diff --git a/Modules/DICOMReader/mitkDICOMFileReaderSelector.cpp b/Modules/DICOMReader/mitkDICOMFileReaderSelector.cpp index d918169a8e..a02c473b58 100644 --- a/Modules/DICOMReader/mitkDICOMFileReaderSelector.cpp +++ b/Modules/DICOMReader/mitkDICOMFileReaderSelector.cpp @@ -1,260 +1,260 @@ /*=================================================================== 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 "mitkDICOMFileReaderSelector.h" #include "mitkDICOMReaderConfigurator.h" #include "mitkDICOMGDCMTagScanner.h" #include #include #include #include #include mitk::DICOMFileReaderSelector ::DICOMFileReaderSelector() { } mitk::DICOMFileReaderSelector ::~DICOMFileReaderSelector() { } std::list mitk::DICOMFileReaderSelector ::GetAllConfiguredReaders() const { return m_Readers; } void mitk::DICOMFileReaderSelector ::AddConfigsFromResources(const std::string& path) { - std::vector configs = GetModuleContext()->GetModule()->FindResources(path, "*.xml", false); + std::vector configs = us::GetModuleContext()->GetModule()->FindResources(path, "*.xml", false); - for (std::vector::iterator iter = configs.begin(); + for (std::vector::iterator iter = configs.begin(); iter != configs.end(); ++iter) { - ModuleResource& resource = *iter; + us::ModuleResource& resource = *iter; if (resource.IsValid()) { - ModuleResourceStream stream(resource); + us::ModuleResourceStream stream(resource); // read all into string s std::string s; stream.seekg(0, std::ios::end); s.reserve(stream.tellg()); stream.seekg(0, std::ios::beg); s.assign((std::istreambuf_iterator(stream)), std::istreambuf_iterator()); this->AddConfig(s); } } } void mitk::DICOMFileReaderSelector -::AddConfigFromResource(ModuleResource& resource) +::AddConfigFromResource(us::ModuleResource& resource) { if (resource.IsValid()) { - ModuleResourceStream stream(resource); + us::ModuleResourceStream stream(resource); // read all into string s std::string s; stream.seekg(0, std::ios::end); s.reserve(stream.tellg()); stream.seekg(0, std::ios::beg); s.assign((std::istreambuf_iterator(stream)), std::istreambuf_iterator()); this->AddConfig(s); } } void mitk::DICOMFileReaderSelector ::AddConfigFromResource(const std::string& resourcename) { - ModuleResource r = GetModuleContext()->GetModule()->GetResource(resourcename); + us::ModuleResource r = us::GetModuleContext()->GetModule()->GetResource(resourcename); this->AddConfigFromResource(r); } void mitk::DICOMFileReaderSelector ::AddFileReaderCanditate(DICOMFileReader::Pointer reader) { if (reader.IsNotNull()) { m_Readers.push_back( reader ); } } void mitk::DICOMFileReaderSelector ::LoadBuiltIn3DConfigs() { //this->AddConfigsFromResources("configurations/3D"); // in this order of preference... this->AddConfigFromResource("configurations/3D/instancenumber.xml"); this->AddConfigFromResource("configurations/3D/slicelocation.xml"); this->AddConfigFromResource("configurations/3D/imageposition.xml"); this->AddConfigFromResource("configurations/3D/imageposition_byacquisition.xml"); //this->AddConfigFromResource("configurations/3D/imagetime.xml"); // no sense in this one? want to see a real-world example first this->AddConfigFromResource("configurations/3D/classicreader.xml"); // currently is 3D+t actually } void mitk::DICOMFileReaderSelector ::LoadBuiltIn3DnTConfigs() { this->AddConfigsFromResources("configurations/3DnT"); } void mitk::DICOMFileReaderSelector ::AddConfig(const std::string& xmlDescription) { DICOMReaderConfigurator::Pointer configurator = DICOMReaderConfigurator::New(); DICOMFileReader::Pointer reader = configurator->CreateFromUTF8ConfigString(xmlDescription); if (reader.IsNotNull()) { m_Readers.push_back( reader ); m_PossibleConfigurations.push_back(xmlDescription); } else { std::stringstream ss; ss << "Could not parse reader configuration. Ignoring it."; throw std::invalid_argument( ss.str() ); } } void mitk::DICOMFileReaderSelector ::AddConfigFile(const std::string& filename) { std::ifstream file(filename.c_str()); std::string s; file.seekg(0, std::ios::end); s.reserve(file.tellg()); file.seekg(0, std::ios::beg); s.assign((std::istreambuf_iterator(file)), std::istreambuf_iterator()); this->AddConfig(s); } void mitk::DICOMFileReaderSelector ::SetInputFiles(StringList filenames) { m_InputFilenames = filenames; } const mitk::StringList& mitk::DICOMFileReaderSelector ::GetInputFiles() const { return m_InputFilenames; } mitk::DICOMFileReader::Pointer mitk::DICOMFileReaderSelector ::GetFirstReaderWithMinimumNumberOfOutputImages() { ReaderList workingCandidates; // do the tag scanning externally and just ONCE DICOMGDCMTagScanner::Pointer gdcmScanner = DICOMGDCMTagScanner::New(); gdcmScanner->SetInputFiles( m_InputFilenames ); // let all readers analyze the file set for (ReaderList::iterator rIter = m_Readers.begin(); rIter != m_Readers.end(); ++rIter) { gdcmScanner->AddTags( (*rIter)->GetTagsOfInterest() ); } gdcmScanner->Scan(); // let all readers analyze the file set unsigned int readerIndex(0); for (ReaderList::iterator rIter = m_Readers.begin(); rIter != m_Readers.end(); ++readerIndex, ++rIter) { (*rIter)->SetInputFiles( m_InputFilenames ); (*rIter)->SetTagCache( gdcmScanner.GetPointer() ); try { (*rIter)->AnalyzeInputFiles(); workingCandidates.push_back( *rIter ); MITK_INFO << "Reader " << readerIndex << " (" << (*rIter)->GetConfigurationLabel() << ") suggests " << (*rIter)->GetNumberOfOutputs() << " 3D blocks"; if ((*rIter)->GetNumberOfOutputs() == 1) { MITK_DEBUG << "Early out with reader #" << readerIndex << " (" << (*rIter)->GetConfigurationLabel() << "), less than 1 block is not possible"; return *rIter; } } catch (std::exception& e) { MITK_ERROR << "Reader " << readerIndex << " (" << (*rIter)->GetConfigurationLabel() << ") threw exception during file analysis, ignoring this reader. Exception: " << e.what(); } catch (...) { MITK_ERROR << "Reader " << readerIndex << " (" << (*rIter)->GetConfigurationLabel() << ") threw unknown exception during file analysis, ignoring this reader."; } } DICOMFileReader::Pointer bestReader; unsigned int minimumNumberOfOutputs = std::numeric_limits::max(); readerIndex = 0; unsigned int bestReaderIndex(0); // select the reader with the minimum number of mitk::Images as output for (ReaderList::iterator rIter = workingCandidates.begin(); rIter != workingCandidates.end(); ++readerIndex, ++rIter) { unsigned int thisReadersNumberOfOutputs = (*rIter)->GetNumberOfOutputs(); if ( thisReadersNumberOfOutputs > 0 // we don't count readers that don't actually produce output && thisReadersNumberOfOutputs < minimumNumberOfOutputs ) { minimumNumberOfOutputs = (*rIter)->GetNumberOfOutputs(); bestReader = *rIter; bestReaderIndex = readerIndex; } } MITK_DEBUG << "Decided for reader #" << bestReaderIndex << " (" << bestReader->GetConfigurationLabel() << ")"; MITK_DEBUG << m_PossibleConfigurations[bestReaderIndex]; return bestReader; } diff --git a/Modules/DICOMReader/mitkDICOMFileReaderSelector.h b/Modules/DICOMReader/mitkDICOMFileReaderSelector.h index 9a7f9401ef..765e2bfa10 100644 --- a/Modules/DICOMReader/mitkDICOMFileReaderSelector.h +++ b/Modules/DICOMReader/mitkDICOMFileReaderSelector.h @@ -1,104 +1,104 @@ /*=================================================================== 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 mitkDICOMFileReaderSelector_h #define mitkDICOMFileReaderSelector_h #include "mitkDICOMFileReader.h" #include namespace mitk { /** \ingroup DICOMReaderModule \brief Simple best-reader selection. This class implements a process of comparing different DICOMFileReader%s and selecting the reader with the minimal number of mitk::Image%s in its output. The code found in this class can - just be used to select a reader using this simple strategy - be taken as an example of how to use DICOMFileReader%s To create a selection of potential readers, the class makes use of mitk::DICOMReaderConfigurator, i.e. DICOMFileReaderSelector also expects the configuration files/strings to be in the format expected by mitk::DICOMReaderConfigurator. Two convenience methods load "default" configurations from compiled-in resources: LoadBuiltIn3DConfigs() and LoadBuiltIn3DnTConfigs(). */ class DICOMReader_EXPORT DICOMFileReaderSelector : public itk::LightObject { public: typedef std::list ReaderList; mitkClassMacro( DICOMFileReaderSelector, itk::LightObject ) itkNewMacro( DICOMFileReaderSelector ) /// \brief Add a configuration as expected by DICOMReaderConfigurator. /// Configs can only be reset by instantiating a new DICOMFileReaderSelector. void AddConfig(const std::string& xmlDescription); /// \brief Add a configuration as expected by DICOMReaderConfigurator. /// Configs can only be reset by instantiating a new DICOMFileReaderSelector. void AddConfigFile(const std::string& filename); /// \brief Add a whole pre-configured reader to the selection process. void AddFileReaderCanditate(DICOMFileReader::Pointer reader); /// \brief Load 3D image creating configurations from the MITK module system (see \ref mitk::Module::FindResources). /// For a default set of configurations, look into the directory Resources of the DICOMReader module. void LoadBuiltIn3DConfigs(); /// \brief Load 3D+t image creating configurations from the MITK module system (see \ref mitk::Module::FindResources). /// For a default set of configurations, look into the directory Resources of the DICOMReader module. void LoadBuiltIn3DnTConfigs(); /// \brief Return all the DICOMFileReader%s that are currently used for selection by this class. /// The readers returned by this method depend on what config files have been added earlier /// (or which of the built-in readers have been loaded) ReaderList GetAllConfiguredReaders() const; /// Input files void SetInputFiles(StringList filenames); /// Input files const StringList& GetInputFiles() const; /// Execute the analysis and selection process. The first reader with a minimal number of outputs will be returned. DICOMFileReader::Pointer GetFirstReaderWithMinimumNumberOfOutputImages(); protected: DICOMFileReaderSelector(); virtual ~DICOMFileReaderSelector(); void AddConfigsFromResources(const std::string& path); void AddConfigFromResource(const std::string& resourcename); - void AddConfigFromResource(ModuleResource& resource); + void AddConfigFromResource(us::ModuleResource& resource); private: StringList m_PossibleConfigurations; StringList m_InputFilenames; ReaderList m_Readers; }; } // namespace #endif // mitkDICOMFileReaderSelector_h