mitk::DataNode::Pointer mitk::Tool::CreateEmptySegmentationNode( Image* original, const std::string& organName, const mitk::Color& color )
{
// we NEED a reference image for size etc.
if (!original) return NULL;
// actually create a new empty segmentation
PixelType pixelType(mitk::MakeScalarPixelType<DefaultSegmentationDataType>() );
Image::Pointer segmentation = Image::New();
if (original->GetDimension() == 2)
{
const unsigned int dimensions[] = { original->GetDimension(0), original->GetDimension(1), 1 };
segmentation->Initialize(pixelType, 3, dimensions);
}
else
{
segmentation->Initialize(pixelType, original->GetDimension(), original->GetDimensions());
}
unsigned int byteSize = sizeof(DefaultSegmentationDataType);
if(segmentation->GetDimension() < 4)
{
for (unsigned int dim = 0; dim < segmentation->GetDimension(); ++dim)
{
byteSize *= segmentation->GetDimension(dim);
}
mitk::ImageWriteAccessor writeAccess(segmentation, segmentation->GetVolumeData(0));
memset( writeAccess.GetData(), 0, byteSize );
}
else
{//if we have a time-resolved image we need to set memory to 0 for each time step
for (unsigned int dim = 0; dim < 3; ++dim)
{
byteSize *= segmentation->GetDimension(dim);
}
for( unsigned int volumeNumber = 0; volumeNumber < segmentation->GetDimension(3); volumeNumber++)
{
mitk::ImageWriteAccessor writeAccess(segmentation, segmentation->GetVolumeData(volumeNumber));
memset( writeAccess.GetData(), 0, byteSize );
}
}
if (original->GetTimeGeometry() )
{
TimeGeometry::Pointer originalGeometry = original->GetTimeGeometry()->Clone();
segmentation->SetTimeGeometry( originalGeometry );
}
else
{
Tool::ErrorMessage("Original image does not have a 'Time sliced geometry'! Cannot create a segmentation.");
return NULL;
}
return CreateSegmentationNode( segmentation, organName, color );
}
void mitk::CorrectorAlgorithm::GenerateData()
{
Image::Pointer inputImage = const_cast<Image*>(ImageToImageFilter::GetInput(0));
if (inputImage.IsNull() || inputImage->GetDimension() != 2)
{
itkExceptionMacro("CorrectorAlgorithm needs a 2D image as input.");
}
if (m_Contour.IsNull())
{
itkExceptionMacro("CorrectorAlgorithm needs a Contour object as input.");
}
// copy the input (since m_WorkingImage will be changed later)
m_WorkingImage = inputImage;
TimeGeometry::Pointer originalGeometry = NULL;
if (inputImage->GetTimeGeometry() )
{
originalGeometry = inputImage->GetTimeGeometry()->Clone();
m_WorkingImage->SetTimeGeometry( originalGeometry );
}
else
{
itkExceptionMacro("Original image does not have a 'Time sliced geometry'! Cannot copy.");
}
Image::Pointer temporarySlice;
// Convert to ipMITKSegmentationTYPE (because TobiasHeimannCorrectionAlgorithm relys on that data type)
{
itk::Image< ipMITKSegmentationTYPE, 2 >::Pointer correctPixelTypeImage;
CastToItkImage( m_WorkingImage, correctPixelTypeImage );
assert (correctPixelTypeImage.IsNotNull() );
// possible bug in CastToItkImage ?
// direction maxtrix is wrong/broken/not working after CastToItkImage, leading to a failed assertion in
// mitk/Core/DataStructures/mitkSlicedGeometry3D.cpp, 479:
// virtual void mitk::SlicedGeometry3D::SetSpacing(const mitk::Vector3D&): Assertion `aSpacing[0]>0 && aSpacing[1]>0 && aSpacing[2]>0' failed
// solution here: we overwrite it with an unity matrix
itk::Image< ipMITKSegmentationTYPE, 2 >::DirectionType imageDirection;
imageDirection.SetIdentity();
//correctPixelTypeImage->SetDirection(imageDirection);
temporarySlice = this->GetOutput();
// temporarySlice = ImportItkImage( correctPixelTypeImage );
m_FillColor = 1;
m_EraseColor = 0;
ImprovedHeimannCorrectionAlgorithm(correctPixelTypeImage);
CastToMitkImage( correctPixelTypeImage, temporarySlice );
}
temporarySlice->SetTimeGeometry(originalGeometry);
}
std::vector<BaseData::Pointer> ItkImageIO::Read()
{
std::vector<BaseData::Pointer> result;
mitk::LocaleSwitch localeSwitch("C");
Image::Pointer image = Image::New();
const unsigned int MINDIM = 2;
const unsigned int MAXDIM = 4;
const std::string path = this->GetLocalFileName();
MITK_INFO << "loading " << path << " via itk::ImageIOFactory... " << std::endl;
// Check to see if we can read the file given the name or prefix
if (path.empty())
{
mitkThrow() << "Empty filename in mitk::ItkImageIO ";
}
// Got to allocate space for the image. Determine the characteristics of
// the image.
m_ImageIO->SetFileName(path);
m_ImageIO->ReadImageInformation();
unsigned int ndim = m_ImageIO->GetNumberOfDimensions();
if (ndim < MINDIM || ndim > MAXDIM)
{
MITK_WARN << "Sorry, only dimensions 2, 3 and 4 are supported. The given file has " << ndim
<< " dimensions! Reading as 4D.";
ndim = MAXDIM;
}
itk::ImageIORegion ioRegion(ndim);
itk::ImageIORegion::SizeType ioSize = ioRegion.GetSize();
itk::ImageIORegion::IndexType ioStart = ioRegion.GetIndex();
unsigned int dimensions[MAXDIM];
dimensions[0] = 0;
dimensions[1] = 0;
dimensions[2] = 0;
dimensions[3] = 0;
ScalarType spacing[MAXDIM];
spacing[0] = 1.0f;
spacing[1] = 1.0f;
spacing[2] = 1.0f;
spacing[3] = 1.0f;
Point3D origin;
origin.Fill(0);
unsigned int i;
for (i = 0; i < ndim; ++i)
{
ioStart[i] = 0;
ioSize[i] = m_ImageIO->GetDimensions(i);
if (i < MAXDIM)
{
dimensions[i] = m_ImageIO->GetDimensions(i);
spacing[i] = m_ImageIO->GetSpacing(i);
if (spacing[i] <= 0)
spacing[i] = 1.0f;
}
if (i < 3)
{
origin[i] = m_ImageIO->GetOrigin(i);
}
}
ioRegion.SetSize(ioSize);
ioRegion.SetIndex(ioStart);
MITK_INFO << "ioRegion: " << ioRegion << std::endl;
m_ImageIO->SetIORegion(ioRegion);
void *buffer = new unsigned char[m_ImageIO->GetImageSizeInBytes()];
m_ImageIO->Read(buffer);
image->Initialize(MakePixelType(m_ImageIO), ndim, dimensions);
image->SetImportChannel(buffer, 0, Image::ManageMemory);
const itk::MetaDataDictionary &dictionary = m_ImageIO->GetMetaDataDictionary();
// access direction of itk::Image and include spacing
mitk::Matrix3D matrix;
matrix.SetIdentity();
unsigned int j, itkDimMax3 = (ndim >= 3 ? 3 : ndim);
for (i = 0; i < itkDimMax3; ++i)
for (j = 0; j < itkDimMax3; ++j)
matrix[i][j] = m_ImageIO->GetDirection(j)[i];
// re-initialize PlaneGeometry with origin and direction
PlaneGeometry *planeGeometry = image->GetSlicedGeometry(0)->GetPlaneGeometry(0);
planeGeometry->SetOrigin(origin);
planeGeometry->GetIndexToWorldTransform()->SetMatrix(matrix);
// re-initialize SlicedGeometry3D
SlicedGeometry3D *slicedGeometry = image->GetSlicedGeometry(0);
slicedGeometry->InitializeEvenlySpaced(planeGeometry, image->GetDimension(2));
slicedGeometry->SetSpacing(spacing);
MITK_INFO << slicedGeometry->GetCornerPoint(false, false, false);
MITK_INFO << slicedGeometry->GetCornerPoint(true, true, true);
// re-initialize TimeGeometry
TimeGeometry::Pointer timeGeometry;
if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TYPE) || dictionary.HasKey(PROPERTY_KEY_TIMEGEOMETRY_TYPE))
{ // also check for the name because of backwards compatibility. Past code version stored with the name and not with
// the key
itk::MetaDataObject<std::string>::ConstPointer timeGeometryTypeData = nullptr;
if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TYPE))
{
timeGeometryTypeData =
dynamic_cast<const itk::MetaDataObject<std::string> *>(dictionary.Get(PROPERTY_NAME_TIMEGEOMETRY_TYPE));
}
else
{
timeGeometryTypeData =
dynamic_cast<const itk::MetaDataObject<std::string> *>(dictionary.Get(PROPERTY_KEY_TIMEGEOMETRY_TYPE));
}
if (timeGeometryTypeData->GetMetaDataObjectValue() == ArbitraryTimeGeometry::GetStaticNameOfClass())
{
MITK_INFO << "used time geometry: " << ArbitraryTimeGeometry::GetStaticNameOfClass() << std::endl;
typedef std::vector<TimePointType> TimePointVector;
TimePointVector timePoints;
if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS))
{
timePoints = ConvertMetaDataObjectToTimePointList(dictionary.Get(PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS));
}
else if (dictionary.HasKey(PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS))
{
timePoints = ConvertMetaDataObjectToTimePointList(dictionary.Get(PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS));
}
if (timePoints.size() - 1 != image->GetDimension(3))
{
MITK_ERROR << "Stored timepoints (" << timePoints.size() - 1 << ") and size of image time dimension ("
<< image->GetDimension(3) << ") do not match. Switch to ProportionalTimeGeometry fallback"
<< std::endl;
}
else
{
ArbitraryTimeGeometry::Pointer arbitraryTimeGeometry = ArbitraryTimeGeometry::New();
TimePointVector::const_iterator pos = timePoints.begin();
TimePointVector::const_iterator prePos = pos++;
for (; pos != timePoints.end(); ++prePos, ++pos)
{
arbitraryTimeGeometry->AppendTimeStepClone(slicedGeometry, *pos, *prePos);
}
timeGeometry = arbitraryTimeGeometry;
}
}
}
if (timeGeometry.IsNull())
{ // Fallback. If no other valid time geometry has been created, create a ProportionalTimeGeometry
MITK_INFO << "used time geometry: " << ProportionalTimeGeometry::GetStaticNameOfClass() << std::endl;
ProportionalTimeGeometry::Pointer propTimeGeometry = ProportionalTimeGeometry::New();
propTimeGeometry->Initialize(slicedGeometry, image->GetDimension(3));
timeGeometry = propTimeGeometry;
}
image->SetTimeGeometry(timeGeometry);
buffer = NULL;
MITK_INFO << "number of image components: " << image->GetPixelType().GetNumberOfComponents() << std::endl;
for (itk::MetaDataDictionary::ConstIterator iter = dictionary.Begin(), iterEnd = dictionary.End(); iter != iterEnd;
++iter)
{
if (iter->second->GetMetaDataObjectTypeInfo() == typeid(std::string))
{
const std::string &key = iter->first;
std::string assumedPropertyName = key;
std::replace(assumedPropertyName.begin(), assumedPropertyName.end(), '_', '.');
std::string mimeTypeName = GetMimeType()->GetName();
// Check if there is already a info for the key and our mime type.
IPropertyPersistence::InfoResultType infoList = mitk::CoreServices::GetPropertyPersistence()->GetInfoByKey(key);
auto predicate = [mimeTypeName](const PropertyPersistenceInfo::ConstPointer &x) {
return x.IsNotNull() && x->GetMimeTypeName() == mimeTypeName;
};
auto finding = std::find_if(infoList.begin(), infoList.end(), predicate);
if (finding == infoList.end())
{
auto predicateWild = [](const PropertyPersistenceInfo::ConstPointer &x) {
return x.IsNotNull() && x->GetMimeTypeName() == PropertyPersistenceInfo::ANY_MIMETYPE_NAME();
};
finding = std::find_if(infoList.begin(), infoList.end(), predicateWild);
}
PropertyPersistenceInfo::ConstPointer info;
if (finding != infoList.end())
{
assumedPropertyName = (*finding)->GetName();
info = *finding;
}
else
{ // we have not found anything suitable so we generate our own info
PropertyPersistenceInfo::Pointer newInfo = PropertyPersistenceInfo::New();
newInfo->SetNameAndKey(assumedPropertyName, key);
newInfo->SetMimeTypeName(PropertyPersistenceInfo::ANY_MIMETYPE_NAME());
info = newInfo;
}
std::string value =
dynamic_cast<itk::MetaDataObject<std::string> *>(iter->second.GetPointer())->GetMetaDataObjectValue();
mitk::BaseProperty::Pointer loadedProp = info->GetDeserializationFunction()(value);
image->SetProperty(assumedPropertyName.c_str(), loadedProp);
// Read properties should be persisted unless they are default properties
// which are written anyway
bool isDefaultKey(false);
for (const auto &defaultKey : m_DefaultMetaDataKeys)
{
if (defaultKey.length() <= assumedPropertyName.length())
{
// does the start match the default key
if (assumedPropertyName.substr(0, defaultKey.length()).find(defaultKey) != std::string::npos)
{
isDefaultKey = true;
break;
}
}
}
if (!isDefaultKey)
{
mitk::CoreServices::GetPropertyPersistence()->AddInfo(info);
}
}
}
MITK_INFO << "...finished!" << std::endl;
result.push_back(image.GetPointer());
return result;
}
std::vector<BaseData::Pointer> LabelSetImageIO::Read()
{
const std::string& locale = "C";
const std::string& currLocale = setlocale( LC_ALL, NULL );
if ( locale.compare(currLocale)!=0 )
{
try
{
setlocale(LC_ALL, locale.c_str());
}
catch(...)
{
mitkThrow() << "Could not set locale.";
}
}
// begin regular image loading, adapted from mitkItkImageIO
itk::NrrdImageIO::Pointer nrrdImageIO = itk::NrrdImageIO::New();
Image::Pointer image = Image::New();
const unsigned int MINDIM = 2;
const unsigned int MAXDIM = 4;
const std::string path = this->GetLocalFileName();
MITK_INFO << "loading " << path << " via itk::ImageIOFactory... " << std::endl;
// Check to see if we can read the file given the name or prefix
if (path.empty())
{
mitkThrow() << "Empty filename in mitk::ItkImageIO ";
}
// Got to allocate space for the image. Determine the characteristics of
// the image.
nrrdImageIO->SetFileName(path);
nrrdImageIO->ReadImageInformation();
unsigned int ndim = nrrdImageIO->GetNumberOfDimensions();
if (ndim < MINDIM || ndim > MAXDIM)
{
MITK_WARN << "Sorry, only dimensions 2, 3 and 4 are supported. The given file has " << ndim << " dimensions! Reading as 4D.";
ndim = MAXDIM;
}
itk::ImageIORegion ioRegion(ndim);
itk::ImageIORegion::SizeType ioSize = ioRegion.GetSize();
itk::ImageIORegion::IndexType ioStart = ioRegion.GetIndex();
unsigned int dimensions[MAXDIM];
dimensions[0] = 0;
dimensions[1] = 0;
dimensions[2] = 0;
dimensions[3] = 0;
ScalarType spacing[MAXDIM];
spacing[0] = 1.0f;
spacing[1] = 1.0f;
spacing[2] = 1.0f;
spacing[3] = 1.0f;
Point3D origin;
origin.Fill(0);
unsigned int i;
for (i = 0; i < ndim; ++i)
{
ioStart[i] = 0;
ioSize[i] = nrrdImageIO->GetDimensions(i);
if (i<MAXDIM)
{
dimensions[i] = nrrdImageIO->GetDimensions(i);
spacing[i] = nrrdImageIO->GetSpacing(i);
if (spacing[i] <= 0)
spacing[i] = 1.0f;
}
if (i<3)
{
origin[i] = nrrdImageIO->GetOrigin(i);
}
}
ioRegion.SetSize(ioSize);
ioRegion.SetIndex(ioStart);
MITK_INFO << "ioRegion: " << ioRegion << std::endl;
nrrdImageIO->SetIORegion(ioRegion);
void* buffer = new unsigned char[nrrdImageIO->GetImageSizeInBytes()];
nrrdImageIO->Read(buffer);
image->Initialize(MakePixelType(nrrdImageIO), ndim, dimensions);
image->SetImportChannel(buffer, 0, Image::ManageMemory);
// access direction of itk::Image and include spacing
mitk::Matrix3D matrix;
matrix.SetIdentity();
unsigned int j, itkDimMax3 = (ndim >= 3 ? 3 : ndim);
for (i = 0; i < itkDimMax3; ++i)
for (j = 0; j < itkDimMax3; ++j)
matrix[i][j] = nrrdImageIO->GetDirection(j)[i];
// re-initialize PlaneGeometry with origin and direction
PlaneGeometry* planeGeometry = image->GetSlicedGeometry(0)->GetPlaneGeometry(0);
planeGeometry->SetOrigin(origin);
planeGeometry->GetIndexToWorldTransform()->SetMatrix(matrix);
// re-initialize SlicedGeometry3D
SlicedGeometry3D* slicedGeometry = image->GetSlicedGeometry(0);
slicedGeometry->InitializeEvenlySpaced(planeGeometry, image->GetDimension(2));
slicedGeometry->SetSpacing(spacing);
MITK_INFO << slicedGeometry->GetCornerPoint(false, false, false);
MITK_INFO << slicedGeometry->GetCornerPoint(true, true, true);
// re-initialize TimeGeometry
ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
timeGeometry->Initialize(slicedGeometry, image->GetDimension(3));
image->SetTimeGeometry(timeGeometry);
buffer = NULL;
MITK_INFO << "number of image components: " << image->GetPixelType().GetNumberOfComponents() << std::endl;
const itk::MetaDataDictionary& dictionary = nrrdImageIO->GetMetaDataDictionary();
for (itk::MetaDataDictionary::ConstIterator iter = dictionary.Begin(), iterEnd = dictionary.End();
iter != iterEnd; ++iter)
{
std::string key = std::string("meta.") + iter->first;
if (iter->second->GetMetaDataObjectTypeInfo() == typeid(std::string))
{
std::string value = dynamic_cast<itk::MetaDataObject<std::string>*>(iter->second.GetPointer())->GetMetaDataObjectValue();
image->SetProperty(key.c_str(), mitk::StringProperty::New(value));
}
}
// end regular image loading
LabelSetImage::Pointer output = LabelSetImageConverter::ConvertImageToLabelSetImage(image);
// get labels and add them as properties to the image
char keybuffer[256];
unsigned int numberOfLayers = GetIntByKey(dictionary, "layers");
std::string _xmlStr;
mitk::Label::Pointer label;
for (unsigned int layerIdx = 0; layerIdx < numberOfLayers; layerIdx++)
{
sprintf(keybuffer, "layer_%03d", layerIdx);
int numberOfLabels = GetIntByKey(dictionary, keybuffer);
mitk::LabelSet::Pointer labelSet = mitk::LabelSet::New();
for (int labelIdx = 0; labelIdx < numberOfLabels; labelIdx++)
{
TiXmlDocument doc;
sprintf(keybuffer, "label_%03d_%05d", layerIdx, labelIdx);
_xmlStr = GetStringByKey(dictionary, keybuffer);
doc.Parse(_xmlStr.c_str());
TiXmlElement * labelElem = doc.FirstChildElement("Label");
if (labelElem == 0)
mitkThrow() << "Error parsing NRRD header for mitk::LabelSetImage IO";
label = LoadLabelFromTiXmlDocument(labelElem);
if (label->GetValue() == 0) // set exterior label is needed to hold exterior information
output->SetExteriorLabel(label);
labelSet->AddLabel(label);
labelSet->SetLayer(layerIdx);
}
output->AddLabelSetToLayer(layerIdx, labelSet);
}
MITK_INFO << "...finished!" << std::endl;
try
{
setlocale(LC_ALL, currLocale.c_str());
}
catch(...)
{
mitkThrow() << "Could not reset locale!";
}
std::vector<BaseData::Pointer> result;
result.push_back(output.GetPointer());
return result;
}
mitk::Image::Pointer mitk::PicFileReader::CreateImage()
{
Image::Pointer output = Image::New();
std::string fileName = this->GetLocalFileName();
mitkIpPicDescriptor *header = mitkIpPicGetHeader(const_cast<char *>(fileName.c_str()), NULL);
if (!header)
{
mitkThrow() << "File could not be read.";
}
header = mitkIpPicGetTags(const_cast<char *>(fileName.c_str()), header);
int channels = 1;
mitkIpPicTSV_t *tsv;
if ((tsv = mitkIpPicQueryTag(header, "SOURCE HEADER")) != NULL)
{
if (tsv->n[0] > 1e+06)
{
mitkIpPicTSV_t *tsvSH;
tsvSH = mitkIpPicDelTag(header, "SOURCE HEADER");
mitkIpPicFreeTag(tsvSH);
}
}
if ((tsv = mitkIpPicQueryTag(header, "ICON80x80")) != NULL)
{
mitkIpPicTSV_t *tsvSH;
tsvSH = mitkIpPicDelTag(header, "ICON80x80");
mitkIpPicFreeTag(tsvSH);
}
if ((tsv = mitkIpPicQueryTag(header, "VELOCITY")) != NULL)
{
++channels;
mitkIpPicDelTag(header, "VELOCITY");
}
if (header == NULL || header->bpe == 0)
{
mitkThrow() << " Could not read file " << fileName;
}
// if pic image only 2D, the n[2] value is not initialized
unsigned int slices = 1;
if (header->dim == 2)
{
header->n[2] = slices;
}
// First initialize the geometry of the output image by the pic-header
SlicedGeometry3D::Pointer slicedGeometry = mitk::SlicedGeometry3D::New();
PicHelper::InitializeEvenlySpaced(header, header->n[2], slicedGeometry);
// if pic image only 3D, the n[3] value is not initialized
unsigned int timesteps = 1;
if (header->dim > 3)
{
timesteps = header->n[3];
}
slicedGeometry->ImageGeometryOn();
ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
timeGeometry->Initialize(slicedGeometry, timesteps);
// Cast the pic descriptor to ImageDescriptor and initialize the output
output->Initialize(CastToImageDescriptor(header));
output->SetTimeGeometry(timeGeometry);
mitkIpPicFree(header);
return output;
}
std::vector<BaseData::Pointer> ItkImageIO::Read()
{
std::vector<BaseData::Pointer> result;
const std::string& locale = "C";
const std::string& currLocale = setlocale( LC_ALL, NULL );
if ( locale.compare(currLocale)!=0 )
{
try
{
setlocale(LC_ALL, locale.c_str());
}
catch(...)
{
MITK_INFO << "Could not set locale " << locale;
}
}
Image::Pointer image = Image::New();
const unsigned int MINDIM = 2;
const unsigned int MAXDIM = 4;
const std::string path = this->GetLocalFileName();
MITK_INFO << "loading " << path << " via itk::ImageIOFactory... " << std::endl;
// Check to see if we can read the file given the name or prefix
if (path.empty())
{
mitkThrow() << "Empty filename in mitk::ItkImageIO ";
}
// Got to allocate space for the image. Determine the characteristics of
// the image.
m_ImageIO->SetFileName( path );
m_ImageIO->ReadImageInformation();
unsigned int ndim = m_ImageIO->GetNumberOfDimensions();
if ( ndim < MINDIM || ndim > MAXDIM )
{
MITK_WARN << "Sorry, only dimensions 2, 3 and 4 are supported. The given file has " << ndim << " dimensions! Reading as 4D.";
ndim = MAXDIM;
}
itk::ImageIORegion ioRegion( ndim );
itk::ImageIORegion::SizeType ioSize = ioRegion.GetSize();
itk::ImageIORegion::IndexType ioStart = ioRegion.GetIndex();
unsigned int dimensions[ MAXDIM ];
dimensions[ 0 ] = 0;
dimensions[ 1 ] = 0;
dimensions[ 2 ] = 0;
dimensions[ 3 ] = 0;
ScalarType spacing[ MAXDIM ];
spacing[ 0 ] = 1.0f;
spacing[ 1 ] = 1.0f;
spacing[ 2 ] = 1.0f;
spacing[ 3 ] = 1.0f;
Point3D origin;
origin.Fill(0);
unsigned int i;
for ( i = 0; i < ndim ; ++i )
{
ioStart[ i ] = 0;
ioSize[ i ] = m_ImageIO->GetDimensions( i );
if(i<MAXDIM)
{
dimensions[ i ] = m_ImageIO->GetDimensions( i );
spacing[ i ] = m_ImageIO->GetSpacing( i );
if(spacing[ i ] <= 0)
spacing[ i ] = 1.0f;
}
if(i<3)
{
origin[ i ] = m_ImageIO->GetOrigin( i );
}
}
ioRegion.SetSize( ioSize );
ioRegion.SetIndex( ioStart );
MITK_INFO << "ioRegion: " << ioRegion << std::endl;
m_ImageIO->SetIORegion( ioRegion );
void* buffer = new unsigned char[m_ImageIO->GetImageSizeInBytes()];
m_ImageIO->Read( buffer );
image->Initialize( MakePixelType(m_ImageIO), ndim, dimensions );
image->SetImportChannel( buffer, 0, Image::ManageMemory );
// access direction of itk::Image and include spacing
mitk::Matrix3D matrix;
matrix.SetIdentity();
unsigned int j, itkDimMax3 = (ndim >= 3? 3 : ndim);
for ( i=0; i < itkDimMax3; ++i)
for( j=0; j < itkDimMax3; ++j )
matrix[i][j] = m_ImageIO->GetDirection(j)[i];
// re-initialize PlaneGeometry with origin and direction
PlaneGeometry* planeGeometry = image->GetSlicedGeometry(0)->GetPlaneGeometry(0);
planeGeometry->SetOrigin(origin);
planeGeometry->GetIndexToWorldTransform()->SetMatrix(matrix);
// re-initialize SlicedGeometry3D
SlicedGeometry3D* slicedGeometry = image->GetSlicedGeometry(0);
slicedGeometry->InitializeEvenlySpaced(planeGeometry, image->GetDimension(2));
slicedGeometry->SetSpacing(spacing);
MITK_INFO << slicedGeometry->GetCornerPoint(false,false,false);
MITK_INFO << slicedGeometry->GetCornerPoint(true,true,true);
// re-initialize TimeGeometry
ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
timeGeometry->Initialize(slicedGeometry, image->GetDimension(3));
image->SetTimeGeometry(timeGeometry);
buffer = NULL;
MITK_INFO << "number of image components: "<< image->GetPixelType().GetNumberOfComponents() << std::endl;
const itk::MetaDataDictionary& dictionary = m_ImageIO->GetMetaDataDictionary();
for (itk::MetaDataDictionary::ConstIterator iter = dictionary.Begin(), iterEnd = dictionary.End();
iter != iterEnd; ++iter)
{
std::string key = std::string("meta.") + iter->first;
if (iter->second->GetMetaDataObjectTypeInfo() == typeid(std::string))
{
std::string value = dynamic_cast<itk::MetaDataObject<std::string>*>(iter->second.GetPointer())->GetMetaDataObjectValue();
image->SetProperty(key.c_str(), mitk::StringProperty::New(value));
}
}
MITK_INFO << "...finished!" << std::endl;
try
{
setlocale(LC_ALL, currLocale.c_str());
}
catch(...)
{
MITK_INFO << "Could not reset locale " << currLocale;
}
result.push_back(image.GetPointer());
return result;
}