mitkDataNodeFactory.cpp
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00001 /*========================================================================= 00002 00003 Program: Medical Imaging & Interaction Toolkit 00004 Language: C++ 00005 Date: $Date$ 00006 Version: $Revision$ 00007 00008 Copyright (c) German Cancer Research Center, Division of Medical and 00009 Biological Informatics. All rights reserved. 00010 See MITKCopyright.txt or https://www.mitk.org/copyright.html for details. 00011 00012 This software is distributed WITHOUT ANY WARRANTY; without even 00013 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 00014 PURPOSE. See the above copyright notices for more information. 00015 00016 =========================================================================*/ 00017 00018 #include <mitkConfig.h> 00019 #include <mitkDataNodeFactory.h> 00020 #include <mitkBaseDataIOFactory.h> 00021 #include <mitkCoreObjectFactory.h> 00022 #include <mitkITKImageImport.h> 00023 00024 // C-Standard library includes 00025 #include <stdlib.h> 00026 #include <locale.h> 00027 00028 // STL-related includes 00029 #include <vector> 00030 #include <map> 00031 #include <istream> 00032 #include <cstdlib> 00033 #include <locale> 00034 00035 00036 // VTK-related includes 00037 #include <vtkSTLReader.h> 00038 #include <vtkOBJReader.h> 00039 #include <vtkPolyData.h> 00040 #include <vtkPolyDataNormals.h> 00041 00042 #include <vtkDataReader.h> 00043 #include <vtkPolyDataReader.h> 00044 #include <vtkStructuredPointsReader.h> 00045 00046 #include <vtkStructuredPoints.h> 00047 #include <vtkLookupTable.h> 00048 #include <vtkPointData.h> 00049 #if ((VTK_MAJOR_VERSION > 4) || ((VTK_MAJOR_VERSION==4) && (VTK_MINOR_VERSION>=4) )) 00050 #include <vtkXMLImageDataReader.h> 00051 #endif 00052 00053 // ITK-related includes 00054 #include <itksys/SystemTools.hxx> 00055 #include <itksys/Directory.hxx> 00056 #include <itkImage.h> 00057 #include <itkImageSeriesReader.h> 00058 #include <itkImageFileReader.h> 00059 #include <itkImageIOFactory.h> 00060 #include <itkImageIORegion.h> 00061 #include <itkImageSeriesReader.h> 00062 #include <itkDICOMImageIO2.h> 00063 #include <itkDICOMSeriesFileNames.h> 00064 #include <itkGDCMImageIO.h> 00065 #include <itkGDCMSeriesFileNames.h> 00066 #include <itkNumericSeriesFileNames.h> 00067 #include <itkCommand.h> 00068 00069 // MITK-related includes 00070 #include "mitkSurface.h" 00071 #include "mitkPointSet.h" 00072 #include "mitkStringProperty.h" 00073 #include "mitkProperties.h" 00074 //#include "mitkMaterialProperty.h" 00075 #include "mitkLevelWindowProperty.h" 00076 #include "mitkVtkRepresentationProperty.h" 00077 #include "mitkVtkInterpolationProperty.h" 00078 #include "mitkVtkScalarModeProperty.h" 00079 #include "mitkImage.h" 00080 #include "mitkLookupTableProperty.h" 00081 #include "mitkLookupTable.h" 00082 #include "mitkImageChannelSelector.h" 00083 #include "mitkImageSliceSelector.h" 00084 #include "mitkCoreObjectFactory.h" 00085 #include "mitkTransferFunctionProperty.h" 00086 #include "mitkVtkResliceInterpolationProperty.h" 00087 #include "mitkProgressBar.h" 00088 #include <mitkDicomSeriesReader.h> 00089 00090 bool mitk::DataNodeFactory::m_TextureInterpolationActive = false; // default value for texture interpolation if nothing is defined in global options (see QmitkMainTemplate.ui.h) 00091 00092 mitk::DataNodeFactory::DataNodeFactory() 00093 : m_UseSeriesDetails(true) 00094 { 00095 m_Serie = false; 00096 m_OldProgress = 0; 00097 this->Modified(); 00098 //ensure that a CoreObjectFactory has been instantiated 00099 mitk::CoreObjectFactory::GetInstance(); 00100 } 00101 00102 mitk::DataNodeFactory::~DataNodeFactory() 00103 {} 00104 00105 void mitk::DataNodeFactory::SetImageSerie(bool serie) 00106 { 00107 m_Serie = serie; 00108 } 00109 00110 void mitk::DataNodeFactory::GenerateData() 00111 { 00112 // IF filename is something.pic, and something.pic does not exist, try to read something.pic.gz 00113 // if there are both, something.pic and something.pic.gz, only the requested file is read 00114 // not only for images, but for all formats 00115 std::ifstream exists(m_FileName.c_str()); 00116 if (!exists) 00117 { 00118 std::string testfilename = m_FileName + ".gz"; 00119 00120 std::ifstream exists(testfilename.c_str()); 00121 if (exists.good()) 00122 { 00123 m_FileName += ".gz"; 00124 } 00125 else 00126 { 00127 testfilename = m_FileName + ".GZ"; 00128 std::ifstream exists(testfilename.c_str()); 00129 if (exists.good()) 00130 { 00131 m_FileName += ".GZ"; 00132 } 00133 else 00134 { 00135 std::string message("File does not exist, or cannot be read. Filename = "); 00136 message += m_FileName; 00137 MITK_ERROR << message; 00138 itkExceptionMacro( << message ); 00139 } 00140 } 00141 } 00142 00143 // part for DICOM 00144 // const char *numbers = "0123456789."; 00145 // std::string::size_type first_non_number; 00146 // first_non_number = itksys::SystemTools::GetFilenameName(m_FileName).find_first_not_of ( numbers ); 00147 00148 if (DicomSeriesReader::IsDicom(this->m_FileName) /*|| first_non_number == std::string::npos*/) 00149 { 00150 this->ReadFileSeriesTypeDCM(); 00151 } 00152 else 00153 { 00154 bool usedNewDTNF = false; 00155 00156 // the mitkBaseDataIO class returns a pointer of a vector of BaseData objects 00157 std::vector<mitk::BaseData::Pointer> baseDataVector = mitk::BaseDataIO::LoadBaseDataFromFile( m_FileName, m_FilePrefix, m_FilePattern, m_Serie ); 00158 00159 if( !baseDataVector.empty() ) 00160 this->ResizeOutputs((unsigned int)baseDataVector.size()); 00161 00162 for(int i=0; i<(int)baseDataVector.size(); i++) 00163 { 00164 mitk::BaseData::Pointer baseData = baseDataVector.at(i); 00165 00166 if( baseData.IsNotNull() ) 00167 { 00168 usedNewDTNF = true; 00169 mitk::DataNode::Pointer node = mitk::DataNode::New(); 00170 node->SetData(baseData); 00171 this->SetDefaultCommonProperties( node ); 00172 00173 this->SetOutput(i, node); 00174 } 00175 } 00176 if(!usedNewDTNF && !( m_FileName != "" ) && !(m_Serie == false)) 00177 ReadFileSeriesTypeITKImageSeriesReader(); 00178 } 00179 } 00180 00181 void mitk::DataNodeFactory::ResizeOutputs( const unsigned int& num ) 00182 { 00183 unsigned int prevNum = this->GetNumberOfOutputs(); 00184 this->SetNumberOfOutputs( num ); 00185 for ( unsigned int i = prevNum; i < num; ++i ) 00186 { 00187 this->SetNthOutput( i, this->MakeOutput( i ).GetPointer() ); 00188 } 00189 } 00190 00191 bool mitk::DataNodeFactory::FileNameEndsWith( const std::string& name ) 00192 { 00193 if (m_FileName.size() < name.size()) return false; 00194 00195 return m_FileName.substr(m_FileName.size() - name.size()) == name; 00196 } 00197 00198 bool mitk::DataNodeFactory::FilePatternEndsWith( const std::string& name ) 00199 { 00200 return m_FilePattern.find( name ) != std::string::npos; 00201 } 00202 00203 std::string mitk::DataNodeFactory::GetBaseFileName() 00204 { 00205 return itksys::SystemTools::GetFilenameName( m_FileName ); 00206 } 00207 00208 std::string mitk::DataNodeFactory::GetBaseFilePrefix() 00209 { 00210 return itksys::SystemTools::GetFilenameName( m_FilePrefix ); 00211 } 00212 00213 std::string mitk::DataNodeFactory::GetDirectory() 00214 { 00215 if ( m_FileName != "" ) 00216 return itksys::SystemTools::GetFilenamePath( m_FileName ); 00217 else if ( m_FilePrefix != "" ) 00218 return itksys::SystemTools::GetFilenamePath( m_FilePrefix ); 00219 else 00220 return std::string( "" ); 00221 } 00222 00223 void mitk::DataNodeFactory::ReadFileSeriesTypeDCM() 00224 { 00225 MITK_INFO << "loading image series with prefix " << m_FilePrefix << " and pattern " << m_FilePattern << " as DICOM..." << std::endl; 00226 const char* previousCLocale = setlocale(LC_NUMERIC, NULL); 00227 setlocale(LC_NUMERIC, "C"); 00228 std::locale previousCppLocale( std::cin.getloc() ); 00229 std::locale l( "C" ); 00230 std::cin.imbue(l); 00231 00232 DicomSeriesReader::UidFileNamesMap names_map = DicomSeriesReader::GetSeries(this->GetDirectory(), this->m_UseSeriesDetails, this->m_SeriesRestrictions); 00233 const unsigned int size = names_map.size(); 00234 00235 this->ResizeOutputs(size); 00236 ProgressBar::GetInstance()->AddStepsToDo(size); 00237 ProgressBar::GetInstance()->Progress(); 00238 00239 unsigned int i = 0u; 00240 const DicomSeriesReader::UidFileNamesMap::const_iterator n_end = names_map.end(); 00241 00242 for (DicomSeriesReader::UidFileNamesMap::const_iterator n_it = names_map.begin(); n_it != n_end; ++n_it) 00243 { 00244 const std::string &uid = n_it->first; 00245 DataNode::Pointer node = this->GetOutput(i); 00246 00247 MITK_INFO << "Reading series #" << i << ": " << uid << std::endl; 00248 00249 if (DicomSeriesReader::LoadDicomSeries(n_it->second, *node)) 00250 { 00251 ++i; 00252 node->SetName(uid); 00253 } 00254 else 00255 { 00256 MITK_ERROR << "skipping series #" << i << " due to exception" << std::endl; 00257 } 00258 00259 ProgressBar::GetInstance()->Progress(); 00260 } 00261 00262 setlocale(LC_NUMERIC, previousCLocale); 00263 std::cin.imbue(previousCppLocale); 00264 } 00265 00266 00267 00268 void mitk::DataNodeFactory::ReadFileSeriesTypeITKImageSeriesReader() 00269 { 00270 typedef itk::Image<int, 3> ImageType; 00271 typedef itk::ImageSeriesReader< ImageType > ReaderType; 00272 typedef itk::NumericSeriesFileNames NameGenerator; 00273 00274 if ( ! this->GenerateFileList() ) 00275 { 00276 itkWarningMacro( "Sorry, file list could not be generated!" ); 00277 return ; 00278 } 00279 if ( m_MatchedFileNames.size() == 0 ) 00280 { 00281 itkWarningMacro( "Sorry, no files matched the given filename ("<< m_FileName <<")!" ); 00282 return ; 00283 } 00284 00285 // 00286 // Finally, initialize the ITK-reader and load the files! 00287 // 00288 ReaderType::Pointer reader = ReaderType::New(); 00289 reader->SetFileNames( m_MatchedFileNames ); 00290 try 00291 { 00292 reader->Update(); 00293 ResizeOutputs( reader->GetNumberOfOutputs() ); 00294 for ( unsigned int i = 0; i < reader->GetNumberOfOutputs(); ++i ) 00295 { 00296 //Initialize mitk image from itk 00297 mitk::Image::Pointer image = mitk::Image::New(); 00298 image->InitializeByItk( reader->GetOutput( i ) ); 00299 image->SetVolume( reader->GetOutput( i )->GetBufferPointer() ); 00300 00301 //add the mitk image to the node 00302 mitk::DataNode::Pointer node = this->GetOutput( i ); 00303 node->SetData( image ); 00304 00305 mitk::StringProperty::Pointer nameProp = mitk::StringProperty::New( m_FileName ); 00306 node->SetProperty( "name", nameProp ); 00307 } 00308 } 00309 catch ( const std::exception & e ) 00310 { 00311 itkWarningMacro( << e.what() ); 00312 return ; 00313 } 00314 } 00315 00316 00317 00318 mitk::ColorProperty::Pointer mitk::DataNodeFactory::DefaultColorForOrgan( const std::string& organ ) 00319 { 00320 static bool initialized = false; 00321 static std::map< std::string, std::string > s_ColorMap; 00322 00323 if (!initialized) 00324 { 00325 // all lowercase here, please! 00326 00327 s_ColorMap.insert( std::make_pair( "ankle", "0xe38686") ); 00328 s_ColorMap.insert( std::make_pair( "appendix", "0xe38686") ); 00329 s_ColorMap.insert( std::make_pair( "blood vessels", "0xff3131") ); 00330 s_ColorMap.insert( std::make_pair( "bronchial tree", "0x3168ff") ); 00331 s_ColorMap.insert( std::make_pair( "bone", "0xd5d5d5") ); 00332 s_ColorMap.insert( std::make_pair( "brain", "0xff9cca") ); 00333 s_ColorMap.insert( std::make_pair( "coccyx", "0xe38686") ); 00334 s_ColorMap.insert( std::make_pair( "colon", "0xe38686") ); 00335 s_ColorMap.insert( std::make_pair( "cyst", "0xe38686") ); 00336 s_ColorMap.insert( std::make_pair( "elbow", "0xe38686") ); 00337 s_ColorMap.insert( std::make_pair( "eye", "0xe38686") ); 00338 s_ColorMap.insert( std::make_pair( "fallopian tube", "0xe38686") ); 00339 s_ColorMap.insert( std::make_pair( "fat", "0xff2bee") ); 00340 s_ColorMap.insert( std::make_pair( "hand", "0xe38686") ); 00341 s_ColorMap.insert( std::make_pair( "gall bladder", "0x567f18") ); 00342 s_ColorMap.insert( std::make_pair( "heart", "0xeb1d32") ); 00343 s_ColorMap.insert( std::make_pair( "hip", "0xe38686") ); 00344 s_ColorMap.insert( std::make_pair( "kidney", "0xd33f00") ); 00345 s_ColorMap.insert( std::make_pair( "knee", "0xe38686") ); 00346 s_ColorMap.insert( std::make_pair( "larynx", "0xe38686") ); 00347 s_ColorMap.insert( std::make_pair( "liver", "0xffcc3d") ); 00348 s_ColorMap.insert( std::make_pair( "lung", "0x6bdcff") ); 00349 s_ColorMap.insert( std::make_pair( "lymph node", "0xff0000") ); 00350 s_ColorMap.insert( std::make_pair( "muscle", "0xff456a") ); 00351 s_ColorMap.insert( std::make_pair( "nerve", "0xffea4f") ); 00352 s_ColorMap.insert( std::make_pair( "nose", "0xe38686") ); 00353 s_ColorMap.insert( std::make_pair( "oesophagus", "0xe38686") ); 00354 s_ColorMap.insert( std::make_pair( "ovaries", "0xe38686") ); 00355 s_ColorMap.insert( std::make_pair( "pancreas", "0xf9ab3d") ); 00356 s_ColorMap.insert( std::make_pair( "pelvis", "0xe38686") ); 00357 s_ColorMap.insert( std::make_pair( "penis", "0xe38686") ); 00358 s_ColorMap.insert( std::make_pair( "pharynx", "0xe38686") ); 00359 s_ColorMap.insert( std::make_pair( "prostate", "0xe38686") ); 00360 s_ColorMap.insert( std::make_pair( "rectum", "0xe38686") ); 00361 s_ColorMap.insert( std::make_pair( "sacrum", "0xe38686") ); 00362 s_ColorMap.insert( std::make_pair( "seminal vesicle", "0xe38686") ); 00363 s_ColorMap.insert( std::make_pair( "shoulder", "0xe38686") ); 00364 s_ColorMap.insert( std::make_pair( "spinal cord", "0xf5f93d") ); 00365 s_ColorMap.insert( std::make_pair( "spleen", "0xf96c3d") ); 00366 s_ColorMap.insert( std::make_pair( "stomach", "0xf96c3d") ); 00367 s_ColorMap.insert( std::make_pair( "teeth", "0xfffcd8") ); 00368 s_ColorMap.insert( std::make_pair( "testicles", "0xe38686") ); 00369 s_ColorMap.insert( std::make_pair( "thyroid", "0xfff694") ); 00370 s_ColorMap.insert( std::make_pair( "tongue", "0xe38686") ); 00371 s_ColorMap.insert( std::make_pair( "tumor", "0x937011") ); 00372 s_ColorMap.insert( std::make_pair( "urethra", "0xf8ff32") ); 00373 s_ColorMap.insert( std::make_pair( "urinary bladder", "0xf8ff32") ); 00374 s_ColorMap.insert( std::make_pair( "uterus", "0xe38686") ); 00375 s_ColorMap.insert( std::make_pair( "vagina", "0xe38686") ); 00376 s_ColorMap.insert( std::make_pair( "vertebra", "0xe38686") ); 00377 s_ColorMap.insert( std::make_pair( "wrist", "0xe38686") ); 00378 initialized = true; 00379 } 00380 00381 std::string lowercaseOrgan(organ); 00382 for(unsigned int i = 0; i < organ.length(); i++) 00383 { 00384 lowercaseOrgan[i] = tolower(lowercaseOrgan[i]); 00385 } 00386 00387 std::map< std::string, std::string >::iterator iter = s_ColorMap.find( lowercaseOrgan ); 00388 if ( iter != s_ColorMap.end() ) 00389 { 00390 std::string hexColor = iter->second; 00391 std::string hexRed = std::string("0x") + hexColor.substr( 2, 2 ); 00392 std::string hexGreen = std::string("0x") + hexColor.substr( 4, 2 ); 00393 std::string hexBlue = std::string("0x") + hexColor.substr( 6, 2 ); 00394 00395 long int red = strtol( hexRed.c_str(), NULL, 16 ); 00396 long int green = strtol( hexGreen.c_str(), NULL, 16 ); 00397 long int blue = strtol( hexBlue.c_str(), NULL, 16 ); 00398 00399 return ColorProperty::New( (float)red/ 255.0, (float)green/ 255.0, (float)blue/ 255.0 ); 00400 } 00401 else 00402 { 00403 // a default color (green) 00404 return ColorProperty::New( 0.0, 1.0, 0.0 ); 00405 } 00406 00407 } 00408 00409 void mitk::DataNodeFactory::SetDefaultCommonProperties(mitk::DataNode::Pointer &node) 00410 { 00411 // path 00412 mitk::StringProperty::Pointer pathProp = mitk::StringProperty::New( itksys::SystemTools::GetFilenamePath( m_FileName ) ); 00413 node->SetProperty( StringProperty::PATH, pathProp ); 00414 00415 00416 // name already defined? 00417 mitk::StringProperty::Pointer nameProp = dynamic_cast<mitk::StringProperty*>(node->GetProperty("name")); 00418 if(nameProp.IsNull() || (strcmp(nameProp->GetValue(),"No Name!")==0)) 00419 { 00420 // name already defined in BaseData 00421 mitk::StringProperty::Pointer baseDataNameProp = dynamic_cast<mitk::StringProperty*>(node->GetData()->GetProperty("name").GetPointer() ); 00422 if(baseDataNameProp.IsNull() || (strcmp(baseDataNameProp->GetValue(),"No Name!")==0)) 00423 { 00424 // name neither defined in node, nor in BaseData -> name = filename 00425 if (FileNameEndsWith( ".gz" )) 00426 m_FileName = m_FileName.substr( 0, m_FileName.length()-3 ); 00427 00428 nameProp = mitk::StringProperty::New( itksys::SystemTools::GetFilenameWithoutLastExtension( m_FileName ) ); 00429 00430 node->SetProperty( "name", nameProp ); 00431 } 00432 else 00433 { 00434 // name defined in BaseData! 00435 nameProp = mitk::StringProperty::New( baseDataNameProp->GetValue() ); 00436 node->SetProperty( "name", nameProp ); 00437 } 00438 } 00439 00440 // visibility 00441 if(!node->GetProperty("visible")) 00442 node->SetVisibility(true); 00443 } 00444
