void mitk::ImageStatisticsHolder::ComputeImageStatistics(int t, unsigned int component)
{
// timestep valid?
if (!m_Image->IsValidTimeStep(t)) return;
// image modified?
if (this->m_Image->GetMTime() > m_LastRecomputeTimeStamp.GetMTime())
this->ResetImageStatistics();
Expand(t+1);
// do we have valid information already?
if( m_ScalarMin[t] != itk::NumericTraits<ScalarType>::max() ||
m_Scalar2ndMin[t] != itk::NumericTraits<ScalarType>::max() ) return; // Values already calculated before...
// used to avoid statistics calculation on qball images. property will be replaced as soons as bug 17928 is merged and the diffusion image refactoring is complete.
mitk::BoolProperty* isqball = dynamic_cast< mitk::BoolProperty* >( m_Image->GetProperty( "IsQballImage" ).GetPointer() );
const mitk::PixelType pType = m_Image->GetPixelType(0);
if(pType.GetNumberOfComponents() == 1 && (pType.GetPixelType() != itk::ImageIOBase::UNKNOWNPIXELTYPE) && (pType.GetPixelType() != itk::ImageIOBase::VECTOR) )
{
// recompute
mitk::ImageTimeSelector::Pointer timeSelector = this->GetTimeSelector();
if(timeSelector.IsNotNull())
{
timeSelector->SetTimeNr(t);
timeSelector->UpdateLargestPossibleRegion();
const mitk::Image* image = timeSelector->GetOutput();
AccessByItk_2( image, _ComputeExtremaInItkImage, this, t );
}
}
else if (pType.GetPixelType() == itk::ImageIOBase::VECTOR && (!isqball || !isqball->GetValue())) // we have a vector image
{
// recompute
mitk::ImageTimeSelector::Pointer timeSelector = this->GetTimeSelector();
if(timeSelector.IsNotNull())
{
timeSelector->SetTimeNr(t);
timeSelector->UpdateLargestPossibleRegion();
const mitk::Image* image = timeSelector->GetOutput();
AccessVectorPixelTypeByItk_n( image, _ComputeExtremaInItkVectorImage, (this, t, component) );
}
}
else
{
m_ScalarMin[t] = 0;
m_ScalarMax[t] = 255;
m_Scalar2ndMin[t] = 0;
m_Scalar2ndMax[t] = 255;
}
}
double mitk::Image::GetPixelValueByIndex(const itk::Index<3> &position, unsigned int timestep, unsigned int component)
{
double value = 0;
if (this->GetTimeSteps() < timestep)
{
timestep = this->GetTimeSteps();
}
value = 0.0;
const unsigned int* imageDims = this->m_ImageDescriptor->GetDimensions();
const mitk::PixelType ptype = this->m_ImageDescriptor->GetChannelTypeById(0);
// Comparison ?>=0 not needed since all position[i] and timestep are unsigned int
// (position[0]>=0 && position[1] >=0 && position[2]>=0 && timestep>=0)
// bug-11978 : we still need to catch index with negative values
if ( position[0] < 0 ||
position[1] < 0 ||
position[2] < 0 )
{
MITK_WARN << "Given position ("<< position << ") is out of image range, returning 0." ;
}
// check if the given position is inside the index range of the image, the 3rd dimension needs to be compared only if the dimension is not 0
else if ( (unsigned int)position[0] >= imageDims[0] ||
(unsigned int)position[1] >= imageDims[1] ||
( imageDims[2] && (unsigned int)position[2] >= imageDims[2] ))
{
MITK_WARN << "Given position ("<< position << ") is out of image range, returning 0." ;
}
else
{
const unsigned int offset = component + ptype.GetNumberOfComponents()*(position[0] + position[1]*imageDims[0] + position[2]*imageDims[0]*imageDims[1] + timestep*imageDims[0]*imageDims[1]*imageDims[2]);
mitkPixelTypeMultiplex3( AccessPixel, ptype, this->GetData(), offset, value );
}
return value;
}
void mitk::ImageStatisticsHolder::ComputeImageStatistics(int t)
{
// timestep valid?
if (!m_Image->IsValidTimeStep(t)) return;
// image modified?
if (this->m_Image->GetMTime() > m_LastRecomputeTimeStamp.GetMTime())
this->ResetImageStatistics();
Expand(t+1);
// do we have valid information already?
if( m_ScalarMin[t] != itk::NumericTraits<ScalarType>::max() ||
m_Scalar2ndMin[t] != itk::NumericTraits<ScalarType>::max() ) return; // Values already calculated before...
const mitk::PixelType pType = m_Image->GetPixelType(0);
if(pType.GetNumberOfComponents() == 1 && (pType.GetPixelType() != itk::ImageIOBase::UNKNOWNPIXELTYPE) && (pType.GetPixelType() != itk::ImageIOBase::VECTOR) )
{
// recompute
mitk::ImageTimeSelector::Pointer timeSelector = this->GetTimeSelector();
if(timeSelector.IsNotNull())
{
timeSelector->SetTimeNr(t);
timeSelector->UpdateLargestPossibleRegion();
const mitk::Image* image = timeSelector->GetOutput();
AccessByItk_2( image, _ComputeExtremaInItkImage, this, t );
}
}
else
{
m_ScalarMin[t] = 0;
m_ScalarMax[t] = 255;
m_Scalar2ndMin[t] = 0;
m_Scalar2ndMax[t] = 255;
}
}
void ItkImageIO::Write()
{
const mitk::Image *image = dynamic_cast<const mitk::Image *>(this->GetInput());
if (image == NULL)
{
mitkThrow() << "Cannot write non-image data";
}
// Switch the current locale to "C"
LocaleSwitch localeSwitch("C");
// Clone the image geometry, because we might have to change it
// for writing purposes
BaseGeometry::Pointer geometry = image->GetGeometry()->Clone();
// Check if geometry information will be lost
if (image->GetDimension() == 2 && !geometry->Is2DConvertable())
{
MITK_WARN << "Saving a 2D image with 3D geometry information. Geometry information will be lost! You might "
"consider using Convert2Dto3DImageFilter before saving.";
// set matrix to identity
mitk::AffineTransform3D::Pointer affTrans = mitk::AffineTransform3D::New();
affTrans->SetIdentity();
mitk::Vector3D spacing = geometry->GetSpacing();
mitk::Point3D origin = geometry->GetOrigin();
geometry->SetIndexToWorldTransform(affTrans);
geometry->SetSpacing(spacing);
geometry->SetOrigin(origin);
}
LocalFile localFile(this);
const std::string path = localFile.GetFileName();
MITK_INFO << "Writing image: " << path << std::endl;
try
{
// Implementation of writer using itkImageIO directly. This skips the use
// of templated itkImageFileWriter, which saves the multiplexing on MITK side.
const unsigned int dimension = image->GetDimension();
const unsigned int *const dimensions = image->GetDimensions();
const mitk::PixelType pixelType = image->GetPixelType();
const mitk::Vector3D mitkSpacing = geometry->GetSpacing();
const mitk::Point3D mitkOrigin = geometry->GetOrigin();
// Due to templating in itk, we are forced to save a 4D spacing and 4D Origin,
// though they are not supported in MITK
itk::Vector<double, 4u> spacing4D;
spacing4D[0] = mitkSpacing[0];
spacing4D[1] = mitkSpacing[1];
spacing4D[2] = mitkSpacing[2];
spacing4D[3] = 1; // There is no support for a 4D spacing. However, we should have a valid value here
itk::Vector<double, 4u> origin4D;
origin4D[0] = mitkOrigin[0];
origin4D[1] = mitkOrigin[1];
origin4D[2] = mitkOrigin[2];
origin4D[3] = 0; // There is no support for a 4D origin. However, we should have a valid value here
// Set the necessary information for imageIO
m_ImageIO->SetNumberOfDimensions(dimension);
m_ImageIO->SetPixelType(pixelType.GetPixelType());
m_ImageIO->SetComponentType(pixelType.GetComponentType() < PixelComponentUserType ?
static_cast<itk::ImageIOBase::IOComponentType>(pixelType.GetComponentType()) :
itk::ImageIOBase::UNKNOWNCOMPONENTTYPE);
m_ImageIO->SetNumberOfComponents(pixelType.GetNumberOfComponents());
itk::ImageIORegion ioRegion(dimension);
for (unsigned int i = 0; i < dimension; i++)
{
m_ImageIO->SetDimensions(i, dimensions[i]);
m_ImageIO->SetSpacing(i, spacing4D[i]);
m_ImageIO->SetOrigin(i, origin4D[i]);
mitk::Vector3D mitkDirection;
mitkDirection.SetVnlVector(geometry->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(i));
itk::Vector<double, 4u> direction4D;
direction4D[0] = mitkDirection[0];
direction4D[1] = mitkDirection[1];
direction4D[2] = mitkDirection[2];
// MITK only supports a 3x3 direction matrix. Due to templating in itk, however, we must
// save a 4x4 matrix for 4D images. in this case, add an homogneous component to the matrix.
if (i == 3)
{
direction4D[3] = 1; // homogenous component
}
else
{
direction4D[3] = 0;
}
vnl_vector<double> axisDirection(dimension);
for (unsigned int j = 0; j < dimension; j++)
{
axisDirection[j] = direction4D[j] / spacing4D[i];
}
m_ImageIO->SetDirection(i, axisDirection);
ioRegion.SetSize(i, image->GetLargestPossibleRegion().GetSize(i));
ioRegion.SetIndex(i, image->GetLargestPossibleRegion().GetIndex(i));
}
// use compression if available
m_ImageIO->UseCompressionOn();
m_ImageIO->SetIORegion(ioRegion);
m_ImageIO->SetFileName(path);
// Handle time geometry
const ArbitraryTimeGeometry *arbitraryTG = dynamic_cast<const ArbitraryTimeGeometry *>(image->GetTimeGeometry());
if (arbitraryTG)
{
itk::EncapsulateMetaData<std::string>(m_ImageIO->GetMetaDataDictionary(),
PROPERTY_KEY_TIMEGEOMETRY_TYPE,
ArbitraryTimeGeometry::GetStaticNameOfClass());
std::stringstream stream;
stream << arbitraryTG->GetTimeBounds(0)[0];
for (TimeStepType pos = 0; pos < arbitraryTG->CountTimeSteps(); ++pos)
{
stream << " " << arbitraryTG->GetTimeBounds(pos)[1];
}
std::string data = stream.str();
itk::EncapsulateMetaData<std::string>(
m_ImageIO->GetMetaDataDictionary(), PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS, data);
}
// Handle properties
mitk::PropertyList::Pointer imagePropertyList = image->GetPropertyList();
for (const auto &property : *imagePropertyList->GetMap())
{
IPropertyPersistence::InfoResultType infoList =
mitk::CoreServices::GetPropertyPersistence()->GetInfo(property.first, GetMimeType()->GetName(), true);
if (infoList.empty())
{
continue;
}
std::string value = infoList.front()->GetSerializationFunction()(property.second);
if (value == mitk::BaseProperty::VALUE_CANNOT_BE_CONVERTED_TO_STRING)
{
continue;
}
std::string key = infoList.front()->GetKey();
itk::EncapsulateMetaData<std::string>(m_ImageIO->GetMetaDataDictionary(), key, value);
}
ImageReadAccessor imageAccess(image);
m_ImageIO->Write(imageAccess.GetData());
}
catch (const std::exception &e)
{
mitkThrow() << e.what();
}
}
void LabelSetImageIO::Write()
{
ValidateOutputLocation();
const LabelSetImage* input = static_cast<const LabelSetImage*>(this->GetInput());
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 " << currLocale;
}
}
mitk::Image::Pointer inputVector = mitk::LabelSetImageConverter::ConvertLabelSetImageToImage(input);
// image write
if ( inputVector.IsNull() )
{
mitkThrow() << "Cannot write non-image data";
}
itk::NrrdImageIO::Pointer nrrdImageIo = itk::NrrdImageIO::New();
// Clone the image geometry, because we might have to change it
// for writing purposes
BaseGeometry::Pointer geometry = inputVector->GetGeometry()->Clone();
// Check if geometry information will be lost
if (inputVector->GetDimension() == 2 &&
!geometry->Is2DConvertable())
{
MITK_WARN << "Saving a 2D image with 3D geometry information. Geometry information will be lost! You might consider using Convert2Dto3DImageFilter before saving.";
// set matrix to identity
mitk::AffineTransform3D::Pointer affTrans = mitk::AffineTransform3D::New();
affTrans->SetIdentity();
mitk::Vector3D spacing = geometry->GetSpacing();
mitk::Point3D origin = geometry->GetOrigin();
geometry->SetIndexToWorldTransform(affTrans);
geometry->SetSpacing(spacing);
geometry->SetOrigin(origin);
}
LocalFile localFile(this);
const std::string path = localFile.GetFileName();
MITK_INFO << "Writing image: " << path << std::endl;
try
{
// Implementation of writer using itkImageIO directly. This skips the use
// of templated itkImageFileWriter, which saves the multiplexing on MITK side.
const unsigned int dimension = inputVector->GetDimension();
const unsigned int* const dimensions = inputVector->GetDimensions();
const mitk::PixelType pixelType = inputVector->GetPixelType();
const mitk::Vector3D mitkSpacing = geometry->GetSpacing();
const mitk::Point3D mitkOrigin = geometry->GetOrigin();
// Due to templating in itk, we are forced to save a 4D spacing and 4D Origin,
// though they are not supported in MITK
itk::Vector<double, 4u> spacing4D;
spacing4D[0] = mitkSpacing[0];
spacing4D[1] = mitkSpacing[1];
spacing4D[2] = mitkSpacing[2];
spacing4D[3] = 1; // There is no support for a 4D spacing. However, we should have a valid value here
itk::Vector<double, 4u> origin4D;
origin4D[0] = mitkOrigin[0];
origin4D[1] = mitkOrigin[1];
origin4D[2] = mitkOrigin[2];
origin4D[3] = 0; // There is no support for a 4D origin. However, we should have a valid value here
// Set the necessary information for imageIO
nrrdImageIo->SetNumberOfDimensions(dimension);
nrrdImageIo->SetPixelType(pixelType.GetPixelType());
nrrdImageIo->SetComponentType(pixelType.GetComponentType() < PixelComponentUserType ?
static_cast<itk::ImageIOBase::IOComponentType>(pixelType.GetComponentType()) :
itk::ImageIOBase::UNKNOWNCOMPONENTTYPE);
nrrdImageIo->SetNumberOfComponents(pixelType.GetNumberOfComponents());
itk::ImageIORegion ioRegion(dimension);
for (unsigned int i = 0; i < dimension; i++)
{
nrrdImageIo->SetDimensions(i, dimensions[i]);
nrrdImageIo->SetSpacing(i, spacing4D[i]);
nrrdImageIo->SetOrigin(i, origin4D[i]);
mitk::Vector3D mitkDirection;
mitkDirection.SetVnlVector(geometry->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(i));
itk::Vector<double, 4u> direction4D;
direction4D[0] = mitkDirection[0];
direction4D[1] = mitkDirection[1];
direction4D[2] = mitkDirection[2];
// MITK only supports a 3x3 direction matrix. Due to templating in itk, however, we must
// save a 4x4 matrix for 4D images. in this case, add an homogneous component to the matrix.
if (i == 3)
{
direction4D[3] = 1; // homogenous component
}
else
{
direction4D[3] = 0;
}
vnl_vector<double> axisDirection(dimension);
for (unsigned int j = 0; j < dimension; j++)
{
axisDirection[j] = direction4D[j] / spacing4D[i];
}
nrrdImageIo->SetDirection(i, axisDirection);
ioRegion.SetSize(i, inputVector->GetLargestPossibleRegion().GetSize(i));
ioRegion.SetIndex(i, inputVector->GetLargestPossibleRegion().GetIndex(i));
}
//use compression if available
nrrdImageIo->UseCompressionOn();
nrrdImageIo->SetIORegion(ioRegion);
nrrdImageIo->SetFileName(path);
// label set specific meta data
char keybuffer[512];
char valbuffer[512];
sprintf(keybuffer, "modality");
sprintf(valbuffer, "org.mitk.image.multilabel");
itk::EncapsulateMetaData<std::string>(nrrdImageIo->GetMetaDataDictionary(), std::string(keybuffer), std::string(valbuffer));
sprintf(keybuffer, "layers");
sprintf(valbuffer, "%1d", input->GetNumberOfLayers());
itk::EncapsulateMetaData<std::string>(nrrdImageIo->GetMetaDataDictionary(), std::string(keybuffer), std::string(valbuffer));
for (unsigned int layerIdx = 0; layerIdx<input->GetNumberOfLayers(); layerIdx++)
{
sprintf(keybuffer, "layer_%03d", layerIdx); // layer idx
sprintf(valbuffer, "%1d", input->GetNumberOfLabels(layerIdx)); // number of labels for the layer
itk::EncapsulateMetaData<std::string>(nrrdImageIo->GetMetaDataDictionary(), std::string(keybuffer), std::string(valbuffer));
mitk::LabelSet::LabelContainerConstIteratorType iter = input->GetLabelSet(layerIdx)->IteratorConstBegin();
unsigned int count(0);
while (iter != input->GetLabelSet(layerIdx)->IteratorConstEnd())
{
std::auto_ptr<TiXmlDocument> document;
document.reset(new TiXmlDocument());
TiXmlDeclaration* decl = new TiXmlDeclaration("1.0", "", ""); // TODO what to write here? encoding? etc....
document->LinkEndChild(decl);
TiXmlElement * labelElem = GetLabelAsTiXmlElement(iter->second);
document->LinkEndChild(labelElem);
TiXmlPrinter printer;
printer.SetIndent("");
printer.SetLineBreak("");
document->Accept(&printer);
sprintf(keybuffer, "org.mitk.label_%03u_%05u", layerIdx, count);
itk::EncapsulateMetaData<std::string>(nrrdImageIo->GetMetaDataDictionary(), std::string(keybuffer), printer.Str());
++iter;
++count;
}
}
// end label set specific meta data
ImageReadAccessor imageAccess(inputVector);
nrrdImageIo->Write(imageAccess.GetData());
}
catch (const std::exception& e)
{
mitkThrow() << e.what();
}
// end image write
try
{
setlocale(LC_ALL, currLocale.c_str());
}
catch(...)
{
mitkThrow() << "Could not reset locale " << currLocale;
}
}
void ItkImageIO::Write()
{
const mitk::Image* image = dynamic_cast<const mitk::Image*>(this->GetInput());
if (image == NULL)
{
mitkThrow() << "Cannot write non-image data";
}
struct LocaleSwitch
{
LocaleSwitch(const std::string& newLocale)
: m_OldLocale(std::setlocale(LC_ALL, NULL))
, m_NewLocale(newLocale)
{
if (m_OldLocale == NULL)
{
m_OldLocale = "";
}
else if (m_NewLocale != m_OldLocale)
{
// set the locale
if (std::setlocale(LC_ALL, m_NewLocale.c_str()) == NULL)
{
MITK_INFO << "Could not set locale " << m_NewLocale;
m_OldLocale = NULL;
}
}
}
~LocaleSwitch()
{
if (m_OldLocale != NULL && std::setlocale(LC_ALL, m_OldLocale) == NULL)
{
MITK_INFO << "Could not reset locale " << m_OldLocale;
}
}
private:
const char* m_OldLocale;
const std::string m_NewLocale;
};
// Switch the current locale to "C"
LocaleSwitch localeSwitch("C");
// Clone the image geometry, because we might have to change it
// for writing purposes
BaseGeometry::Pointer geometry = image->GetGeometry()->Clone();
// Check if geometry information will be lost
if (image->GetDimension() == 2 &&
!geometry->Is2DConvertable())
{
MITK_WARN << "Saving a 2D image with 3D geometry information. Geometry information will be lost! You might consider using Convert2Dto3DImageFilter before saving.";
// set matrix to identity
mitk::AffineTransform3D::Pointer affTrans = mitk::AffineTransform3D::New();
affTrans->SetIdentity();
mitk::Vector3D spacing = geometry->GetSpacing();
mitk::Point3D origin = geometry->GetOrigin();
geometry->SetIndexToWorldTransform(affTrans);
geometry->SetSpacing(spacing);
geometry->SetOrigin(origin);
}
LocalFile localFile(this);
const std::string path = localFile.GetFileName();
MITK_INFO << "Writing image: " << path << std::endl;
try
{
// Implementation of writer using itkImageIO directly. This skips the use
// of templated itkImageFileWriter, which saves the multiplexing on MITK side.
const unsigned int dimension = image->GetDimension();
const unsigned int* const dimensions = image->GetDimensions();
const mitk::PixelType pixelType = image->GetPixelType();
const mitk::Vector3D mitkSpacing = geometry->GetSpacing();
const mitk::Point3D mitkOrigin = geometry->GetOrigin();
// Due to templating in itk, we are forced to save a 4D spacing and 4D Origin,
// though they are not supported in MITK
itk::Vector<double, 4u> spacing4D;
spacing4D[0] = mitkSpacing[0];
spacing4D[1] = mitkSpacing[1];
spacing4D[2] = mitkSpacing[2];
spacing4D[3] = 1; // There is no support for a 4D spacing. However, we should have a valid value here
itk::Vector<double, 4u> origin4D;
origin4D[0] = mitkOrigin[0];
origin4D[1] = mitkOrigin[1];
origin4D[2] = mitkOrigin[2];
origin4D[3] = 0; // There is no support for a 4D origin. However, we should have a valid value here
// Set the necessary information for imageIO
m_ImageIO->SetNumberOfDimensions(dimension);
m_ImageIO->SetPixelType(pixelType.GetPixelType());
m_ImageIO->SetComponentType(pixelType.GetComponentType() < PixelComponentUserType ?
static_cast<itk::ImageIOBase::IOComponentType>(pixelType.GetComponentType()) :
itk::ImageIOBase::UNKNOWNCOMPONENTTYPE);
m_ImageIO->SetNumberOfComponents( pixelType.GetNumberOfComponents() );
itk::ImageIORegion ioRegion( dimension );
for(unsigned int i = 0; i < dimension; i++)
{
m_ImageIO->SetDimensions(i, dimensions[i]);
m_ImageIO->SetSpacing(i, spacing4D[i]);
m_ImageIO->SetOrigin(i, origin4D[i]);
mitk::Vector3D mitkDirection;
mitkDirection.SetVnlVector(geometry->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(i));
itk::Vector<double, 4u> direction4D;
direction4D[0] = mitkDirection[0];
direction4D[1] = mitkDirection[1];
direction4D[2] = mitkDirection[2];
// MITK only supports a 3x3 direction matrix. Due to templating in itk, however, we must
// save a 4x4 matrix for 4D images. in this case, add an homogneous component to the matrix.
if (i == 3)
{
direction4D[3] = 1; // homogenous component
}
else
{
direction4D[3] = 0;
}
vnl_vector<double> axisDirection(dimension);
for(unsigned int j = 0; j < dimension; j++)
{
axisDirection[j] = direction4D[j] / spacing4D[i];
}
m_ImageIO->SetDirection(i, axisDirection);
ioRegion.SetSize(i, image->GetLargestPossibleRegion().GetSize(i));
ioRegion.SetIndex(i, image->GetLargestPossibleRegion().GetIndex(i));
}
//use compression if available
m_ImageIO->UseCompressionOn();
m_ImageIO->SetIORegion(ioRegion);
m_ImageIO->SetFileName(path);
// ***** Remove const_cast after bug 17952 is fixed ****
ImageReadAccessor imageAccess(const_cast<mitk::Image*>(image));
m_ImageIO->Write(imageAccess.GetData());
}
catch (const std::exception& e)
{
mitkThrow() << e.what();
}
}