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Program: Insight Segmentation & Registration Toolkit
Module: itkImageBase.h
Language: C++
Date: $Date$
Version: $Revision$
Copyright (c) Insight Software Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
Portions of this code are covered under the VTK copyright.
See VTKCopyright.txt or http://www.kitware.com/VTKCopyright.htm for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
#ifndef __itkImageBase_h
#define __itkImageBase_h
#include "itkDataObject.h"
#include "itkImageRegion.h"
#include "itkIndex.h"
#include "itkObjectFactory.h"
#include "itkOffset.h"
#include "itkPoint.h"
#include "itkSize.h"
#include "itkFixedArray.h"
#include "itkPoint.h"
#include "itkMatrix.h"
#include "itkContinuousIndex.h"
#include "itkImageHelper.h"
#include <vnl/vnl_matrix_fixed.txx>
#include "itkImageRegion.h"
#ifdef ITK_USE_TEMPLATE_META_PROGRAMMING_LOOP_UNROLLING
#include "itkImageTransformHelper.h"
#endif
namespace itk
{
/**
* Due to a bug in MSVC, an enum value cannot be accessed out of a template
* parameter until the template class opens. In order for templated classes
* to access the dimension of an image template parameter in defining their
* own dimension, this class is needed as a work-around.
*/
template <typename TImage>
struct GetImageDimension
{
itkStaticConstMacro(ImageDimension, unsigned int, TImage::ImageDimension);
};
/** \class ImageBase
* \brief Base class for templated image classes.
*
* ImageBase is the base class for the templated Image
* classes. ImageBase is templated over the dimension of the image. It
* provides the API and ivars that depend solely on the dimension of
* the image. ImageBase does not store any of the image (pixel) data.
* Storage for the pixels and the pixel access methods are defined in
* subclasses of ImageBase, namely Image and ImageAdaptor.
*
* There are three sets of meta-data describing an image. These are "Region"
* objects that define a portion of an image via a starting index for the
* image array and a size. The ivar LargestPossibleRegion defines the size
* and starting index of the image dataset. The entire image dataset, however,
* may not be resident in memory. The region of the image that is resident in
* memory is defined by the "BufferedRegion". The Buffer is a contiguous block
* of memory. The third set of meta-data defines a region of interest, called
* the "RequestedRegion". The RequestedRegion is used by the pipeline
* execution model to define what a filter is requested to produce.
*
* [RegionIndex, RegionSize] C [BufferIndex, BufferSize]
* C [ImageIndex, ImageSize]
*
* \ingroup ImageObjects
* \ingroup ITKSystemObjects
*
*/
template<unsigned int VImageDimension=2>
class ITK_EXPORT ImageBase : public DataObject
{
public:
/** Standard typedefs. */
typedef ImageBase Self;
typedef DataObject Superclass;
typedef SmartPointer<Self> Pointer;
typedef SmartPointer<const Self> ConstPointer;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkTypeMacro(ImageBase, DataObject);
/** Dimension of the image. This constant is used by functions that are
* templated over image type (as opposed to being templated over pixel
* type and dimension) when they need compile time access to the dimension
* of the image. */
itkStaticConstMacro(ImageDimension, unsigned int, VImageDimension );
/** Index typedef support. An index is used to access pixel values. */
typedef Index<VImageDimension> IndexType;
typedef typename IndexType::IndexValueType IndexValueType;
/** Offset typedef support. An offset represent relative position
* between indices. */
typedef Offset<VImageDimension> OffsetType;
typedef typename OffsetType::OffsetValueType OffsetValueType;
/** Size typedef support. A size is used to define region bounds. */
typedef Size<VImageDimension> SizeType;
typedef typename SizeType::SizeValueType SizeValueType;
/** Region typedef support. A region is used to specify a subset of an image. */
typedef ImageRegion<VImageDimension> RegionType;
/** Spacing typedef support. Spacing holds the size of a pixel. The
* spacing is the geometric distance between image samples. ITK only
* supports positive spacing value: negative values may cause
* undesirable results. */
typedef double SpacingValueType;
typedef Vector<SpacingValueType, VImageDimension> SpacingType;
/** Origin typedef support. The origin is the geometric coordinates
* of the index (0,0). */
typedef double PointValueType;
typedef Point<PointValueType, VImageDimension> PointType;
/** Direction typedef support. The Direction is a matix of
* direction cosines that specify the direction between samples.
* */
typedef Matrix<double, VImageDimension, VImageDimension> DirectionType;
/** Restore object to initialized state. */
void Initialize();
/** Image dimension. The dimension of an image is fixed at construction. */
static unsigned int GetImageDimension()
{ return VImageDimension; }
/** Set the origin of the image. The origin is the geometric
* coordinates of the image origin. It is stored internally
* as double but may be set from float.
* \sa GetOrigin() */
itkSetMacro(Origin, PointType);
virtual void SetOrigin( const double origin[VImageDimension] );
virtual void SetOrigin( const float origin[VImageDimension] );
/** Set the direction cosines of the image. The direction cosines
* are vectors that point from one pixel to the next.
*
* One row of the matrix indicates the direction cosines of the unit vector
* that is parallel to the lines of the image grid corresponding to that
* dimension. For example, and image with Direction matrix
*
* 0.866 0.500
* -0.500 0.866
*
* has an image grid were the fastest changing index (dimension[0]) walks
* over a line that in Physical space is oriented parallel to the vector
* (0.866,0.5). The second fastest changing index (dimension[1]) walks along
* a line that in Physical space is oriented parallel to the vector
* (-0.5,0.866)
*
* The vectors whose direction cosines are stored in the Direction matrix,
* are expected to be orthogonal to each other, and they are expected to form
* a right handed coordinate system, but this is not checked nor enforced in
* the itk::ImageBase.
*
* For details, please see:
*
* http://www.itk.org/Wiki/Proposals:Orientation#Some_notes_on_the_DICOM_convention_and_current_ITK_usage
*
* \sa GetDirection() */
virtual void SetDirection( const DirectionType direction );
/** Get the direction cosines of the image. The direction cosines
* are vectors that point from one pixel to the next.
* For ImageBase and Image, the default direction is identity. */
itkGetConstReferenceMacro(Direction, DirectionType);
/** Get the spacing (size of a pixel) `of the image. The
* spacing is the geometric distance between image samples.
* The value returned is a pointer to a double array.
* For ImageBase and Image, the default data spacing is unity. */
itkGetConstReferenceMacro(Spacing, SpacingType);
/** Get the origin of the image. The origin is the geometric
* coordinates of the index (0,0). The value returned is a pointer
* to a double array. For ImageBase and Image, the default origin is
* 0. */
itkGetConstReferenceMacro(Origin, PointType);
/** Allocate the image memory. The size of the image must
* already be set, e.g. by calling SetRegions().
*
* This method should be pure virtual, if backwards compatibility
* was not required.
*/
virtual void Allocate() {};
/** Set the region object that defines the size and starting index
* for the largest possible region this image could represent. This
* is used in determining how much memory would be needed to load an
* entire dataset. It is also used to determine boundary
* conditions.
* \sa ImageRegion, SetBufferedRegion(), SetRequestedRegion() */
virtual void SetLargestPossibleRegion(const RegionType ®ion);
/** Get the region object that defines the size and starting index
* for the largest possible region this image could represent. This
* is used in determining how much memory would be needed to load an
* entire dataset. It is also used to determine boundary
* conditions.
* \sa ImageRegion, GetBufferedRegion(), GetRequestedRegion() */
virtual const RegionType& GetLargestPossibleRegion() const
{ return m_LargestPossibleRegion;};
/** Set the region object that defines the size and starting index
* of the region of the image currently loaded in memory.
* \sa ImageRegion, SetLargestPossibleRegion(), SetRequestedRegion() */
virtual void SetBufferedRegion(const RegionType ®ion);
/** Get the region object that defines the size and starting index
* of the region of the image currently loaded in memory.
* \sa ImageRegion, SetLargestPossibleRegion(), SetRequestedRegion() */
virtual const RegionType& GetBufferedRegion() const
{ return m_BufferedRegion;};
/** Set the region object that defines the size and starting index
* for the region of the image requested (i.e., the region of the
* image to be operated on by a filter). Setting the RequestedRegion
* does not cause the object to be modified. This method is called
* internally by the pipeline and therefore bypasses the modified
* time calculation.
* \sa ImageRegion, SetLargestPossibleRegion(), SetBufferedRegion() */
virtual void SetRequestedRegion(const RegionType ®ion);
/** Set the requested region from this data object to match the requested
* region of the data object passed in as a parameter. This method
* implements the API from DataObject. The data object parameter must be
* castable to an ImageBase. Setting the RequestedRegion does not cause
* the object to be modified. This method is called internally by
* the pipeline and therefore bypasses the modified time
* calculation. */
virtual void SetRequestedRegion(DataObject *data);
/** Get the region object that defines the size and starting index
* for the region of the image requested (i.e., the region of the
* image to be operated on by a filter).
* \sa ImageRegion, SetLargestPossibleRegion(), SetBufferedRegion() */
virtual const RegionType& GetRequestedRegion() const
{ return m_RequestedRegion;};
/** Get the offset table. The offset table gives increments for
* moving from one pixel to next in the current row, column, slice,
* etc.. This table if of size [VImageDimension+1], because its
* values are computed progressively as: {1, N1, N1*N2,
* N1*N2*N3,...,(N1*...*Nn)} Where the values {N1,...,Nn} are the
* elements of the BufferedRegion::Size array. The last element of
* the OffsetTable is equivalent to the BufferSize. Having a
* [VImageDimension+1] size array, simplifies the implementation of
* some data accessing algorithms. The entries in the offset table
* are only valid after the BufferedRegion is set. */
const OffsetValueType *GetOffsetTable() const { return m_OffsetTable; };
/** Compute an offset from the beginning of the buffer for a pixel
* at the specified index. The index is not checked as to whether it
* is inside the current buffer, so the computed offset could
* conceivably be outside the buffer. If bounds checking is needed,
* one can call ImageRegion::IsInside(ind) on the BufferedRegion
* prior to calling ComputeOffset. */
#ifdef ITK_USE_TEMPLATE_META_PROGRAMMING_LOOP_UNROLLING
inline OffsetValueType ComputeOffset(const IndexType &ind) const
{
OffsetValueType offset = 0;
ImageHelper<VImageDimension,VImageDimension>::ComputeOffset(this->GetBufferedRegion().GetIndex(),
ind,
m_OffsetTable,
offset);
return offset;
}
#else
OffsetValueType ComputeOffset(const IndexType &ind) const
{
// need to add bounds checking for the region/buffer?
OffsetValueType offset=0;
const IndexType &bufferedRegionIndex = this->GetBufferedRegion().GetIndex();
// data is arranged as [][][][slice][row][col]
// with Index[0] = col, Index[1] = row, Index[2] = slice
for (int i=VImageDimension-1; i > 0; i--)
{
offset += (ind[i] - bufferedRegionIndex[i])*m_OffsetTable[i];
}
offset += (ind[0] - bufferedRegionIndex[0]);
return offset;
}
#endif
/** Compute the index of the pixel at a specified offset from the
* beginning of the buffered region. Bounds checking is not
* performed. Thus, the computed index could be outside the
* BufferedRegion. To ensure a valid index, the parameter "offset"
* should be between 0 and the number of pixels in the
* BufferedRegion (the latter can be found using
* ImageRegion::GetNumberOfPixels()). */
#ifdef ITK_USE_TEMPLATE_META_PROGRAMMING_LOOP_UNROLLING
inline IndexType ComputeIndex(OffsetValueType offset) const
{
IndexType index;
const IndexType &bufferedRegionIndex = this->GetBufferedRegion().GetIndex();
ImageHelper<VImageDimension,VImageDimension>::ComputeIndex(bufferedRegionIndex,
offset,
m_OffsetTable,
index);
return index;
}
#else
IndexType ComputeIndex(OffsetValueType offset) const
{
IndexType index;
const IndexType &bufferedRegionIndex = this->GetBufferedRegion().GetIndex();
for (int i=VImageDimension-1; i > 0; i--)
{
index[i] = static_cast<IndexValueType>(offset / m_OffsetTable[i]);
offset -= (index[i] * m_OffsetTable[i]);
index[i] += bufferedRegionIndex[i];
}
index[0] = bufferedRegionIndex[0] + static_cast<IndexValueType>(offset);
return index;
}
#endif
/** Set the spacing (size of a pixel) of the image. The
* spacing is the geometric distance between image samples.
* It is stored internally as double, but may be set from
* float. These methods also pre-compute the Index to Physical
* point transforms of the image.
* \sa GetSpacing() */
virtual void SetSpacing (const SpacingType & spacing);
virtual void SetSpacing (const double spacing[VImageDimension]);
virtual void SetSpacing (const float spacing[VImageDimension]);
/** Get the index (discrete) of a voxel from a physical point.
* Floating point index results are rounded to integers
* if ITK_USE_CENTERED_PIXEL_COORDINATES_CONSISTENTLY is on
* and truncated otherwise.
* Returns true if the resulting index is within the image, false otherwise
* \sa Transform */
#ifdef ITK_USE_TEMPLATE_META_PROGRAMMING_LOOP_UNROLLING
template<class TCoordRep>
bool TransformPhysicalPointToIndex(
const Point<TCoordRep, VImageDimension>& point,
IndexType & index ) const
{
ImageTransformHelper<VImageDimension,VImageDimension-1,VImageDimension-1>::TransformPhysicalPointToIndex(
this->m_PhysicalPointToIndex, this->m_Origin, point, index);
// Now, check to see if the index is within allowed bounds
const bool isInside = this->GetLargestPossibleRegion().IsInside( index );
return isInside;
}
#else
template<class TCoordRep>
bool TransformPhysicalPointToIndex(
const Point<TCoordRep, VImageDimension>& point,
IndexType & index ) const
{
for (unsigned int i = 0; i < VImageDimension; i++)
{
TCoordRep sum = NumericTraits<TCoordRep>::Zero;
for (unsigned int j = 0; j < VImageDimension; j++)
{
sum += this->m_PhysicalPointToIndex[i][j] * (point[j] - this->m_Origin[j]);
}
#ifdef ITK_USE_CENTERED_PIXEL_COORDINATES_CONSISTENTLY
index[i] = Math::RoundHalfIntegerUp< IndexValueType>( sum );
#else
index[i] = static_cast< IndexValueType>( sum );
#endif
}
// Now, check to see if the index is within allowed bounds
const bool isInside = this->GetLargestPossibleRegion().IsInside( index );
return isInside;
}
#endif
/** \brief Get the continuous index from a physical point
*
* Returns true if the resulting index is within the image, false otherwise.
* \sa Transform */
template<class TCoordRep>
bool TransformPhysicalPointToContinuousIndex(
const Point<TCoordRep, VImageDimension>& point,
ContinuousIndex<TCoordRep, VImageDimension>& index ) const
{
Vector<double, VImageDimension> cvector;
for( unsigned int k = 0; k < VImageDimension; k++ )
{
cvector[k] = point[k] - this->m_Origin[k];
}
cvector = m_PhysicalPointToIndex * cvector;
for( unsigned int i = 0; i < VImageDimension; i++ )
{
index[i] = static_cast<TCoordRep>(cvector[i]);
}
// Now, check to see if the index is within allowed bounds
const bool isInside = this->GetLargestPossibleRegion().IsInside( index );
return isInside;
}
/** Get a physical point (in the space which
* the origin and spacing infomation comes from)
* from a continuous index (in the index space)
* \sa Transform */
template<class TCoordRep>
void TransformContinuousIndexToPhysicalPoint(
const ContinuousIndex<TCoordRep, VImageDimension>& index,
Point<TCoordRep, VImageDimension>& point ) const
{
for( unsigned int r=0; r<VImageDimension; r++)
{
TCoordRep sum = NumericTraits<TCoordRep>::Zero;
for( unsigned int c=0; c<VImageDimension; c++ )
{
sum += this->m_IndexToPhysicalPoint(r,c) * index[c];
}
point[r] = sum + this->m_Origin[r];
}
}
/** Get a physical point (in the space which
* the origin and spacing infomation comes from)
* from a discrete index (in the index space)
*
* \sa Transform */
#ifdef ITK_USE_TEMPLATE_META_PROGRAMMING_LOOP_UNROLLING
template<class TCoordRep>
void TransformIndexToPhysicalPoint(
const IndexType & index,
Point<TCoordRep, VImageDimension>& point ) const
{
ImageTransformHelper<VImageDimension,VImageDimension-1,VImageDimension-1>::TransformIndexToPhysicalPoint(
this->m_IndexToPhysicalPoint, this->m_Origin, index, point);
}
#else
template<class TCoordRep>
void TransformIndexToPhysicalPoint(
const IndexType & index,
Point<TCoordRep, VImageDimension>& point ) const
{
for (unsigned int i = 0; i < VImageDimension; i++)
{
point[i] = this->m_Origin[i];
for (unsigned int j = 0; j < VImageDimension; j++)
{
point[i] += m_IndexToPhysicalPoint[i][j] * index[j];
}
}
}
#endif
/** Get a physical point (in the space which
* the origin and spacing infomation comes from)
* from a discrete index (in the index space)
*
* \sa Transform */
/** Take a vector or covariant vector that has been computed in the
* coordinate system parallel to the image grid and rotate it by the
* direction cosines in order to get it in terms of the coordinate system of
* the image acquisition device. This implementation in the OrientedImage
* multiply the array (vector or covariant vector) by the matrix of Direction
* Cosines. The arguments of the method are of type FixedArray to make
* possible to use this method with both Vector and CovariantVector.
* The Method is implemented differently in the itk::Image.
*
* \sa Image
*/
template<class TCoordRep>
void TransformLocalVectorToPhysicalVector(
const FixedArray<TCoordRep, VImageDimension> & inputGradient,
FixedArray<TCoordRep, VImageDimension> & outputGradient ) const
{
//
// This temporary implementation should be replaced with Template MetaProgramming.
//
#ifdef ITK_USE_ORIENTED_IMAGE_DIRECTION
const DirectionType & direction = this->GetDirection();
for (unsigned int i = 0; i < VImageDimension; i++)
{
typedef typename NumericTraits<TCoordRep>::AccumulateType CoordSumType;
CoordSumType sum = NumericTraits<CoordSumType>::Zero;
for (unsigned int j = 0; j < VImageDimension; j++)
{
sum += direction[i][j] * inputGradient[j];
}
outputGradient[i] = static_cast<TCoordRep>( sum );
}
#else
for (unsigned int i = 0; i < VImageDimension; i++)
{
outputGradient[i] = inputGradient[i];
}
#endif
}
/** Copy information from the specified data set. This method is
* part of the pipeline execution model. By default, a ProcessObject
* will copy meta-data from the first input to all of its
* outputs. See ProcessObject::GenerateOutputInformation(). Each
* subclass of DataObject is responsible for being able to copy
* whatever meta-data it needs from from another DataObject.
* ImageBase has more meta-data than its DataObject. Thus, it must
* provide its own version of CopyInformation() in order to copy the
* LargestPossibleRegion from the input parameter. */
virtual void CopyInformation(const DataObject *data);
/** Graft the data and information from one image to another. This
* is a convenience method to setup a second image with all the meta
* information of another image and use the same pixel
* container. Note that this method is different than just using two
* SmartPointers to the same image since separate DataObjects are
* still maintained. This method is similar to
* ImageSource::GraftOutput(). The implementation in ImageBase
* simply calls CopyInformation() and copies the region ivars.
* Subclasses of ImageBase are responsible for copying the pixel
* container. */
virtual void Graft(const DataObject *data);
/** Update the information for this DataObject so that it can be used
* as an output of a ProcessObject. This method is used the pipeline
* mechanism to propagate information and initialize the meta data
* associated with a DataObject. This method calls its source's
* ProcessObject::UpdateOutputInformation() which determines modified
* times, LargestPossibleRegions, and any extra meta data like spacing,
* origin, etc. */
virtual void UpdateOutputInformation();
/** Overriden from base class to check if the requested image region
* has zero pixels.
*
* This is needed so that filters can set an input's requested
* region to zero, to indicate that it does not need to be updated
* or executed.
*/
virtual void UpdateOutputData();
/** Set the RequestedRegion to the LargestPossibleRegion. This
* forces a filter to produce all of the output in one execution
* (i.e. not streaming) on the next call to Update(). */
virtual void SetRequestedRegionToLargestPossibleRegion();
/** Determine whether the RequestedRegion is outside of the
* BufferedRegion. This method returns true if the RequestedRegion
* is outside the BufferedRegion (true if at least one pixel is
* outside). This is used by the pipeline mechanism to determine
* whether a filter needs to re-execute in order to satisfy the
* current request. If the current RequestedRegion is already
* inside the BufferedRegion from the previous execution (and the
* current filter is up to date), then a given filter does not need
* to re-execute */
virtual bool RequestedRegionIsOutsideOfTheBufferedRegion();
/** Verify that the RequestedRegion is within the
* LargestPossibleRegion. If the RequestedRegion is not within the
* LargestPossibleRegion, then the filter cannot possible satisfy
* the request. This method returns true if the request can be
* satisfied and returns fails if the request cannot. This method is
* used by PropagateRequestedRegion(). PropagateRequestedRegion()
* throws a InvalidRequestedRegionError exception is the requested
* region is not within the LargestPossibleRegion. */
virtual bool VerifyRequestedRegion();
/** INTERNAL This method is used internally by filters to copy meta-data from
* the output to the input. Users should not have a need to use this method.
*
* Filters that override the ProcessObject's GenerateOutputInformation()
* should generally have the following line if they want to propagate meta-
* data for both Image and VectorImage
* \code
* outputImage->SetNumberOfComponentsPerPixel(
* inputImage->GetNumberOfComponentsPerPixel() )
* \endcode
*
* \sa ImageBase, VectorImage
*
* Returns/Sets the number of components in the image. Note that for all
* images this is 1. Even for Image< RGBPixel< T >, 3 >.
* This is >= 1 only for time-series images such as itk::VectorImage. */
virtual unsigned int GetNumberOfComponentsPerPixel() const;
virtual void SetNumberOfComponentsPerPixel( unsigned int );
protected:
ImageBase();
~ImageBase();
virtual void PrintSelf(std::ostream& os, Indent indent) const;
/** Calculate the offsets needed to move from one pixel to the next
* along a row, column, slice, volume, etc. These offsets are based
* on the size of the BufferedRegion. This should be called after
* the BufferedRegion is set. */
void ComputeOffsetTable();
/** Compute helper matrices used to transform Index coordinates to
* PhysicalPoint coordinates and back. This method is virtual and will be
* overloaded in derived classes in order to provide backward compatibility
* behavior in classes that did not used to take image orientation into
* account. */
virtual void ComputeIndexToPhysicalPointMatrices();
protected:
/** Origin and spacing of physical coordinates. This variables are
* protected for efficiency. They are referenced frequently by
* inner loop calculations. */
SpacingType m_Spacing;
PointType m_Origin;
DirectionType m_Direction;
/** Matrices intended to help with the conversion of Index coordinates
* to PhysicalPoint coordinates */
DirectionType m_IndexToPhysicalPoint;
DirectionType m_PhysicalPointToIndex;
/** Restores the buffered region to it's default state
* This method does not call Modify because Initialization is
* called by ReleaseData and can not modify the MTime
* \sa ReleaseData, Initialize, SetBufferedRegion */
virtual void InitializeBufferedRegion(void);
private:
ImageBase(const Self&); //purposely not implemented
void operator=(const Self&); //purposely not implemented
OffsetValueType m_OffsetTable[VImageDimension+1];
RegionType m_LargestPossibleRegion;
RegionType m_RequestedRegion;
RegionType m_BufferedRegion;
};
} // end namespace itk
// Define instantiation macro for this template.
#define ITK_TEMPLATE_ImageBase(_, EXPORT, x, y) namespace itk { \
_(1(class EXPORT ImageBase< ITK_TEMPLATE_1 x >)) \
namespace Templates { typedef ImageBase< ITK_TEMPLATE_1 x > ImageBase##y; } \
}
#if ITK_TEMPLATE_EXPLICIT
# include "Templates/itkImageBase+-.h"
#endif
#if ITK_TEMPLATE_TXX
# include "itkImageBase.txx"
#endif
#endif
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