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vtkITKArchetypeImageSeriesReader.cxx
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vtkITKArchetypeImageSeriesReader.cxx
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/*=========================================================================
Copyright Brigham and Women's Hospital (BWH) All Rights Reserved.
See COPYRIGHT.txt
or http://www.slicer.org/copyright/copyright.txt for details.
Program: vtkITK
Module: $HeadURL$
Date: $Date$
Version: $Revision$
==========================================================================*/
// VTKITK includes
#include "vtkITKArchetypeImageSeriesReader.h"
#include "vtkITKImageWriter.h"
// VTK includes
#include <vtkDataArray.h>
#include <vtkErrorCode.h>
#include <vtkImageData.h>
#include <vtkMath.h>
#include <vtkMatrix4x4.h>
#include <vtkInformation.h>
#include <vtkInformationVector.h>
#include <vtkNew.h>
#include <vtkObjectFactory.h>
#include <vtkPointData.h>
#include <vtkStreamingDemandDrivenPipeline.h>
// ITK includes
#include <itkNiftiImageIO.h>
#include <itkNrrdImageIO.h>
#include <itkMetaDataDictionary.h>
#include <itkMetaDataObjectBase.h>
#include <itkMetaDataObject.h>
#include <itkMetaImageIO.h>
#include <itkTimeProbe.h>
// STD includes
#include <algorithm>
#include <vector>
#include "itkArchetypeSeriesFileNames.h"
#include "itkOrientImageFilter.h"
#include "itkImageSeriesReader.h"
#ifdef VTKITK_BUILD_DICOM_SUPPORT
#include "itkDCMTKImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkGDCMImageIO.h"
#endif
vtkStandardNewMacro(vtkITKArchetypeImageSeriesReader);
//----------------------------------------------------------------------------
vtkITKArchetypeImageSeriesReader::vtkITKArchetypeImageSeriesReader()
{
this->Archetype = nullptr;
this->IndexArchetype = 0;
this->SingleFile = 1;
this->UseOrientationFromFile = 1;
this->RasToIjkMatrix = nullptr;
this->MeasurementFrameMatrix = vtkMatrix4x4::New();
this->MeasurementFrameMatrix->Identity();
this->SetDesiredCoordinateOrientationToAxial();
this->UseNativeCoordinateOrientation = 0;
this->FileNameSliceOffset = 0;
this->FileNameSliceSpacing = 1;
this->FileNameSliceCount = 0;
this->UseNativeOrigin = true;
#ifdef VTKITK_BUILD_DICOM_SUPPORT
this->DICOMImageIOApproach = vtkITKArchetypeImageSeriesReader::GDCM;
#endif
this->OutputScalarType = VTK_FLOAT;
this->NumberOfComponents = 0;
this->UseNativeScalarType = 0;
for (int i = 0; i < 3; i++)
{
this->DefaultDataSpacing[i] = 1.0;
this->DefaultDataOrigin[i] = 0.0;
}
this->SeriesInstanceUIDs.resize( 0 );
this->ContentTime.resize( 0 );
this->TriggerTime.resize( 0 );
this->EchoNumbers.resize( 0 );
this->DiffusionGradientOrientation.resize( 0 );
this->SliceLocation.resize( 0 );
this->ImageOrientationPatient.resize( 0 );
this->AnalyzeHeader = true;
this->GroupingByTags = false;
this->IsOnlyFile = false;
this->ArchetypeIsDICOM = false;
this->SelectedUID = -1;
this->SelectedContentTime = -1;
this->SelectedTriggerTime = -1;
this->SelectedEchoNumbers = -1;
this->SelectedDiffusion = -1;
this->SelectedSlice = -1;
this->SelectedOrientation = -1;
this->SetNumberOfInputPorts(0);
this->SetNumberOfOutputPorts(1);
this->VoxelVectorType = vtkITKImageWriter::VoxelVectorTypeUndefined;
}
//----------------------------------------------------------------------------
vtkITKArchetypeImageSeriesReader::~vtkITKArchetypeImageSeriesReader()
{
if (this->Archetype)
{
delete [] this->Archetype;
this->Archetype = nullptr;
}
if (RasToIjkMatrix)
{
this->RasToIjkMatrix->Delete();
this->RasToIjkMatrix = nullptr;
}
if (MeasurementFrameMatrix)
{
MeasurementFrameMatrix->Delete();
MeasurementFrameMatrix = nullptr;
}
}
//----------------------------------------------------------------------------
vtkMatrix4x4* vtkITKArchetypeImageSeriesReader::GetRasToIjkMatrix()
{
this->UpdateInformation();
return this->RasToIjkMatrix;
}
//----------------------------------------------------------------------------
vtkMatrix4x4* vtkITKArchetypeImageSeriesReader::GetMeasurementFrameMatrix()
{
this->UpdateInformation();
return MeasurementFrameMatrix;
}
//----------------------------------------------------------------------------
void vtkITKArchetypeImageSeriesReader::PrintSelf(ostream& os, vtkIndent indent)
{
int idx;
this->Superclass::PrintSelf(os,indent);
os << indent << "Archetype: " <<
(this->Archetype ? this->Archetype : "(none)") << "\n";
os << indent << "FileNameSliceOffset: "
<< this->FileNameSliceOffset << "\n";
os << indent << "FileNameSliceSpacing: "
<< this->FileNameSliceSpacing << "\n";
os << indent << "FileNameSliceCount: "
<< this->FileNameSliceCount << "\n";
os << indent << "OutputScalarType: "
<< vtkImageScalarTypeNameMacro(this->OutputScalarType)
<< std::endl;
os << indent << "DefaultDataSpacing: (" << this->DefaultDataSpacing[0];
for (idx = 1; idx < 3; ++idx)
{
os << ", " << this->DefaultDataSpacing[idx];
}
os << ")\n";
os << indent << "DefaultDataOrigin: (" << this->DefaultDataOrigin[0];
for (idx = 1; idx < 3; ++idx)
{
os << ", " << this->DefaultDataOrigin[idx];
}
os << ")\n";
#ifdef VTKITK_BUILD_DICOM_SUPPORT
os << indent << "DICOMImageIOApproach: " << this->GetDICOMImageIOApproach();
#else
os << indent << "DICOMImageIOApproach: " << "NA";
#endif
}
//----------------------------------------------------------------------------
int vtkITKArchetypeImageSeriesReader::CanReadFile(const char* filename)
{
if (!filename)
{
return false;
}
itk::ImageIOBase::Pointer imageIO = this->GetImageIO(filename);
if (imageIO == nullptr)
{
return false;
}
return true;
}
//----------------------------------------------------------------------------
itk::ImageIOBase::Pointer vtkITKArchetypeImageSeriesReader::GetImageIO(const char* filename)
{
if (filename == nullptr)
{
return nullptr;
}
std::string fileNameCollapsed = itksys::SystemTools::CollapseFullPath(filename);
// First see if the archetype exists
if (!itksys::SystemTools::FileExists(fileNameCollapsed.c_str()))
{
vtkDebugMacro(<<"The filename does not exist.");
return nullptr;
}
// Reduce the selection of filenames
if (this->IsOnlyFile || this->SingleFile)
{
this->FileNames.resize(0);
this->FileNames.emplace_back(filename);
}
else
{
if (!GroupingByTags)
{
AssembleVolumeContainingArchetype();
}
else
{
GroupFiles(SelectedUID,
SelectedContentTime,
SelectedTriggerTime,
SelectedEchoNumbers,
SelectedDiffusion,
SelectedSlice,
SelectedOrientation);
}
}
#ifdef VTKITK_BUILD_DICOM_SUPPORT
itk::ImageIOBase::Pointer dicomIO;
#endif
typedef itk::Image<float, 3> ImageType;
itk::ImageIOBase::Pointer imageIO = nullptr;
try
{
// Some file types require special processing
#ifdef VTKITK_BUILD_DICOM_SUPPORT
if (this->GetDICOMImageIOApproach() == vtkITKArchetypeImageSeriesReader::DCMTK)
{
dicomIO = itk::DCMTKImageIO::New();
}
else
{
dicomIO = itk::GDCMImageIO::New();
}
// Test whether the input file is a DICOM file
this->ArchetypeIsDICOM = dicomIO->CanReadFile(filename);
#endif
if (this->FileNames.size() == 0)
{
vtkErrorMacro( "vtkITKArchetypeImageSeriesReader::ExecuteInformation: Files not found!");
this->SetErrorCode(vtkErrorCode::FileNotFoundError);
return nullptr;
}
else if (this->FileNames.size() == 1) // If there is only one file in the series, just use an image file reader
{
itk::ImageFileReader<ImageType>::Pointer imageReader =
itk::ImageFileReader<ImageType>::New();
imageReader->SetFileName(this->FileNames[0].c_str());
#ifdef VTKITK_BUILD_DICOM_SUPPORT
if (this->ArchetypeIsDICOM)
{
imageReader->SetImageIO(dicomIO);
}
#endif
imageReader->UpdateOutputInformation();
imageIO = imageReader->GetImageIO();
if (imageIO.GetPointer() == nullptr)
{
vtkErrorMacro( "vtkITKArchetypeImageSeriesReader::ExecuteInformation: ImageIO for file " << fileNameCollapsed.c_str() << " does not exist.");
this->SetErrorCode(vtkErrorCode::UnrecognizedFileTypeError);
return nullptr;
}
}
else
{
//
// more than one file, use series reader
//
itk::ImageSeriesReader<ImageType>::Pointer seriesReader =
itk::ImageSeriesReader<ImageType>::New();
seriesReader->SetFileNames(this->FileNames);
#ifdef VTKITK_BUILD_DICOM_SUPPORT
if (this->ArchetypeIsDICOM)
{
seriesReader->SetImageIO(dicomIO);
}
else
#endif
{
itk::ImageFileReader<ImageType>::Pointer imageReader =
itk::ImageFileReader<ImageType>::New();
imageReader->SetFileName(this->FileNames[0].c_str());
imageReader->UpdateOutputInformation();
imageIO = imageReader->GetImageIO();
seriesReader->SetImageIO(imageIO);
}
seriesReader->UpdateOutputInformation();
imageIO = seriesReader->GetImageIO();
}
}
catch (itk::ExceptionObject& e)
{
vtkDebugMacro( "vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open " << fileNameCollapsed.c_str() << ". "
<< "ITK exception info: error in " << e.GetLocation() << ": "<< e.GetDescription());
this->SetErrorCode(vtkErrorCode::FileFormatError);
return nullptr;
}
catch (const std::string& err)
{
// GDCM can throw std::string exception if some verification fail
vtkDebugMacro("vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open " << fileNameCollapsed.c_str() << ". "
<< "Error: " << err);
this->SetErrorCode(vtkErrorCode::FileFormatError);
return nullptr;
}
return imageIO;
}
//----------------------------------------------------------------------------
// This method returns the largest data that can be generated.
int vtkITKArchetypeImageSeriesReader::RequestInformation(
vtkInformation * vtkNotUsed(request),
vtkInformationVector **vtkNotUsed(inputVector),
vtkInformationVector *outputVector)
{
// get the info objects
vtkInformation* outInfo = outputVector->GetInformationObject(0);
std::vector<std::string> candidateFiles;
std::vector<std::string> candidateSeries;
int extent[6];
std::string fileNameCollapsed = itksys::SystemTools::CollapseFullPath( this->Archetype);
if ( this->SingleFile )
{
this->AnalyzeHeader = false;
}
// Since we only need origin, spacing and extents, we can use one
// image type.
typedef itk::Image<float,3> ImageType;
itk::ImageRegion<3> region;
typedef itk::ImageSource<ImageType> FilterType;
FilterType::Pointer filter;
// First see if the archetype exists, if it's not a pointer into memory
if (fileNameCollapsed.find("slicer:") != std::string::npos &&
fileNameCollapsed.find("#") != std::string::npos)
{
vtkDebugMacro("File " << fileNameCollapsed.c_str() << " is a pointer to the mrml scene in memory, not checking for it on disk");
}
else
{
if (!itksys::SystemTools::FileExists (fileNameCollapsed.c_str()))
{
vtkErrorMacro( "vtkITKArchetypeImageSeriesReader::ExecuteInformation: Archetype file " << fileNameCollapsed.c_str() << " does not exist.");
this->SetErrorCode(vtkErrorCode::FileNotFoundError);
return 0;
}
}
this->AllFileNames.resize( 0 );
// the code in this try/catch block uses ITK dicom code to evaluate
// the files to see if they will be readable. Some forms of dicom will
// trigger exceptions which ultimately mean that the file isn't
// going to be readable
try
{
// if user already set up FileNames, we do not try to find candidate files
if ( this->GetNumberOfFileNames() > 0 )
{
unsigned int nFiles = this->GetNumberOfFileNames();
this->AllFileNames.resize( 0 );
for (unsigned int k = 0; k < nFiles; k++)
{
this->AllFileNames.push_back( this->FileNames[k] );
}
this->FileNames.resize( 0 );
// if this is the only file set by user
if (nFiles == 1)
{
this->IsOnlyFile = true;
}
// if we need to analyze the header
if ( this->AnalyzeHeader )
{
this->AnalyzeDicomHeaders();
}
}
else
{
#ifdef VTKITK_BUILD_DICOM_SUPPORT
if ( this->ArchetypeIsDICOM && !this->GetSingleFile() )
{
typedef itk::GDCMSeriesFileNames DICOMNameGeneratorType;
DICOMNameGeneratorType::Pointer inputImageFileGenerator = DICOMNameGeneratorType::New();
std::string fileNamePath = itksys::SystemTools::GetFilenamePath( this->Archetype );
if (fileNamePath == "")
{
fileNamePath = ".";
}
inputImageFileGenerator->SetDirectory( fileNamePath );
// determine if the file is diffusion weighted MR file
// Find the series that contains the archetype
candidateSeries = inputImageFileGenerator->GetSeriesUIDs();
// Find all dicom files in the directory
for (unsigned int s = 0; s < candidateSeries.size(); s++)
{
std::vector<std::string> seriesFileNames;
seriesFileNames = inputImageFileGenerator->GetFileNames( candidateSeries[s] );
for (unsigned int f = 0; f < seriesFileNames.size(); f++)
{
this->AllFileNames.push_back( seriesFileNames[f] );
}
}
//int nFiles = this->AllFileNames.size(); UNUSED
// analysis dicom files and fill the Dicom Tag arrays
if ( this->AnalyzeHeader )
{
this->AnalyzeDicomHeaders();
}
// the following for loop set up candidate files with same series number
// that include the given Archetype;
int found = 0;
for (unsigned int s = 0; s < candidateSeries.size() && found == 0; s++)
{
candidateFiles = inputImageFileGenerator->GetFileNames(candidateSeries[s]);
for (unsigned int f = 0; f < candidateFiles.size(); f++)
{
if (itksys::SystemTools::CollapseFullPath(candidateFiles[f].c_str()) ==
fileNameCollapsed)
{
found = 1;
break;
}
}
}
// do we have just one candidate file
if ( candidateFiles.size() == 1 )
{
this->IsOnlyFile = true;
}
}
else
#endif
if( !this->GetSingleFile() )
{ // not dicom
// check the dimensions of the archetype - if there
// is more then one slice, use only the archetype
// but if it is a single slice, try to generate a
// series of filenames
itk::ImageFileReader<ImageType>::Pointer imageReader =
itk::ImageFileReader<ImageType>::New();
imageReader->SetFileName(this->Archetype);
imageReader->UpdateOutputInformation();
region = imageReader->GetOutput()->GetLargestPossibleRegion();
if ( region.GetSize()[2] > 1 )
{
candidateFiles.emplace_back(this->Archetype);
this->AllFileNames.emplace_back(this->Archetype);
this->IsOnlyFile = true;
}
else
{
// Generate filenames from the Archetype
itk::ArchetypeSeriesFileNames::Pointer fit = itk::ArchetypeSeriesFileNames::New();
fit->SetArchetype (this->Archetype);
candidateFiles = fit->GetFileNames();
this->AllFileNames.resize( candidateFiles.size() );
for (int f = 0; f < (int)(candidateFiles.size()); f ++)
{
this->AllFileNames[f] = candidateFiles[f];
}
if ( candidateFiles.size() == 1 )
{
this->IsOnlyFile = true;
}
else if ( AnalyzeHeader )
{
this->AnalyzeDicomHeaders();
}
}
}
else
{
this->AllFileNames.emplace_back(this->Archetype);
this->IsOnlyFile = true;
}
}
}
catch (itk::ExceptionObject& e)
{
vtkErrorMacro( "vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open " << fileNameCollapsed.c_str() << ". "
<< "ITK exception info: error in " << e.GetLocation() << ": "<< e.GetDescription());
this->SetErrorCode(vtkErrorCode::FileFormatError);
return 0;
}
catch (const std::string& err)
{
// GDCM can throw std::string exception if some verification fail
vtkErrorMacro( "vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open " << fileNameCollapsed.c_str() << ". "
<< "Error: " << err);
this->SetErrorCode(vtkErrorCode::FileFormatError);
return 0;
}
// figure out the index of Archetype in AllFileNames
// Collapsing of path is necessary to normalize filenames (path separator, capitalization of drive
// letter and path) for comparison.
std::string archetypeCollapsed = itksys::SystemTools::CollapseFullPath(this->Archetype);
for (unsigned int k = 0; k < this->AllFileNames.size(); k++)
{
if (itksys::SystemTools::CollapseFullPath(this->AllFileNames[k]) == archetypeCollapsed)
{
this->IndexArchetype = k;
break;
}
}
// Reduce the selection of filenames
if ( this->IsOnlyFile || this->SingleFile )
{
this->FileNames.resize( 0 );
this->FileNames.emplace_back(this->Archetype);
}
else
{
if ( !GroupingByTags )
{
AssembleVolumeContainingArchetype();
}
else
{
GroupFiles( SelectedUID,
SelectedContentTime,
SelectedTriggerTime,
SelectedEchoNumbers,
SelectedDiffusion,
SelectedSlice,
SelectedOrientation );
}
}
if (RasToIjkMatrix)
{
this->RasToIjkMatrix->Delete();
}
this->RasToIjkMatrix = vtkMatrix4x4::New();
vtkNew<vtkMatrix4x4> IjkToLpsMatrix;
this->RasToIjkMatrix->Identity();
IjkToLpsMatrix->Identity();
double spacing[3];
double origin[3];
itk::ImageIOBase::Pointer imageIO = this->GetImageIO(this->Archetype);
try
{
if (this->FileNames.size() == 0)
{
vtkErrorMacro( "vtkITKArchetypeImageSeriesReader::ExecuteInformation: Failed to read file series");
this->SetErrorCode(vtkErrorCode::FileNotFoundError);
return 0;
}
else if (this->FileNames.size() == 1) // If there is only one file in the series, just use an image file reader
{
itk::OrientImageFilter<ImageType,ImageType>::Pointer orient =
itk::OrientImageFilter<ImageType,ImageType>::New();
itk::ImageFileReader<ImageType>::Pointer imageReader =
itk::ImageFileReader<ImageType>::New();
imageReader->SetFileName(this->FileNames[0].c_str());
imageReader->SetImageIO(imageIO);
if (this->UseNativeCoordinateOrientation)
{
imageReader->UpdateOutputInformation();
filter = imageReader;
}
else
{
orient->SetInput(imageReader->GetOutput());
orient->UseImageDirectionOn();
orient->SetDesiredCoordinateOrientation(this->DesiredCoordinateOrientation);
orient->UpdateOutputInformation();
filter = orient;
}
for (int i = 0; i < 3; i++)
{
spacing[i] = filter->GetOutput()->GetSpacing()[i];
origin[i] = filter->GetOutput()->GetOrigin()[i];
// Get IJK to RAS direction vector
for ( unsigned int j=0; j < filter->GetOutput()->GetImageDimension (); j++ )
{
IjkToLpsMatrix->SetElement(j, i, spacing[i]*filter->GetOutput()->GetDirection()[j][i]);
}
}
region = filter->GetOutput()->GetLargestPossibleRegion();
extent[0] = region.GetIndex()[0];
extent[1] = region.GetIndex()[0] + region.GetSize()[0] - 1;
extent[2] = region.GetIndex()[1];
extent[3] = region.GetIndex()[1] + region.GetSize()[1] - 1;
extent[4] = region.GetIndex()[2];
extent[5] = region.GetIndex()[2] + region.GetSize()[2] - 1;
typedef std::vector<std::vector<double> > DoubleVectorType;
typedef itk::MetaDataObject<DoubleVectorType> MetaDataDoubleVectorType;
const itk::MetaDataDictionary & dictionary = imageReader->GetMetaDataDictionary();
itk::MetaDataDictionary::ConstIterator itr = dictionary.Begin();
itk::MetaDataDictionary::ConstIterator end = dictionary.End();
while( itr != end )
{
itk::MetaDataObjectBase::Pointer entry = itr->second;
MetaDataDoubleVectorType::Pointer entryvalue1
= dynamic_cast<MetaDataDoubleVectorType *>( entry.GetPointer() );
if( entryvalue1 )
{
int pos = itr->first.find( "NRRD_measurement frame" );
if( pos != -1 )
{
DoubleVectorType tagvalue = entryvalue1->GetMetaDataObjectValue();
for( int i = 0; i < 3; i++ )
{
for( int j = 0; j < 3; j++ )
{
this->MeasurementFrameMatrix->SetElement(i,j, tagvalue.at( j ).at( i ));
}
}
}
}
++itr;
}
imageIO = imageReader->GetImageIO();
if (imageIO.GetPointer() == nullptr)
{
vtkErrorMacro( "vtkITKArchetypeImageSeriesReader::ExecuteInformation: ImageIO for file " << fileNameCollapsed.c_str() << " does not exist.");
this->SetErrorCode(vtkErrorCode::UnrecognizedFileTypeError);
return 0;
}
}
else
{
//
// more than one file, use series reader
//
itk::OrientImageFilter<ImageType,ImageType>::Pointer orient =
itk::OrientImageFilter<ImageType,ImageType>::New();
itk::ImageSeriesReader<ImageType>::Pointer seriesReader =
itk::ImageSeriesReader<ImageType>::New();
seriesReader->SetFileNames(this->FileNames);
seriesReader->SetImageIO(imageIO);
if (this->UseNativeCoordinateOrientation)
{
filter = seriesReader;
}
else
{
orient->SetInput(seriesReader->GetOutput());
orient->UseImageDirectionOn();
orient->SetDesiredCoordinateOrientation(this->DesiredCoordinateOrientation);
filter = orient;
}
filter->UpdateOutputInformation();
for (int i = 0; i < 3; i++)
{
spacing[i] = filter->GetOutput()->GetSpacing()[i];
origin[i] = filter->GetOutput()->GetOrigin()[i];
// Get IJK to RAS direction vector
for ( unsigned int j=0; j < filter->GetOutput()->GetImageDimension (); j++ )
{
IjkToLpsMatrix->SetElement(j, i, spacing[i]*filter->GetOutput()->GetDirection()[j][i]);
}
}
region = filter->GetOutput()->GetLargestPossibleRegion();
extent[0] = region.GetIndex()[0];
extent[1] = region.GetIndex()[0] + region.GetSize()[0] - 1;
extent[2] = region.GetIndex()[1];
extent[3] = region.GetIndex()[1] + region.GetSize()[1] - 1;
extent[4] = region.GetIndex()[2];
extent[5] = region.GetIndex()[2] + region.GetSize()[2] - 1;
imageIO = seriesReader->GetImageIO();
}
}
catch (itk::ExceptionObject& e)
{
vtkErrorMacro( "vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open " << fileNameCollapsed.c_str() << ". "
<< "ITK exception info: error in " << e.GetLocation() << ": "<< e.GetDescription());
this->SetErrorCode(vtkErrorCode::FileFormatError);
return 0;
}
// Transform from LPS to RAS
vtkMatrix4x4* LpsToRasMatrix = vtkMatrix4x4::New();
LpsToRasMatrix->Identity();
LpsToRasMatrix->SetElement(0,0,-1);
LpsToRasMatrix->SetElement(1,1,-1);
vtkMatrix4x4* LPSMeasurementFrameMatrix = vtkMatrix4x4::New();
LPSMeasurementFrameMatrix->DeepCopy(this->MeasurementFrameMatrix);
vtkMatrix4x4::Multiply4x4(LpsToRasMatrix, IjkToLpsMatrix, this->RasToIjkMatrix);
vtkMatrix4x4::Multiply4x4(LpsToRasMatrix, LPSMeasurementFrameMatrix, this->MeasurementFrameMatrix);
LpsToRasMatrix->Delete();
LPSMeasurementFrameMatrix->Delete();
// If it looks like the pipeline did not provide the spacing and
// origin, modify the spacing and origin with the defaults
for (int j = 0; j < 3; j++)
{
if (spacing[j] == 1.0)
{
spacing[j] = this->DefaultDataSpacing[j];
}
if (origin[j] == 0.0)
{
origin[j] = this->DefaultDataOrigin[j];
}
}
origin[0] *= -1; // L -> R
origin[1] *= -1; // P -> A
if (this->UseNativeOrigin)
{
for (int j = 0; j < 3; j++)
{
this->RasToIjkMatrix->SetElement(j, 3, origin[j]);
}
this->RasToIjkMatrix->Invert();
}
else
{
this->RasToIjkMatrix->Invert();
for (int j = 0; j < 3; j++)
{
this->RasToIjkMatrix->SetElement(j, 3, (extent[2*j+1] - extent[2*j])/2.0);
}
}
outInfo->Set(vtkDataObject::SPACING(), spacing, 3);
outInfo->Set(vtkDataObject::ORIGIN(), origin, 3);
// TODO: this may corrupt the slice spacig in multiframe DICOM files,
// so probably it would be better to remove it.
this->RasToIjkMatrix->SetElement(3,3,1.0);
if ( !this->GetUseOrientationFromFile() )
{
this->RasToIjkMatrix->Identity();
for ( unsigned int j=0; j < 3; j++ )
{
this->RasToIjkMatrix->SetElement(j, j, 1.0/spacing[j]);
}
}
outInfo->Set(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT(), extent, 6);
int scalarType = this->OutputScalarType;
try
{
if (this->UseNativeScalarType)
{
// If there is only one file in the series
if (this->FileNames.size() == 1)
{
if (imageIO.GetPointer() == nullptr)
{
scalarType = VTK_SHORT; // TODO - figure out why multi-file series doesn't have an imageIO
}
else if (imageIO->GetComponentType() == itk::ImageIOBase::UCHAR)
{
scalarType = VTK_UNSIGNED_CHAR;
}
else if (imageIO->GetComponentType() == itk::ImageIOBase::CHAR)
{
scalarType = VTK_CHAR;
}
else if (imageIO->GetComponentType() == itk::ImageIOBase::USHORT)
{
scalarType = VTK_UNSIGNED_SHORT;
}
else if (imageIO->GetComponentType() == itk::ImageIOBase::SHORT)
{
scalarType = VTK_SHORT;
}
else if (imageIO->GetComponentType() == itk::ImageIOBase::UINT)
{
scalarType = VTK_UNSIGNED_INT;
}
else if (imageIO->GetComponentType() == itk::ImageIOBase::INT)
{
scalarType = VTK_INT;
}
else if (imageIO->GetComponentType() == itk::ImageIOBase::ULONG)
{
scalarType = VTK_UNSIGNED_LONG;
}
else if (imageIO->GetComponentType() == itk::ImageIOBase::LONG)
{
scalarType = VTK_LONG;
}
else if (imageIO->GetComponentType() == itk::ImageIOBase::FLOAT)
{
scalarType = VTK_FLOAT;
}
else if (imageIO->GetComponentType() == itk::ImageIOBase::DOUBLE)
{
scalarType = VTK_DOUBLE;
}
}
else
{
double min = 0, max = 0;
for( unsigned int f = 0; f < this->FileNames.size(); f++ )
{
imageIO->SetFileName( this->FileNames[f] );
imageIO->ReadImageInformation();
if ( imageIO->GetComponentType() == itk::ImageIOBase::UCHAR )
{
min = std::numeric_limits<uint8_t>::min() < min ? std::numeric_limits<uint8_t>::min() : min;
max = std::numeric_limits<uint8_t>::max() > max ? std::numeric_limits<uint8_t>::max() : max;
}
if ( imageIO->GetComponentType() == itk::ImageIOBase::CHAR )
{
min = std::numeric_limits<int8_t>::min() < min ? std::numeric_limits<int8_t>::min() : min;
max = std::numeric_limits<int8_t>::max() > max ? std::numeric_limits<int8_t>::max() : max;
}
if ( imageIO->GetComponentType() == itk::ImageIOBase::USHORT )
{
min = std::numeric_limits<uint16_t>::min() < min ? std::numeric_limits<uint16_t>::min() : min;
max = std::numeric_limits<uint16_t>::max() > max ? std::numeric_limits<uint16_t>::max() : max;
}
if ( imageIO->GetComponentType() == itk::ImageIOBase::SHORT )
{
min = std::numeric_limits<int16_t>::min() < min ? std::numeric_limits<int16_t>::min() : min;
max = std::numeric_limits<int16_t>::max() > max ? std::numeric_limits<int16_t>::max() : max;
}
if ( imageIO->GetComponentType() == itk::ImageIOBase::UINT )
{
min = std::numeric_limits<uint32_t>::min() < min ? std::numeric_limits<uint32_t>::min() : min;
max = std::numeric_limits<uint32_t>::max() > max ? std::numeric_limits<uint32_t>::max() : max;
}
if ( imageIO->GetComponentType() == itk::ImageIOBase::INT )
{
min = static_cast<double>(std::numeric_limits<int32_t>::min() < min ? std::numeric_limits<int32_t>::min() : min);
max = static_cast<double>(std::numeric_limits<int32_t>::max() > max ? std::numeric_limits<int32_t>::max() : max);
}
if ( imageIO->GetComponentType() == itk::ImageIOBase::ULONG )
{ // note that on windows ULONG is only 32 bit
min = static_cast<double>(std::numeric_limits<uint64_t>::min() < min ? std::numeric_limits<uint64_t>::min() : min);
max = static_cast<double>(std::numeric_limits<uint64_t>::max() > max ? std::numeric_limits<uint64_t>::max() : max);
}
if ( imageIO->GetComponentType() == itk::ImageIOBase::LONG )
{ // note that on windows LONG is only 32 bit
min = static_cast<double>(std::numeric_limits<int64_t>::min() < min ? std::numeric_limits<int64_t>::min() : min);
max = static_cast<double>(std::numeric_limits<int64_t>::max() > max ? std::numeric_limits<int64_t>::max() : max);
}
if ( imageIO->GetComponentType() == itk::ImageIOBase::FLOAT )
{
// use -max() as min() for both float and double as temp workaround
// should switch to lowest() function in C++ 11 in the future
min = -std::numeric_limits<float>::max() < min ? -std::numeric_limits<float>::max() : min;
max = std::numeric_limits<float>::max() > max ? std::numeric_limits<float>::max() : max;
}
if ( imageIO->GetComponentType() == itk::ImageIOBase::DOUBLE )
{
min = -std::numeric_limits<double>::max() < min ? -std::numeric_limits<double>::max() : min;
max = std::numeric_limits<double>::max() > max ? std::numeric_limits<double>::max() : max;
}
}
if (!(min <= max))
{
throw std::string("Invalid voxel value range");
}
if( min >= 0 ) // unsigned
{
if( max <= std::numeric_limits<uint8_t>::max() )
{
scalarType = VTK_UNSIGNED_CHAR;
}
else if( max <= std::numeric_limits<uint16_t>::max() )
{
scalarType = VTK_UNSIGNED_SHORT;
}
else if( max <= std::numeric_limits<uint32_t>::max() )
{
scalarType = VTK_UNSIGNED_INT;
}
else if( max <= static_cast<double>(std::numeric_limits<uint64_t>::max()) )
{
scalarType = VTK_UNSIGNED_LONG;
}
else if( max <= std::numeric_limits<float>::max() )
{
scalarType = VTK_FLOAT;
}
else if( max <= std::numeric_limits<double>::max() )
{
scalarType = VTK_DOUBLE;
}
else
{
throw std::string("Cannot find suitable scalar type for value range");
}
}
else
{
if( max <= std::numeric_limits<int8_t>::max()
&& min >= std::numeric_limits<int8_t>::min() )
{
scalarType = VTK_CHAR;
}
else if( max <= std::numeric_limits<int16_t>::max()
&& min >= std::numeric_limits<int16_t>::min() )
{
scalarType = VTK_SHORT;
}
else if( max <= std::numeric_limits<int32_t>::max()
&& min >= std::numeric_limits<int32_t>::min() )
{
scalarType = VTK_INT;
}
else if( max <= std::numeric_limits<int64_t>::max()
&& min >= std::numeric_limits<int64_t>::min() )
{
scalarType = VTK_LONG;
}
else if ( max <= std::numeric_limits<float>::max()
&& min >= -std::numeric_limits<float>::max() )
{
scalarType = VTK_FLOAT;
}
else if( max <= std::numeric_limits<double>::max()
&& min >= -std::numeric_limits<double>::max() )
{
scalarType = VTK_DOUBLE;
}
else
{
throw std::string("Cannot find suitable scalar type for value range");
}
}
}
}
}
catch (itk::ExceptionObject& e)
{
vtkErrorMacro( "vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open " << fileNameCollapsed.c_str() << ". "
<< "ITK exception info: error in " << e.GetLocation() << ": "<< e.GetDescription());
this->SetErrorCode(vtkErrorCode::FileFormatError);
return 0;
}
catch (const std::string& err)
{
// GDCM can throw std::string exception if some verification fail
vtkDebugMacro("vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open " << fileNameCollapsed.c_str() << ". "
<< "Error: " << err);
this->SetErrorCode(vtkErrorCode::FileFormatError);
return 0;
}
int numberOfComponents = 1;
if (imageIO.GetPointer() != nullptr)
{