Reader to read files in Philips PAR/REC file format. More...

#include <mitkParRecFileReader.h>

Inheritance diagram for mitk::ParRecFileReader:

Collaboration diagram for mitk::ParRecFileReader:

Public Types
typedef ParRecFileReader	Self
typedef FileReader	Superclass
typedef itk::SmartPointer< Self >	Pointer
typedef itk::SmartPointer < const Self >	ConstPointer
Public Member Functions
virtual const char *	GetClassName () const
virtual void	SetFileName (const char *_arg)
	Specify the file to load.
virtual const char *	GetFileName () const
	Get the specified the file to load.
virtual void	SetFilePrefix (const char *_arg)
	Specify file prefix for the file(s) to load.
virtual const char *	GetFilePrefix () const
	Get the specified file prefix for the file(s) to load.
virtual void	SetFilePattern (const char *_arg)
	Specified file pattern for the file(s) to load. The sprintf format used to build filename from FilePrefix and number.
virtual const char *	GetFilePattern () const
	Get the specified file pattern for the file(s) to load. The sprintf format used to build filename from FilePrefix and number.
Static Public Member Functions
static Pointer	New ()
static bool	CanReadFile (const std::string filename, const std::string filePrefix, const std::string filePattern)
Protected Member Functions
virtual void	GenerateData ()
	A version of GenerateData() specific for image processing filters.
virtual void	GenerateOutputInformation ()
	ParRecFileReader ()
	~ParRecFileReader ()
Protected Attributes
itk::TimeStamp	m_ReadHeaderTime
int	m_StartFileIndex
std::string	m_FileName
std::string	m_RecFileName
std::string	m_FilePrefix
std::string	m_FilePattern

Detailed Description

Reader to read files in Philips PAR/REC file format.

Definition at line 31 of file mitkParRecFileReader.h.

Member Typedef Documentation

typedef itk::SmartPointer<const Self> mitk::ParRecFileReader::ConstPointer

Definition at line 34 of file mitkParRecFileReader.h.

typedef itk::SmartPointer<Self> mitk::ParRecFileReader::Pointer

Definition at line 34 of file mitkParRecFileReader.h.

typedef ParRecFileReader mitk::ParRecFileReader::Self

Definition at line 34 of file mitkParRecFileReader.h.

typedef FileReader mitk::ParRecFileReader::Superclass

Definition at line 34 of file mitkParRecFileReader.h.

Constructor & Destructor Documentation

mitk::ParRecFileReader::ParRecFileReader ( ) [protected]

Definition at line 274 of file mitkParRecFileReader.cpp.

: m_FileName(""), m_FilePrefix(""), m_FilePattern("")
{
}

mitk::ParRecFileReader::~ParRecFileReader ( ) [protected]

Definition at line 279 of file mitkParRecFileReader.cpp.

{
}

Member Function Documentation

bool mitk::ParRecFileReader::CanReadFile	(	const std::string	filename,
		const std::string	filePrefix,
		const std::string	filePattern
	)		`[static]`

Definition at line 241 of file mitkParRecFileReader.cpp.

{
  // First check the extension
  if(  filename == "" )
    {
      //MITK_INFO<<"No filename specified."<<std::endl;
    return false;
    }

  bool extensionFound = false;
  std::string::size_type PARPos = filename.rfind(".par");
  if ((PARPos != std::string::npos)
      && (PARPos == filename.length() - 4))
    {
    extensionFound = true;
    }

  PARPos = filename.rfind(".PAR");
  if ((PARPos != std::string::npos)
      && (PARPos == filename.length() - 4))
    {
    extensionFound = true;
    }

  if( !extensionFound )
    {
      //MITK_INFO<<"The filename extension is not recognized."<<std::endl;
    return false;
    }

  return true;
}

void mitk::ParRecFileReader::GenerateData ( ) [protected, virtual]

A version of GenerateData() specific for image processing filters.

This implementation will split the processing across multiple threads. The buffer is allocated by this method. Then the BeforeThreadedGenerateData() method is called (if provided). Then, a series of threads are spawned each calling ThreadedGenerateData(). After all the threads have completed processing, the AfterThreadedGenerateData() method is called (if provided). If an image processing filter cannot be threaded, the filter should provide an implementation of GenerateData(). That implementation is responsible for allocating the output buffer. If a filter an be threaded, it should NOT provide a GenerateData() method but should provide a ThreadedGenerateData() instead.

See also:: ThreadedGenerateData()

Reimplemented from mitk::ImageSource.

Definition at line 176 of file mitkParRecFileReader.cpp.

References QuadProgPP::t().

{
  mitk::Image::Pointer output = this->GetOutput();
  
  // Check to see if we can read the file given the name or prefix
  //
  if ( m_RecFileName == "" )
  {
    throw itk::ImageFileReaderException(__FILE__, __LINE__, "FileName for rec-file empty");
  }
  
  if( m_RecFileName != "")
  {
    FILE *f = fopen(m_RecFileName.c_str(), "r");
    if(f==NULL)
    {
      throw itk::ImageFileReaderException(__FILE__, __LINE__, "Could not open rec-file.");
    }

    int zstart, zmax;
    int tstart, tmax;

    zstart=output->GetRequestedRegion().GetIndex(2);
    tstart=output->GetRequestedRegion().GetIndex(3);

    zmax=zstart+output->GetRequestedRegion().GetSize(2);
    tmax=tstart+output->GetRequestedRegion().GetSize(3);

    int sliceSize=output->GetDimension(0)*output->GetDimension(1)*output->GetPixelType().GetBpe()/8;    
    void *data = malloc(sliceSize);

    bool ignore4Dtopogram=false;
    {
      int slicePlusTimeSize=output->GetDimension(0)*output->GetDimension(1)*output->GetDimension(3)*output->GetPixelType().GetBpe()/8;
    if(output->GetDimension(3)>1)
      ignore4Dtopogram=true;

      int z,t;
      for(t=tstart;t<tmax;++t)
        for(z=zstart;z<zmax;++z)
        {
          if(ignore4Dtopogram)
            fseek(f,slicePlusTimeSize*z+(sliceSize+1)*t,SEEK_SET);
          else
            fseek(f,slicePlusTimeSize*z+sliceSize*t,SEEK_SET);
          size_t ignored = fread(data, sliceSize, 1, f);
          ++ignored;
          output->SetSlice(data,z,t,0);
        }
    }
    //else
    //{
    //  for(;z<zmax;++z)
    //  {
    //    fseek(f,sliceSize*z,SEEK_SET);          
    //    fread(data, sliceSize, 1, f);
    //    output->SetSlice(data,z,0,0);
    //  }
    //}
    free(data);

    fclose(f);
  }
}

void mitk::ParRecFileReader::GenerateOutputInformation ( void ) [protected, virtual]

Definition at line 26 of file mitkParRecFileReader.cpp.

References mitk::ImageSource::GetOutput(), m_FileName, m_FilePrefix, m_ReadHeaderTime, and m_RecFileName.

{
  mitk::Image::Pointer output = this->GetOutput();
  
  if ((output->IsInitialized()) && (this->GetMTime() <= m_ReadHeaderTime.GetMTime()))
    return;
  
  itkDebugMacro(<<"Reading PAR file for GenerateOutputInformation()" << m_FileName);
  
  // Check to see if we can read the file given the name or prefix
  //
  if ( m_FileName == "" && m_FilePrefix == "" )
  {
    throw itk::ImageFileReaderException(__FILE__, __LINE__, "One of FileName or FilePrefix must be non-empty");
  }
  
  m_RecFileName = "";
  if( m_FileName != "")
  {
    int extPos=m_FileName.find_last_of(".");
    if(extPos>=-1)
    {
      const char *ext=m_FileName.c_str()+extPos+1;
      if(stricmp(ext,"par")==0)
        m_RecFileName = m_FileName.substr(0,extPos);
      else
        m_RecFileName = m_FileName;
    }
    else
        m_RecFileName = m_FileName;

    m_RecFileName.append(".rec");

    bool headerRead = false;

    mitk::PixelType type;
    unsigned int dimension=0;
    unsigned int dimensions[4]={0,0,1,1};
    float sliceThickness=0.0;
    float sliceGap=0.0;
    float sliceSpacing=0.0;
    mitk::Vector3D thickness; thickness.Fill(1.0);
    mitk::Vector3D gap; gap.Fill(0.0);
    mitk::Vector3D spacing;
    
    FILE *f;
    f=fopen(m_FileName.c_str(), "r");
    if(f!=NULL)
    {
      while(!feof(f))
      {
        char s[300], *p;
        char* ignored = fgets(s,200,f);
        ++ignored;
        if(strstr(s,"Max. number of cardiac phases"))
        {
          p=strchr(s,':')+1;
          dimensions[3]=atoi(p);
          if(dimensions[3]>1)
            dimension=4;
        }
        else
        if(strstr(s,"Max. number of slices/locations"))
        {
          p=strchr(s,':')+1;
          dimensions[2]=atoi(p);
          if(dimension==0)
          {
            if(dimensions[2]>1)
              dimension=3;
            else
              dimension=2;
          }
        }
        else
        if(strstr(s,"Image pixel size"))
        {
          p=strchr(s,':')+1;
          int bpe=atoi(p);
          if(bpe==8)
            type=typeid(mitkIpUInt1_t);
          else
            type=typeid(mitkIpUInt2_t);
        }
        else
        if(strstr(s,"Recon resolution"))
        {
          p=s+strcspn(s,"0123456789");
          sscanf(p,"%u %u", dimensions, dimensions+1);
        }
        else
        if(strstr(s,"FOV (ap,fh,rl) [mm]"))
        {
          p=s+strcspn(s,"0123456789");
          sscanf(p,"%f %f %f", &thickness[0], &thickness[1], &thickness[2]);
        }
        else
        if(strstr(s,"Slice thickness [mm]"))
        {
          p=s+strcspn(s,"0123456789");
          sscanf(p,"%f", &sliceThickness);
        }
        else
        if(strstr(s,"Slice gap [mm]"))
        {
          p=s+strcspn(s,"-0123456789");
          sscanf(p,"%f", &sliceGap);
        }
      }
      fclose(f);

//C:\home\ivo\data\coronaries\ucsf-wholeheart-2.par
      sliceSpacing = sliceThickness+sliceGap;
      if((dimension>0) && (dimensions[0]>0) && (dimensions[1]>0) && (sliceThickness>0) && (sliceSpacing>0))
      {
        headerRead = true;
        if(fabs(thickness[0]/dimensions[2]-sliceSpacing)<0.0001)
          thickness[0]=thickness[1];
        else
        if(fabs(thickness[1]/dimensions[2]-sliceSpacing)<0.0001)
          thickness[1]=thickness[0];
        thickness[2]=sliceSpacing;

        thickness[0]/=dimensions[0];
        thickness[1]/=dimensions[1];
        spacing=thickness+gap;
      }
    }
    
    if( headerRead == false)
    {
      itk::ImageFileReaderException e(__FILE__, __LINE__);
      itk::OStringStream msg;
      msg << " Could not read file "
        << m_FileName.c_str();
      e.SetDescription(msg.str().c_str());
      throw e;
      return;
    }
    
    output->Initialize(type, dimension, dimensions);
    output->GetSlicedGeometry()->SetSpacing(spacing);

    //output->GetSlicedGeometry()->SetGeometry2D(mitk::Image::BuildStandardPlaneGeometry2D(output->GetSlicedGeometry(), dimensions).GetPointer(), 0);
    output->GetSlicedGeometry()->SetEvenlySpaced();
  }
  
  m_ReadHeaderTime.Modified();
}

virtual const char* mitk::ParRecFileReader::GetClassName ( ) const [virtual]

virtual const char* mitk::ParRecFileReader::GetFileName ( ) const [virtual]

Get the specified the file to load.

Either the FileName or FilePrefix plus FilePattern are used to read.

Implements mitk::FileReader.

virtual const char* mitk::ParRecFileReader::GetFilePattern ( ) const [virtual]

Get the specified file pattern for the file(s) to load. The sprintf format used to build filename from FilePrefix and number.

You should specify either a FileName or FilePrefix. Use FilePrefix if the data is stored in multiple files.

Implements mitk::FileReader.

virtual const char* mitk::ParRecFileReader::GetFilePrefix ( ) const [virtual]

Get the specified file prefix for the file(s) to load.

You should specify either a FileName or FilePrefix. Use FilePrefix if the data is stored in multiple files.

Implements mitk::FileReader.

static Pointer mitk::ParRecFileReader::New ( ) [static]

Method for creation through the object factory.

Reimplemented from mitk::ImageSource.

virtual void mitk::ParRecFileReader::SetFileName ( const char * aFileName ) [virtual]

Specify the file to load.

Either the FileName or FilePrefix plus FilePattern are used to read.

Implements mitk::FileReader.

virtual void mitk::ParRecFileReader::SetFilePattern ( const char * aFilePattern ) [virtual]

Specified file pattern for the file(s) to load. The sprintf format used to build filename from FilePrefix and number.

You should specify either a FileName or FilePrefix. Use FilePrefix if the data is stored in multiple files.

Implements mitk::FileReader.

virtual void mitk::ParRecFileReader::SetFilePrefix ( const char * aFilePrefix ) [virtual]

Specify file prefix for the file(s) to load.

You should specify either a FileName or FilePrefix. Use FilePrefix if the data is stored in multiple files.

Implements mitk::FileReader.

Member Data Documentation

std::string mitk::ParRecFileReader::m_FileName [protected]

Definition at line 65 of file mitkParRecFileReader.h.

Referenced by GenerateOutputInformation().

std::string mitk::ParRecFileReader::m_FilePattern [protected]

Definition at line 70 of file mitkParRecFileReader.h.

std::string mitk::ParRecFileReader::m_FilePrefix [protected]

Definition at line 68 of file mitkParRecFileReader.h.

Referenced by GenerateOutputInformation().

itk::TimeStamp mitk::ParRecFileReader::m_ReadHeaderTime [protected]

Definition at line 61 of file mitkParRecFileReader.h.

Referenced by GenerateOutputInformation().

std::string mitk::ParRecFileReader::m_RecFileName [protected]

Definition at line 66 of file mitkParRecFileReader.h.

Referenced by GenerateOutputInformation().

int mitk::ParRecFileReader::m_StartFileIndex [protected]

Definition at line 63 of file mitkParRecFileReader.h.

The documentation for this class was generated from the following files:

mitk::ParRecFileReader Class Reference [IO Classes]

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

mitk::ParRecFileReader Class Reference
[IO Classes]