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vtkMRMLSegmentationStorageNode.cxx
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vtkMRMLSegmentationStorageNode.cxx
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/*==============================================================================
Copyright (c) Laboratory for Percutaneous Surgery (PerkLab)
Queen's University, Kingston, ON, Canada. All Rights Reserved.
See COPYRIGHT.txt
or http://www.slicer.org/copyright/copyright.txt for details.
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
This file was originally developed by Adam Rankin and Csaba Pinter, PerkLab, Queen's
University and was supported through the Applied Cancer Research Unit program of Cancer
Care Ontario with funds provided by the Ontario Ministry of Health and Long-Term Care
==============================================================================*/
// Segmentations includes
#include "vtkMRMLSegmentationStorageNode.h"
#include "vtkSegmentation.h"
#include "vtkOrientedImageData.h"
#include "vtkOrientedImageDataResample.h"
// MRML includes
#include "vtkMRMLI18N.h"
#include "vtkMRMLMessageCollection.h"
#include <vtkMRMLScalarVolumeNode.h>
#include <vtkMRMLScene.h>
#include "vtkMRMLSegmentationNode.h"
#include "vtkMRMLSegmentationDisplayNode.h"
// VTK includes
#include <vtkDataObject.h>
#include <vtkDoubleArray.h>
#include <vtkErrorCode.h>
#include <vtkFieldData.h>
#include <vtkImageAccumulate.h>
#include <vtkImageAppendComponents.h>
#include <vtkImageCast.h>
#include <vtkImageConstantPad.h>
#include <vtkImageExtractComponents.h>
#include <vtkInformation.h>
#include <vtkInformationIntegerVectorKey.h>
#include <vtkInformationStringKey.h>
#include <vtkITKArchetypeImageSeriesVectorReaderFile.h>
#include <vtkMultiBlockDataSet.h>
#include <vtkNew.h>
#include <vtkTeemNRRDWriter.h>
#include <vtkObjectFactory.h>
#include <vtkPointData.h>
#include <vtkPolyData.h>
#include <vtkStringArray.h>
#include <vtkTransform.h>
#include <vtkXMLMultiBlockDataWriter.h>
#include <vtkXMLMultiBlockDataReader.h>
#include <vtksys/SystemTools.hxx>
#ifdef SUPPORT_4D_SPATIAL_NRRD
// ITK includes
#include <itkMacro.h>
#include <itkImageFileWriter.h>
#include <itkImageFileReader.h>
#include <itkMetaDataDictionary.h>
#include <itkMetaDataObject.h>
#include <itkNrrdImageIO.h>
#endif
// STL & C++ includes
#include <iterator>
#include <sstream>
//----------------------------------------------------------------------------
static const std::string SERIALIZATION_SEPARATOR = "|";
static const std::string KEY_SEGMENT_ID = "ID";
static const std::string KEY_SEGMENT_NAME = "Name";
static const std::string KEY_SEGMENT_COLOR = "Color";
static const std::string KEY_SEGMENT_TAGS = "Tags";
static const std::string KEY_SEGMENT_EXTENT = "Extent";
static const std::string KEY_SEGMENT_LABEL_VALUE = "LabelValue";
static const std::string KEY_SEGMENT_LAYER = "Layer";
static const std::string KEY_SEGMENT_NAME_AUTO_GENERATED = "NameAutoGenerated";
static const std::string KEY_SEGMENT_COLOR_AUTO_GENERATED = "ColorAutoGenerated";
static const std::string KEY_SEGMENTATION_SOURCE_REPRESENTATION = "MasterRepresentation";
static const std::string KEY_SEGMENTATION_CONVERSION_PARAMETERS = "ConversionParameters";
static const std::string KEY_SEGMENTATION_EXTENT = "Extent"; // Deprecated, kept only for being able to read legacy files.
static const std::string KEY_SEGMENTATION_REFERENCE_IMAGE_EXTENT_OFFSET = "ReferenceImageExtentOffset";
static const std::string KEY_SEGMENTATION_CONTAINED_REPRESENTATION_NAMES = "ContainedRepresentationNames";
static const int SINGLE_SEGMENT_INDEX = -1; // used as segment index when there is only a single segment
//----------------------------------------------------------------------------
vtkMRMLNodeNewMacro(vtkMRMLSegmentationStorageNode);
//----------------------------------------------------------------------------
vtkMRMLSegmentationStorageNode::vtkMRMLSegmentationStorageNode() = default;
//----------------------------------------------------------------------------
vtkMRMLSegmentationStorageNode::~vtkMRMLSegmentationStorageNode() = default;
//----------------------------------------------------------------------------
void vtkMRMLSegmentationStorageNode::PrintSelf(ostream& os, vtkIndent indent)
{
Superclass::PrintSelf(os,indent);
vtkMRMLPrintBeginMacro(os, indent);
vtkMRMLPrintBooleanMacro(CropToMinimumExtent);
vtkMRMLPrintEndMacro();
}
//----------------------------------------------------------------------------
void vtkMRMLSegmentationStorageNode::ReadXMLAttributes(const char** atts)
{
MRMLNodeModifyBlocker blocker(this);
Superclass::ReadXMLAttributes(atts);
vtkMRMLReadXMLBeginMacro(atts);
vtkMRMLReadXMLBooleanMacro(CropToMinimumExtent, CropToMinimumExtent);
vtkMRMLReadXMLEndMacro();
}
//----------------------------------------------------------------------------
void vtkMRMLSegmentationStorageNode::WriteXML(ostream& of, int nIndent)
{
Superclass::WriteXML(of, nIndent);
vtkMRMLWriteXMLBeginMacro(of);
vtkMRMLWriteXMLBooleanMacro(CropToMinimumExtent, CropToMinimumExtent);
vtkMRMLWriteXMLEndMacro();
}
//----------------------------------------------------------------------------
// Copy the node's attributes to this object.
// Does NOT copy: ID, FilePrefix, Name, StorageID
void vtkMRMLSegmentationStorageNode::Copy(vtkMRMLNode *anode)
{
MRMLNodeModifyBlocker blocker(anode);
Superclass::Copy(anode);
vtkMRMLCopyBeginMacro(anode);
vtkMRMLCopyBooleanMacro(CropToMinimumExtent);
vtkMRMLCopyEndMacro();
}
//----------------------------------------------------------------------------
void vtkMRMLSegmentationStorageNode::InitializeSupportedReadFileTypes()
{
//: File format name
std::string fileType = vtkMRMLTr("vtkMRMLSegmentationStorageNode", "Segmentation");
this->SupportedReadFileTypes->InsertNextValue(fileType + " (.seg.nrrd)");
this->SupportedReadFileTypes->InsertNextValue(fileType + " (.seg.nhdr)");
this->SupportedReadFileTypes->InsertNextValue(fileType + " (.seg.vtm)");
this->SupportedReadFileTypes->InsertNextValue(fileType + " (.nrrd)");
this->SupportedReadFileTypes->InsertNextValue(fileType + " (.vtm)");
this->SupportedReadFileTypes->InsertNextValue(fileType + " (.nii.gz)");
this->SupportedReadFileTypes->InsertNextValue(fileType + " (.hdr)");
this->SupportedReadFileTypes->InsertNextValue(fileType + " (.nii)");
}
//----------------------------------------------------------------------------
void vtkMRMLSegmentationStorageNode::InitializeSupportedWriteFileTypes()
{
Superclass::InitializeSupportedWriteFileTypes();
vtkMRMLSegmentationNode* segmentationNode = this->GetAssociatedDataNode();
bool masterIsImage = true;
bool masterIsPolyData = true;
if (segmentationNode)
{
// restrict write file types to those that are suitable for current source representation
masterIsImage = segmentationNode->GetSegmentation()->IsSourceRepresentationImageData();
masterIsPolyData = segmentationNode->GetSegmentation()->IsSourceRepresentationPolyData();
if (!masterIsImage && !masterIsPolyData)
{
// if contains unknown representation then enable all formats
masterIsImage = true;
masterIsPolyData = true;
}
}
//: File format name
std::string fileType = vtkMRMLTr("vtkMRMLSegmentationStorageNode", "Segmentation");
if (masterIsImage)
{
this->SupportedWriteFileTypes->InsertNextValue(fileType + " (.seg.nrrd)");
this->SupportedWriteFileTypes->InsertNextValue(fileType + " (.seg.nhdr)");
this->SupportedWriteFileTypes->InsertNextValue(fileType + " (.nrrd)");
this->SupportedWriteFileTypes->InsertNextValue(fileType + " (.nhdr)");
}
if (masterIsPolyData)
{
this->SupportedWriteFileTypes->InsertNextValue(fileType + " (.seg.vtm)");
this->SupportedWriteFileTypes->InsertNextValue(fileType + " (.vtm)");
}
}
//----------------------------------------------------------------------------
vtkMRMLSegmentationNode* vtkMRMLSegmentationStorageNode::GetAssociatedDataNode()
{
if (!this->GetScene())
{
return nullptr;
}
std::vector<vtkMRMLNode*> segmentationNodes;
unsigned int numberOfNodes = this->GetScene()->GetNodesByClass("vtkMRMLSegmentationNode", segmentationNodes);
for (unsigned int nodeIndex=0; nodeIndex<numberOfNodes; nodeIndex++)
{
vtkMRMLSegmentationNode* node = vtkMRMLSegmentationNode::SafeDownCast(segmentationNodes[nodeIndex]);
if (node)
{
const char* storageNodeID = node->GetStorageNodeID();
if (storageNodeID && !strcmp(storageNodeID, this->ID))
{
return vtkMRMLSegmentationNode::SafeDownCast(node);
}
}
}
return nullptr;
}
//----------------------------------------------------------------------------
const char* vtkMRMLSegmentationStorageNode::GetDefaultWriteFileExtension()
{
vtkMRMLSegmentationNode* segmentationNode = this->GetAssociatedDataNode();
if (!segmentationNode)
{
return nullptr;
}
if (segmentationNode->GetSegmentation()->IsSourceRepresentationImageData())
{
return "seg.nrrd";
}
else if (segmentationNode->GetSegmentation()->IsSourceRepresentationPolyData())
{
return "seg.vtm";
}
// Source representation is not supported for writing to file
return nullptr;
}
//----------------------------------------------------------------------------
void vtkMRMLSegmentationStorageNode::ResetSupportedWriteFileTypes()
{
this->InitializeSupportedWriteFileTypes();
}
//----------------------------------------------------------------------------
bool vtkMRMLSegmentationStorageNode::CanReadInReferenceNode(vtkMRMLNode *refNode)
{
return refNode->IsA("vtkMRMLSegmentationNode");
}
//----------------------------------------------------------------------------
int vtkMRMLSegmentationStorageNode::ReadDataInternal(vtkMRMLNode *refNode)
{
vtkMRMLSegmentationNode* segmentationNode = vtkMRMLSegmentationNode::SafeDownCast(refNode);
if (!segmentationNode)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLSegmentationStorageNode::ReadDataInternal",
"Node for storing reading result (" << (this->ID ? this->ID : "(unknown)") << ") is not a valid segmentation node.");
return 0;
}
MRMLNodeModifyBlocker blocker(segmentationNode);
std::string fullName = this->GetFullNameFromFileName();
if (fullName.empty())
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLSegmentationStorageNode::ReadDataInternal",
"Filename is not specified (" << (this->ID ? this->ID : "(unknown)") << ").");
return 0;
}
// Check that the file exists
if (vtksys::SystemTools::FileExists(fullName.c_str()) == false)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLSegmentationStorageNode::ReadDataInternal",
"Segmentation file '" << fullName.c_str() << "' is not found while trying to read node (" << (this->ID ? this->ID : "(unknown)") << ").");
return 0;
}
bool success = false;
// Try to read as labelmap first then as poly data
if (this->ReadBinaryLabelmapRepresentation(segmentationNode, fullName))
{
success = true;
}
#ifdef SUPPORT_4D_SPATIAL_NRRD
else if (this->ReadBinaryLabelmapRepresentation4DSpatial(segmentationNode, fullName))
{
success = true;
}
#endif
else if (this->ReadPolyDataRepresentation(segmentationNode, fullName))
{
success = true;
}
// Create display node if segmentation there is none
if (success && !segmentationNode->GetDisplayNode())
{
segmentationNode->CreateDefaultDisplayNodes();
}
if (!success)
{
// Failed to read
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLSegmentationStorageNode::ReadDataInternal",
"File '" << fullName << "' could not be read neither as labelmap nor polydata"
<< " while trying to read node (" << (this->ID ? this->ID : "(unknown)") << ").");
return 0;
}
return 1;
}
#ifdef SUPPORT_4D_SPATIAL_NRRD
//----------------------------------------------------------------------------
int vtkMRMLSegmentationStorageNode::ReadBinaryLabelmapRepresentation4DSpatial(vtkMRMLSegmentationNode* segmentationNode, std::string path)
{
if (!vtksys::SystemTools::FileExists(path.c_str()))
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLSegmentationStorageNode::ReadBinaryLabelmapRepresentation4DSpatial",
"Input file " << path << " does not exist.");
return 0;
}
// Set up output segmentation
if (!segmentationNode)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLSegmentationStorageNode::ReadBinaryLabelmapRepresentation4DSpatial",
"Output segmentation must exist.");
return 0;
}
// Read 4D NRRD image file
typedef itk::ImageFileReader<BinaryLabelmap4DImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetFileName(path);
try
{
reader->Update();
}
catch (itk::ImageFileReaderException &error)
{
// Do not report error as the file might contain poly data in which case ReadPolyDataRepresentation will read it alright
vtkDebugMacro("ReadBinaryLabelmapRepresentation: Failed to load file " << path << " as segmentation. Exception:\n" << error);
return 0;
}
BinaryLabelmap4DImageType::Pointer allSegmentLabelmapsImage = reader->GetOutput();
// Read succeeded
// Make sure there is a valid segmentation object in the node
vtkSegmentation* segmentation = segmentationNode->GetSegmentation();
if (!segmentation)
{
vtkNew<vtkSegmentation> newSegmentation;
segmentation = newSegmentation;
segmentationNode->SetAndObserveSegmentation(newSegmentation);
}
MRMLNodeModifyBlocker blocker(segmentationNode);
// Clean out the segmentation before adding the new segments
if (segmentation->GetNumberOfSegments() > 0)
{
segmentation->RemoveAllSegments();
}
// Set source representation
segmentation->SetSourceRepresentationName(vtkSegmentationConverter::GetSegmentationBinaryLabelmapRepresentationName());
// Get metadata dictionary from image
itk::MetaDataDictionary metadata = allSegmentLabelmapsImage->GetMetaDataDictionary();
// Read common geometry extent
std::string commonExtent;
itk::ExposeMetaData<std::string>(metadata, GetSegmentationMetaDataKey(KEY_SEGMENTATION_EXTENT).c_str(), commonExtent);
int commonGeometryExtent[6] = {0,-1,0,-1,0,-1};
GetImageExtentFromString(commonGeometryExtent, commonExtent);
// Read conversion parameters
std::string conversionParameters;
itk::ExposeMetaData<std::string>(metadata, GetSegmentationMetaDataKey(KEY_SEGMENTATION_CONVERSION_PARAMETERS).c_str(), conversionParameters);
segmentation->DeserializeConversionParameters(conversionParameters);
// Read contained representation names
std::string containedRepresentationNames;
itk::ExposeMetaData<std::string>(metadata, GetSegmentationMetaDataKey(KEY_SEGMENTATION_CONTAINED_REPRESENTATION_NAMES).c_str(), containedRepresentationNames);
// Get image properties
BinaryLabelmap4DImageType::RegionType itkRegion = allSegmentLabelmapsImage->GetLargestPossibleRegion();
BinaryLabelmap4DImageType::PointType itkOrigin = allSegmentLabelmapsImage->GetOrigin();
BinaryLabelmap4DImageType::SpacingType itkSpacing = allSegmentLabelmapsImage->GetSpacing();
BinaryLabelmap4DImageType::DirectionType itkDirections = allSegmentLabelmapsImage->GetDirection();
// Make image properties accessible for VTK
double origin[3] = {itkOrigin[0], itkOrigin[1], itkOrigin[2]};
double spacing[3] = {itkSpacing[0], itkSpacing[1], itkSpacing[2]};
double directions[3][3] = {{1.0,0.0,0.0},{0.0,1.0,0.0},{0.0,0.0,1.0}};
for (unsigned int col=0; col<3; col++)
{
for (unsigned int row=0; row<3; row++)
{
directions[row][col] = itkDirections[row][col];
}
}
// Read segment binary labelmaps
for (unsigned int segmentIndex = itkRegion.GetIndex()[3];
segmentIndex < itkRegion.GetIndex()[3]+itkRegion.GetSize()[3];
++segmentIndex)
{
// Create segment
vtkSmartPointer<vtkSegment> currentSegment = vtkSmartPointer<vtkSegment>::New();
// Get metadata for current segment
// ID
std::string currentSegmentID;
itk::ExposeMetaData<std::string>(
metadata,
GetSegmentMetaDataKey(segmentIndex, KEY_SEGMENT_ID),
currentSegmentID);
// Name
std::string currentSegmentName;
itk::ExposeMetaData<std::string>(
metadata,
GetSegmentMetaDataKey(segmentIndex, KEY_SEGMENT_NAME),
currentSegmentName);
currentSegment->SetName(currentSegmentName.c_str());
// Color
std::string colorString;
itk::ExposeMetaData<std::string>(
metadata,
GetSegmentMetaDataKey(segmentIndex, KEY_SEGMENT_COLOR),
colorString);
if (colorString.empty())
{
// Backwards compatibility
itk::ExposeMetaData<std::string>(metadata, GetSegmentMetaDataKey(segmentIndex, "DefaultColor"), colorString);
}
double currentSegmentColor[3] = {0.0,0.0,0.0};
GetSegmentColorFromString(currentSegmentColor, colorString);
// Extent
std::string extentValue;
itk::ExposeMetaData<std::string>(
metadata,
GetSegmentMetaDataKey(segmentIndex, KEY_SEGMENT_EXTENT),
extentValue);
int currentSegmentExtent[6] = {0,-1,0,-1,0,-1};
GetImageExtentFromString(currentSegmentExtent, extentValue);
// Tags
std::string tagsValue;
itk::ExposeMetaData<std::string>(
metadata,
GetSegmentMetaDataKey(segmentIndex, KEY_SEGMENT_TAGS),
tagsValue);
SetSegmentTagsFromString(currentSegment, tagsValue);
// NameAutoGenerated
std::string currentSegmentNameAutoGenerated;
itk::ExposeMetaData<std::string>(
metadata,
GetSegmentMetaDataKey(segmentIndex, KEY_SEGMENT_NAME_AUTO_GENERATED),
currentSegmentNameAutoGenerated);
currentSegment->SetNameAutoGenerated(!currentSegmentNameAutoGenerated.compare("1"));
// ColorAutoGenerated
std::string currentSegmentColorAutoGenerated;
itk::ExposeMetaData<std::string>(
metadata,
GetSegmentMetaDataKey(segmentIndex, KEY_SEGMENT_COLOR_AUTO_GENERATED),
currentSegmentColorAutoGenerated);
currentSegment->SetColorAutoGenerated(!currentSegmentColorAutoGenerated.compare("1"));
// Create binary labelmap volume
vtkSmartPointer<vtkOrientedImageData> currentBinaryLabelmap = vtkSmartPointer<vtkOrientedImageData>::New();
currentBinaryLabelmap->SetOrigin(origin);
currentBinaryLabelmap->SetSpacing(spacing);
currentBinaryLabelmap->SetDirections(directions);
currentBinaryLabelmap->SetExtent(currentSegmentExtent);
currentBinaryLabelmap->AllocateScalars(VTK_UNSIGNED_CHAR, 1);
unsigned char* labelmapPtr = (unsigned char*)currentBinaryLabelmap->GetScalarPointerForExtent(currentSegmentExtent);
// Define ITK region for current segment
BinaryLabelmap4DImageType::RegionType segmentRegion;
BinaryLabelmap4DImageType::SizeType segmentRegionSize;
BinaryLabelmap4DImageType::IndexType segmentRegionIndex;
segmentRegionIndex[0] = segmentRegionIndex[1] = segmentRegionIndex[2] = 0;
segmentRegionIndex[3] = segmentIndex;
segmentRegionSize = itkRegion.GetSize();
segmentRegionSize[3] = 1;
segmentRegion.SetIndex(segmentRegionIndex);
segmentRegion.SetSize(segmentRegionSize);
// Iterate through current segment's region and read voxel values into segment labelmap
BinaryLabelmap4DIteratorType segmentLabelmapIterator(allSegmentLabelmapsImage, segmentRegion);
for (segmentLabelmapIterator.GoToBegin(); !segmentLabelmapIterator.IsAtEnd(); ++segmentLabelmapIterator)
{
// Skip region outside extent of current segment (consider common extent boundaries)
BinaryLabelmap4DImageType::IndexType segmentIndex = segmentLabelmapIterator.GetIndex();
if ( segmentIndex[0] + commonGeometryExtent[0] < currentSegmentExtent[0]
|| segmentIndex[0] + commonGeometryExtent[0] > currentSegmentExtent[1]
|| segmentIndex[1] + commonGeometryExtent[2] < currentSegmentExtent[2]
|| segmentIndex[1] + commonGeometryExtent[2] > currentSegmentExtent[3]
|| segmentIndex[2] + commonGeometryExtent[4] < currentSegmentExtent[4]
|| segmentIndex[2] + commonGeometryExtent[4] > currentSegmentExtent[5] )
{
continue;
}
// Get voxel value
unsigned char voxelValue = segmentLabelmapIterator.Get();
// Set voxel value in current segment labelmap
(*labelmapPtr) = voxelValue;
++labelmapPtr;
}
// Set loaded binary labelmap to segment
currentSegment->AddRepresentation(vtkSegmentationConverter::GetSegmentationBinaryLabelmapRepresentationName(), currentBinaryLabelmap);
// Add segment to segmentation
segmentation->AddSegment(currentSegment, currentSegmentID);
}
// Create contained representations now that all the data is loaded
this->CreateRepresentationsBySerializedNames(segmentation, containedRepresentationNames);
return 1;
}
#endif // SUPPORT_4D_SPATIAL_NRRD
//----------------------------------------------------------------------------
int vtkMRMLSegmentationStorageNode::ReadBinaryLabelmapRepresentation(vtkMRMLSegmentationNode* segmentationNode, std::string path)
{
if (!vtksys::SystemTools::FileExists(path.c_str()))
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLSegmentationStorageNode::ReadBinaryLabelmapRepresentation",
"Input file " << path << " does not exist.");
return 0;
}
if (!segmentationNode)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLSegmentationStorageNode::ReadBinaryLabelmapRepresentation",
"Output segmentation must exist.");
return 0;
}
// Make sure there is a valid segmentation object in the node
vtkSegmentation* segmentation = segmentationNode->GetSegmentation();
if (!segmentation)
{
vtkNew<vtkSegmentation> newSegmentation;
segmentation = newSegmentation;
segmentationNode->SetAndObserveSegmentation(newSegmentation);
}
vtkSmartPointer<vtkImageData> imageData = nullptr;
vtkNew<vtkITKArchetypeImageSeriesVectorReaderFile> archetypeImageReader;
archetypeImageReader->SetSingleFile(1);
archetypeImageReader->SetUseOrientationFromFile(1);
archetypeImageReader->ResetFileNames();
archetypeImageReader->SetArchetype(path.c_str());
archetypeImageReader->SetOutputScalarTypeToNative();
archetypeImageReader->SetDesiredCoordinateOrientationToNative();
archetypeImageReader->SetUseNativeOriginOn();
int numberOfSegments = 0;
std::map<int, std::vector<int> > segmentIndexInLayer;
std::string containedRepresentationNames;
vtkMatrix4x4* rasToFileIjk = nullptr;
int imageExtentInFile[6] = { 0, -1, 0, -1, 0, -1 };
int commonGeometryExtent[6] = { 0, -1, 0, -1, 0, -1 };
bool isExtentValid = false;
int referenceImageExtentOffset[3] = { 0, 0, 0 };
if (archetypeImageReader->CanReadFile(path.c_str()))
{
// Read the volume
this->GetUserMessages()->SetObservedObject(archetypeImageReader);
archetypeImageReader->Update();
this->GetUserMessages()->SetObservedObject(nullptr);
if (archetypeImageReader->GetErrorCode() != vtkErrorCode::NoError)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLSegmentationStorageNode::ReadBinaryLabelmapRepresentation",
"Error reading image.");
return 0;
}
// Copy image data to sequence of volume nodes
imageData = archetypeImageReader->GetOutput();
rasToFileIjk = archetypeImageReader->GetRasToIjkMatrix();
imageData->GetExtent(imageExtentInFile);
imageData->GetExtent(commonGeometryExtent);
// Get metadata dictionary from image
itk::MetaDataDictionary dictionary = archetypeImageReader->GetMetaDataDictionary();
std::string segmentationExtentString;
if (this->GetSegmentationMetaDataFromDicitionary(segmentationExtentString, dictionary, KEY_SEGMENTATION_EXTENT))
{
// Legacy format. Return and read using ReadBinaryLabelmapRepresentation4DSpatial if available.
return 0;
}
// Read common geometry
std::string referenceImageExtentOffsetStr;
if (this->GetSegmentationMetaDataFromDicitionary(referenceImageExtentOffsetStr, dictionary, KEY_SEGMENTATION_REFERENCE_IMAGE_EXTENT_OFFSET))
{
// Common geometry extent is specified by an offset (extent[0], extent[2], extent[4]) and the size of the image
// NRRD file cannot store start extent, so we store that in KEY_SEGMENTATION_REFERENCE_IMAGE_EXTENT_OFFSET and from imageExtentInFile we
// only use the extent size.
std::stringstream ssExtentValue(referenceImageExtentOffsetStr);
ssExtentValue >> referenceImageExtentOffset[0] >> referenceImageExtentOffset[1] >> referenceImageExtentOffset[2];
commonGeometryExtent[0] = referenceImageExtentOffset[0];
commonGeometryExtent[1] = referenceImageExtentOffset[0] + imageExtentInFile[1] - imageExtentInFile[0];
commonGeometryExtent[2] = referenceImageExtentOffset[1];
commonGeometryExtent[3] = referenceImageExtentOffset[1] + imageExtentInFile[3] - imageExtentInFile[2];
commonGeometryExtent[4] = referenceImageExtentOffset[2];
commonGeometryExtent[5] = referenceImageExtentOffset[2] + imageExtentInFile[5] - imageExtentInFile[4];
}
else
{
// KEY_SEGMENTATION_REFERENCE_IMAGE_EXTENT_OFFSET is not specified,
// which means that this is probably a regular NRRD file that should be imported as a segmentation.
// Use the image extent as common geometry extent.
vtkInfoMacro(<< KEY_SEGMENTATION_REFERENCE_IMAGE_EXTENT_OFFSET << " attribute was not found in NRRD segmentation file. Assume no offset.");
imageData->GetExtent(commonGeometryExtent);
}
// Special case: extent = [0, 0, 0, 0, 0, 0] means there is no image data
isExtentValid = true;
if (imageExtentInFile[0] == 0
&& imageExtentInFile[1] == 0
&& imageExtentInFile[2] == 0
&& imageExtentInFile[3] == 0
&& imageExtentInFile[4] == 0
&& imageExtentInFile[5] == 0)
{
imageExtentInFile[1] = -1;
imageExtentInFile[3] = -1;
imageExtentInFile[5] = -1;
commonGeometryExtent[0] = 0;
commonGeometryExtent[1] = -1;
commonGeometryExtent[2] = 0;
commonGeometryExtent[3] = -1;
commonGeometryExtent[4] = 0;
commonGeometryExtent[5] = -1;
isExtentValid = false;
}
// Read conversion parameters
std::string conversionParameters;
if (this->GetSegmentationMetaDataFromDicitionary(conversionParameters, dictionary, KEY_SEGMENTATION_CONVERSION_PARAMETERS))
{
segmentation->DeserializeConversionParameters(conversionParameters);
}
// Read contained representation names
this->GetSegmentationMetaDataFromDicitionary(containedRepresentationNames, dictionary, KEY_SEGMENTATION_CONTAINED_REPRESENTATION_NAMES);
// Read contained segment layer numbers
while (dictionary.HasKey(GetSegmentMetaDataKey(numberOfSegments, KEY_SEGMENT_ID)))
{
int segmentIndex = numberOfSegments;
std::string layerValue;
if (this->GetSegmentMetaDataFromDicitionary(layerValue, dictionary, segmentIndex, KEY_SEGMENT_LAYER))
{
segmentIndexInLayer[vtkVariant(layerValue).ToInt()].push_back(segmentIndex);
}
else
{
segmentIndexInLayer[segmentIndex].push_back(segmentIndex);
}
++numberOfSegments;
}
}
else
{
vtkDebugMacro("ReadBinaryLabelmapRepresentation: File is not using a supported format!");
return 0;
}
if (imageData == nullptr)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLSegmentationStorageNode::ReadBinaryLabelmapRepresentation",
"Error reading image: invalid image data.");
return 0;
}
// Read succeeded
int numberOfFrames = imageData->GetNumberOfScalarComponents();
MRMLNodeModifyBlocker blocker(segmentationNode);
// Clean out the segmentation before adding the new segments
if (segmentation->GetNumberOfSegments() > 0)
{
segmentation->RemoveAllSegments();
}
// Set source representation
segmentation->SetSourceRepresentationName(vtkSegmentationConverter::GetSegmentationBinaryLabelmapRepresentationName());
// Compensate for the extent shift in the image origin.
// We change the origin so that if a reader ignores private fields, such as
// referenceImageExtentOffset, the image is placed correctly in physical coordinate system.
vtkNew<vtkMatrix4x4> fileIjkToIjk;
fileIjkToIjk->SetElement(0, 3, referenceImageExtentOffset[0]);
fileIjkToIjk->SetElement(1, 3, referenceImageExtentOffset[1]);
fileIjkToIjk->SetElement(2, 3, referenceImageExtentOffset[2]);
vtkNew<vtkMatrix4x4> rasToIjk;
vtkMatrix4x4::Multiply4x4(fileIjkToIjk.GetPointer(), rasToFileIjk, rasToIjk.GetPointer());
vtkNew<vtkMatrix4x4> imageToWorldMatrix; // = ijkToRas;
vtkMatrix4x4::Invert(rasToIjk.GetPointer(), imageToWorldMatrix.GetPointer());
imageData->SetExtent(commonGeometryExtent);
vtkNew<vtkImageExtractComponents> extractComponents;
extractComponents->SetInputData(imageData);
vtkNew<vtkImageConstantPad> padder;
padder->SetInputConnection(extractComponents->GetOutputPort());
// Get metadata for current segment
itk::MetaDataDictionary dictionary = archetypeImageReader->GetMetaDataDictionary();
std::vector<vtkSmartPointer<vtkSegment> > segments(numberOfSegments);
std::map<int, vtkSmartPointer<vtkOrientedImageData> > layerToImage;
for (int frameIndex = 0; frameIndex < numberOfFrames; ++frameIndex)
{
// Create binary labelmap volume
vtkSmartPointer<vtkOrientedImageData> currentBinaryLabelmap = nullptr;
if (numberOfSegments == 0 && isExtentValid)
{
// No segment metadata. We are loading from a plain volume (not seg.nrrd).
currentBinaryLabelmap = vtkSmartPointer<vtkOrientedImageData>::New();
extractComponents->SetComponents(frameIndex);
padder->SetOutputWholeExtent(imageExtentInFile);
padder->Update();
currentBinaryLabelmap->ShallowCopy(padder->GetOutput());
double scalarRange[2] = { 0 };
currentBinaryLabelmap->GetScalarRange(scalarRange);
vtkIdType lowLabel = (vtkIdType)(floor(scalarRange[0]));
vtkIdType highLabel = (vtkIdType)(ceil(scalarRange[1]));
vtkSmartPointer<vtkImageAccumulate> imageAccumulate = vtkSmartPointer<vtkImageAccumulate>::New();
imageAccumulate->SetInputData(currentBinaryLabelmap);
imageAccumulate->IgnoreZeroOn(); // Ignore background value
imageAccumulate->SetComponentExtent(lowLabel, highLabel, 0, 0, 0, 0);
imageAccumulate->SetComponentOrigin(0, 0, 0);
imageAccumulate->SetComponentSpacing(1, 1, 1);
imageAccumulate->Update();
std::vector<vtkIdType> labelValues;
for (vtkIdType labelValue = lowLabel; labelValue <= highLabel; ++labelValue)
{
if (labelValue == 0)
{
continue;
}
double frequency = imageAccumulate->GetOutput()->GetPointData()->GetScalars()->GetTuple1(labelValue - lowLabel);
if (frequency == 0.0)
{
continue;
}
vtkSmartPointer<vtkSegment> currentSegment = vtkSmartPointer<vtkSegment>::New();
currentSegment->SetLabelValue(labelValue);
currentBinaryLabelmap->SetImageToWorldMatrix(imageToWorldMatrix.GetPointer());
currentSegment->AddRepresentation(vtkSegmentationConverter::GetBinaryLabelmapRepresentationName(), currentBinaryLabelmap);
segments.push_back(currentSegment);
}
// Set segmentation geometry from loaded image
std::string imageGeometryString = vtkSegmentationConverter::SerializeImageGeometry(currentBinaryLabelmap);
segmentation->SetConversionParameter(vtkSegmentationConverter::GetReferenceImageGeometryParameterName(), imageGeometryString);
}
else
{
for (int segmentIndex : segmentIndexInLayer[frameIndex])
{
// Create segment
vtkSmartPointer<vtkSegment> currentSegment = vtkSmartPointer<vtkSegment>::New();
std::string segmentColor;
if (this->GetSegmentMetaDataFromDicitionary(segmentColor, dictionary, segmentIndex, KEY_SEGMENT_COLOR))
{
double currentSegmentColor[3] = { 0.0, 0.0, 0.0 };
this->GetSegmentColorFromString(currentSegmentColor, segmentColor);
currentSegment->SetColor(currentSegmentColor);
}
else if (this->GetSegmentMetaDataFromDicitionary(segmentColor, dictionary, segmentIndex, "DefaultColor"))
{
double defaultSegmentColor[3] = { 0.0, 0.0, 0.0 };
this->GetSegmentColorFromString(defaultSegmentColor, segmentColor);
currentSegment->SetColor(defaultSegmentColor);
}
// Tags
std::string segmentTags;
if (this->GetSegmentMetaDataFromDicitionary(segmentTags, dictionary, segmentIndex, KEY_SEGMENT_TAGS))
{
this->SetSegmentTagsFromString(currentSegment, segmentTags);
}
// NameAutoGenerated
std::string nameAutoGenerated;
if (this->GetSegmentMetaDataFromDicitionary(nameAutoGenerated, dictionary, segmentIndex, KEY_SEGMENT_NAME_AUTO_GENERATED))
{
currentSegment->SetNameAutoGenerated(!strcmp(nameAutoGenerated.c_str(), "1"));
}
// ColorAutoGenerated
std::string colorAutoGenerated;
if (this->GetSegmentMetaDataFromDicitionary(colorAutoGenerated, dictionary, segmentIndex, KEY_SEGMENT_COLOR_AUTO_GENERATED))
{
currentSegment->SetColorAutoGenerated(!strcmp(colorAutoGenerated.c_str(),"1"));
}
// Label value
std::string labelValue;
if (this->GetSegmentMetaDataFromDicitionary(labelValue, dictionary, segmentIndex, KEY_SEGMENT_LABEL_VALUE))
{
currentSegment->SetLabelValue(vtkVariant(labelValue).ToInt());
}
if (currentBinaryLabelmap == nullptr)
{
currentBinaryLabelmap = vtkSmartPointer<vtkOrientedImageData>::New();
// Extent
int currentSegmentExtent[6] = { 0, -1, 0, -1, 0, -1 };
std::string currentExtentString;
if (this->GetSegmentMetaDataFromDicitionary(currentExtentString, dictionary, segmentIndex, KEY_SEGMENT_EXTENT))
{
GetImageExtentFromString(currentSegmentExtent, currentExtentString);
}
else
{
vtkWarningToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLSegmentationStorageNode::ReadBinaryLabelmapRepresentation",
"Segment extent is missing for segment " << segmentIndex);
for (int i = 0; i < 6; i++)
{
currentSegmentExtent[i] = imageExtentInFile[i];
}
}
for (int i = 0; i < 3; i++)
{
currentSegmentExtent[i * 2] += referenceImageExtentOffset[i];
currentSegmentExtent[i * 2 + 1] += referenceImageExtentOffset[i];
}
// Copy with clipping to specified extent
if (currentSegmentExtent[0] <= currentSegmentExtent[1]
&& currentSegmentExtent[2] <= currentSegmentExtent[3]
&& currentSegmentExtent[4] <= currentSegmentExtent[5])
{
// non-empty segment
extractComponents->SetComponents(frameIndex);
padder->SetOutputWholeExtent(currentSegmentExtent);
padder->Update();
currentBinaryLabelmap->DeepCopy(padder->GetOutput());
}
else
{
// empty segment
for (int i = 0; i < 3; ++i)
{
currentSegmentExtent[2 * i] = 0;
currentSegmentExtent[2 * i + 1] = -1;
}
currentBinaryLabelmap->SetExtent(currentSegmentExtent);
currentBinaryLabelmap->AllocateScalars(VTK_UNSIGNED_CHAR, 1);
}
currentBinaryLabelmap->SetImageToWorldMatrix(imageToWorldMatrix.GetPointer());
}
// Set loaded binary labelmap to segment
currentSegment->AddRepresentation(vtkSegmentationConverter::GetSegmentationBinaryLabelmapRepresentationName(), currentBinaryLabelmap);
segments[segmentIndex] = currentSegment;
}
}
}
vtkMRMLColorTableNode* exportColorTableNode = segmentationNode->GetLabelmapConversionColorTableNode();
// Add the created segments to the segmentation
for (int segmentIndex = 0; segmentIndex < static_cast<int>(segments.size()); ++segmentIndex)
{
vtkSegment* currentSegment = segments[segmentIndex];
if (!currentSegment)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLSegmentationStorageNode::ReadBinaryLabelmapRepresentation",
"Could not find segment" << segmentIndex);
continue;
}
std::string currentSegmentID;
if (numberOfSegments != 0)
{
// ID
if (!this->GetSegmentMetaDataFromDicitionary(currentSegmentID, dictionary, segmentIndex, KEY_SEGMENT_ID))
{
// No segment ID is specified, which may mean that it is an empty segmentation.
// We consider a segmentation empty if it has only one scalar component that is empty.
if (numberOfFrames == 1)
{
extractComponents->SetComponents(segmentIndex);
extractComponents->Update();
vtkImageData* labelmap = extractComponents->GetOutput();
double* scalarRange = labelmap->GetScalarRange();
if (scalarRange[0] >= scalarRange[1])
{
// Segmentation contains a single blank segment without segment ID,
// which means that it is an empty segmentation.
// It may still contain valuable metadata, but we don't create any segments.
break;
}
}
currentSegmentID = segmentation->GenerateUniqueSegmentID("Segment");
vtkWarningToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLSegmentationStorageNode::ReadBinaryLabelmapRepresentation",
"Segment ID is missing for segment " << segmentIndex << " adding segment with ID: " << currentSegmentID);
}
// Name
std::string segmentName;
if (this->GetSegmentMetaDataFromDicitionary(segmentName, dictionary, segmentIndex, KEY_SEGMENT_NAME))
{
currentSegment->SetName(segmentName.c_str());
}
else
{
vtkWarningToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLSegmentationStorageNode::ReadBinaryLabelmapRepresentation",
"Segment name is missing for segment " << segmentIndex);
currentSegment->SetName(currentSegmentID.c_str());
}
}
else
{
std::stringstream segmentNameSS;
segmentNameSS << "Segment_" << currentSegment->GetLabelValue();
std::string segmentName = segmentNameSS.str();
if (exportColorTableNode)
{
const char* colorName = exportColorTableNode->GetColorName(currentSegment->GetLabelValue());
if (colorName)
{
segmentName = colorName;
}
double color[4] = { 0.0, 0.0, 0.0, 1.0 };
exportColorTableNode->GetColor(currentSegment->GetLabelValue(), color);
currentSegment->SetColor(color);
}
else
{
vtkMRMLSegmentationDisplayNode* displayNode = vtkMRMLSegmentationDisplayNode::SafeDownCast(
segmentationNode->GetDisplayNode());
if (displayNode)
{
double color[4] = { 0.0, 0.0, 0.0, 1.0 };
displayNode->GenerateSegmentColor(color);
currentSegment->SetColor(color);
}
}
currentSegmentID = segmentation->GenerateUniqueSegmentID(segmentName);
currentSegment->SetName(currentSegmentID.c_str());
}
segmentation->AddSegment(currentSegment, currentSegmentID);
}
// Create contained representations now that all the data is loaded
this->CreateRepresentationsBySerializedNames(segmentation, containedRepresentationNames);
return 1;
}
//----------------------------------------------------------------------------
int vtkMRMLSegmentationStorageNode::ReadPolyDataRepresentation(vtkMRMLSegmentationNode* segmentationNode, std::string path)
{
if (!vtksys::SystemTools::FileExists(path.c_str()))
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLSegmentationStorageNode::ReadPolyDataRepresentation",
"ReadPolyDataRepresentation: Input file " << path << " does not exist.");
return 0;
}
// Set up output segmentation
if (!segmentationNode)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLSegmentationStorageNode::ReadPolyDataRepresentation",
"Output segmentation must exist.");
return 0;