common/clitkEsrfHstImageIO.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 #include "clitkEsrfHstImageIO.h"
  20 #include "clitkEsrfHstXMLFileReader.h"
  21 #include "clitkDD.h"
  22
  23 // itk include (for itkReadRawBytesAfterSwappingMacro)
  24 #include <itkRawImageIO.h>
  25 #include <itksys/SystemTools.hxx>
  26 #include <itkMetaDataObject.h>
  27
  28 //--------------------------------------------------------------------
  29 // Read Image Information
  30 void clitk::EsrfHstImageIO::ReadImageInformation()
  31 {
  32   clitk::EsrfHstXMLFileReader::Pointer hstXmlReader;
  33   hstXmlReader = clitk::EsrfHstXMLFileReader::New();
  34   hstXmlReader->SetFilename(m_XmlFileName);
  35   hstXmlReader->GenerateOutputInformation();
  36   itk::MetaDataDictionary &dic = *(hstXmlReader->GetOutputObject() );
  37
  38   typedef itk::MetaDataObject< double > MetaDataDoubleType;
  39   typedef itk::MetaDataObject< std::string > MetaDataStringType;
  40   typedef itk::MetaDataObject< int > MetaDataIntType;
  41   SetComponentType(itk::ImageIOBase::FLOAT);
  42   SetNumberOfDimensions(3);
  43   SetDimensions(0, dynamic_cast<MetaDataIntType *>(dic["SIZEX"].GetPointer() )->GetMetaDataObjectValue());
  44   SetDimensions(1, dynamic_cast<MetaDataIntType *>(dic["SIZEY"].GetPointer() )->GetMetaDataObjectValue());
  45   SetDimensions(2, dynamic_cast<MetaDataIntType *>(dic["SIZEZ"].GetPointer() )->GetMetaDataObjectValue());
  46   SetSpacing(0, dynamic_cast<MetaDataDoubleType *>(dic["voxelsize"].GetPointer() )->GetMetaDataObjectValue());
  47   SetSpacing(1, GetSpacing(0));
  48   SetSpacing(2, GetSpacing(0));
  49   SetOrigin(0, GetSpacing(0)*(dynamic_cast<MetaDataIntType *>(dic["ORIGINX"].GetPointer() )->GetMetaDataObjectValue()-1));
  50   SetOrigin(1, GetSpacing(0)*(dynamic_cast<MetaDataIntType *>(dic["ORIGINY"].GetPointer() )->GetMetaDataObjectValue()-1));
  51   SetOrigin(2, GetSpacing(0)*(dynamic_cast<MetaDataIntType *>(dic["ORIGINZ"].GetPointer() )->GetMetaDataObjectValue()-1));
  52   if(std::string("LOWBYTEFIRST") == dynamic_cast<MetaDataStringType*>(dic["SUBVOLUME_NAME"].GetPointer() )->GetMetaDataObjectValue())
  53     this->SetByteOrder(BigEndian);
  54   else
  55     this->SetByteOrder(LittleEndian);
  56
  57   // Prepare raw file name
  58   m_RawFileName = itksys::SystemTools::GetFilenamePath(m_XmlFileName);
  59   if(m_RawFileName != "")
  60     m_RawFileName += std::string("/");
  61   m_RawFileName += dynamic_cast<MetaDataStringType*>(dic["SUBVOLUME_NAME"].GetPointer() )->GetMetaDataObjectValue();
  62 } ////
  63
  64 //--------------------------------------------------------------------
  65 // Read Image Information
  66 bool clitk::EsrfHstImageIO::CanReadFile(const char* FileNameToRead)
  67 {
  68   std::string ext = itksys::SystemTools::GetFilenameLastExtension(FileNameToRead);
  69   if( ext!=std::string(".xml") && ext!=std::string(".vol") )
  70     return false;
  71
  72   m_XmlFileName = std::string(FileNameToRead);
  73   if( ext==std::string(".vol") )
  74     m_XmlFileName += std::string(".xml");
  75
  76   std::ifstream is(m_XmlFileName.c_str());
  77   if(! is.is_open() )
  78     return false;
  79
  80   std::string firstLine;
  81   std::getline(is, firstLine);
  82   if(firstLine.find( std::string("<!-- PyHST VOLUME XML FILE -->") ) == std::string::npos)
  83     return false;
  84
  85   return true;
  86 } ////
  87
  88 //--------------------------------------------------------------------
  89 // Read Image Content
  90 void clitk::EsrfHstImageIO::Read(void * buffer)
  91 {
  92   // Adapted from itkRawImageIO
  93   std::ifstream is(m_RawFileName.c_str(), std::ios::binary);
  94   if(! is.is_open() )
  95     itkExceptionMacro(<<"Could not open file " << m_RawFileName);
  96
  97   unsigned long numberOfBytesToBeRead = GetComponentSize();
  98   for(unsigned int i=0; i<GetNumberOfDimensions(); i++) numberOfBytesToBeRead *= GetDimensions(i);
  99
 100   if(!this->ReadBufferAsBinary(is, buffer, numberOfBytesToBeRead)) {
 101     itkExceptionMacro(<<"Read failed: Wanted "
 102                       << numberOfBytesToBeRead
 103                       << " bytes, but read "
 104                       << is.gcount() << " bytes.");
 105   }
 106   itkDebugMacro(<< "Reading Done");
 107
 108   // Adapted from itkRawImageIO
 109   {
 110 #if ( ITK_VERSION_MAJOR < 5 )
 111     using namespace itk;
 112     // Swap bytes if necessary
 113     if itkReadRawBytesAfterSwappingMacro( unsigned short, USHORT )
 114       else if itkReadRawBytesAfterSwappingMacro( short, SHORT )
 115         else if itkReadRawBytesAfterSwappingMacro( char, CHAR )
 116           else if itkReadRawBytesAfterSwappingMacro( unsigned char, UCHAR )
 117             else if itkReadRawBytesAfterSwappingMacro( unsigned int, UINT )
 118               else if itkReadRawBytesAfterSwappingMacro( int, INT )
 119                 else if itkReadRawBytesAfterSwappingMacro( float, FLOAT )
 120                   else if itkReadRawBytesAfterSwappingMacro( double, DOUBLE );
 121 #else
 122   #define itkReadRawBytesAfterSwappingMacro(StrongType, WeakType)   \
 123     ( this->GetComponentType() == WeakType )                        \
 124       {                                                             \
 125       using InternalByteSwapperType = itk::ByteSwapper<StrongType>; \
 126       if ( m_ByteOrder == LittleEndian )                            \
 127         {                                                           \
 128         InternalByteSwapperType::SwapRangeFromSystemToLittleEndian( \
 129           (StrongType *)buffer, this->GetImageSizeInComponents() ); \
 130         }                                                           \
 131       else if ( m_ByteOrder == BigEndian )                          \
 132         {                                                           \
 133         InternalByteSwapperType::SwapRangeFromSystemToBigEndian(    \
 134           (StrongType *)buffer, this->GetImageSizeInComponents() ); \
 135         }                                                           \
 136       }
 137
 138     // Swap bytes if necessary
 139     if itkReadRawBytesAfterSwappingMacro( unsigned short, USHORT )
 140       else if itkReadRawBytesAfterSwappingMacro( short, SHORT )
 141         else if itkReadRawBytesAfterSwappingMacro( char, CHAR )
 142           else if itkReadRawBytesAfterSwappingMacro( unsigned char, UCHAR )
 143             else if itkReadRawBytesAfterSwappingMacro( unsigned int, UINT )
 144               else if itkReadRawBytesAfterSwappingMacro( int, INT )
 145                 else if itkReadRawBytesAfterSwappingMacro( float, FLOAT )
 146                   else if itkReadRawBytesAfterSwappingMacro( double, DOUBLE );
 147 #endif
 148   }
 149 }
 150
 151 //--------------------------------------------------------------------
 152 // Write Image Information
 153 void clitk::EsrfHstImageIO::WriteImageInformation(bool keepOfStream)
 154 {
 155 }
 156
 157 //--------------------------------------------------------------------
 158 // Write Image Information
 159 bool clitk::EsrfHstImageIO::CanWriteFile(const char* FileNameToWrite)
 160 {
 161   return false;
 162 }
 163
 164 //--------------------------------------------------------------------
 165 // Write Image
 166 void clitk::EsrfHstImageIO::Write(const void * buffer)
 167 {
 168 } ////