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Program: Visualization Toolkit
Module: vtkImageReslice.h
Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
All rights reserved.
See Copyright.txt or http://www.kitware.com/Copyright.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 notice for more information.
=========================================================================*/
/**
* @class vtkImageReslice
* @brief Reslices a volume along a new set of axes.
*
* vtkImageReslice is the swiss-army-knife of image geometry filters:
* It can permute, rotate, flip, scale, resample, deform, and pad image
* data in any combination with reasonably high efficiency. Simple
* operations such as permutation, resampling and padding are done
* with similar efficiently to the specialized vtkImagePermute,
* vtkImageResample, and vtkImagePad filters. There are a number of
* tasks that vtkImageReslice is well suited for:
* <p>1) Application of simple rotations, scales, and translations to
* an image. It is often a good idea to use vtkImageChangeInformation
* to center the image first, so that scales and rotations occur around
* the center rather than around the lower-left corner of the image.
* <p>2) Resampling of one data set to match the voxel sampling of
* a second data set via the SetInformationInput() method, e.g. for
* the purpose of comparing two images or combining two images.
* A transformation, either linear or nonlinear, can be applied
* at the same time via the SetResliceTransform method if the two
* images are not in the same coordinate space.
* <p>3) Extraction of slices from an image volume. The most convenient
* way to do this is to use SetResliceAxesDirectionCosines() to
* specify the orientation of the slice. The direction cosines give
* the x, y, and z axes for the output volume. The method
* SetOutputDimensionality(2) is used to specify that want to output a
* slice rather than a volume. The SetResliceAxesOrigin() command is
* used to provide an (x,y,z) point that the slice will pass through.
* You can use both the ResliceAxes and the ResliceTransform at the
* same time, in order to extract slices from a volume that you have
* applied a transformation to.
* @warning
* This filter is very inefficient if the output X dimension is 1.
* @sa
* vtkAbstractTransform vtkMatrix4x4
*/
#ifndef vtkImageReslice_h
#define vtkImageReslice_h
#include "vtkImagingCoreModule.h" // For export macro
#include "vtkThreadedImageAlgorithm.h"
// interpolation mode constants
#define VTK_RESLICE_NEAREST VTK_NEAREST_INTERPOLATION
#define VTK_RESLICE_LINEAR VTK_LINEAR_INTERPOLATION
#define VTK_RESLICE_CUBIC VTK_CUBIC_INTERPOLATION
class vtkImageData;
class vtkAbstractTransform;
class vtkMatrix4x4;
class vtkImageStencilData;
class vtkScalarsToColors;
class vtkAbstractImageInterpolator;
class VTKIMAGINGCORE_EXPORT vtkImageReslice : public vtkThreadedImageAlgorithm
{
public:
static vtkImageReslice *New();
vtkTypeMacro(vtkImageReslice, vtkThreadedImageAlgorithm);
void PrintSelf(ostream& os, vtkIndent indent) VTK_OVERRIDE;
//@{
/**
* This method is used to set up the axes for the output voxels.
* The output Spacing, Origin, and Extent specify the locations
* of the voxels within the coordinate system defined by the axes.
* The ResliceAxes are used most often to permute the data, e.g.
* to extract ZY or XZ slices of a volume as 2D XY images.
* <p>The first column of the matrix specifies the x-axis
* vector (the fourth element must be set to zero), the second
* column specifies the y-axis, and the third column the
* z-axis. The fourth column is the origin of the
* axes (the fourth element must be set to one).
* <p>An alternative to SetResliceAxes() is to use
* SetResliceAxesDirectionCosines() to set the directions of the
* axes and SetResliceAxesOrigin() to set the origin of the axes.
*/
virtual void SetResliceAxes(vtkMatrix4x4*);
vtkGetObjectMacro(ResliceAxes, vtkMatrix4x4);
//@}
//@{
/**
* Specify the direction cosines for the ResliceAxes (i.e. the
* first three elements of each of the first three columns of
* the ResliceAxes matrix). This will modify the current
* ResliceAxes matrix, or create a new matrix if none exists.
*/
void SetResliceAxesDirectionCosines(double x0, double x1, double x2,
double y0, double y1, double y2,
double z0, double z1, double z2);
void SetResliceAxesDirectionCosines(const double x[3],
const double y[3],
const double z[3]) {
this->SetResliceAxesDirectionCosines(x[0], x[1], x[2],
y[0], y[1], y[2],
z[0], z[1], z[2]); };
void SetResliceAxesDirectionCosines(const double xyz[9]) {
this->SetResliceAxesDirectionCosines(xyz[0], xyz[1], xyz[2],
xyz[3], xyz[4], xyz[5],
xyz[6], xyz[7], xyz[8]); };
void GetResliceAxesDirectionCosines(double x[3], double y[3], double z[3]);
void GetResliceAxesDirectionCosines(double xyz[9]) {
this->GetResliceAxesDirectionCosines(&xyz[0], &xyz[3], &xyz[6]); };
double *GetResliceAxesDirectionCosines() {
this->GetResliceAxesDirectionCosines(this->ResliceAxesDirectionCosines);
return this->ResliceAxesDirectionCosines; };
//@}
//@{
/**
* Specify the origin for the ResliceAxes (i.e. the first three
* elements of the final column of the ResliceAxes matrix).
* This will modify the current ResliceAxes matrix, or create
* new matrix if none exists.
*/
void SetResliceAxesOrigin(double x, double y, double z);
void SetResliceAxesOrigin(const double xyz[3]) {
this->SetResliceAxesOrigin(xyz[0], xyz[1], xyz[2]); };
void GetResliceAxesOrigin(double xyz[3]);
double *GetResliceAxesOrigin() {
this->GetResliceAxesOrigin(this->ResliceAxesOrigin);
return this->ResliceAxesOrigin; };
//@}
//@{
/**
* Set a transform to be applied to the resampling grid that has
* been defined via the ResliceAxes and the output Origin, Spacing
* and Extent. Note that applying a transform to the resampling
* grid (which lies in the output coordinate system) is
* equivalent to applying the inverse of that transform to
* the input volume. Nonlinear transforms such as vtkGridTransform
* and vtkThinPlateSplineTransform can be used here.
*/
virtual void SetResliceTransform(vtkAbstractTransform*);
vtkGetObjectMacro(ResliceTransform, vtkAbstractTransform);
//@}
//@{
/**
* Set a vtkImageData from which the default Spacing, Origin,
* and WholeExtent of the output will be copied. The spacing,
* origin, and extent will be permuted according to the
* ResliceAxes. Any values set via SetOutputSpacing,
* SetOutputOrigin, and SetOutputExtent will override these
* values. By default, the Spacing, Origin, and WholeExtent
* of the Input are used.
*/
virtual void SetInformationInput(vtkImageData*);
vtkGetObjectMacro(InformationInput, vtkImageData);
//@}
//@{
/**
* Specify whether to transform the spacing, origin and extent
* of the Input (or the InformationInput) according to the
* direction cosines and origin of the ResliceAxes before applying
* them as the default output spacing, origin and extent
* (default: On).
*/
vtkSetMacro(TransformInputSampling, int);
vtkBooleanMacro(TransformInputSampling, int);
vtkGetMacro(TransformInputSampling, int);
//@}
//@{
/**
* Turn this on if you want to guarantee that the extent of the
* output will be large enough to ensure that none of the
* data will be cropped (default: Off).
*/
vtkSetMacro(AutoCropOutput, int);
vtkBooleanMacro(AutoCropOutput, int);
vtkGetMacro(AutoCropOutput, int);
//@}
//@{
/**
* Turn on wrap-pad feature (default: Off).
*/
vtkSetMacro(Wrap, int);
vtkGetMacro(Wrap, int);
vtkBooleanMacro(Wrap, int);
//@}
//@{
/**
* Turn on mirror-pad feature (default: Off).
* This will override the wrap-pad.
*/
vtkSetMacro(Mirror, int);
vtkGetMacro(Mirror, int);
vtkBooleanMacro(Mirror, int);
//@}
//@{
/**
* Extend the apparent input border by a half voxel (default: On).
* This changes how interpolation is handled at the borders of the
* input image: if the center of an output voxel is beyond the edge
* of the input image, but is within a half voxel width of the edge
* (using the input voxel width), then the value of the output voxel
* is calculated as if the input's edge voxels were duplicated past
* the edges of the input.
* This has no effect if Mirror or Wrap are on.
*/
vtkSetMacro(Border, int);
vtkGetMacro(Border, int);
vtkBooleanMacro(Border, int);
//@}
//@{
/**
* Set interpolation mode (default: nearest neighbor).
*/
vtkSetClampMacro(InterpolationMode, int,
VTK_RESLICE_NEAREST, VTK_RESLICE_CUBIC);
vtkGetMacro(InterpolationMode, int);
void SetInterpolationModeToNearestNeighbor() {
this->SetInterpolationMode(VTK_RESLICE_NEAREST); };
void SetInterpolationModeToLinear() {
this->SetInterpolationMode(VTK_RESLICE_LINEAR); };
void SetInterpolationModeToCubic() {
this->SetInterpolationMode(VTK_RESLICE_CUBIC); };
virtual const char *GetInterpolationModeAsString();
//@}
//@{
/**
* Set the interpolator to use. The default interpolator
* supports the Nearest, Linear, and Cubic interpolation modes.
*/
virtual void SetInterpolator(vtkAbstractImageInterpolator *sampler);
virtual vtkAbstractImageInterpolator *GetInterpolator();
//@}
//@{
/**
* Set the slab mode, for generating thick slices. The default is Mean.
* If SetSlabNumberOfSlices(N) is called with N greater than one, then
* each output slice will actually be a composite of N slices. This method
* specifies the compositing mode to be used.
*/
vtkSetClampMacro(SlabMode, int, VTK_IMAGE_SLAB_MIN, VTK_IMAGE_SLAB_SUM);
vtkGetMacro(SlabMode, int);
void SetSlabModeToMin() {
this->SetSlabMode(VTK_IMAGE_SLAB_MIN); };
void SetSlabModeToMax() {
this->SetSlabMode(VTK_IMAGE_SLAB_MAX); };
void SetSlabModeToMean() {
this->SetSlabMode(VTK_IMAGE_SLAB_MEAN); };
void SetSlabModeToSum() {
this->SetSlabMode(VTK_IMAGE_SLAB_SUM); };
virtual const char *GetSlabModeAsString();
//@}
//@{
/**
* Set the number of slices that will be combined to create the slab.
*/
vtkSetMacro(SlabNumberOfSlices, int);
vtkGetMacro(SlabNumberOfSlices, int);
//@}
//@{
/**
* Use trapezoid integration for slab computation. All this does is
* weigh the first and last slices by half when doing sum and mean.
* It is off by default.
*/
vtkSetMacro(SlabTrapezoidIntegration, int);
vtkBooleanMacro(SlabTrapezoidIntegration, int);
vtkGetMacro(SlabTrapezoidIntegration, int);
//@}
//@{
/**
* The slab spacing as a fraction of the output slice spacing.
* When one of the various slab modes is chosen, each output slice is
* produced by generating several "temporary" output slices and then
* combining them according to the slab mode. By default, the spacing
* between these temporary slices is the Z component of the OutputSpacing.
* This method sets the spacing between these temporary slices to be a
* fraction of the output spacing.
*/
vtkSetMacro(SlabSliceSpacingFraction, double);
vtkGetMacro(SlabSliceSpacingFraction, double);
//@}
//@{
/**
* Turn on and off optimizations (default on, they should only be
* turned off for testing purposes).
*/
vtkSetMacro(Optimization, int);
vtkGetMacro(Optimization, int);
vtkBooleanMacro(Optimization, int);
//@}
//@{
/**
* Set a value to add to all the output voxels.
* After a sample value has been interpolated from the input image, the
* equation u = (v + ScalarShift)*ScalarScale will be applied to it before
* it is written to the output image. The result will always be clamped to
* the limits of the output data type.
*/
vtkSetMacro(ScalarShift, double);
vtkGetMacro(ScalarShift, double);
//@}
//@{
/**
* Set multiplication factor to apply to all the output voxels.
* After a sample value has been interpolated from the input image, the
* equation u = (v + ScalarShift)*ScalarScale will be applied to it before
* it is written to the output image. The result will always be clamped to
* the limits of the output data type.
*/
vtkSetMacro(ScalarScale, double);
vtkGetMacro(ScalarScale, double)
//@}
//@{
/**
* Set the scalar type of the output to be different from the input.
* The default value is -1, which means that the input scalar type will be
* used to set the output scalar type. Otherwise, this must be set to one
* of the following types: VTK_CHAR, VTK_SIGNED_CHAR, VTK_UNSIGNED_CHAR,
* VTK_SHORT, VTK_UNSIGNED_SHORT, VTK_INT, VTK_UNSIGNED_INT, VTK_FLOAT,
* or VTK_DOUBLE. Other types are not permitted. If the output type
* is an integer type, the output will be rounded and clamped to the
* limits of the type.
*/
vtkSetMacro(OutputScalarType, int);
vtkGetMacro(OutputScalarType, int);
//@}
//@{
/**
* Set the background color (for multi-component images).
*/
vtkSetVector4Macro(BackgroundColor, double);
vtkGetVector4Macro(BackgroundColor, double);
//@}
//@{
/**
* Set background grey level (for single-component images).
*/
void SetBackgroundLevel(double v) { this->SetBackgroundColor(v,v,v,v); };
double GetBackgroundLevel() { return this->GetBackgroundColor()[0]; };
//@}
//@{
/**
* Set the voxel spacing for the output data. The default output
* spacing is the input spacing permuted through the ResliceAxes.
*/
virtual void SetOutputSpacing(double x, double y, double z);
virtual void SetOutputSpacing(const double a[3]) {
this->SetOutputSpacing(a[0], a[1], a[2]); };
vtkGetVector3Macro(OutputSpacing, double);
void SetOutputSpacingToDefault();
//@}
//@{
/**
* Set the origin for the output data. The default output origin
* is the input origin permuted through the ResliceAxes.
*/
virtual void SetOutputOrigin(double x, double y, double z);
virtual void SetOutputOrigin(const double a[3]) {
this->SetOutputOrigin(a[0], a[1], a[2]); };
vtkGetVector3Macro(OutputOrigin, double);
void SetOutputOriginToDefault();
//@}
//@{
/**
* Set the extent for the output data. The default output extent
* is the input extent permuted through the ResliceAxes.
*/
virtual void SetOutputExtent(int a, int b, int c, int d, int e, int f);
virtual void SetOutputExtent(const int a[6]) {
this->SetOutputExtent(a[0], a[1], a[2], a[3], a[4], a[5]); };
vtkGetVector6Macro(OutputExtent, int);
void SetOutputExtentToDefault();
//@}
//@{
/**
* Force the dimensionality of the output to either 1, 2,
* 3 or 0 (default: 3). If the dimensionality is 2D, then
* the Z extent of the output is forced to (0,0) and the Z
* origin of the output is forced to 0.0 (i.e. the output
* extent is confined to the xy plane). If the dimensionality
* is 1D, the output extent is confined to the x axis.
* For 0D, the output extent consists of a single voxel at
* (0,0,0).
*/
vtkSetMacro(OutputDimensionality, int);
vtkGetMacro(OutputDimensionality, int);
//@}
/**
* When determining the modified time of the filter,
* this check the modified time of the transform and matrix.
*/
vtkMTimeType GetMTime() VTK_OVERRIDE;
/**
* Report object referenced by instances of this class.
*/
void ReportReferences(vtkGarbageCollector*) VTK_OVERRIDE;
//@{
/**
* Convenient methods for switching between nearest-neighbor and linear
* interpolation.
* InterpolateOn() is equivalent to SetInterpolationModeToLinear() and
* InterpolateOff() is equivalent to SetInterpolationModeToNearestNeighbor()
* You should not use these methods if you use the SetInterpolationMode
* methods.
*/
void SetInterpolate(int t) {
if (t && !this->GetInterpolate()) {
this->SetInterpolationModeToLinear(); }
else if (!t && this->GetInterpolate()) {
this->SetInterpolationModeToNearestNeighbor(); } };
void InterpolateOn() {
this->SetInterpolate(1); };
void InterpolateOff() {
this->SetInterpolate(0); };
int GetInterpolate() {
return (this->GetInterpolationMode() != VTK_RESLICE_NEAREST); };
//@}
//@{
/**
* Use a stencil to limit the calculations to a specific region of
* the output. Portions of the output that are 'outside' the stencil
* will be cleared to the background color.
*/
void SetStencilData(vtkImageStencilData *stencil);
vtkImageStencilData *GetStencil();
//@}
//@{
/**
* Generate an output stencil that defines which pixels were
* interpolated and which pixels were out-of-bounds of the input.
*/
vtkSetMacro(GenerateStencilOutput, int);
vtkGetMacro(GenerateStencilOutput, int);
vtkBooleanMacro(GenerateStencilOutput, int);
//@}
//@{
/**
* Get the output stencil.
*/
vtkAlgorithmOutput *GetStencilOutputPort() {
return this->GetOutputPort(1); }
vtkImageStencilData *GetStencilOutput();
void SetStencilOutput(vtkImageStencilData *stencil);
//@}
protected:
vtkImageReslice();
~vtkImageReslice();
vtkMatrix4x4 *ResliceAxes;
double ResliceAxesDirectionCosines[9];
double ResliceAxesOrigin[3];
vtkAbstractTransform *ResliceTransform;
vtkAbstractImageInterpolator *Interpolator;
vtkImageData *InformationInput;
int Wrap;
int Mirror;
int Border;
int InterpolationMode;
int Optimization;
int SlabMode;
int SlabNumberOfSlices;
int SlabTrapezoidIntegration;
double SlabSliceSpacingFraction;
double ScalarShift;
double ScalarScale;
double BackgroundColor[4];
double OutputOrigin[3];
double OutputSpacing[3];
int OutputExtent[6];
int OutputScalarType;
int OutputDimensionality;
int TransformInputSampling;
int AutoCropOutput;
int HitInputExtent;
int UsePermuteExecute;
int ComputeOutputSpacing;
int ComputeOutputOrigin;
int ComputeOutputExtent;
int GenerateStencilOutput;
vtkMatrix4x4 *IndexMatrix;
vtkAbstractTransform *OptimizedTransform;
/**
* This should be set to 1 by derived classes that override the
* ConvertScalars method.
*/
int HasConvertScalars;
/**
* This should be overridden by derived classes that operate on
* the interpolated data before it is placed in the output.
*/
virtual int ConvertScalarInfo(int &scalarType, int &numComponents);
/**
* This should be overridden by derived classes that operate on
* the interpolated data before it is placed in the output.
* The input data will usually be double or float (since the
* interpolation routines use floating-point) but it could be
* of any type. This method will be called from multiple threads,
* so it must be thread-safe in derived classes.
*/
virtual void ConvertScalars(void *inPtr, void *outPtr,
int inputType, int inputNumComponents,
int count, int idX, int idY, int idZ,
int threadId);
void ConvertScalarsBase(void *inPtr, void *outPtr,
int inputType, int inputNumComponents,
int count, int idX, int idY, int idZ, int threadId) {
this->ConvertScalars(inPtr, outPtr, inputType, inputNumComponents,
count, idX, idY, idZ, threadId); }
void GetAutoCroppedOutputBounds(vtkInformation *inInfo, double bounds[6]);
virtual void AllocateOutputData(vtkImageData *output, vtkInformation *outInfo, int *uExtent) VTK_OVERRIDE;
virtual vtkImageData *AllocateOutputData(vtkDataObject *, vtkInformation *) VTK_OVERRIDE;
virtual int RequestInformation(vtkInformation *, vtkInformationVector **,
vtkInformationVector *) VTK_OVERRIDE;
virtual int RequestUpdateExtent(vtkInformation *, vtkInformationVector **,
vtkInformationVector *) VTK_OVERRIDE;
virtual int RequestData(vtkInformation *, vtkInformationVector **,
vtkInformationVector *) VTK_OVERRIDE;
virtual void ThreadedRequestData(vtkInformation *request,
vtkInformationVector **inputVector,
vtkInformationVector *outputVector,
vtkImageData ***inData,
vtkImageData **outData, int ext[6], int id) VTK_OVERRIDE;
virtual int FillInputPortInformation(int port, vtkInformation *info) VTK_OVERRIDE;
virtual int FillOutputPortInformation(int port, vtkInformation *info) VTK_OVERRIDE;
vtkMatrix4x4 *GetIndexMatrix(vtkInformation *inInfo,
vtkInformation *outInfo);
vtkAbstractTransform *GetOptimizedTransform() {
return this->OptimizedTransform; };
private:
vtkImageReslice(const vtkImageReslice&) VTK_DELETE_FUNCTION;
void operator=(const vtkImageReslice&) VTK_DELETE_FUNCTION;
};
#endif
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