Templateitk::OrientImageFilter< TInputImage, TOutputImage

This class satisfies a common requirement in medical imaging, which is to properly orient a 3 dimensional image with respect to anatomical features. Due to the wide variety of hardware used to generate 3D images of human anatomy, and the even wider variety of image processing software, it is often necessary to re-orient image volume data.

OrientImageFilter depends on a set of constants that describe all possible permutations of Axes. These reside in itkSpatialOrientation.h. These are labeled according to the following scheme: Directions are labeled in terms of following pairs:

The initials of these directions are used in a 3 letter code in the enumerated type itk::SpatialOrientation::ValidCoordinateOrientationFlags. The initials are given fastest moving index first, second fastest second, third fastest third. Examples:

In order to use this filter, you need to supply an input image, the current orientation of the input image (set with SetGivenCoordinateOrientation) and the desired orientation. (set with SetDesiredCoordinateOrientation). You may explicitly set the DesiredOrientation with SetDesiredCoordinateOrientation (if UseImageDirection is "off") or you can use the image's direction cosines to set the DesiredOrientation (if UseImageDirection is "on"). When reading image files that define the coordinate orientation of the image, the current orientation is stored in the MetadataDictionary for the itk::Image object and the Image.Direction direction cosine matrix created from the file.

As an example, if you wished to keep all images within your program in the orientation corresponding to the Analyze file format's 'CORONAL' orientation you could do something like the following

 #include "itkAnalyzeImageIO.h"
 #include "itkMetaDataObject.h"
 #include "itkImage.h"
 #include "itkSpatialOrientation.h"
 #include "itkOrientImageFilter.h"
 #include "itkIOCommon.h"
 typedef itk::Image<unsigned char,3> ImageType;
 typedef itk::ImageFileReader< TstImageType > ImageReaderType ;
 ImageType::Pointer ReadAnalyzeFile(const char *path)
 {
   itk::AnalyzeImageIO::Pointer io = itk::AnalyzeImageIO::New();
   ImageReaderType::Pointer fileReader = ImageReaderType::New();
   fileReader->SetImageIO(io);
   fileReader->SetFileName(path);
   fileReader->Update();
   ImageType::Pointer rval = fileReader->GetOutput();
   
   itk::SpatialOrientation::ValidCoordinateOrientationFlags fileOrientation;
   itk::ExposeMetaData<itk::SpatialOrientation::ValidCoordinateOrientationFlags>
     (rval->GetMetaDataDictionary(),itk::ITK_CoordinateOrientation,fileOrientation);
   itk::OrientImageFilter<ImageType,ImageType>::Pointer orienter =
     itk::OrientImageFilter<ImageType,ImageType>::New();
   orienter->SetGivenCoordinateOrientation(fileOrientation);
   orienter->SetDesiredCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RIP);
   orienter->SetInput(rval);
   orienter->Update();
   rval = orienter->GetOutput();
   return rval;
 }

 #include "itkAnalyzeImageIO.h"
 #include "itkImage.h"
 #include "itkOrientImageFilter.h"
 typedef itk::Image<unsigned char,3> ImageType;
 typedef itk::ImageFileReader< TstImageType > ImageReaderType ;
 ImageType::Pointer ReadAnalyzeFile(const char *path)
 {
   itk::AnalyzeImageIO::Pointer io = itk::AnalyzeImageIO::New();
   ImageReaderType::Pointer fileReader = ImageReaderType::New();
   fileReader->SetImageIO(io);
   fileReader->SetFileName(path);
   fileReader->Update();
   ImageType::Pointer rval = fileReader->GetOutput();
   
   itk::OrientImageFilter<ImageType,ImageType>::Pointer orienter =
     itk::OrientImageFilter<ImageType,ImageType>::New();
   orienter->UseImageDirectionOn();
   orienter->SetDesiredCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RIP);
   orienter->SetInput(rval);
   orienter->Update();
   rval = orienter->GetOutput();
   return rval;
 }

Member Typedef Documentation

Member Enumeration Documentation

template<class TInputImage, class TOutputImage>
anonymous enum

The dimensions of the input image must equal those of the output image.

Enumeration values:

SameDimension

Definition at line 183 of file itkOrientImageFilter.h.

template<class TInputImage, class TOutputImage>
anonymous enum

The dimension of the input image must be 3.

Enumeration values:

DimensionShouldBe3

Definition at line 187 of file itkOrientImageFilter.h.

Constructor & Destructor Documentation

Member Function Documentation

template<class TInputImage, class TOutputImage>
virtual void itk::OrientImageFilter< TInputImage, TOutputImage >::GenerateOutputInformation	(		)	`[virtual]`

OrientImageFilter produces an image which is a different dimensionality than its input image, in general. As such, OrientImageFilter needs to provide an implementation for GenerateOutputInformation() in order to inform the pipeline execution model. The original documentation of this method is below.

See also:: ProcessObject::GenerateOutputInformaton()

Reimplemented from itk::ProcessObject.

template<class TInputImage, class TOutputImage>
virtual CoordinateOrientationCode itk::OrientImageFilter< TInputImage, TOutputImage >::GetDesiredCoordinateOrientation	(		)	`[virtual]`

Set/Get the orientation codes to define the coordinate transform.

template<class TInputImage, class TOutputImage>
virtual const FlipAxesArrayType& itk::OrientImageFilter< TInputImage, TOutputImage >::GetFlipAxes	(		)	`[virtual]`

Get flip axes.

template<class TInputImage, class TOutputImage>
virtual CoordinateOrientationCode itk::OrientImageFilter< TInputImage, TOutputImage >::GetGivenCoordinateOrientation	(		)	`[virtual]`

Set/Get the orientation codes to define the coordinate transform.

template<class TInputImage, class TOutputImage>
virtual const PermuteOrderArrayType& itk::OrientImageFilter< TInputImage, TOutputImage >::GetPermuteOrder	(		)	`[virtual]`

Get axes permute order.

template<class TInputImage, class TOutputImage>
virtual bool itk::OrientImageFilter< TInputImage, TOutputImage >::GetUseImageDirection	(		)	`[virtual]`

Controls how the GivenCoordinateOrientation is determined. If "on", the direction cosines determine the coordinate orientation. If "off", the user must use the SetGivenCoordinateOrientation method to establis the orientation. For compatbility with the original API, the default if "off".

template<class TInputImage, class TOutputImage>
bool itk::OrientImageFilter< TInputImage, TOutputImage >::NeedToFlip	(		)	`[protected]`

* Member functions used by GenerateData:

template<class TInputImage, class TOutputImage>
bool itk::OrientImageFilter< TInputImage, TOutputImage >::NeedToPermute	(		)	`[protected]`

* Member functions used by GenerateData:

template<class TInputImage, class TOutputImage>
Pointer itk::OrientImageFilter< TInputImage, TOutputImage >::New	(		)	`[static]`

Standard New method.

Reimplemented from itk::Object.

template<class TInputImage, class TOutputImage>
void itk::OrientImageFilter< TInputImage, TOutputImage >::PrintSelf	(	std::ostream &	os,
		Indent	indent
	)	const `[protected, virtual]`

Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

template<class TInputImage, class TOutputImage>
void itk::OrientImageFilter< TInputImage, TOutputImage >::SetDesiredCoordinateOrientation	(	CoordinateOrientationCode	newCode	)

Set/Get the orientation codes to define the coordinate transform.

template<class TInputImage, class TOutputImage>
void itk::OrientImageFilter< TInputImage, TOutputImage >::SetDesiredCoordinateOrientationToAxial	(		)	`[inline]`

Convenience methods to set desired slice orientation These methods allow a limited selection of slice orientations without having to specify the SpatialOrientation.

SetDesiredCoordinateOrientationToAxial is equivalent to SetDesiredCoordinateOrientation (ITK_COORDINATE_ORIENTATION_RAI).

SetDesiredCoordinateOrientationToCoronal is equivalent to SetDesiredCoordinateOrientation (ITK_COORDINATE_ORIENTATION_RSA).

SetDesiredCoordinateOrientationToSagittal is equivalent to SetDesiredCoordinateOrientation (ITK_COORDINATE_ORIENTATION_ASL).

Definition at line 233 of file itkOrientImageFilter.h.

template<class TInputImage, class TOutputImage>
void itk::OrientImageFilter< TInputImage, TOutputImage >::SetDesiredCoordinateOrientationToCoronal	(		)	`[inline]`

Convenience methods to set desired slice orientation These methods allow a limited selection of slice orientations without having to specify the SpatialOrientation.

SetDesiredCoordinateOrientationToAxial is equivalent to SetDesiredCoordinateOrientation (ITK_COORDINATE_ORIENTATION_RAI).

SetDesiredCoordinateOrientationToCoronal is equivalent to SetDesiredCoordinateOrientation (ITK_COORDINATE_ORIENTATION_RSA).

SetDesiredCoordinateOrientationToSagittal is equivalent to SetDesiredCoordinateOrientation (ITK_COORDINATE_ORIENTATION_ASL).

Definition at line 237 of file itkOrientImageFilter.h.

template<class TInputImage, class TOutputImage>
void itk::OrientImageFilter< TInputImage, TOutputImage >::SetDesiredCoordinateOrientationToSagittal	(		)	`[inline]`

Convenience methods to set desired slice orientation These methods allow a limited selection of slice orientations without having to specify the SpatialOrientation.

SetDesiredCoordinateOrientationToAxial is equivalent to SetDesiredCoordinateOrientation (ITK_COORDINATE_ORIENTATION_RAI).

SetDesiredCoordinateOrientationToCoronal is equivalent to SetDesiredCoordinateOrientation (ITK_COORDINATE_ORIENTATION_RSA).

SetDesiredCoordinateOrientationToSagittal is equivalent to SetDesiredCoordinateOrientation (ITK_COORDINATE_ORIENTATION_ASL).

Definition at line 241 of file itkOrientImageFilter.h.

template<class TInputImage, class TOutputImage>
void itk::OrientImageFilter< TInputImage, TOutputImage >::SetGivenCoordinateOrientation	(	CoordinateOrientationCode	newCode	)

Set/Get the orientation codes to define the coordinate transform.

template<class TInputImage, class TOutputImage>
virtual void itk::OrientImageFilter< TInputImage, TOutputImage >::SetUseImageDirection	(	bool	_arg	)	`[virtual]`

template<class TInputImage, class TOutputImage>
virtual void itk::OrientImageFilter< TInputImage, TOutputImage >::UseImageDirectionOff	(		)	`[virtual]`

template<class TInputImage, class TOutputImage>
virtual void itk::OrientImageFilter< TInputImage, TOutputImage >::UseImageDirectionOn	(		)	`[virtual]`


Public Types
typedef OrientImageFilter	Self
typedef ImageToImageFilter< TInputImage, TOutputImage >	Superclass
typedef SmartPointer< Self >	Pointer
typedef SmartPointer< const Self >	ConstPointer
typedef TInputImage	InputImageType
typedef TOutputImage	OutputImageType
typedef InputImageType::Pointer	InputImagePointer
typedef InputImageType::ConstPointer	InputImageConstPointer
typedef InputImageType::RegionType	InputImageRegionType
typedef InputImageType::PixelType	InputImagePixelType
typedef OutputImageType::Pointer	OutputImagePointer
typedef OutputImageType::ConstPointer	OutputImageConstPointer
typedef OutputImageType::RegionType	OutputImageRegionType
typedef OutputImageType::PixelType	OutputImagePixelType
typedef SpatialOrientation::ValidCoordinateOrientationFlags	CoordinateOrientationCode
typedef PermuteAxesImageFilter< TInputImage >	PermuterType
typedef PermuterType::PermuteOrderArrayType	PermuteOrderArrayType
typedef FlipImageFilter< TInputImage >	FlipperType
typedef FlipperType::FlipAxesArrayType	FlipAxesArrayType
enum	{ SameDimension = 0 }
enum	{ DimensionShouldBe3 = 0 }
Public Member Functions
virtual const char *	GetNameOfClass () const
virtual const PermuteOrderArrayType &	GetPermuteOrder ()
virtual const FlipAxesArrayType &	GetFlipAxes ()
virtual void	GenerateOutputInformation ()

	itkStaticConstMacro (InputImageDimension, unsigned int, TInputImage::ImageDimension)
	itkStaticConstMacro (OutputImageDimension, unsigned int, TOutputImage::ImageDimension)

virtual CoordinateOrientationCode	GetGivenCoordinateOrientation ()
void	SetGivenCoordinateOrientation (CoordinateOrientationCode newCode)
virtual CoordinateOrientationCode	GetDesiredCoordinateOrientation ()
void	SetDesiredCoordinateOrientation (CoordinateOrientationCode newCode)

virtual void	UseImageDirectionOn ()
virtual void	UseImageDirectionOff ()
virtual bool	GetUseImageDirection ()
virtual void	SetUseImageDirection (bool _arg)

void	SetDesiredCoordinateOrientationToAxial ()
void	SetDesiredCoordinateOrientationToCoronal ()
void	SetDesiredCoordinateOrientationToSagittal ()
Static Public Member Functions
Pointer	New ()
Protected Member Functions
	OrientImageFilter ()
	~OrientImageFilter ()
void	PrintSelf (std::ostream &os, Indent indent) const
void	GenerateInputRequestedRegion ()
void	EnlargeOutputRequestedRegion (DataObject *)
void	GenerateData ()

void	DeterminePermutationsAndFlips (const SpatialOrientation::ValidCoordinateOrientationFlags fixed_orient, const SpatialOrientation::ValidCoordinateOrientationFlags moving_orient)
bool	NeedToPermute ()
bool	NeedToFlip ()

itk::OrientImageFilter< TInputImage, TOutputImage > Class Template Reference

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Detailed Description

template<class TInputImage, class TOutputImage>
class itk::OrientImageFilter< TInputImage, TOutputImage >

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

itk::OrientImageFilter< TInputImage, TOutputImage > Class Template Reference

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Detailed Description

template<class TInputImage, class TOutputImage> class itk::OrientImageFilter< TInputImage, TOutputImage >

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

template<class TInputImage, class TOutputImage>
class itk::OrientImageFilter< TInputImage, TOutputImage >