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vtkMRMLVolumeSequenceStorageNode.cxx
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vtkMRMLVolumeSequenceStorageNode.cxx
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/*=auto=========================================================================
Portions (c) Copyright 2005 Brigham and Women's Hospital (BWH) All Rights Reserved.
See COPYRIGHT.txt
or http://www.slicer.org/copyright/copyright.txt for details.
=========================================================================auto=*/
#include <algorithm>
#include "vtkMRMLVolumeSequenceStorageNode.h"
#include "vtkMRMLScalarVolumeNode.h"
#include "vtkMRMLSequenceNode.h"
#include "vtkMRMLVectorVolumeNode.h"
#include "vtkSlicerVersionConfigure.h"
#if Slicer_VERSION_MAJOR > 4 || (Slicer_VERSION_MAJOR == 4 && Slicer_VERSION_MINOR >= 9)
#include "vtkTeemNRRDReader.h"
#include "vtkTeemNRRDWriter.h"
#else
#include "vtkNRRDReader.h"
#include "vtkNRRDWriter.h"
#endif
#include "vtkObjectFactory.h"
#include "vtkImageAppendComponents.h"
#include "vtkImageData.h"
#include "vtkImageExtractComponents.h"
#include "vtkNew.h"
#include "vtkStringArray.h"
//----------------------------------------------------------------------------
vtkMRMLNodeNewMacro(vtkMRMLVolumeSequenceStorageNode);
//----------------------------------------------------------------------------
vtkMRMLVolumeSequenceStorageNode::vtkMRMLVolumeSequenceStorageNode()
{
}
//----------------------------------------------------------------------------
vtkMRMLVolumeSequenceStorageNode::~vtkMRMLVolumeSequenceStorageNode()
{
}
//----------------------------------------------------------------------------
bool vtkMRMLVolumeSequenceStorageNode::CanReadInReferenceNode(vtkMRMLNode *refNode)
{
return refNode->IsA("vtkMRMLSequenceNode");
}
//----------------------------------------------------------------------------
int vtkMRMLVolumeSequenceStorageNode::ReadDataInternal(vtkMRMLNode* refNode)
{
if (!this->CanReadInReferenceNode(refNode))
{
return 0;
}
vtkMRMLSequenceNode* volSequenceNode = dynamic_cast<vtkMRMLSequenceNode*>(refNode);
if (!volSequenceNode)
{
vtkErrorMacro("ReadDataInternal: not a Sequence node.");
return 0;
}
std::string fullName = this->GetFullNameFromFileName();
if (fullName == std::string(""))
{
vtkErrorMacro("ReadData: File name not specified");
return 0;
}
#if Slicer_VERSION_MAJOR > 4 || (Slicer_VERSION_MAJOR == 4 && Slicer_VERSION_MINOR >= 9)
vtkNew<vtkTeemNRRDReader> reader;
#else
vtkNew<vtkNRRDReader> reader;
#endif
reader->SetFileName(fullName.c_str());
// Check if this is a NRRD file that we can read
if (!reader->CanReadFile(fullName.c_str()))
{
vtkDebugMacro("vtkMRMLVolumeSequenceStorageNode: This is not a nrrd file");
return 0;
}
// Set up reader
if (this->CenterImage)
{
reader->SetUseNativeOriginOff();
}
else
{
reader->SetUseNativeOriginOn();
}
// Read the header to see if the NRRD file corresponds to the
// MRML Node
reader->UpdateInformation();
// Read the volume
reader->Update();
// Read index information and custom attributes
std::vector< std::string > indexValues;
typedef std::vector<std::string> KeyVector;
KeyVector keys = reader->GetHeaderKeysVector();
for ( KeyVector::iterator kit = keys.begin(); kit != keys.end(); ++kit)
{
if (*kit == "axis 0 index type")
{
volSequenceNode->SetIndexTypeFromString(reader->GetHeaderValue((*kit).c_str()));
}
else if (*kit == "axis 0 index values")
{
std::string indexValue;
for (std::istringstream indexValueList(reader->GetHeaderValue((*kit).c_str()));
indexValueList >> indexValue;)
{
// Encode string to make sure there are no spaces in the serialized index value (space is used as separator)
indexValues.push_back(vtkMRMLNode::URLDecodeString(indexValue.c_str()));
}
}
else
{
volSequenceNode->SetAttribute((*kit).c_str(), reader->GetHeaderValue((*kit).c_str()));
}
}
const char* sequenceAxisLabel = reader->GetAxisLabel(0);
volSequenceNode->SetIndexName(sequenceAxisLabel ? sequenceAxisLabel : "frame");
const char* sequenceAxisUnit = reader->GetAxisUnit(0);
volSequenceNode->SetIndexUnit(sequenceAxisUnit ? sequenceAxisUnit : "");
// Copy image data to sequence of volume nodes
vtkImageData* imageData = reader->GetOutput();
if (imageData == NULL || imageData->GetPointData()==NULL || imageData->GetPointData()->GetScalars() == NULL)
{
vtkErrorMacro("vtkMRMLVolumeSequenceStorageNode::ReadDataInternal: invalid image data");
return 0;
}
int numberOfFrames = imageData->GetNumberOfScalarComponents();
vtkNew<vtkImageExtractComponents> extractComponents;
extractComponents->SetInputConnection(reader->GetOutputPort());
for (int frameIndex = 0; frameIndex<numberOfFrames; frameIndex++)
{
extractComponents->SetComponents(frameIndex);
extractComponents->Update();
vtkNew<vtkImageData> frameVoxels;
frameVoxels->DeepCopy(extractComponents->GetOutput());
// Slicer expects normalized image position and spacing
frameVoxels->SetSpacing( 1, 1, 1 );
frameVoxels->SetOrigin( 0, 0, 0 );
vtkNew<vtkMRMLScalarVolumeNode> frameVolume;
frameVolume->SetAndObserveImageData(frameVoxels.GetPointer());
frameVolume->SetRASToIJKMatrix(reader->GetRasToIjkMatrix());
std::ostringstream indexStr;
if (static_cast<int>(indexValues.size()) > frameIndex)
{
indexStr << indexValues[frameIndex] << std::ends;
}
else
{
indexStr << frameIndex << std::ends;
}
std::ostringstream nameStr;
nameStr << refNode->GetName() << "_" << std::setw(4) << std::setfill('0') << frameIndex << std::ends;
frameVolume->SetName( nameStr.str().c_str() );
volSequenceNode->SetDataNodeAtValue(frameVolume.GetPointer(), indexStr.str().c_str() );
}
// success
return 1;
}
//----------------------------------------------------------------------------
bool vtkMRMLVolumeSequenceStorageNode::CanWriteFromReferenceNode(vtkMRMLNode *refNode)
{
vtkMRMLSequenceNode* volSequenceNode = vtkMRMLSequenceNode::SafeDownCast(refNode);
if (volSequenceNode == NULL)
{
vtkDebugMacro("vtkMRMLVolumeSequenceStorageNode::CanWriteFromReferenceNode: invalid volSequenceNode");
return false;
}
if (volSequenceNode->GetNumberOfDataNodes() == 0)
{
vtkDebugMacro("vtkMRMLVolumeSequenceStorageNode::CanWriteFromReferenceNode: no data nodes");
return false;
}
vtkMRMLVolumeNode* firstFrameVolume = vtkMRMLVolumeNode::SafeDownCast(volSequenceNode->GetNthDataNode(0));
if (firstFrameVolume == NULL)
{
vtkDebugMacro("vtkMRMLVolumeSequenceStorageNode::CanWriteFromReferenceNode: only volume nodes can be written");
return false;
}
int firstFrameVolumeExtent[6] = { 0, -1, 0, -1, 0, -1 };
int firstFrameVolumeScalarType = VTK_VOID;
int firstFrameVolumeNumberOfComponents = 0;
if (firstFrameVolume->GetImageData())
{
firstFrameVolume->GetImageData()->GetExtent(firstFrameVolumeExtent);
firstFrameVolumeScalarType = firstFrameVolume->GetImageData()->GetScalarType();
firstFrameVolumeNumberOfComponents = firstFrameVolume->GetImageData()->GetNumberOfScalarComponents();
if (firstFrameVolumeNumberOfComponents != 1)
{
vtkDebugMacro("vtkMRMLVolumeSequenceStorageNode::CanWriteFromReferenceNode: only single scalar component volumes can be written by VTK NRRD writer");
return false;
}
}
int numberOfFrameVolumes = volSequenceNode->GetNumberOfDataNodes();
for (int frameIndex = 1; frameIndex<numberOfFrameVolumes; frameIndex++)
{
vtkMRMLVolumeNode* currentFrameVolume = vtkMRMLVolumeNode::SafeDownCast(volSequenceNode->GetNthDataNode(frameIndex));
if (currentFrameVolume == NULL)
{
vtkDebugMacro("vtkMRMLVolumeSequenceStorageNode::CanWriteFromReferenceNode: only volume nodes can be written (frame "<<frameIndex<<")");
return false;
}
vtkNew<vtkMatrix4x4> currentVolumeIjkToRas;
currentFrameVolume->GetIJKToRASMatrix(currentVolumeIjkToRas.GetPointer());
int currentFrameVolumeExtent[6] = { 0, -1, 0, -1, 0, -1 };
int currentFrameVolumeScalarType = VTK_VOID;
int currentFrameVolumeNumberOfComponents = 0;
if (currentFrameVolume->GetImageData())
{
currentFrameVolume->GetImageData()->GetExtent(currentFrameVolumeExtent);
currentFrameVolumeScalarType = currentFrameVolume->GetImageData()->GetScalarType();
currentFrameVolumeNumberOfComponents = currentFrameVolume->GetImageData()->GetNumberOfScalarComponents();
}
for (int i = 0; i < 6; i++)
{
if (firstFrameVolumeExtent[i] != currentFrameVolumeExtent[i])
{
vtkDebugMacro("vtkMRMLVolumeSequenceStorageNode::CanWriteFromReferenceNode: extent mismatch (frame " << frameIndex << ")");
return false;
}
}
if (currentFrameVolumeScalarType != firstFrameVolumeScalarType)
{
vtkDebugMacro("vtkMRMLVolumeSequenceStorageNode::CanWriteFromReferenceNode: scalar type mismatch (frame " << frameIndex << ")");
return false;
}
if (currentFrameVolumeNumberOfComponents != firstFrameVolumeNumberOfComponents)
{
vtkDebugMacro("vtkMRMLVolumeSequenceStorageNode::CanWriteFromReferenceNode: number of components mismatch (frame " << frameIndex << ")");
return false;
}
}
return true;
}
//----------------------------------------------------------------------------
int vtkMRMLVolumeSequenceStorageNode::WriteDataInternal(vtkMRMLNode *refNode)
{
vtkMRMLSequenceNode* volSequenceNode = vtkMRMLSequenceNode::SafeDownCast(refNode);
if (volSequenceNode==NULL)
{
vtkErrorMacro(<< "vtkMRMLVolumeSequenceStorageNode::WriteDataInternal: Do not recognize node type " << refNode->GetClassName());
return 0;
}
vtkNew<vtkMatrix4x4> ijkToRas;
int frameVolumeDimensions[3] = {0};
int frameVolumeScalarType = VTK_VOID;
if (volSequenceNode->GetNumberOfDataNodes()>0)
{
vtkMRMLVolumeNode* frameVolume = vtkMRMLVolumeNode::SafeDownCast(volSequenceNode->GetNthDataNode(0));
if (frameVolume==NULL)
{
vtkErrorMacro(<< "vtkMRMLVolumeSequenceStorageNode::WriteDataInternal: Data node is not a volume");
return 0;
}
frameVolume->GetIJKToRASMatrix(ijkToRas.GetPointer());
if (frameVolume->GetImageData())
{
frameVolume->GetImageData()->GetDimensions(frameVolumeDimensions);
frameVolumeScalarType = frameVolume->GetImageData()->GetScalarType();
}
}
vtkNew<vtkImageAppendComponents> appender;
int numberOfFrameVolumes = volSequenceNode->GetNumberOfDataNodes();
for (int frameIndex=0; frameIndex<numberOfFrameVolumes; frameIndex++)
{
vtkMRMLVolumeNode* frameVolume = vtkMRMLVolumeNode::SafeDownCast(volSequenceNode->GetNthDataNode(frameIndex));
if (frameVolume==NULL)
{
vtkErrorMacro(<< "vtkMRMLVolumeSequenceStorageNode::WriteDataInternal: Data node "<<frameIndex<<" is not a volume");
return 0;
}
//TODO: check if frameVolume->GetIJKToRASMatrix() is the same as ijkToRas
// either save the IJK to RAS into each frame or resample or return with error
int currentFrameVolumeDimensions[3] = {0};
int currentFrameVolumeScalarType = VTK_VOID;
if (frameVolume->GetImageData())
{
frameVolume->GetImageData()->GetDimensions(currentFrameVolumeDimensions);
currentFrameVolumeScalarType = frameVolume->GetImageData()->GetScalarType();
}
if (currentFrameVolumeDimensions[0] != frameVolumeDimensions[0]
|| currentFrameVolumeDimensions[0] != frameVolumeDimensions[0]
|| currentFrameVolumeDimensions[0] != frameVolumeDimensions[0]
|| currentFrameVolumeScalarType != frameVolumeScalarType)
{
vtkErrorMacro(<< "vtkMRMLVolumeSequenceStorageNode::WriteDataInternal: Data node "<<frameIndex<<" size or scalar type mismatch ("
<<"got "<<currentFrameVolumeDimensions[0]<<"x"<<currentFrameVolumeDimensions[1]<<"x"<<currentFrameVolumeDimensions[2]<<" "<<vtkImageScalarTypeNameMacro(currentFrameVolumeScalarType)<<", "
<<"expected "<<frameVolumeDimensions[0]<<"x"<<frameVolumeDimensions[1]<<"x"<<frameVolumeDimensions[2]<<" "<<vtkImageScalarTypeNameMacro(frameVolumeScalarType) );
return 0;
}
if (frameVolume->GetImageData())
{
appender->AddInputData(frameVolume->GetImageData());
}
}
std::string fullName = this->GetFullNameFromFileName();
if (fullName == std::string(""))
{
vtkErrorMacro("WriteData: File name not specified");
return 0;
}
// Use here the NRRD Writer
#if Slicer_VERSION_MAJOR > 4 || (Slicer_VERSION_MAJOR == 4 && Slicer_VERSION_MINOR >= 9)
vtkNew<vtkTeemNRRDWriter> writer;
writer->SetVectorAxisKind(nrrdKindList);
#else
vtkNew<vtkNRRDWriter> writer;
#endif
writer->SetFileName(fullName.c_str());
appender->Update();
writer->SetInputConnection(appender->GetOutputPort());
writer->SetUseCompression(this->GetUseCompression());
// set volume attributes
writer->SetIJKToRASMatrix(ijkToRas.GetPointer());
//writer->SetMeasurementFrameMatrix(mf.GetPointer());
// Write index information
if (!volSequenceNode->GetIndexName().empty())
{
writer->SetAxisLabel(0, volSequenceNode->GetIndexName().c_str());
}
if (!volSequenceNode->GetIndexUnit().empty())
{
writer->SetAxisUnit(0, volSequenceNode->GetIndexUnit().c_str());
}
if (!volSequenceNode->GetIndexTypeAsString().empty())
{
writer->SetAttribute("axis 0 index type", volSequenceNode->GetIndexTypeAsString());
}
if (numberOfFrameVolumes > 0)
{
std::stringstream ssIndexValues;
for (int frameIndex = 0; frameIndex < numberOfFrameVolumes; frameIndex++)
{
if (frameIndex > 0)
{
ssIndexValues << " ";
}
// Encode string to make sure there are no spaces in the serialized index value (space is used as separator)
ssIndexValues << vtkMRMLNode::URLEncodeString(volSequenceNode->GetNthIndexValue(frameIndex).c_str());
}
writer->SetAttribute("axis 0 index values", ssIndexValues.str());
}
// pass down all MRML attributes to NRRD
std::vector<std::string> attributeNames = volSequenceNode->GetAttributeNames();
std::vector<std::string>::iterator ait = attributeNames.begin();
for (; ait != attributeNames.end(); ++ait)
{
writer->SetAttribute((*ait), volSequenceNode->GetAttribute((*ait).c_str()));
}
writer->Write();
int writeFlag = 1;
if (writer->GetWriteError())
{
vtkErrorMacro("ERROR writing NRRD file " << (writer->GetFileName() == NULL ? "null" : writer->GetFileName()));
writeFlag = 0;
}
this->StageWriteData(refNode);
return writeFlag;
}
//----------------------------------------------------------------------------
void vtkMRMLVolumeSequenceStorageNode::InitializeSupportedReadFileTypes()
{
this->SupportedReadFileTypes->InsertNextValue("Volume sequence (.seq.nrrd)");
this->SupportedReadFileTypes->InsertNextValue("Volume sequence (.seq.nhdr)");
this->SupportedReadFileTypes->InsertNextValue("Volume sequence (.nrrd)");
this->SupportedReadFileTypes->InsertNextValue("Volume sequence (.nhdr)");
}
//----------------------------------------------------------------------------
void vtkMRMLVolumeSequenceStorageNode::InitializeSupportedWriteFileTypes()
{
this->SupportedWriteFileTypes->InsertNextValue("Volume sequence (.seq.nrrd)");
this->SupportedWriteFileTypes->InsertNextValue("Volume sequence (.seq.nhdr)");
this->SupportedWriteFileTypes->InsertNextValue("Volume sequence (.nrrd)");
this->SupportedWriteFileTypes->InsertNextValue("Volume sequence (.nhdr)");
}
//----------------------------------------------------------------------------
const char* vtkMRMLVolumeSequenceStorageNode::GetDefaultWriteFileExtension()
{
return "seq.nrrd";
}