ShapeWorks Python API
ShapeWorks Python API
Biharmonic = <WarpMethod.Biharmonic: 1>
module-attribute
Members:
Laplacian
Biharmonic
ContourDomain = <DomainType.ContourDomain: 2>
module-attribute
Members:
MeshDomain
ImageDomain
ContourDomain
ImageDomain = <DomainType.ImageDomain: 0>
module-attribute
Members:
MeshDomain
ImageDomain
ContourDomain
Laplacian = <WarpMethod.Laplacian: 0>
module-attribute
Members:
Laplacian
Biharmonic
Linear = <InterpolationType.Linear: 0>
module-attribute
Members:
Linear
NearestNeighbor
MeshDomain = <DomainType.MeshDomain: 1>
module-attribute
Members:
MeshDomain
ImageDomain
ContourDomain
NearestNeighbor = <InterpolationType.NearestNeighbor: 1>
module-attribute
Members:
Linear
NearestNeighbor
Pi = 3.141592653589793
module-attribute
Convert a string or number to a floating point number, if possible.
X = <Axis.X: 0>
module-attribute
Members:
invalid
X
Y
Z
Y = <Axis.Y: 1>
module-attribute
Members:
invalid
X
Y
Z
Z = <Axis.Z: 2>
module-attribute
Members:
invalid
X
Y
Z
invalid = <Axis.invalid: -1>
module-attribute
Members:
invalid
X
Y
Z
Analyze
Bases: pybind11_builtins.pybind11_object
create_shape_from_points()
method descriptor
create_shape_from_points(self: shapeworks_py.Analyze, arg0: shapeworks_py.Particles) -> shapeworks_py.Shape
get_mean_shape()
method descriptor
get_mean_shape(self: shapeworks_py.Analyze) -> shapeworks_py.Mesh
get_mean_shape_points()
method descriptor
get_mean_shape_points(self: shapeworks_py.Analyze) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, 1]"]
get_median_shape()
method descriptor
get_median_shape(self: shapeworks_py.Analyze) -> shapeworks_py.Mesh
get_median_shape_points()
method descriptor
get_median_shape_points(self: shapeworks_py.Analyze) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, 1]"]
get_mode_shape()
method descriptor
get_mode_shape(self: shapeworks_py.Analyze, arg0: typing.SupportsInt, arg1: typing.SupportsFloat) -> shapeworks_py.Shape
get_num_modes()
method descriptor
get_num_modes(self: shapeworks_py.Analyze) -> int
get_num_particles()
method descriptor
get_num_particles(self: shapeworks_py.Analyze) -> int
get_num_subjects()
method descriptor
get_num_subjects(self: shapeworks_py.Analyze) -> int
get_shape_points()
method descriptor
get_shape_points(self: shapeworks_py.Analyze, arg0: typing.SupportsInt, arg1: typing.SupportsFloat) -> shapeworks_py.Particles
get_shapes()
method descriptor
get_shapes(self: shapeworks_py.Analyze) -> list[shapeworks_py.Shape]
get_subject_features()
method descriptor
get_subject_features(self: shapeworks_py.Analyze, arg0: typing.SupportsInt, arg1: str) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, 1]"]
groups_active()
method descriptor
groups_active(self: shapeworks_py.Analyze) -> bool
run_offline_analysis()
method descriptor
run_offline_analysis(self: shapeworks_py.Analyze, arg0: str, arg1: typing.SupportsFloat, arg2: typing.SupportsFloat) -> None
Axis
Bases: pybind11_builtins.pybind11_object
Members:
invalid
X
Y
Z
X = <Axis.X: 0>
class-attribute
Members:
invalid
X
Y
Z
Y = <Axis.Y: 1>
class-attribute
Members:
invalid
X
Y
Z
Z = <Axis.Z: 2>
class-attribute
Members:
invalid
X
Y
Z
invalid = <Axis.invalid: -1>
class-attribute
Members:
invalid
X
Y
Z
name
property
name(self: object, /) -> str
value
property
DomainType
Bases: pybind11_builtins.pybind11_object
Members:
MeshDomain
ImageDomain
ContourDomain
ContourDomain = <DomainType.ContourDomain: 2>
class-attribute
Members:
MeshDomain
ImageDomain
ContourDomain
ImageDomain = <DomainType.ImageDomain: 0>
class-attribute
Members:
MeshDomain
ImageDomain
ContourDomain
MeshDomain = <DomainType.MeshDomain: 1>
class-attribute
Members:
MeshDomain
ImageDomain
ContourDomain
name
property
name(self: object, /) -> str
value
property
Groom
Bases: pybind11_builtins.pybind11_object
run()
method descriptor
run(self: shapeworks_py.Groom) -> bool
Image
Bases: pybind11_builtins.pybind11_object
antialias()
method descriptor
antialias(self: shapeworks_py.Image, iterations: typing.SupportsInt = 50, maxRMSErr: typing.SupportsFloat = 0.009999999776482582, layers: typing.SupportsInt = 3) -> shapeworks_py.Image
antialiases binary volumes (layers is set to 3 when not specified)
applyCurvatureFilter()
method descriptor
applyCurvatureFilter(self: shapeworks_py.Image, iterations: typing.SupportsInt = 10) -> shapeworks_py.Image
denoises an image using curvature driven flow using curvature flow image filter
applyGradientFilter()
method descriptor
applyGradientFilter(self: shapeworks_py.Image) -> shapeworks_py.Image
computes gradient magnitude at each pixel using gradient magnitude filter
applyIntensityFilter()
method descriptor
applyIntensityFilter(self: shapeworks_py.Image, min: typing.SupportsFloat = 0.0, max: typing.SupportsFloat = 0.0) -> shapeworks_py.Image
applies intensity windowing image filter
applySigmoidFilter()
method descriptor
applySigmoidFilter(self: shapeworks_py.Image, alpha: typing.SupportsFloat = 10.0, beta: typing.SupportsFloat = 10.0) -> shapeworks_py.Image
computes sigmoid function pixel-wise using sigmoid image filter
applyTPLevelSetFilter()
method descriptor
applyTPLevelSetFilter(self: shapeworks_py.Image, featureImage: shapeworks_py.Image, scaling: typing.SupportsFloat = 20.0) -> shapeworks_py.Image
segments structures in image using topology preserving geodesic active contour level set filter
applyTransform()
method descriptor
applyTransform(args, *kwargs) Overloaded function.
- applyTransform(self: shapeworks_py.Image, transform: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[4, 4]"], interp: shapeworks_py.InterpolationType =
applies the given transformation to the image by using the specified resampling filter (Linear or NearestNeighbor)
- applyTransform(self: shapeworks_py.Image, transform: shapeworks_py.WarpTransform, interp: shapeworks_py.InterpolationType =
applies the given warp transformation to the image using the specified resampling filter (Linear or NearestNeighbor)
- applyTransform(self: shapeworks_py.Image, transform: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[4, 4]"], origin: collections.abc.Sequence[typing.SupportsFloat], dims: collections.abc.Sequence[typing.SupportsInt], spacing: collections.abc.Sequence[typing.SupportsFloat], direction: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[3, 3]"], interp: shapeworks_py.InterpolationType =
applies the given transformation to the image by using resampling filter with new origin, dims, spacing, and sampling along given direction axes (a 3x3 row-major matrix) using the specified interpolation method (Linear or NearestNeighbor)
assign()
method descriptor
assign(self: shapeworks_py.Image, arg0: numpy.ndarray) -> shapeworks_py.Image
Initialize an image from a numpy array (must be dtype float32). Transfers ownership of the array without copying. If a copy is desired, construct using Image(np.array(arr)).
binarize()
method descriptor
binarize(self: shapeworks_py.Image, minVal: typing.SupportsFloat = 0.0, maxVal: typing.SupportsFloat = 3.4028234663852886e+38, innerVal: typing.SupportsFloat = 1.0, outerVal: typing.SupportsFloat = 0.0) -> shapeworks_py.Image
sets portion of image greater than min and less than or equal to max to the specified value
center()
method descriptor
center(self: shapeworks_py.Image) -> numpy.ndarray
physical coordinates of center of this image
centerOfMass()
method descriptor
centerOfMass(self: shapeworks_py.Image, minVal: typing.SupportsFloat = 0.0, maxVal: typing.SupportsFloat = 1.0) -> numpy.ndarray
returns average physical coordinate of pixels in range (minval, maxval]
clip()
method descriptor
clip(args, *kwargs) Overloaded function.
- clip(self: shapeworks_py.Image, o: collections.abc.Sequence[typing.SupportsFloat], p1: collections.abc.Sequence[typing.SupportsFloat], p2: collections.abc.Sequence[typing.SupportsFloat], val: typing.SupportsFloat = 0.0) -> shapeworks_py.Image
sets values on the back side of cutting plane (containing three non-colinear points) to val (default 0.0)
- clip(self: shapeworks_py.Image, n: collections.abc.Sequence[typing.SupportsFloat], q: collections.abc.Sequence[typing.SupportsFloat], val: typing.SupportsFloat = 0.0) -> shapeworks_py.Image
sets values on the back side of cutting plane (normal n containing point p) to val (default 0.0)
closeHoles()
method descriptor
closeHoles(self: shapeworks_py.Image, foreground: typing.SupportsFloat = 0.0) -> shapeworks_py.Image
closes holes in a volume defined by values larger than specified value
compare()
method descriptor
compare(args, *kwargs) Overloaded function.
- compare(self: shapeworks_py.Image, other: shapeworks_py.Image, verifyall: bool = True, tolerance: typing.SupportsFloat = 0.0, precision: typing.SupportsFloat = 1e-06) -> bool
compares two images
- compare(self: shapeworks_py.Image, other: shapeworks_py.Image, verifyall: bool = True, tolerance: typing.SupportsFloat = 0.0, precision: typing.SupportsFloat = 1e-12) -> bool
compares two images
computeDT()
method descriptor
computeDT(self: shapeworks_py.Image, isovalue: typing.SupportsFloat = 0.0) -> shapeworks_py.Image
computes signed distance transform volume from an image at the specified isovalue
coordsys()
method descriptor
coordsys(self: shapeworks_py.Image) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[3, 3]"]
return 3x3 coordinate system in which this image lives in physical space
copy()
method descriptor
copy(self: shapeworks_py.Image) -> shapeworks_py.Image
createCenterOfMassTransform()
method descriptor
createCenterOfMassTransform(self: shapeworks_py.Image) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, n]"]
creates a transform that translates center of mass to center of image
createRigidRegistrationTransform()
method descriptor
createRigidRegistrationTransform(self: shapeworks_py.Image, target: shapeworks_py.Image, isoValue: typing.SupportsFloat = 0.0, iterations: typing.SupportsInt = 20) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, n]"]
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
crop()
method descriptor
crop(self: shapeworks_py.Image, region: shapeworks::PhysicalRegion, padding: typing.SupportsInt = 0) -> shapeworks_py.Image
crops the image down to the given (physical) region, with optional padding
dims()
method descriptor
dims(self: shapeworks_py.Image) -> numpy.ndarray
logical dimensions of the image
evaluate()
method descriptor
evaluate(self: shapeworks_py.Image, pt: collections.abc.Sequence[typing.SupportsFloat]) -> float
evaluate the image at any given point in space
extractLabel()
method descriptor
extractLabel(self: shapeworks_py.Image, label: typing.SupportsFloat = 1.0) -> shapeworks_py.Image
extracts/isolates a specific pixel label from a given multi-label volume and outputs the corresponding binary image
fitRegion()
method descriptor
fitRegion(self: shapeworks_py.Image, region: shapeworks::PhysicalRegion, value: typing.SupportsFloat = 0) -> shapeworks_py.Image
crops or pads the image to fit a region with optional padding value
gaussianBlur()
method descriptor
gaussianBlur(self: shapeworks_py.Image, sigma: typing.SupportsFloat = 0.0) -> shapeworks_py.Image
applies gaussian blur
getDICOMSeriesUIDs()
staticmethod
getDICOMSeriesUIDs(pathname: str) -> list[str]
return the list of DICOM series UIDs found in the given directory
isolate()
method descriptor
isolate(self: shapeworks_py.Image, minimum_size: typing.SupportsInt = 0) -> shapeworks_py.Image
isolate the largest object (minimum_size=0), or keep every connected component with at least minimum_size voxels
logicalBoundingBox()
method descriptor
logicalBoundingBox(self: shapeworks_py.Image) -> shapeworks::IndexRegion
returns the index coordinates of this image's region
logicalToPhysical()
method descriptor
logicalToPhysical(args, *kwargs) Overloaded function.
- logicalToPhysical(self: shapeworks_py.Image, region: shapeworks::IndexRegion) -> shapeworks::PhysicalRegion
converts from a logical region (index coordinates) to a physical region
- logicalToPhysical(self: shapeworks_py.Image, c: collections.abc.Sequence[typing.SupportsInt]) -> numpy.ndarray
converts a logical (index) coordinate to physical space
max()
method descriptor
max(self: shapeworks_py.Image) -> float
maximum of image
mean()
method descriptor
mean(self: shapeworks_py.Image) -> float
mean of image
min()
method descriptor
min(self: shapeworks_py.Image) -> float
minimum of image
origin()
method descriptor
origin(self: shapeworks_py.Image) -> numpy.ndarray
physical coordinates of image origin
pad()
method descriptor
pad(args, *kwargs) Overloaded function.
- pad(self: shapeworks_py.Image, pad: typing.SupportsInt, value: typing.SupportsFloat = 0.0) -> shapeworks_py.Image
pads an image by same number of pixels in all directions with constant value
- pad(self: shapeworks_py.Image, padx: typing.SupportsInt, pady: typing.SupportsInt, padz: typing.SupportsInt, value: typing.SupportsFloat = 0.0) -> shapeworks_py.Image
pads an image by desired number of pixels in each direction with constant value
- pad(self: shapeworks_py.Image, region: shapeworks::IndexRegion, value: typing.SupportsFloat = 0.0) -> shapeworks_py.Image
pads an image to include the given region with constant value
physicalBoundingBox()
method descriptor
physicalBoundingBox(self: shapeworks_py.Image, isovalue: typing.SupportsFloat = 1.0) -> shapeworks::PhysicalRegion
returns region of physical space occupied by the region of data <= the given isoValue
physicalToLogical()
method descriptor
physicalToLogical(args, *kwargs) Overloaded function.
- physicalToLogical(self: shapeworks_py.Image, region: shapeworks::PhysicalRegion) -> shapeworks::IndexRegion
converts from a physical region to a logical region (index coordinates)
- physicalToLogical(self: shapeworks_py.Image, p: collections.abc.Sequence[typing.SupportsFloat]) -> numpy.ndarray
converts a physical coordinate to a logical (index) space
physicalboundingBox()
method descriptor
physicalboundingBox(self: shapeworks_py.Image) -> shapeworks::PhysicalRegion
returns region of physical space occupied by this image
recenter()
method descriptor
recenter(self: shapeworks_py.Image) -> shapeworks_py.Image
recenters an image by changing its origin in the image header to the physical coordinates of the center of the image
reflect()
method descriptor
reflect(self: shapeworks_py.Image, axis: shapeworks_py.Axis) -> shapeworks_py.Image
reflect image with respect to logical image center and the specified axis
resample()
method descriptor
resample(args, *kwargs) Overloaded function.
- resample(self: shapeworks_py.Image, transform: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[4, 4]"], origin: collections.abc.Sequence[typing.SupportsFloat], dims: collections.abc.Sequence[typing.SupportsInt], spacing: collections.abc.Sequence[typing.SupportsFloat], direction: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[3, 3]"], interp: shapeworks_py.InterpolationType =
resamples by applying transform then sampling from given origin along direction axes at spacing physical units per pixel for dims pixels using specified interpolator
- resample(self: shapeworks_py.Image, physicalSpacing: collections.abc.Sequence[typing.SupportsFloat], interp: shapeworks_py.InterpolationType =
resamples image using new physical spacing, updating logical dims to keep all image data for this spacing
- resample(self: shapeworks_py.Image, isoSpacing: typing.SupportsFloat = 1.0, interp: shapeworks_py.InterpolationType =
isotropically resamples image using giving isospacing
resize()
method descriptor
resize(self: shapeworks_py.Image, logicalDims: collections.abc.Sequence[typing.SupportsInt], interp: shapeworks_py.InterpolationType =
change logical dims (computes new physical spacing)
rotate()
method descriptor
rotate(args, *kwargs) Overloaded function.
- rotate(self: shapeworks_py.Image, angle: typing.SupportsFloat, axis: itk::Vector
rotate around center (not origin) using axis (default z-axis) by angle (in radians)
- rotate(self: shapeworks_py.Image, angle: typing.SupportsFloat, axis: shapeworks_py.Axis) -> shapeworks_py.Image
rotate around center (not origin) using axis (default z-axis) by angle (in radians)
- rotate(self: shapeworks_py.Image, angle: typing.SupportsFloat, axis: collections.abc.Sequence[typing.SupportsFloat]) -> shapeworks_py.Image
rotate around center (not origin) using axis (default z-axis) by angle (in radians)
scale()
method descriptor
scale(self: shapeworks_py.Image, scale_vec: collections.abc.Sequence[typing.SupportsFloat]) -> shapeworks_py.Image
scale image by scale_vec around center (not origin)
setCoordsys()
method descriptor
setCoordsys(self: shapeworks_py.Image, coordsys: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[3, 3]"] = [1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0]) -> shapeworks_py.Image
sets the orientation of this image
setOrigin()
method descriptor
setOrigin(self: shapeworks_py.Image, origin: collections.abc.Sequence[typing.SupportsFloat] = [0.0, 0.0, 0.0]) -> shapeworks_py.Image
sets the image origin in physical space to the given value
setSpacing()
method descriptor
setSpacing(self: shapeworks_py.Image, spacing: collections.abc.Sequence[typing.SupportsFloat] = [1.0, 1.0, 1.0]) -> shapeworks_py.Image
set image spacing, the size of each pixel
size()
method descriptor
size(self: shapeworks_py.Image) -> numpy.ndarray
physical dimensions of the image (dims * spacing)
spacing()
method descriptor
spacing(self: shapeworks_py.Image) -> numpy.ndarray
physical spacing of the image
std()
method descriptor
std(self: shapeworks_py.Image) -> float
standard deviation of image
toArray()
method descriptor
toArray(self: shapeworks_py.Image, copy: bool = False, for_viewing: bool = False) -> numpy.ndarray
returns raw array of image data, directly sharing data by default, copying if specified. NOTE: many Image operations reallocate image array, so while the array returned from this function is writable, it is best used immediately for Python operations; use for_viewing argument to get array in column-major ('F') order ('sw2vtkImage' already does this).
toMesh()
method descriptor
toMesh(self: shapeworks_py.Image, isovalue: typing.SupportsFloat) -> shapeworks::Mesh
converts image to mesh at specified isovalue
topologyPreservingSmooth()
method descriptor
topologyPreservingSmooth(self: shapeworks_py.Image, scaling: typing.SupportsFloat = 20.0, sigmoidAlpha: typing.SupportsFloat = 10.5, sigmoidBeta: typing.SupportsFloat = 10.0) -> shapeworks_py.Image
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]
translate()
method descriptor
translate(self: shapeworks_py.Image, v: collections.abc.Sequence[typing.SupportsFloat]) -> shapeworks_py.Image
translates image
write()
method descriptor
write(self: shapeworks_py.Image, filename: str, compressed: bool = True) -> shapeworks_py.Image
writes the current image (determines type by its extension)
ImageUtils
Bases: pybind11_builtins.pybind11_object
boundingBox()
staticmethod
boundingBox(args, *kwargs) Overloaded function.
- boundingBox(filenames: collections.abc.Sequence[str], isoValue: typing.SupportsFloat = 1.0) -> shapeworks_py.PhysicalRegion
compute largest bounding box surrounding the specified isovalue of the specified set of filenames
- boundingBox(images: collections.abc.Sequence[shapeworks_py.Image], isoValue: typing.SupportsFloat = 1.0) -> shapeworks_py.PhysicalRegion
compute largest bounding box surrounding the specified isovalue of the specified set of images
createWarpTransform()
staticmethod
createWarpTransform(source_landmarks: str, target_landmarks: str, stride: typing.SupportsInt = 1) -> shapeworks_py.WarpTransform
computes a warp transform from the source to the target landmarks (in the given files) using every stride points
IndexRegion
Bases: pybind11_builtins.pybind11_object
max
property
max point of region
min
property
min point of region
origin()
method descriptor
origin(self: shapeworks_py.IndexRegion) -> numpy.ndarray
return origin of region
pad()
method descriptor
pad(self: shapeworks_py.IndexRegion, padding: typing.SupportsInt) -> shapeworks_py.IndexRegion
grows or shrinks the region by the specified amount
size()
method descriptor
size(self: shapeworks_py.IndexRegion) -> numpy.ndarray
return size of region
valid()
method descriptor
valid(self: shapeworks_py.IndexRegion) -> bool
ensure if region is valid
InterpolationType
Bases: pybind11_builtins.pybind11_object
Members:
Linear
NearestNeighbor
Linear = <InterpolationType.Linear: 0>
class-attribute
Members:
Linear
NearestNeighbor
NearestNeighbor = <InterpolationType.NearestNeighbor: 1>
class-attribute
Members:
Linear
NearestNeighbor
name
property
name(self: object, /) -> str
value
property
Mesh
Bases: pybind11_builtins.pybind11_object
Affine = <AlignmentType.Affine: 2>
class-attribute
Members:
Rigid
Similarity
Affine
Butterfly = <SubdivisionType.Butterfly: 0>
class-attribute
Members:
Butterfly
Loop
Face = <FieldType.Face: 1>
class-attribute
Members:
Point
Face
Gaussian = <CurvatureType.Gaussian: 1>
class-attribute
Members:
Principal
Gaussian
Mean
Loop = <SubdivisionType.Loop: 1>
class-attribute
Members:
Butterfly
Loop
Mean = <CurvatureType.Mean: 2>
class-attribute
Members:
Principal
Gaussian
Mean
Point = <FieldType.Point: 0>
class-attribute
Members:
Point
Face
PointToCell = <DistanceMethod.PointToCell: 1>
class-attribute
Members:
PointToPoint
PointToCell
PointToPoint = <DistanceMethod.PointToPoint: 0>
class-attribute
Members:
PointToPoint
PointToCell
Principal = <CurvatureType.Principal: 0>
class-attribute
Members:
Principal
Gaussian
Mean
Rigid = <AlignmentType.Rigid: 0>
class-attribute
Members:
Rigid
Similarity
Affine
Similarity = <AlignmentType.Similarity: 1>
class-attribute
Members:
Rigid
Similarity
Affine
AlignmentType
Bases: pybind11_builtins.pybind11_object
Members:
Rigid
Similarity
Affine
Affine = <AlignmentType.Affine: 2>
class-attribute
Members:
Rigid
Similarity
Affine
Rigid = <AlignmentType.Rigid: 0>
class-attribute
Members:
Rigid
Similarity
Affine
Similarity = <AlignmentType.Similarity: 1>
class-attribute
Members:
Rigid
Similarity
Affine
name
property
name(self: object, /) -> str
value
property
CurvatureType
Bases: pybind11_builtins.pybind11_object
Members:
Principal
Gaussian
Mean
Gaussian = <CurvatureType.Gaussian: 1>
class-attribute
Members:
Principal
Gaussian
Mean
Mean = <CurvatureType.Mean: 2>
class-attribute
Members:
Principal
Gaussian
Mean
Principal = <CurvatureType.Principal: 0>
class-attribute
Members:
Principal
Gaussian
Mean
name
property
name(self: object, /) -> str
value
property
DistanceMethod
Bases: pybind11_builtins.pybind11_object
Members:
PointToPoint
PointToCell
PointToCell = <DistanceMethod.PointToCell: 1>
class-attribute
Members:
PointToPoint
PointToCell
PointToPoint = <DistanceMethod.PointToPoint: 0>
class-attribute
Members:
PointToPoint
PointToCell
name
property
name(self: object, /) -> str
value
property
FieldType
Bases: pybind11_builtins.pybind11_object
Members:
Point
Face
Face = <FieldType.Face: 1>
class-attribute
Members:
Point
Face
Point = <FieldType.Point: 0>
class-attribute
Members:
Point
Face
name
property
name(self: object, /) -> str
value
property
SubdivisionType
Bases: pybind11_builtins.pybind11_object
Members:
Butterfly
Loop
Butterfly = <SubdivisionType.Butterfly: 0>
class-attribute
Members:
Butterfly
Loop
Loop = <SubdivisionType.Loop: 1>
class-attribute
Members:
Butterfly
Loop
name
property
name(self: object, /) -> str
value
property
applySubdivisionFilter()
method descriptor
applySubdivisionFilter(self: shapeworks_py.Mesh, type: shapeworks_py.Mesh.SubdivisionType =
applies subdivision filter (butterfly (default) or loop)
applyTransform()
method descriptor
applyTransform(self: shapeworks_py.Mesh, transform: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[4, 4]"], imageTransform: bool = False) -> shapeworks_py.Mesh
applies the given transformation to the mesh
boundingBox()
method descriptor
boundingBox(self: shapeworks_py.Mesh) -> shapeworks_py.PhysicalRegion
computes bounding box of current mesh
center()
method descriptor
center(self: shapeworks_py.Mesh) -> numpy.ndarray
center of mesh
centerOfMass()
method descriptor
centerOfMass(self: shapeworks_py.Mesh) -> numpy.ndarray
center of mass of mesh
clip()
method descriptor
clip(args, *kwargs) Overloaded function.
- clip(self: shapeworks_py.Mesh, point: collections.abc.Sequence[typing.SupportsFloat], normal: collections.abc.Sequence[typing.SupportsFloat]) -> shapeworks_py.Mesh
clips a mesh using a cutting plane
- clip(self: shapeworks_py.Mesh, o: collections.abc.Sequence[typing.SupportsFloat], p1: collections.abc.Sequence[typing.SupportsFloat], p2: collections.abc.Sequence[typing.SupportsFloat]) -> shapeworks_py.Mesh
clips a mesh using a cutting plane
clipClosedSurface()
method descriptor
clipClosedSurface(self: shapeworks_py.Mesh, point: collections.abc.Sequence[typing.SupportsFloat], normal: collections.abc.Sequence[typing.SupportsFloat]) -> shapeworks_py.Mesh
clips a mesh using a cutting plane resulting in a closed surface
closestPoint()
method descriptor
closestPoint(self: shapeworks_py.Mesh, point: collections.abc.Sequence[typing.SupportsFloat]) -> tuple
returns closest point to given point on mesh
closestPointId()
method descriptor
closestPointId(self: shapeworks_py.Mesh, point: collections.abc.Sequence[typing.SupportsFloat]) -> int
returns closest point id in this mesh to the given point in space
compareField()
method descriptor
compareField(self: shapeworks_py.Mesh, other_mesh: shapeworks_py.Mesh, name1: str, name2: str = '', eps: typing.SupportsFloat = -1.0) -> bool
compares two meshes based on fields
computeNormals()
method descriptor
computeNormals(self: shapeworks_py.Mesh) -> shapeworks_py.Mesh
computes and adds oriented point and cell normals
computeThickness()
method descriptor
computeThickness(self: shapeworks_py.Mesh, ct: shapeworks_py.Image, dt: shapeworks_py.Image = None, maxDist: typing.SupportsFloat = 10000, medianRadius: typing.SupportsFloat = 5.0, distanceMesh: str = '') -> shapeworks_py.Mesh
Computes cortical thickness
copy()
method descriptor
copy(self: shapeworks_py.Mesh) -> shapeworks_py.Mesh
coverage()
method descriptor
coverage(self: shapeworks_py.Mesh, otherMesh: shapeworks_py.Mesh, allowBackIntersections: bool = True, angleThreshold: typing.SupportsFloat = 0, backSearchRadius: typing.SupportsFloat = 0) -> shapeworks_py.Mesh
determines coverage between current mesh and another mesh (e.g. acetabular cup / femoral head)
createTransform()
method descriptor
createTransform(self: shapeworks_py.Mesh, target: shapeworks_py.Mesh, align: shapeworks_py.Mesh.AlignmentType =
creates a transform using specified AlignmentType (Mesh.Rigid, Mesh.Similarity, Mesh.Affine) for specified number of iterations (default alignment: Similarity, default iterations: 10)
curvature()
method descriptor
curvature(self: shapeworks_py.Mesh, type: shapeworks_py.Mesh.CurvatureType =
computes and adds curvature (principal (default) or gaussian or mean)
distance()
method descriptor
distance(self: shapeworks_py.Mesh, target: shapeworks_py.Mesh, method: shapeworks_py.Mesh.DistanceMethod =
computes closest distance from vertices of this mesh to target mesh, returning the distances and the indices of faces or vertices in the target mesh that contain the closest points; the distances are also stored on this mesh as a 'distance' point field
extractLargestComponent()
method descriptor
extractLargestComponent(self: shapeworks_py.Mesh) -> shapeworks_py.Mesh
extract the largest connected component from the mesh
faces()
method descriptor
faces(self: shapeworks_py.Mesh) -> typing.Annotated[numpy.typing.NDArray[numpy.int32], "[m, n]"]
matrix with number of faces with indices of the three points from which each face is composed
fillHoles()
method descriptor
fillHoles(self: shapeworks_py.Mesh, hole_size: typing.SupportsFloat = 1000) -> shapeworks_py.Mesh
finds holes in a mesh and closes them
fixElement()
method descriptor
fixElement(self: shapeworks_py.Mesh) -> shapeworks_py.Mesh
fix element winding of mesh
geodesicDistance()
method descriptor
geodesicDistance(args, *kwargs) Overloaded function.
- geodesicDistance(self: shapeworks_py.Mesh, source: typing.SupportsInt, target: typing.SupportsInt) -> float
computes geodesic distance between two vertices (specified by their indices) on mesh
- geodesicDistance(self: shapeworks_py.Mesh, landmark: collections.abc.Sequence[typing.SupportsFloat]) -> numpy.ndarray
computes geodesic distance between a point (landmark) and each vertex on mesh
- geodesicDistance(self: shapeworks_py.Mesh, curve: collections.abc.Sequence[collections.abc.Sequence[typing.SupportsFloat]]) -> numpy.ndarray
computes geodesic distance between a set of points (curve) and all vertices on mesh
getFace()
method descriptor
getFace(self: shapeworks_py.Mesh, id: typing.SupportsInt) -> numpy.ndarray
return indices of the three points with which the face at the given index is composed
getField()
method descriptor
getField(self: shapeworks_py.Mesh, name: str, type: shapeworks_py.Mesh.FieldType) -> numpy.ndarray
gets the field
getFieldNames()
method descriptor
getFieldNames(self: shapeworks_py.Mesh) -> list[str]
print all field names in mesh
getFieldValue()
method descriptor
getFieldValue(self: shapeworks_py.Mesh, idx: str, name: typing.SupportsInt) -> float
gets the value at the given index of field
getMultiFieldValue()
method descriptor
getMultiFieldValue(self: shapeworks_py.Mesh, idx: str, name: typing.SupportsInt) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, 1]"]
gets the vector value at the given index of field
getPoint()
method descriptor
getPoint(self: shapeworks_py.Mesh, id: typing.SupportsInt) -> numpy.ndarray
(x,y,z) coordinates of vertex at given index
interpolateFieldAtPoint()
method descriptor
interpolateFieldAtPoint(self: shapeworks_py.Mesh, field: str, point: collections.abc.Sequence[typing.SupportsFloat]) -> float
Interpolate the feature at the location using barycentric coordinate
interpolate_scalars_to_mesh()
method descriptor
interpolate_scalars_to_mesh(self: shapeworks_py.Mesh, name: str, positions: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[m, 1]"], scalar_values: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[m, 1]"]) -> None
Interpolate scalars to mesh
invertNormals()
method descriptor
invertNormals(self: shapeworks_py.Mesh) -> shapeworks_py.Mesh
handle flipping normals
numFaces()
method descriptor
numFaces(self: shapeworks_py.Mesh) -> int
number of faces
numPoints()
method descriptor
numPoints(self: shapeworks_py.Mesh) -> int
number of points
points()
method descriptor
points(self: shapeworks_py.Mesh) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, n]"]
matrix with number of points with (x,y,z) coordinates of each point
probeVolume()
method descriptor
probeVolume(self: shapeworks_py.Mesh, image: shapeworks_py.Image) -> shapeworks_py.Mesh
samples image data values at point locations specified by image
reflect()
method descriptor
reflect(self: shapeworks_py.Mesh, axis: shapeworks_py.Axis, origin: collections.abc.Sequence[typing.SupportsFloat] = [0.0, 0.0, 0.0]) -> shapeworks_py.Mesh
reflect meshes with respect to a specified center and specific axis
remesh()
method descriptor
remesh(self: shapeworks_py.Mesh, numVertices: typing.SupportsInt, adaptivity: typing.SupportsFloat) -> shapeworks_py.Mesh
applies remeshing using approximated centroidal voronoi diagrams for a given number of vertices and adaptivity
remeshPercent()
method descriptor
remeshPercent(self: shapeworks_py.Mesh, percentage: typing.SupportsFloat, adaptivity: typing.SupportsFloat) -> shapeworks_py.Mesh
applies remeshing using approximated centroidal voronoi diagrams for a given percentage of vertices and adaptivity
rotate()
method descriptor
rotate(self: shapeworks_py.Mesh, angle: typing.SupportsFloat, axis: shapeworks_py.Axis) -> shapeworks_py.Mesh
rotate using axis by angle (in degrees)
scale()
method descriptor
scale(self: shapeworks_py.Mesh, v: collections.abc.Sequence[typing.SupportsFloat]) -> shapeworks_py.Mesh
scale mesh
setField()
method descriptor
setField(self: shapeworks_py.Mesh, name: str, array: numpy.ndarray, type: shapeworks_py.Mesh.FieldType =
sets the given field for points with array (type defaults to Point)
setFieldValue()
method descriptor
setFieldValue(self: shapeworks_py.Mesh, idx: str, value: typing.SupportsInt, name: typing.SupportsFloat = '') -> None
sets the given index of field to value
smooth()
method descriptor
smooth(self: shapeworks_py.Mesh, iterations: typing.SupportsInt = 0, relaxation: typing.SupportsFloat = 0.0) -> shapeworks_py.Mesh
applies laplacian smoothing
smoothSinc()
method descriptor
smoothSinc(self: shapeworks_py.Mesh, iterations: typing.SupportsInt = 0, passband: typing.SupportsFloat = 0.0) -> shapeworks_py.Mesh
applies windowed sinc smoothing
toDistanceTransform()
method descriptor
toDistanceTransform(self: shapeworks_py.Mesh, region: shapeworks_py.PhysicalRegion = { min: [1e+09, 1e+09, 1e+09], max: [-1e+09, -1e+09, -1e+09] }, spacing: collections.abc.Sequence[typing.SupportsFloat] = [1.0, 1.0, 1.0], padding: collections.abc.Sequence[typing.SupportsInt] = [1, 1, 1]) -> shapeworks_py.Image
converts specified region to distance transform image with specified spacing and padding (default: unit spacing and 1 pixel of padding)
toImage()
method descriptor
toImage(self: shapeworks_py.Mesh, region: shapeworks_py.PhysicalRegion = { min: [1e+09, 1e+09, 1e+09], max: [-1e+09, -1e+09, -1e+09] }, spacing: collections.abc.Sequence[typing.SupportsFloat] = [1.0, 1.0, 1.0]) -> shapeworks_py.Image
rasterize specified region to create binary image of desired dims (default: unit spacing)
translate()
method descriptor
translate(self: shapeworks_py.Mesh, v: collections.abc.Sequence[typing.SupportsFloat]) -> shapeworks_py.Mesh
translates mesh
write()
method descriptor
write(self: shapeworks_py.Mesh, pathname: str, binaryFile: bool = False) -> shapeworks_py.Mesh
writes mesh, format specified by filename extension
MeshUtils
Bases: pybind11_builtins.pybind11_object
boundaryLoopExtractor()
staticmethod
boundaryLoopExtractor(mesh: shapeworks_py.Mesh) -> shapeworks_py.Mesh
for a mesh extracts the boundary loop and export the boundary loop as a contour .vtp file
boundingBox()
staticmethod
boundingBox(args, *kwargs) Overloaded function.
- boundingBox(filenames: collections.abc.Sequence[str], center: bool = False) -> shapeworks_py.PhysicalRegion
calculate bounding box incrementally for meshes
- boundingBox(meshes: collections.abc.Sequence[shapeworks_py.Mesh], center: bool = False) -> shapeworks_py.PhysicalRegion
calculate bounding box incrementally for meshes
computeMeanNormals()
staticmethod
computeMeanNormals(args, *kwargs) Overloaded function.
- computeMeanNormals(filenames: collections.abc.Sequence[str], autoGenerateNormals: bool = True) -> numpy.ndarray
computes average normals for each point in given set of meshes
- computeMeanNormals(meshes: collections.abc.Sequence[shapeworks_py.Mesh]) -> numpy.ndarray
computes average normals for each point in given set of meshes
findReferenceMesh()
staticmethod
findReferenceMesh(meshes: collections.abc.Sequence[shapeworks_py.Mesh], random_subset: typing.SupportsInt = -1) -> int
find reference mesh from a set of meshes
generateNormals()
staticmethod
generateNormals(meshes: collections.abc.Sequence[shapeworks_py.Mesh], forceRegen: bool = False) -> None
generates and adds normals for points and faces for each mesh in given set of meshes
sharedBoundaryExtractor()
staticmethod
sharedBoundaryExtractor(mesh_l: shapeworks_py.Mesh, mesh_r: shapeworks_py.Mesh, tol: typing.SupportsFloat = 0.001) -> tuple
extract the shared boundary for the given left and right meshes and save the individual meshes
MeshWarper
Bases: pybind11_builtins.pybind11_object
buildMesh()
method descriptor
buildMesh(self: shapeworks_py.MeshWarper, particles: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[m, n]"]) -> shapeworks_py.Mesh
Build the mesh from particle positions (matrix [Nx3])
extractLandmarks()
method descriptor
extractLandmarks(self: shapeworks_py.MeshWarper, warped_mesh: shapeworks_py.Mesh) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, n]"]
Extract the landmarks from the warped mesh and return the landmarks (matrix [Nx3])
generateWarp()
method descriptor
generateWarp(args, *kwargs) Overloaded function.
- generateWarp(self: shapeworks_py.MeshWarper, reference_mesh: shapeworks_py.Mesh, reference_particles: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[m, n]"]) -> bool
Assign the reference mesh/particles (matrix [Nx3]) and pre-compute the warping
- generateWarp(self: shapeworks_py.MeshWarper, reference_mesh: shapeworks_py.Mesh, reference_particles: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[m, n]"], landmarks: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[m, n]"]) -> bool
Assign the reference mesh/particles (matrix [Nx3]) and landmarks (matrix [Nx3]) and pre-compute the warping
getGoodParticlesIndices()
method descriptor
getGoodParticlesIndices(self: shapeworks_py.MeshWarper) -> list[int]
Return the indexes of good particles.
getLandmarksMap()
method descriptor
getLandmarksMap(self: shapeworks_py.MeshWarper) -> dict[int, int]
Return the map of landmarks to vertices.
getNumWarpVertices()
method descriptor
getNumWarpVertices(self: shapeworks_py.MeshWarper) -> int
Return the number of vertices in the warped mesh.
getReferenceMesh()
method descriptor
getReferenceMesh(self: shapeworks_py.MeshWarper) -> shapeworks_py.Mesh
Return the mesh used for warping.
getReferenceParticles()
method descriptor
getReferenceParticles(self: shapeworks_py.MeshWarper) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, n]"]
Return the particles used for warping.
getWarpMatrix()
method descriptor
getWarpMatrix(self: shapeworks_py.MeshWarper) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, n]"]
Return the warping matrix (Vertices = Warp * Control).
getWarpMethod()
method descriptor
getWarpMethod(self: shapeworks_py.MeshWarper) -> shapeworks_py.WarpMethod
Return the current warp method.
hasBadParticles()
method descriptor
hasBadParticles(self: shapeworks_py.MeshWarper) -> bool
Return true if warping has removed any bad particle(s).
prepareMesh()
staticmethod
prepareMesh(mesh: shapeworks_py.Mesh) -> shapeworks_py.Mesh
Return the prepared mesh used for warping (before vertices were inserted).
setWarpMethod()
method descriptor
setWarpMethod(self: shapeworks_py.MeshWarper, method: shapeworks_py.WarpMethod) -> None
Set the warp method (WarpMethod.Laplacian or WarpMethod.Biharmonic)
MorphologicalDeviationScore
Bases: pybind11_builtins.pybind11_object
GetMorphoDevScore()
method descriptor
GetMorphoDevScore(self: shapeworks_py.MorphologicalDeviationScore, X: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[m, n]"]) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, 1]"]
Compute Mahalanobis-based deviation score for test samples.
Parameters
X : numpy.ndarray Matrix of test samples (n_samples x n_features)
Returns
numpy.ndarray Vector of Mahalanobis distances for each sample.
GetPCACoefficients()
method descriptor
GetPCACoefficients(self: shapeworks_py.MorphologicalDeviationScore, X: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[m, n]"]) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, n]"]
Project samples onto the fitted PCA basis.
Parameters
X : numpy.ndarray Matrix of samples (n_samples x n_features)
Returns
numpy.ndarray Matrix of PCA coefficients with shape (n_samples, rank).
GetRetainedVarianceRatio()
method descriptor
GetRetainedVarianceRatio(self: shapeworks_py.MorphologicalDeviationScore) -> float
Get the retained variance ratio used to choose PPCA components.
Returns
float The current retained variance ratio.
SetControlShapes()
method descriptor
SetControlShapes(self: shapeworks_py.MorphologicalDeviationScore, X: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[m, n]"]) -> bool
Fit PPCA model on control shapes.
Parameters
X : numpy.ndarray Matrix of control shapes (n_samples x n_features)
Returns
bool True if fitting was successful, False otherwise.
SetRetainedVarianceRatio()
method descriptor
SetRetainedVarianceRatio(self: shapeworks_py.MorphologicalDeviationScore, ratio: typing.SupportsFloat) -> None
Set the retained variance ratio used to choose PPCA components.
Parameters
ratio : float Target cumulative variance ratio in the interval (0, 1].
Optimize
Bases: pybind11_builtins.pybind11_object
GetParticleSystem()
method descriptor
GetParticleSystem(self: shapeworks_py.Optimize) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, n]"]
LoadParameterFile()
method descriptor
LoadParameterFile(self: shapeworks_py.Optimize, arg0: str) -> bool
Run()
method descriptor
Run(self: shapeworks_py.Optimize) -> bool
SetIterationCallbackFunction()
method descriptor
SetIterationCallbackFunction(self: shapeworks_py.Optimize, arg0: collections.abc.Callable[[], None]) -> None
SetUpOptimize()
method descriptor
SetUpOptimize(self: shapeworks_py.Optimize, projectFile: shapeworks::Project) -> bool
Parameters
Bases: pybind11_builtins.pybind11_object
as_map()
method descriptor
as_map(self: shapeworks_py.Parameters) -> dict[str, str]
get underlying map
get()
method descriptor
get(self: shapeworks_py.Parameters, key: str, default: str = '') -> str
get a parameter based on a key, return default if it doesn't exist
key_exists()
method descriptor
key_exists(self: shapeworks_py.Parameters, key: str) -> bool
return if a key exists or not
remove_entry()
method descriptor
remove_entry(self: shapeworks_py.Parameters, key: str) -> None
remove an entry
reset_parameters()
method descriptor
reset_parameters(self: shapeworks_py.Parameters) -> None
reset parameters to blank
set()
method descriptor
set(args, *kwargs) Overloaded function.
- set(self: shapeworks_py.Parameters, key: str, Variant: shapeworks::Variant) -> None
set a parameter based on a key
- set(self: shapeworks_py.Parameters, key: str, value: str) -> None
set a parameter based on a key
ParticleShapeStatistics
Bases: pybind11_builtins.pybind11_object
PCA()
method descriptor
PCA(args, *kwargs) Overloaded function.
- PCA(self: shapeworks_py.ParticleShapeStatistics, particleSystem: shapeworks_py.ParticleSystem, domainsPerShape: typing.SupportsInt = 1) -> int
calculates the eigen values and eigen vectors of the data
- PCA(self: shapeworks_py.ParticleShapeStatistics, project: shapeworks::Project) -> int
calculates the eigen values and eigen vectors of the data from a project
eigenValues()
method descriptor
eigenValues(self: shapeworks_py.ParticleShapeStatistics) -> list[float]
return the eigen values
eigenVectors()
method descriptor
eigenVectors(self: shapeworks_py.ParticleShapeStatistics) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, n]"]
returns the eigenvectors
getMean()
method descriptor
getMean(self: shapeworks_py.ParticleShapeStatistics) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, 1]"]
returns the mean shape particles
numDims()
method descriptor
numDims(self: shapeworks_py.ParticleShapeStatistics) -> int
returns the number of features of the particle system
pcaLoadings()
method descriptor
pcaLoadings(self: shapeworks_py.ParticleShapeStatistics) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, n]"]
returns the coefficients of the linear combination of the original variables from which the principal components are constructed
percentVarByMode()
method descriptor
percentVarByMode(self: shapeworks_py.ParticleShapeStatistics) -> list[float]
return the variance accounted for by the principal components
principalComponentProjections()
method descriptor
principalComponentProjections(self: shapeworks_py.ParticleShapeStatistics) -> int
projects the original data on the calculated principal components
projectNewSample()
method descriptor
projectNewSample(self: shapeworks_py.ParticleShapeStatistics, newSample: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[m, 1]"]) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, 1]"]
project a new sample into the PCA space
sampleSize()
method descriptor
sampleSize(self: shapeworks_py.ParticleShapeStatistics) -> int
returns the sample size of the particle system
ParticleSystem
Bases: pybind11_builtins.pybind11_object
D()
method descriptor
D(self: shapeworks_py.ParticleSystem) -> int
EvaluationCompare()
method descriptor
EvaluationCompare(self: shapeworks_py.ParticleSystem, arg0: shapeworks_py.ParticleSystem) -> bool
ExactCompare()
method descriptor
ExactCompare(self: shapeworks_py.ParticleSystem, arg0: shapeworks_py.ParticleSystem) -> bool
N()
method descriptor
N(self: shapeworks_py.ParticleSystem) -> int
Particles()
method descriptor
Particles(self: shapeworks_py.ParticleSystem) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, n]"]
Paths()
method descriptor
Paths(self: shapeworks_py.ParticleSystem) -> list[str]
ShapeAsPointSet()
method descriptor
ShapeAsPointSet(self: shapeworks_py.ParticleSystem, id_shape: typing.SupportsInt) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, n]"]
Return the particle pointset [Nx3] of the specified shape
Particles
Bases: pybind11_builtins.pybind11_object
get_combined_global_particles()
method descriptor
get_combined_global_particles(self: shapeworks_py.Particles) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, 1]"]
combined world particles across all domains as a flat vector
get_combined_local_particles()
method descriptor
get_combined_local_particles(self: shapeworks_py.Particles) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, 1]"]
combined local particles across all domains as a flat vector
get_number_of_domains()
method descriptor
get_number_of_domains(self: shapeworks_py.Particles) -> int
get_total_number_of_particles()
method descriptor
get_total_number_of_particles(self: shapeworks_py.Particles) -> int
PhysicalRegion
Bases: pybind11_builtins.pybind11_object
max
property
max point of region
min
property
min point of region
expand()
method descriptor
expand(args, *kwargs) Overloaded function.
- expand(self: shapeworks_py.PhysicalRegion, other: shapeworks_py.PhysicalRegion) -> shapeworks_py.PhysicalRegion
expand this region up to the largest portions of both
- expand(self: shapeworks_py.PhysicalRegion, point: itk::Point
expand this region to include this point
origin()
method descriptor
origin(self: shapeworks_py.PhysicalRegion) -> numpy.ndarray
return origin of region
pad()
method descriptor
pad(self: shapeworks_py.PhysicalRegion, padding: typing.SupportsFloat) -> shapeworks_py.PhysicalRegion
grows or shrinks the region by the specified amount
shrink()
method descriptor
shrink(self: shapeworks_py.PhysicalRegion, other: shapeworks_py.PhysicalRegion) -> shapeworks_py.PhysicalRegion
shrink this region down to the smallest portions of both
size()
method descriptor
size(self: shapeworks_py.PhysicalRegion) -> numpy.ndarray
return size of region
to_string()
method descriptor
to_string(self: shapeworks_py.PhysicalRegion) -> str
returns a string representation of this region
valid()
method descriptor
valid(self: shapeworks_py.PhysicalRegion) -> bool
ensure if region is valid
Project
Bases: pybind11_builtins.pybind11_object
clear_parameters()
method descriptor
clear_parameters(self: shapeworks_py.Project, name: str) -> None
get_domain_names()
method descriptor
get_domain_names(self: shapeworks_py.Project) -> list[str]
Return the domain names (e.g. femur, pelvis, etc)
get_feature_names()
method descriptor
get_feature_names(self: shapeworks_py.Project) -> list[str]
get_filename()
method descriptor
get_filename(self: shapeworks_py.Project) -> str
Return the filename
get_groomed_domain_types()
method descriptor
get_groomed_domain_types(self: shapeworks_py.Project) -> list[shapeworks_py.DomainType]
Return the groomed domain types
get_groomed_present()
method descriptor
get_groomed_present(self: shapeworks_py.Project) -> bool
Return if groomed files are present
get_group_names()
method descriptor
get_group_names(self: shapeworks_py.Project) -> list[str]
get_group_values()
method descriptor
get_group_values(self: shapeworks_py.Project, group_names: str) -> list[str]
get_headers()
method descriptor
get_headers(self: shapeworks_py.Project) -> list[str]
Return the headers of the subject sheet
get_images_present()
method descriptor
get_images_present(self: shapeworks_py.Project) -> bool
get_number_of_domains_per_subject()
method descriptor
get_number_of_domains_per_subject(self: shapeworks_py.Project) -> int
Return the number of domains
get_number_of_subjects()
method descriptor
get_number_of_subjects(self: shapeworks_py.Project) -> int
Return the number of subjects in the project
get_original_domain_types()
method descriptor
get_original_domain_types(self: shapeworks_py.Project) -> list[shapeworks_py.DomainType]
Return the original domain types
get_originals_present()
method descriptor
get_originals_present(self: shapeworks_py.Project) -> bool
Return if original files are present
get_parameters()
method descriptor
get_parameters(self: shapeworks_py.Project, name: str, domain_name: str = '') -> shapeworks::Parameters
get_particles_present()
method descriptor
get_particles_present(self: shapeworks_py.Project) -> bool
Return if particle files are present
get_project_path()
method descriptor
get_project_path(self: shapeworks_py.Project) -> str
Return the project path
get_string_column()
method descriptor
get_string_column(self: shapeworks_py.Project, name: str) -> list[str]
Return a column by name
get_subjects()
method descriptor
get_subjects(self: shapeworks_py.Project) -> list[shapeworks::Subject]
Return the list of Subjects
get_supported_version()
method descriptor
get_supported_version(self: shapeworks_py.Project) -> int
get_version()
method descriptor
get_version(self: shapeworks_py.Project) -> int
load()
method descriptor
load(self: shapeworks_py.Project, filename: str) -> bool
Load from XLSX file
save()
method descriptor
save(self: shapeworks_py.Project, filename: str = '') -> None
Save to XLSX file
set_filename()
method descriptor
set_filename(self: shapeworks_py.Project, filename: str) -> None
Set project filename
set_groomed_domain_types()
method descriptor
set_groomed_domain_types(self: shapeworks_py.Project, types: collections.abc.Sequence[shapeworks_py.DomainType]) -> None
Set the groomed domain types
set_original_domain_types()
method descriptor
set_original_domain_types(self: shapeworks_py.Project, types: collections.abc.Sequence[shapeworks_py.DomainType]) -> None
Set the original domain types
set_parameters()
method descriptor
set_parameters(self: shapeworks_py.Project, name: str, params: shapeworks::Parameters, domain_name: str = '') -> None
set_subjects()
method descriptor
set_subjects(self: shapeworks_py.Project, subjects: collections.abc.Sequence[shapeworks::Subject]) -> None
store_subjects()
method descriptor
store_subjects(self: shapeworks_py.Project) -> None
ReconstructSurface_RBFSSparseTransform
Bases: pybind11_builtins.pybind11_object
meanSurface()
method descriptor
meanSurface(self: shapeworks_py.ReconstructSurface_RBFSSparseTransform, distanceTransformFiles: collections.abc.Sequence[str], localPointsFiles: collections.abc.Sequence[str], worldPointsFiles: collections.abc.Sequence[str]) -> None
samplesAlongPCAModes()
method descriptor
samplesAlongPCAModes(self: shapeworks_py.ReconstructSurface_RBFSSparseTransform, worldPointsFiles: collections.abc.Sequence[str]) -> None
setDoProcrustes()
method descriptor
setDoProcrustes(self: shapeworks_py.ReconstructSurface_RBFSSparseTransform, doProcrustes: bool) -> None
setDoProcrustesScaling()
method descriptor
setDoProcrustesScaling(self: shapeworks_py.ReconstructSurface_RBFSSparseTransform, doProcrustesScaling: bool) -> None
setEnableOutput()
method descriptor
setEnableOutput(self: shapeworks_py.ReconstructSurface_RBFSSparseTransform, enableOutput: bool) -> None
setMaxAngleDegrees()
method descriptor
setMaxAngleDegrees(self: shapeworks_py.ReconstructSurface_RBFSSparseTransform, maxAngleDegrees: typing.SupportsFloat) -> None
setMaxStdDev()
method descriptor
setMaxStdDev(self: shapeworks_py.ReconstructSurface_RBFSSparseTransform, maxStdDev: typing.SupportsFloat) -> None
setMaxVarianceCaptured()
method descriptor
setMaxVarianceCaptured(self: shapeworks_py.ReconstructSurface_RBFSSparseTransform, maxVarianceCaptured: typing.SupportsFloat) -> None
setMeanBeforeWarp()
method descriptor
setMeanBeforeWarp(self: shapeworks_py.ReconstructSurface_RBFSSparseTransform, meanBeforeWarp: bool) -> None
setModeIndex()
method descriptor
setModeIndex(self: shapeworks_py.ReconstructSurface_RBFSSparseTransform, modeIndex: typing.SupportsInt) -> None
setNumOfClusters()
method descriptor
setNumOfClusters(self: shapeworks_py.ReconstructSurface_RBFSSparseTransform, numOfClusters: typing.SupportsInt) -> None
setNumOfModes()
method descriptor
setNumOfModes(self: shapeworks_py.ReconstructSurface_RBFSSparseTransform, numOfModes: typing.SupportsInt) -> None
setNumOfParticles()
method descriptor
setNumOfParticles(self: shapeworks_py.ReconstructSurface_RBFSSparseTransform, numOfParticles: typing.SupportsInt) -> None
setNumOfSamplesPerMode()
method descriptor
setNumOfSamplesPerMode(self: shapeworks_py.ReconstructSurface_RBFSSparseTransform, numOfSamplesPerMode: typing.SupportsInt) -> None
setOutPath()
method descriptor
setOutPath(self: shapeworks_py.ReconstructSurface_RBFSSparseTransform, path: str) -> None
setOutPrefix()
method descriptor
setOutPrefix(self: shapeworks_py.ReconstructSurface_RBFSSparseTransform, prefix: str) -> None
surface()
method descriptor
surface(self: shapeworks_py.ReconstructSurface_RBFSSparseTransform, localPointsFiles: collections.abc.Sequence[str]) -> None
ReconstructSurface_ThinPlateSplineTransform
Bases: pybind11_builtins.pybind11_object
meanSurface()
method descriptor
meanSurface(self: shapeworks_py.ReconstructSurface_ThinPlateSplineTransform, distanceTransformFiles: collections.abc.Sequence[str], localPointsFiles: collections.abc.Sequence[str], worldPointsFiles: collections.abc.Sequence[str]) -> None
samplesAlongPCAModes()
method descriptor
samplesAlongPCAModes(self: shapeworks_py.ReconstructSurface_ThinPlateSplineTransform, worldPointsFiles: collections.abc.Sequence[str]) -> None
setDoProcrustes()
method descriptor
setDoProcrustes(self: shapeworks_py.ReconstructSurface_ThinPlateSplineTransform, doProcrustes: bool) -> None
setDoProcrustesScaling()
method descriptor
setDoProcrustesScaling(self: shapeworks_py.ReconstructSurface_ThinPlateSplineTransform, doProcrustesScaling: bool) -> None
setEnableOutput()
method descriptor
setEnableOutput(self: shapeworks_py.ReconstructSurface_ThinPlateSplineTransform, enableOutput: bool) -> None
setMaxAngleDegrees()
method descriptor
setMaxAngleDegrees(self: shapeworks_py.ReconstructSurface_ThinPlateSplineTransform, maxAngleDegrees: typing.SupportsFloat) -> None
setMaxStdDev()
method descriptor
setMaxStdDev(self: shapeworks_py.ReconstructSurface_ThinPlateSplineTransform, maxStdDev: typing.SupportsFloat) -> None
setMaxVarianceCaptured()
method descriptor
setMaxVarianceCaptured(self: shapeworks_py.ReconstructSurface_ThinPlateSplineTransform, maxVarianceCaptured: typing.SupportsFloat) -> None
setMeanBeforeWarp()
method descriptor
setMeanBeforeWarp(self: shapeworks_py.ReconstructSurface_ThinPlateSplineTransform, meanBeforeWarp: bool) -> None
setModeIndex()
method descriptor
setModeIndex(self: shapeworks_py.ReconstructSurface_ThinPlateSplineTransform, modeIndex: typing.SupportsInt) -> None
setNumOfClusters()
method descriptor
setNumOfClusters(self: shapeworks_py.ReconstructSurface_ThinPlateSplineTransform, numOfClusters: typing.SupportsInt) -> None
setNumOfModes()
method descriptor
setNumOfModes(self: shapeworks_py.ReconstructSurface_ThinPlateSplineTransform, numOfModes: typing.SupportsInt) -> None
setNumOfParticles()
method descriptor
setNumOfParticles(self: shapeworks_py.ReconstructSurface_ThinPlateSplineTransform, numOfParticles: typing.SupportsInt) -> None
setNumOfSamplesPerMode()
method descriptor
setNumOfSamplesPerMode(self: shapeworks_py.ReconstructSurface_ThinPlateSplineTransform, numOfSamplesPerMode: typing.SupportsInt) -> None
setOutPath()
method descriptor
setOutPath(self: shapeworks_py.ReconstructSurface_ThinPlateSplineTransform, path: str) -> None
setOutPrefix()
method descriptor
setOutPrefix(self: shapeworks_py.ReconstructSurface_ThinPlateSplineTransform, prefix: str) -> None
surface()
method descriptor
surface(self: shapeworks_py.ReconstructSurface_ThinPlateSplineTransform, localPointsFiles: collections.abc.Sequence[str]) -> None
Shape
Bases: pybind11_builtins.pybind11_object
get_display_name()
method descriptor
get_display_name(self: shapeworks_py.Shape) -> str
get_id()
method descriptor
get_id(self: shapeworks_py.Shape) -> int
get_particles()
method descriptor
get_particles(self: shapeworks_py.Shape) -> shapeworks_py.Particles
returns the particles for this shape
ShapeEvaluation
Bases: pybind11_builtins.pybind11_object
ComputeCompactness()
staticmethod
ComputeCompactness(particleSystem: shapeworks_py.ParticleSystem, nModes: typing.SupportsInt, saveTo: str = '') -> float
Computes the compactness measure for a particle system
ComputeFullCompactness()
staticmethod
ComputeFullCompactness(particleSystem: shapeworks_py.ParticleSystem, progress_callback: collections.abc.Callable[[typing.SupportsFloat], None] = None) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, 1]"]
Computes the compactness measure for a particle system, all modes
ComputeFullGeneralization()
staticmethod
ComputeFullGeneralization(particleSystem: shapeworks_py.ParticleSystem, progress_callback: collections.abc.Callable[[typing.SupportsFloat], None] = None, check_abort: collections.abc.Callable[[], bool] = None, surface_distance_mode: bool = False) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, 1]"]
Computes the generalization measure for a particle system, all modes
ComputeFullSpecificity()
staticmethod
ComputeFullSpecificity(particleSystem: shapeworks_py.ParticleSystem, progress_callback: collections.abc.Callable[[typing.SupportsFloat], None] = None, check_abort: collections.abc.Callable[[], bool] = None, surface_distance_mode: bool = False) -> typing.Annotated[numpy.typing.NDArray[numpy.float64], "[m, 1]"]
Computes the specificity measure for a particle system, all modes
ComputeGeneralization()
staticmethod
ComputeGeneralization(particleSystem: shapeworks_py.ParticleSystem, nModes: typing.SupportsInt, saveTo: str = '', surface_distance_mode: bool = False) -> float
Computes the generalization measure for a particle system
ComputeSpecificity()
staticmethod
ComputeSpecificity(particleSystem: shapeworks_py.ParticleSystem, nModes: typing.SupportsInt, saveTo: str = '', surface_distance_mode: bool = False) -> float
Computes the specificity measure for a particle system
Subject
Bases: pybind11_builtins.pybind11_object
get_constraints_filenames()
method descriptor
get_constraints_filenames(self: shapeworks_py.Subject) -> list[str]
Get the constraints filenames (one per domain)
get_display_name()
method descriptor
get_display_name(self: shapeworks_py.Subject) -> str
Get the display name
get_extra_values()
method descriptor
get_extra_values(self: shapeworks_py.Subject) -> dict[str, str]
Get extra values (extra columns we don't interpret)
get_feature_filenames()
method descriptor
get_feature_filenames(self: shapeworks_py.Subject) -> dict[str, str]
Get the feature map filenames
get_groomed_clipped_mesh()
method descriptor
get_groomed_clipped_mesh(self: shapeworks_py.Subject, domain_id: typing.SupportsInt = 0) -> shapeworks_py.Mesh
Get the mesh clipped by constraints
get_groomed_filenames()
method descriptor
get_groomed_filenames(self: shapeworks_py.Subject) -> list[str]
Get groomed filenames
get_groomed_transforms()
method descriptor
get_groomed_transforms(self: shapeworks_py.Subject) -> list[list[float]]
Get the groomed transforms (one vector per domain)
get_group_value()
method descriptor
get_group_value(self: shapeworks_py.Subject, group_name: str) -> str
Get a specific group value
get_group_values()
method descriptor
get_group_values(self: shapeworks_py.Subject) -> tsl::ordered_map
Get the group values map
get_landmarks_filenames()
method descriptor
get_landmarks_filenames(self: shapeworks_py.Subject) -> list[str]
Get the landmarks filenames (one per domain)
get_local_particle_filenames()
method descriptor
get_local_particle_filenames(self: shapeworks_py.Subject) -> list[str]
Get local particle filenames
get_number_of_domains()
method descriptor
get_number_of_domains(self: shapeworks_py.Subject) -> int
Get the number of domains
get_original_filenames()
method descriptor
get_original_filenames(self: shapeworks_py.Subject) -> list[str]
Get original filenames
get_procrustes_transforms()
method descriptor
get_procrustes_transforms(self: shapeworks_py.Subject) -> list[list[float]]
Get the procrustes transforms (one vector per domain)
get_world_particle_filenames()
method descriptor
get_world_particle_filenames(self: shapeworks_py.Subject) -> list[str]
Get the world particle filenames
set_constraints_filenames()
method descriptor
set_constraints_filenames(self: shapeworks_py.Subject, filenames: collections.abc.Sequence[str]) -> None
Set the constraint filenames (one per domain)
set_display_name()
method descriptor
set_display_name(self: shapeworks_py.Subject, display_name: str) -> None
Set the display name
set_excluded()
method descriptor
set_excluded(self: shapeworks_py.Subject, excluded: bool) -> None
Set excluded
set_extra_values()
method descriptor
set_extra_values(self: shapeworks_py.Subject, extra_values: collections.abc.Mapping[str, str]) -> None
Set extra values
set_feature_filenames()
method descriptor
set_feature_filenames(self: shapeworks_py.Subject, filenames: collections.abc.Mapping[str, str]) -> None
Set the feature map filenames
set_fixed()
method descriptor
set_fixed(self: shapeworks_py.Subject, fixed: bool) -> None
Set fixed
set_groomed_filenames()
method descriptor
set_groomed_filenames(self: shapeworks_py.Subject, filenames: collections.abc.Sequence[str]) -> None
Set groomed filenames
set_groomed_transforms()
method descriptor
set_groomed_transforms(self: shapeworks_py.Subject, transforms: collections.abc.Sequence[collections.abc.Sequence[typing.SupportsFloat]]) -> None
Set the groomed transforms (one vector per domain)
set_group_values()
method descriptor
set_group_values(self: shapeworks_py.Subject, Set group values mapgroup_values: collections.abc.Mapping[str, str]) -> None
set_landmarks_filenames()
method descriptor
set_landmarks_filenames(self: shapeworks_py.Subject, filenames: collections.abc.Sequence[str]) -> None
Set the landmarks filenames (one per domain)
set_local_particle_filenames()
method descriptor
set_local_particle_filenames(self: shapeworks_py.Subject, filenames: collections.abc.Sequence[str]) -> None
Set local particle filenames (one per domain)
set_number_of_domains()
method descriptor
set_number_of_domains(self: shapeworks_py.Subject, number_of_domains: typing.SupportsInt) -> None
Set the number of domains
set_original_filenames()
method descriptor
set_original_filenames(self: shapeworks_py.Subject, filenames: collections.abc.Sequence[str]) -> None
Set original filenames (one per domain)
set_procrustes_transforms()
method descriptor
set_procrustes_transforms(self: shapeworks_py.Subject, transforms: collections.abc.Sequence[collections.abc.Sequence[typing.SupportsFloat]]) -> None
Set the procrustes transforms (one vector per domain)
set_world_particle_filenames()
method descriptor
set_world_particle_filenames(self: shapeworks_py.Subject, filenames: collections.abc.Sequence[str]) -> None
Set the world particle filenames
Variant
Bases: pybind11_builtins.pybind11_object
as_str()
method descriptor
as_str(self: shapeworks_py.Variant) -> str
Return the variant string content
VectorImage
Bases: pybind11_builtins.pybind11_object
evaluate()
method descriptor
evaluate(self: shapeworks_py.VectorImage, pt: collections.abc.Sequence[typing.SupportsFloat]) -> list[float]
evaluate the vector image at any given point in space
WarpMethod
Bases: pybind11_builtins.pybind11_object
Members:
Laplacian
Biharmonic
Biharmonic = <WarpMethod.Biharmonic: 1>
class-attribute
Members:
Laplacian
Biharmonic
Laplacian = <WarpMethod.Laplacian: 0>
class-attribute
Members:
Laplacian
Biharmonic
name
property
name(self: object, /) -> str
value
property
WarpTransform
Bases: pybind11_builtins.pybind11_object
axis_is_valid()
builtin
axis_is_valid(axis: collections.abc.Sequence[typing.SupportsFloat]) -> bool
ensure an axis is valid
degToRad()
builtin
degToRad(deg: typing.SupportsFloat) -> float
convert degrees to radians
mean()
builtin
mean(arg0: numpy.ndarray) -> float
incrementally compute (single-component) mean of field
range()
builtin
range(arg0: numpy.ndarray) -> list[float]
compute (single-component) range of field
seed()
builtin
seed(seed: typing.SupportsInt = 1784653900016739) -> None
sets the seed for random number generation (internal use)
set_progress_callback()
builtin
set_progress_callback(callback: typing_extensions.CapsuleType) -> None
sets up a progress callback
setup_console_logging()
builtin
setup_console_logging(show_progress: bool = True, xml_status: bool = False) -> None
sets up console logging options
stddev()
builtin
stddev(arg0: numpy.ndarray) -> float
compute (single-component) standard deviation of field
toAxis()
builtin
toAxis(str: str) -> shapeworks_py.Axis
convert to axis