoutExtension.clear(); + this->m_Extension.clear(); + } + this->Modified(); +} + +void mitk::ImageWriter::SetFileName(const std::string & fileName) +{ + this->SetFileName( fileName.c_str() ); +} + +void mitk::ImageWriter::SetExtension(const char* extension) +{ + if ( extension && ( extension == this->m_Extension ) ) + { + return; + } + if ( extension ) + { + this->m_Extension = extension; + this->m_FileName = this->m_FileNameWithoutExtension + this->m_Extension; + } + else + { + this->m_Extension.clear(); + this->m_FileName = this->m_FileNameWithoutExtension; + } + this->Modified(); +} + +void mitk::ImageWriter::SetExtension(const std::string & extension) +{ + this->SetFileName( extension.c_str() ); +} + void mitk::ImageWriter::SetDefaultExtension() { - m_Extension = ".mhd"; + this->m_Extension = ".mhd"; + this->m_FileName = this->m_FileNameWithoutExtension + this->m_Extension; + this->Modified(); } #include #include #include static void writeVti(const char * filename, mitk::Image* image, int t=0) { vtkXMLImageDataWriter * vtkwriter = vtkXMLImageDataWriter::New(); vtkwriter->SetFileName( filename ); vtkwriter->SetInput(image->GetVtkImageData(t)); vtkwriter->Write(); vtkwriter->Delete(); } #include void mitk::ImageWriter::WriteByITK(mitk::Image* image, const std::string& fileName) { + MITK_INFO << "Writing image: " << fileName << std::endl; // Pictures and picture series like .png are written via a different mechanism then volume images. // So, they are still multiplexed and thus not support vector images. if (fileName.find(".png") != std::string::npos || fileName.find(".tif") != std::string::npos || fileName.find(".jpg") != std::string::npos) { try { // switch processing of single/multi-component images if( image->GetPixelType(0).GetNumberOfComponents() == 1) { AccessByItk_1( image, _mitkItkPictureWrite, fileName ); } else { AccessFixedPixelTypeByItk_1( image, _mitkItkPictureWriteComposite, MITK_ACCESSBYITK_PIXEL_TYPES_SEQ MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES_SEQ , fileName); } } catch(itk::ExceptionObject &e) { std::cerr << "Caught " << e.what() << std::endl; } catch(std::exception &e) { std::cerr << "Caught std::exception " << e.what() << std::endl; } return; } // Implementation of writer using itkImageIO directly. This skips the use // of templated itkImageFileWriter, which saves the multiplexing on MITK side. unsigned int dimension = image->GetDimension(); unsigned int* dimensions = image->GetDimensions(); mitk::PixelType pixelType = image->GetPixelType(); mitk::Vector3D spacing = image->GetGeometry()->GetSpacing(); mitk::Point3D origin = image->GetGeometry()->GetOrigin(); itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO( fileName.c_str(), itk::ImageIOFactory::WriteMode ); if(imageIO.IsNull()) { itkExceptionMacro(<< "Error: Could not create itkImageIO via factory for file " << fileName); } // Set the necessary information for imageIO imageIO->SetNumberOfDimensions(dimension); imageIO->SetPixelType( pixelType.GetPixelType() ); imageIO->SetComponentType( pixelType.GetComponentType() < PixelComponentUserType ? static_cast(pixelType.GetComponentType()) : itk::ImageIOBase::UNKNOWNCOMPONENTTYPE); imageIO->SetNumberOfComponents( pixelType.GetNumberOfComponents() ); itk::ImageIORegion ioRegion( dimension ); for(unsigned int i=0; iSetDimensions(i,dimensions[i]); imageIO->SetSpacing(i,spacing[i]); imageIO->SetOrigin(i,origin[i]); mitk::Vector3D direction; direction.SetVnlVector(image->GetGeometry()->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(i)); vnl_vector< double > axisDirection(dimension); for(unsigned int j=0; jSetDirection( i, axisDirection ); ioRegion.SetSize(i, image->GetLargestPossibleRegion().GetSize(i) ); ioRegion.SetIndex(i, image->GetLargestPossibleRegion().GetIndex(i) ); } //use compression if available imageIO->UseCompressionOn(); imageIO->SetIORegion(ioRegion); imageIO->SetFileName(fileName); ImageReadAccessor imageAccess(image); imageIO->Write(imageAccess.GetData()); } void mitk::ImageWriter::GenerateData() { const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, NULL ); if ( locale.compare(currLocale)!=0 ) { try { setlocale(LC_ALL, locale.c_str()); } catch(...) { MITK_INFO << "Could not set locale " << locale; } } if ( m_FileName == "" ) { itkWarningMacro( << "Sorry, filename has not been set!" ); return ; } FILE* tempFile = fopen(m_FileName.c_str(),"w"); if (tempFile==NULL) { itkExceptionMacro(<<"File location not writeable"); return; } fclose(tempFile); remove(m_FileName.c_str()); // Creating clone of input image, since i might change the geometry mitk::Image::Pointer input = const_cast(this->GetInput())->Clone(); // Check if geometry information will be lost if (input->GetDimension() == 2) { if (!input->GetGeometry()->Is2DConvertable()) { MITK_WARN << "Saving a 2D image with 3D geometry information. Geometry information will be lost! You might consider using Convert2Dto3DImageFilter before saving."; // set matrix to identity mitk::AffineTransform3D::Pointer affTrans = mitk::AffineTransform3D::New(); affTrans->SetIdentity(); mitk::Vector3D spacing = input->GetGeometry()->GetSpacing(); mitk::Point3D origin = input->GetGeometry()->GetOrigin(); input->GetGeometry()->SetIndexToWorldTransform(affTrans); input->GetGeometry()->SetSpacing(spacing); input->GetGeometry()->SetOrigin(origin); } } bool vti = (m_Extension.find(".vti") != std::string::npos); // If the extension is NOT .pic and NOT .nrrd and NOT .nii and NOT .nii.gz the following block is entered if ( m_Extension.find(".pic") == std::string::npos && m_Extension.find(".nrrd") == std::string::npos && m_Extension.find(".nii") == std::string::npos && m_Extension.find(".nii.gz") == std::string::npos ) { if(input->GetDimension() > 3) { int t, timesteps; timesteps = input->GetDimension(3); ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New(); timeSelector->SetInput(input); mitk::Image::Pointer image = timeSelector->GetOutput(); for(t = 0; t < timesteps; ++t) { std::ostringstream filename; timeSelector->SetTimeNr(t); timeSelector->Update(); if(input->GetTimeSlicedGeometry()->IsValidTime(t)) { const mitk::TimeBounds& timebounds = input->GetTimeSlicedGeometry()->GetGeometry3D(t)->GetTimeBounds(); - filename << m_FileName.c_str() << "_S" << std::setprecision(0) << timebounds[0] << "_E" << std::setprecision(0) << timebounds[1] << "_T" << t << m_Extension; + filename << m_FileNameWithoutExtension << "_S" << std::setprecision(0) << timebounds[0] << "_E" << std::setprecision(0) << timebounds[1] << "_T" << t << m_Extension; } else { itkWarningMacro(<<"Error on write: TimeSlicedGeometry invalid of image " << filename << "."); - filename << m_FileName.c_str() << "_T" << t << m_Extension; + filename << m_FileNameWithoutExtension << "_T" << t << m_Extension; } if ( vti ) { writeVti(filename.str().c_str(), input, t); } else { WriteByITK(image, filename.str()); } } } else if ( vti ) { - std::ostringstream filename; - filename << m_FileName.c_str() << m_Extension; - writeVti(filename.str().c_str(), input); + writeVti(m_FileName.c_str(), input); } else { - std::ostringstream filename; - filename << m_FileName.c_str() << m_Extension; - WriteByITK(input, filename.str()); + WriteByITK(input, m_FileName); } } else { // use the PicFileWriter for the .pic data type if( m_Extension.find(".pic") != std::string::npos ) { /* PicFileWriter::Pointer picWriter = PicFileWriter::New(); size_t found; found = m_FileName.find( m_Extension ); // !!! HAS to be at the very end of the filename (not somewhere in the middle) if( m_FileName.length() > 3 && found != m_FileName.length() - 4 ) { //if Extension not in Filename std::ostringstream filename; filename << m_FileName.c_str() << m_Extension; picWriter->SetFileName( filename.str().c_str() ); } else { picWriter->SetFileName( m_FileName.c_str() ); } picWriter->SetInputImage( input ); picWriter->Write(); */ } // use the ITK .nrrd Image writer if( m_Extension.find(".nrrd") != std::string::npos || m_Extension.find(".nii") != std::string::npos || m_Extension.find(".nii.gz") != std::string::npos ) { - std::ostringstream filename; - filename << this->m_FileName.c_str() << this->m_Extension; - WriteByITK(input, filename.str()); + WriteByITK(input, this->m_FileName); } } m_MimeType = "application/MITK.Pic"; try { setlocale(LC_ALL, currLocale.c_str()); } catch(...) { MITK_INFO << "Could not reset locale " << currLocale; } } bool mitk::ImageWriter::CanWriteDataType( DataNode* input ) { if ( input ) { - mitk::BaseData* data = input->GetData(); - if ( data ) - { - mitk::Image::Pointer image = dynamic_cast( data ); - if( image.IsNotNull() ) - { - //"SetDefaultExtension()" set m_Extension to ".mhd" ????? - m_Extension = ".pic"; - return true; - } - } + return this->CanWriteBaseDataType(input->GetData()); } return false; } void mitk::ImageWriter::SetInput( DataNode* input ) { if( input && CanWriteDataType( input ) ) this->ProcessObject::SetNthInput( 0, dynamic_cast( input->GetData() ) ); } std::string mitk::ImageWriter::GetWritenMIMEType() { return m_MimeType; } std::vector mitk::ImageWriter::GetPossibleFileExtensions() { std::vector possibleFileExtensions; possibleFileExtensions.push_back(".pic"); + possibleFileExtensions.push_back(".pic.gz"); possibleFileExtensions.push_back(".bmp"); possibleFileExtensions.push_back(".dcm"); possibleFileExtensions.push_back(".DCM"); possibleFileExtensions.push_back(".dicom"); possibleFileExtensions.push_back(".DICOM"); possibleFileExtensions.push_back(".gipl"); possibleFileExtensions.push_back(".gipl.gz"); possibleFileExtensions.push_back(".mha"); possibleFileExtensions.push_back(".nii"); + possibleFileExtensions.push_back(".nii.gz"); possibleFileExtensions.push_back(".nrrd"); possibleFileExtensions.push_back(".nhdr"); possibleFileExtensions.push_back(".png"); possibleFileExtensions.push_back(".PNG"); possibleFileExtensions.push_back(".spr"); possibleFileExtensions.push_back(".mhd"); possibleFileExtensions.push_back(".vtk"); possibleFileExtensions.push_back(".vti"); possibleFileExtensions.push_back(".hdr"); possibleFileExtensions.push_back(".png"); possibleFileExtensions.push_back(".tif"); possibleFileExtensions.push_back(".jpg"); return possibleFileExtensions; } std::string mitk::ImageWriter::GetFileExtension() { return m_Extension; } void mitk::ImageWriter::SetInput( mitk::Image* image ) { this->ProcessObject::SetNthInput( 0, image ); } const mitk::Image* mitk::ImageWriter::GetInput() { if ( this->GetNumberOfInputs() < 1 ) { return NULL; } else { return static_cast< const mitk::Image * >( this->ProcessObject::GetInput( 0 ) ); } } + +const char* mitk::ImageWriter::GetDefaultFilename() +{ + return "Image.nrrd"; +} + +const char* mitk::ImageWriter::GetFileDialogPattern() +{ + return "Image (*.pic, *.pic.gz, *.bmp, *.dcm, *.DCM, *.dicom, *.DICOM, *.gipl, *.gipl.gz, *.mha, " + "*.nii, *.nii.gz, *.nrrd, *.nhdr, *.png, *.PNG, *.spr, *.mhd, *.vtk, *.vti, *.hdr, *.png, " + "*.tif, *.jpg)"; +} + +const char *mitk::ImageWriter::GetDefaultExtension() +{ + return ".nrrd"; +} + +bool mitk::ImageWriter::CanWriteBaseDataType(BaseData::Pointer data) +{ + return dynamic_cast( data.GetPointer() ); +} + +void mitk::ImageWriter::DoWrite(BaseData::Pointer data) +{ + if (this->CanWriteBaseDataType(data)) + { + this->SetInput(dynamic_cast(data.GetPointer())); + this->Update(); + } +} diff --git a/Core/Code/IO/mitkImageWriter.h b/Core/Code/IO/mitkImageWriter.h index 1b5c5a82f8..b8bd51241f 100644 --- a/Core/Code/IO/mitkImageWriter.h +++ b/Core/Code/IO/mitkImageWriter.h @@ -1,159 +1,170 @@ /*=================================================================== 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. ===================================================================*/ #ifndef _MITK_IMAGE_WRITER__H_ #define _MITK_IMAGE_WRITER__H_ -#include +#include namespace mitk { class Image; /** * @brief Writer for mitk::Image * * Uses the given extension (SetExtension) to decide the format to write * (.mhd is default, .pic, .tif, .png, .jpg supported yet). * @ingroup IO */ -class MITK_CORE_EXPORT ImageWriter : public mitk::FileWriter +class MITK_CORE_EXPORT ImageWriter : public mitk::FileWriterWithInformation { public: mitkClassMacro( ImageWriter, mitk::FileWriter ); itkNewMacro( Self ); mitkWriterMacro; /** * Sets the filename of the file to write. * @param _arg the name of the file to write. */ - itkSetStringMacro( FileName ); + virtual void SetFileName (const char* fileName); + virtual void SetFileName (const std::string& fileName); /** * @returns the name of the file to be written to disk. */ itkGetStringMacro( FileName ); /** * \brief Explicitly set the extension to be added to the filename. * @param _arg to be added to the filename, including a "." * (e.g., ".mhd"). */ - itkSetStringMacro( Extension ); + virtual void SetExtension (const char* extension); + virtual void SetExtension (const std::string& extension); /** * \brief Get the extension to be added to the filename. * @returns the extension to be added to the filename (e.g., * ".mhd"). */ itkGetStringMacro( Extension ); /** * \brief Set the extension to be added to the filename to the default */ void SetDefaultExtension(); /** * @warning multiple write not (yet) supported */ itkSetStringMacro( FilePrefix ); /** * @warning multiple write not (yet) supported */ itkGetStringMacro( FilePrefix ); /** * @warning multiple write not (yet) supported */ itkSetStringMacro( FilePattern ); /** * @warning multiple write not (yet) supported */ itkGetStringMacro( FilePattern ); /** * Sets the 0'th input object for the filter. * @param input the first input for the filter. */ void SetInput( mitk::Image* input ); //##Documentation //## @brief Return the possible file extensions for the data type associated with the writer virtual std::vector GetPossibleFileExtensions(); /** * @brief Return the extension to be added to the filename. */ virtual std::string GetFileExtension(); /** * @brief Check if the Writer can write the Content of the */ virtual bool CanWriteDataType( DataNode* ); /** * @brief Return the MimeType of the saved File. */ virtual std::string GetWritenMIMEType(); using Superclass::SetInput; /** * @brief Set the DataTreenode as Input. Important: The Writer always have a SetInput-Function. */ virtual void SetInput( DataNode* ); /** * @returns the 0'th input object of the filter. */ const mitk::Image* GetInput(); + // FileWriterWithInformation methods + virtual const char* GetDefaultFilename(); + virtual const char *GetFileDialogPattern(); + virtual const char *GetDefaultExtension(); + virtual bool CanWriteBaseDataType(BaseData::Pointer data); + virtual void DoWrite(BaseData::Pointer data); + protected: /** * Constructor. */ ImageWriter(); /** * Virtual destructor. */ virtual ~ImageWriter(); virtual void GenerateData(); virtual void WriteByITK(mitk::Image* image, const std::string& fileName); std::string m_FileName; + std::string m_FileNameWithoutExtension; + std::string m_FilePrefix; std::string m_FilePattern; std::string m_Extension; std::string m_MimeType; }; } #endif //_MITK_IMAGE_WRITER__H_ diff --git a/Core/Code/Testing/mitkIOUtilTest.cpp b/Core/Code/Testing/mitkIOUtilTest.cpp index c232c77387..1694c4b31d 100644 --- a/Core/Code/Testing/mitkIOUtilTest.cpp +++ b/Core/Code/Testing/mitkIOUtilTest.cpp @@ -1,71 +1,69 @@ /*=================================================================== 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 "mitkTestingMacros.h" #include #include int mitkIOUtilTest(int argc , char* argv[]) { // always start with this! MITK_TEST_BEGIN("mitkIOUtilTest") MITK_TEST_CONDITION_REQUIRED( argc >= 4, "Testing if input parameters are set."); std::string pathToImage = argv[1]; std::string pathToPointSet = argv[2]; std::string pathToSurface = argv[3]; mitk::Image::Pointer img1 = mitk::IOUtil::LoadImage(pathToImage); MITK_TEST_CONDITION( img1.IsNotNull(), "Testing if image 1 could be loaded"); mitk::PointSet::Pointer pointset = mitk::IOUtil::LoadPointSet(pathToPointSet); MITK_TEST_CONDITION( pointset.IsNotNull(), "Testing if pointset could be loaded"); mitk::Surface::Pointer surface = mitk::IOUtil::LoadSurface(pathToSurface); MITK_TEST_CONDITION( surface.IsNotNull(), "Testing if surface could be loaded"); std::string outDir = MITK_TEST_OUTPUT_DIR; std::string imagePath = outDir+"/diffpic3d.nrrd"; + std::string imagePath2 = outDir+"/diffpic3d.nii.gz"; std::string pointSetPath = outDir + "/diffpointset.mps"; std::string surfacePath = outDir + "/diffsurface.stl"; std::string pointSetPathWithDefaultExtension = outDir + "/diffpointset2.mps"; std::string pointSetPathWithoutDefaultExtension = outDir + "/diffpointset2.xXx"; - // the cases where no exception is thrown - try{ - MITK_TEST_CONDITION(mitk::IOUtil::SaveImage(img1, imagePath.c_str()), "Testing if the image could be saved"); - MITK_TEST_CONDITION(mitk::IOUtil::SavePointSet(pointset, pointSetPath.c_str()), "Testing if the pointset could be saved"); - MITK_TEST_CONDITION(mitk::IOUtil::SaveSurface(surface, surfacePath.c_str()), "Testing if the surface could be saved"); - - // test if defaultextension is inserted if no extension is present - MITK_TEST_CONDITION(mitk::IOUtil::SavePointSet(pointset, pointSetPathWithoutDefaultExtension.c_str()), "Testing if the pointset could be saved"); - }catch ( mitk::Exception e){ - MITK_INFO << "Exception is thrown during writeing"; - } + // the cases where no exception should be thrown + MITK_TEST_CONDITION(mitk::IOUtil::SaveImage(img1, imagePath), "Testing if the image could be saved"); + MITK_TEST_CONDITION(mitk::IOUtil::SaveBaseData(img1.GetPointer(), imagePath2), "Testing if the image could be saved"); + MITK_TEST_CONDITION(mitk::IOUtil::SavePointSet(pointset, pointSetPath), "Testing if the pointset could be saved"); + MITK_TEST_CONDITION(mitk::IOUtil::SaveSurface(surface, surfacePath), "Testing if the surface could be saved"); + + // test if defaultextension is inserted if no extension is present + MITK_TEST_CONDITION(mitk::IOUtil::SavePointSet(pointset, pointSetPathWithoutDefaultExtension.c_str()), "Testing if the pointset could be saved"); // test if exception is thrown as expected on unknown extsension MITK_TEST_FOR_EXCEPTION(mitk::Exception, mitk::IOUtil::SaveSurface(surface,"testSurface.xXx")); //load data which does not exist MITK_TEST_FOR_EXCEPTION(mitk::Exception, mitk::IOUtil::LoadImage("fileWhichDoesNotExist.nrrd")); //delete the files after the test is done remove(imagePath.c_str()); remove(pointSetPath.c_str()); remove(surfacePath.c_str()); //remove the pointset with default extension and not the one without remove(pointSetPathWithDefaultExtension.c_str()); MITK_TEST_END(); }