shapeworks::Image
Module: Image Classes
#include <Image.h>
Public Types
| Name | |
|---|---|
| enum | InterpolationType |
| using float | PixelType |
| using itk::Image< PixelType, 3 > | ImageType |
| using itk::StatisticsImageFilter< ImageType >::Pointer | StatsPtr |
| using itk::ImageRegionIterator< ImageType > | ImageIterator |
| using itk::LinearInterpolateImageFunction< ImageType > | InterpolatorType |
Public Functions
| Name | |
|---|---|
| Image(const Dims dims) | |
| Image(const std::string & pathname) | |
| Image(ImageType::Pointer imagePtr) | |
| Image(const vtkSmartPointer< vtkImageData > vtkImage) | |
| Image(Image && img) | |
| Image(const Image & img) | |
| Image & | operator=(const Image & img) |
| Image & | operator=(Image && img) lvalue assignment operator |
| operator ImageType::Pointer() rvalue assignment operator |
|
| ImageType::Pointer | getITKImage() const |
| vtkSmartPointer< vtkImageData > | getVTKImage() const creates a VTK filter for the given image |
| Image & | operator-() negation operator |
| Image | operator+(const Image & other) const plus operator to add two images |
| Image & | operator+=(const Image & other) |
| Image | operator-(const Image & other) const minus operator to add two images |
| Image & | operator-=(const Image & other) |
| Image | operator*(const Image & other) const multiply operator to multiply two images |
| Image | operator*(const PixelType x) const multiply operator to scale contents of an image |
| Image & | operator*=(const PixelType x) |
| Image | operator/(const PixelType x) const divide operator to scale contents of an image |
| Image & | operator/=(const PixelType x) |
| Image | operator+(const PixelType x) const plus operator to shift contents of an image |
| Image & | operator+=(const PixelType x) |
| Image | operator-(const PixelType x) const minus operator to shift contents of an image |
| Image & | operator-=(const PixelType x) |
| Image & | antialias(unsigned iterations =50, double maxRMSErr =0.01f, int layers =3) antialiases image |
| Image & | recenter() |
| Image & | resample(const TransformPtr transform, const Point3 origin, const Dims dims, const Vector3 spacing, const ImageType::DirectionType direction, InterpolationType interp =NearestNeighbor) |
| Image & | resample(const Vector & physicalSpacing, InterpolationType interp =Linear) resamples image using new physical spacing, updating logical dims to keep all image data for this spacing |
| Image & | resample(double isoSpacing =1.0, InterpolationType interp =Linear) resamples image using isotropic physical spacing |
| Image & | resize(Dims logicalDims, InterpolationType interp =Linear) |
| Image & | pad(int padding, PixelType value =0.0) pads an image by same number of voxels in all directions with constant value |
| Image & | pad(int padx, int pady, int padz, PixelType value =0.0) pads an image by desired number of voxels in each direction with constant value |
| Image & | pad(IndexRegion & region, PixelType value =0.0) pads an image to include the given region with constant value |
| Image & | translate(const Vector3 & v) helper to simply translate image |
| Image & | scale(const Vector3 & v) helper to simply scale image around center (not origin) |
| Image & | rotate(const double angle, const Vector3 & axis) helper to simply rotate around axis through center (not origin) by given angle (in radians) |
| Image & | rotate(const double angle, Axis axis) helper to simply rotate around axis through center (not origin) by given angle (in radians) |
| TransformPtr | createCenterOfMassTransform() creates a transform that translates center of mass to center of image |
| TransformPtr | createRigidRegistrationTransform(const Image & target_dt, float isoValue =0.0, unsigned iterations =20) |
| Image & | applyTransform(const TransformPtr transform, InterpolationType interp =Linear) applies the given transformation to the image by using resampling filter |
| Image & | applyTransform(const TransformPtr transform, const Point3 origin, const Dims dims, const Vector3 spacing, const ImageType::DirectionType direction, InterpolationType interp =NearestNeighbor) |
| Image & | applyTransform(const TransformPtr transform, const Image & referenceImage, InterpolationType interp =Linear) applies the given transformation to the image by using resampling filter with reference image |
| Image & | extractLabel(const PixelType label =1.0) |
| Image & | closeHoles(const PixelType foreground =0.0) closes holes in a given volume, default foreground value assumes a binary volume |
| Image & | binarize(PixelType minVal =0.0, PixelType maxVal =std::numeric_limits< PixelType >::max(), PixelType innerVal =1.0, PixelType outerVal =0.0) threholds image into binary label based on upper and lower intensity bounds given by user |
| Image & | computeDT(PixelType isoValue =0.0) computes distance transform volume from a (preferably antialiased) binary image using the specified isovalue |
| Image & | applyCurvatureFilter(unsigned iterations =10) denoises an image using curvature driven flow using curvature flow image filter |
| Image & | applyGradientFilter() computes gradient magnitude at each pixel using gradient magnitude filter |
| Image & | applySigmoidFilter(double alpha =10.0, double beta =10.0) computes sigmoid function pixel-wise using sigmoid image filter |
| Image & | applyTPLevelSetFilter(const Image & featureImage, double scaling =20.0) segements structures in images using topology preserving geodesic active contour level set filter |
| Image & | topologyPreservingSmooth(float scaling =20.0, float sigmoidAlpha =10.5, float sigmoidBeta =10.0) |
| Image & | applyIntensityFilter(double minVal, double maxVal) applies intensity windowing image filter |
| Image & | gaussianBlur(double sigma =0.0) applies gaussian blur with given sigma |
| Image & | crop(PhysicalRegion region, const int padding =0) crops the image down to the given region, with optional padding added |
| Image & | clip(const Plane plane, const PixelType val =0.0) clips an image using a cutting plane |
| Image & | reflect(const Axis & axis) |
| Image & | setOrigin(Point3 origin =Point3({0, 0, 0})) sets the image origin in physical space to the given value |
| Image & | setSpacing(Vector3 spacing) sets the image spacing to the given value |
| Image & | setCoordsys(ImageType::DirectionType coordsys) sets the coordinate system in which this image lives in physical space |
| Image & | isolate() isolate the largest object in a binary segmentation |
| Dims | dims() const logical dimensions of the image |
| Point3 | size() const physical dimensions of the image (dims * spacing) |
| Vector | spacing() const physical spacing of the image |
| double | get_minimum_spacing() const minimum physical spacing of the image |
| Point3 | origin() const physical coordinates of image origin |
| Point3 | center() const physical coordinates of center of this image |
| ImageType::DirectionType | coordsys() const return coordinate system in which this image lives in physical space |
| Point3 | centerOfMass(PixelType minVal =0.0, PixelType maxVal =1.0) const returns average physical coordinate of pixels in range (minval, maxval] |
| PixelType | min() minimum of image |
| PixelType | max() maximum of image |
| PixelType | mean() mean of image |
| PixelType | std() standard deviation of image |
| IndexRegion | logicalBoundingBox() const bounding box of complete image in logical (index) space |
| PhysicalRegion | physicalBoundingBox() const bounding box of complete image in physical space |
| PhysicalRegion | physicalBoundingBox(PixelType isovalue) const bounding box of largest region of data >= the given isoValue in physical space |
| PhysicalRegion | logicalToPhysical(IndexRegion region) const converts a bounding box in logical (index) space to this image's index coordinates |
| IndexRegion | physicalToLogical(PhysicalRegion region) const converts a bounding box in physical space to this image's logical (index) coordinates |
| Point3 | logicalToPhysical(const Coord & c) const converts from pixel coordinates to physical space |
| Coord | physicalToLogical(const Point3 & p) const converts from a physical coordinate to a logical coordinate |
| bool | isInside(const Point3 & p) const checks if a given point is inside the image |
| ImageIterator | iterator() creates an image iterator and returns it |
| bool | compare(const Image & other, bool verifyall =true, double tolerance =0.0, double precision =1e-12) const compares this with another image using the region of interest filter |
| bool | operator==(const Image & other) const compares this with another image using the region of interest filter |
| Image & | write(const std::string & filename, bool compressed =true) writes image, format specified by filename extension |
| Mesh | toMesh(PixelType isovalue) const converts image to mesh |
| Image::PixelType | evaluate(Point p) Evaluates the image at a given position. |
| std::vector< std::string > | getSupportedTypes() Return supported file types. |
Friends
| Name | |
|---|---|
| struct | SharedCommandData |
Detailed Description
class shapeworks::Image;
This class represents a 3D image volume and operations that can be performed on images.
Public Types Documentation
enum InterpolationType
| Enumerator | Value | Description |
|---|---|---|
| Linear | ||
| NearestNeighbor |
using PixelType
using shapeworks::Image::PixelType = float;
using ImageType
using shapeworks::Image::ImageType = itk::Image<PixelType, 3>;
using StatsPtr
using shapeworks::Image::StatsPtr = itk::StatisticsImageFilter<ImageType>::Pointer;
using ImageIterator
using shapeworks::Image::ImageIterator = itk::ImageRegionIterator<ImageType>;
using InterpolatorType
using shapeworks::Image::InterpolatorType = itk::LinearInterpolateImageFunction<ImageType>;
Public Functions Documentation
function Image
Image(
const Dims dims
)
function Image
inline Image(
const std::string & pathname
)
function Image
inline Image(
ImageType::Pointer imagePtr
)
function Image
Image(
const vtkSmartPointer< vtkImageData > vtkImage
)
function Image
inline Image(
Image && img
)
function Image
inline Image(
const Image & img
)
function operator=
Image & operator=(
const Image & img
)
function operator=
Image & operator=(
Image && img
)
lvalue assignment operator
function operator ImageType::Pointer
inline operator ImageType::Pointer()
rvalue assignment operator
return this as an ITK image
function getITKImage
inline ImageType::Pointer getITKImage() const
function getVTKImage
vtkSmartPointer< vtkImageData > getVTKImage() const
creates a VTK filter for the given image
function operator-
Image & operator-()
negation operator
function operator+
Image operator+(
const Image & other
) const
plus operator to add two images
function operator+=
Image & operator+=(
const Image & other
)
function operator-
Image operator-(
const Image & other
) const
minus operator to add two images
function operator-=
Image & operator-=(
const Image & other
)
function operator*
Image operator*(
const Image & other
) const
multiply operator to multiply two images
function operator*
Image operator*(
const PixelType x
) const
multiply operator to scale contents of an image
function operator*=
Image & operator*=(
const PixelType x
)
function operator/
Image operator/(
const PixelType x
) const
divide operator to scale contents of an image
function operator/=
Image & operator/=(
const PixelType x
)
function operator+
Image operator+(
const PixelType x
) const
plus operator to shift contents of an image
function operator+=
Image & operator+=(
const PixelType x
)
function operator-
Image operator-(
const PixelType x
) const
minus operator to shift contents of an image
function operator-=
Image & operator-=(
const PixelType x
)
function antialias
Image & antialias(
unsigned iterations =50,
double maxRMSErr =0.01f,
int layers =3
)
antialiases image
function recenter
Image & recenter()
helper identical to setOrigin(image.center()) changing origin (in the image header) to physcial center of the image
function resample
Image & resample(
const TransformPtr transform,
const Point3 origin,
const Dims dims,
const Vector3 spacing,
const ImageType::DirectionType direction,
InterpolationType interp =NearestNeighbor
)
resamples by applying transform then sampling from given origin along direction axes at spacing physical units per pixel for dims pixels using specified interpolator
function resample
Image & resample(
const Vector & physicalSpacing,
InterpolationType interp =Linear
)
resamples image using new physical spacing, updating logical dims to keep all image data for this spacing
function resample
Image & resample(
double isoSpacing =1.0,
InterpolationType interp =Linear
)
resamples image using isotropic physical spacing
function resize
Image & resize(
Dims logicalDims,
InterpolationType interp =Linear
)
changes logical image size, computing new physical spacing based on this size (i.e., physical image size remains the same)
function pad
Image & pad(
int padding,
PixelType value =0.0
)
pads an image by same number of voxels in all directions with constant value
function pad
Image & pad(
int padx,
int pady,
int padz,
PixelType value =0.0
)
pads an image by desired number of voxels in each direction with constant value
function pad
Image & pad(
IndexRegion & region,
PixelType value =0.0
)
pads an image to include the given region with constant value
function translate
Image & translate(
const Vector3 & v
)
helper to simply translate image
function scale
Image & scale(
const Vector3 & v
)
helper to simply scale image around center (not origin)
function rotate
Image & rotate(
const double angle,
const Vector3 & axis
)
helper to simply rotate around axis through center (not origin) by given angle (in radians)
function rotate
Image & rotate(
const double angle,
Axis axis
)
helper to simply rotate around axis through center (not origin) by given angle (in radians)
function createCenterOfMassTransform
TransformPtr createCenterOfMassTransform()
creates a transform that translates center of mass to center of image
function createRigidRegistrationTransform
TransformPtr createRigidRegistrationTransform(
const Image & target_dt,
float isoValue =0.0,
unsigned iterations =20
)
creates transform to target image using iterative closest point (ICP) registration; images MUST be distance transforms; isovalue is used to create meshes from these distance transform images, which are then passed to ICP for the given number of iterations
function applyTransform
Image & applyTransform(
const TransformPtr transform,
InterpolationType interp =Linear
)
applies the given transformation to the image by using resampling filter
function applyTransform
Image & applyTransform(
const TransformPtr transform,
const Point3 origin,
const Dims dims,
const Vector3 spacing,
const ImageType::DirectionType direction,
InterpolationType interp =NearestNeighbor
)
applies the given transformation to the image by using resampling filter with new origin, dims, spacing and direction values
function applyTransform
Image & applyTransform(
const TransformPtr transform,
const Image & referenceImage,
InterpolationType interp =Linear
)
applies the given transformation to the image by using resampling filter with reference image
function extractLabel
Image & extractLabel(
const PixelType label =1.0
)
extracts/isolates a specific voxel label from a given multi-label volume and outputs the corresponding binary image
function closeHoles
Image & closeHoles(
const PixelType foreground =0.0
)
closes holes in a given volume, default foreground value assumes a binary volume
function binarize
Image & binarize(
PixelType minVal =0.0,
PixelType maxVal =std::numeric_limits< PixelType >::max(),
PixelType innerVal =1.0,
PixelType outerVal =0.0
)
threholds image into binary label based on upper and lower intensity bounds given by user
function computeDT
Image & computeDT(
PixelType isoValue =0.0
)
computes distance transform volume from a (preferably antialiased) binary image using the specified isovalue
function applyCurvatureFilter
Image & applyCurvatureFilter(
unsigned iterations =10
)
denoises an image using curvature driven flow using curvature flow image filter
function applyGradientFilter
Image & applyGradientFilter()
computes gradient magnitude at each pixel using gradient magnitude filter
function applySigmoidFilter
Image & applySigmoidFilter(
double alpha =10.0,
double beta =10.0
)
computes sigmoid function pixel-wise using sigmoid image filter
function applyTPLevelSetFilter
Image & applyTPLevelSetFilter(
const Image & featureImage,
double scaling =20.0
)
segements structures in images using topology preserving geodesic active contour level set filter
function topologyPreservingSmooth
Image & topologyPreservingSmooth(
float scaling =20.0,
float sigmoidAlpha =10.5,
float sigmoidBeta =10.0
)
creates a feature image (by applying gradient then sigmoid filters), then passes it to the TPLevelSet filter [curvature flow filter is often applied to the image before this filter]
function applyIntensityFilter
Image & applyIntensityFilter(
double minVal,
double maxVal
)
applies intensity windowing image filter
function gaussianBlur
Image & gaussianBlur(
double sigma =0.0
)
applies gaussian blur with given sigma
function crop
Image & crop(
PhysicalRegion region,
const int padding =0
)
crops the image down to the given region, with optional padding added
function clip
Image & clip(
const Plane plane,
const PixelType val =0.0
)
clips an image using a cutting plane
function reflect
Image & reflect(
const Axis & axis
)
reflect image around the plane specified by the logical center and the given normal (ex: <1,0,0> reflects across YZ-plane).
function setOrigin
Image & setOrigin(
Point3 origin =Point3({0, 0, 0})
)
sets the image origin in physical space to the given value
function setSpacing
Image & setSpacing(
Vector3 spacing
)
sets the image spacing to the given value
function setCoordsys
Image & setCoordsys(
ImageType::DirectionType coordsys
)
sets the coordinate system in which this image lives in physical space
function isolate
Image & isolate()
isolate the largest object in a binary segmentation
function dims
inline Dims dims() const
logical dimensions of the image
function size
inline Point3 size() const
physical dimensions of the image (dims * spacing)
function spacing
inline Vector spacing() const
physical spacing of the image
function get_minimum_spacing
double get_minimum_spacing() const
minimum physical spacing of the image
function origin
inline Point3 origin() const
physical coordinates of image origin
function center
inline Point3 center() const
physical coordinates of center of this image
function coordsys
inline ImageType::DirectionType coordsys() const
return coordinate system in which this image lives in physical space
function centerOfMass
Point3 centerOfMass(
PixelType minVal =0.0,
PixelType maxVal =1.0
) const
returns average physical coordinate of pixels in range (minval, maxval]
function min
PixelType min()
minimum of image
function max
PixelType max()
maximum of image
function mean
PixelType mean()
mean of image
function std
PixelType std()
standard deviation of image
function logicalBoundingBox
IndexRegion logicalBoundingBox() const
bounding box of complete image in logical (index) space
function physicalBoundingBox
PhysicalRegion physicalBoundingBox() const
bounding box of complete image in physical space
function physicalBoundingBox
PhysicalRegion physicalBoundingBox(
PixelType isovalue
) const
bounding box of largest region of data >= the given isoValue in physical space
function logicalToPhysical
PhysicalRegion logicalToPhysical(
IndexRegion region
) const
converts a bounding box in logical (index) space to this image's index coordinates
function physicalToLogical
IndexRegion physicalToLogical(
PhysicalRegion region
) const
converts a bounding box in physical space to this image's logical (index) coordinates
function logicalToPhysical
Point3 logicalToPhysical(
const Coord & c
) const
converts from pixel coordinates to physical space
function physicalToLogical
Coord physicalToLogical(
const Point3 & p
) const
converts from a physical coordinate to a logical coordinate
function isInside
bool isInside(
const Point3 & p
) const
checks if a given point is inside the image
function iterator
ImageIterator iterator()
creates an image iterator and returns it
function compare
bool compare(
const Image & other,
bool verifyall =true,
double tolerance =0.0,
double precision =1e-12
) const
compares this with another image using the region of interest filter
function operator==
inline bool operator==(
const Image & other
) const
compares this with another image using the region of interest filter
function write
Image & write(
const std::string & filename,
bool compressed =true
)
writes image, format specified by filename extension
function toMesh
Mesh toMesh(
PixelType isovalue
) const
converts image to mesh
function evaluate
Image::PixelType evaluate(
Point p
)
Evaluates the image at a given position.
function getSupportedTypes
static inline std::vector< std::string > getSupportedTypes()
Return supported file types.
Friends
friend SharedCommandData
friend struct SharedCommandData(
SharedCommandData
);
Updated on 2024-03-17 at 12:58:44 -0600