ShapeWorks Commands
shapeworks is a single executable for ShapeWorks with a set of sub-executables (commands) that are flexible, modular, loosely coupled, and standardized subcommands, with interactive help to perform individual operations needed for a typical shape modeling workflow that includes the Groom, Optimize, and Analyze phases.
Activate shapeworks environment
Each time you use ShapeWorks from the command line, you must first activate its environment using the conda activate shapeworks command on the terminal.
Add shapeworks to your path
Please make sure that shapeworks is in your path. See Adding to PATH Environment Variable.
shapeworks
Usage:
shapeworks <command> [args]...
Description: Unified ShapeWorks executable that includes command line utilities for automated construction of compact statistical landmark-based shape models of ensembles of shapes
Options:
-h, --help: show this help message and exit
--version: show program's version number and exit
-q, --quiet: don't print status messages
Groom Commands
groom
Usage:
shapeworks groom [args]...
Description: groom a shapeworks project
Options:
-h, --help: show this help message and exit
--name=STRING: Path to parameter file.
Image Commands
add
Usage:
shapeworks add [args]...
Description: add a value to each pixel in the given image and/or add another image in a pixelwise manner
Options:
-h, --help: show this help message and exit
-x DOUBLE, --value=DOUBLE: Value to add to each pixel [default: 0.0].
--name=STRING: Name of image to add pixelwise.
antialias
Usage:
shapeworks antialias [args]...
Description: antialiases binary volumes
Options:
-h, --help: show this help message and exit
--iterations=INT: Maximum number of iterations [default: 50].
--maxrmserror=DOUBLE: Maximum RMS error determines how fast the solver converges. Range [0.0, 1.0], larger is faster [default: 0.01].
--layers=INT: Number of layers around a 3d pixel to use for this computation [default: 3].
binarize
Usage:
shapeworks binarize [args]...
Description: sets portion of image greater than min and less than or equal to max to the specified value
Options:
-h, --help: show this help message and exit
--min=DOUBLE: Lower threshold level [default: 0.0].
--max=DOUBLE: Upper threshold level [default: inf ].
--value=DOUBLE: Value to set region [default: 1].
blur
Usage:
shapeworks blur [args]...
Description: applies gaussian blur
Options:
-h, --help: show this help message and exit
--sigma=DOUBLE: Value of sigma [default: 0].
bounding-box-image
Usage:
shapeworks bounding-box-image [args]...
Description: compute largest physical bounding box surrounding the specified isovalue of the specified set of images
Options:
-h, --help: show this help message and exit
--names :
Paths to images (must be followed by --), ex: "bounding-box-image --names *.nrrd -- --isovalue 1.5")
--isovalue=DOUBLE: Threshold value [default: 1].
clip-image
Usage:
shapeworks clip-image [args]...
Description: clips volume with the specified cutting planes defined by three 3D points
Options:
-h, --help: show this help message and exit
--x1=DOUBLE: Value of x1 for cutting plane [default: 0].
--y1=DOUBLE: Value of y1 for cutting plane [default: 0].
--z1=DOUBLE: Value of z1 for cutting plane [default: 0].
--x2=DOUBLE: Value of x2 for cutting plane [default: 0].
--y2=DOUBLE: Value of y2 for cutting plane [default: 0].
--z2=DOUBLE: Value of z2 for cutting plane [default: 0].
--x3=DOUBLE: Value of x3 for cutting plane [default: 0].
--y3=DOUBLE: Value of y3 for cutting plane [default: 0].
--z3=DOUBLE: Value of z3 for cutting plane [default: 0].
--value=DOUBLE: Value of clipped pixels [default: 0].
close-holes
Usage:
shapeworks close-holes [args]...
Description: closes holes in a volume defined by values larger than specified value
Options:
-h, --help: show this help message and exit
--value=DOUBLE: Largest value not in volume [default: 0].
compare-image
Usage:
shapeworks compare-image [args]...
Description: compare two images
Options:
-h, --help: show this help message and exit
--name=STRING: Compare this image with another.
--verifyall=BOOL: Also verify origin, spacing, and direction matches [default: true].
--tolerance=DOUBLE: Allowed percentage of pixel differences [default: 0].
--precision=DOUBLE: Allowed difference between two pixels for them to still be considered equal [default: 1e-12].
compute-dt
Usage:
shapeworks compute-dt [args]...
Description: computes signed distance transform volume from an image at the specified isovalue
Options:
-h, --help: show this help message and exit
--isovalue=DOUBLE: Level set value that defines the interface between foreground and background [default: 0].
crop
Usage:
shapeworks crop [args]...
Description: crop image down to the current region of physical space (from bounding-box or set-region commands)
Options:
-h, --help: show this help message and exit
curvature
Usage:
shapeworks curvature [args]...
Description: denoises an image using curvature driven flow using curvature flow image filter
Options:
-h, --help: show this help message and exit
--iterations=INT: Number of iterations [default: 10].
divide
Usage:
shapeworks divide [args]...
Description: divide an image by a constant
Options:
-h, --help: show this help message and exit
-x DOUBLE, --value=DOUBLE: Value with which to divide [default: 0.0].
extract-label
Usage:
shapeworks extract-label [args]...
Description: extracts/isolates a specific voxel label from a given multi-label volume and outputs the corresponding binary image
Options:
-h, --help: show this help message and exit
--label=DOUBLE: Label value to be extracted [default: 1].
gradient
Usage:
shapeworks gradient [args]...
Description: computes gradient magnitude of an image region at each pixel using gradient magnitude filter
Options:
-h, --help: show this help message and exit
icp-image
Usage:
shapeworks icp-image [args]...
Description: transform current image using iterative closest point (ICP) 3D rigid registration computed from current distance map to target distance map
Options:
-h, --help: show this help message and exit
--target=STRING: Distance map of target image.
--isovalue=DOUBLE: Isovalue of distance maps used to create ICPtransform [default: 0].
--iterations=UNSIGNED: Number of iterations run ICP registration [default: 20].
image-bounds
Usage:
shapeworks image-bounds [args]...
Description: return bounds of image, optionally with an isovalue to restrict region
Options:
-h, --help: show this help message and exit
--isovalue=DOUBLE: Isovalue [default: entire image].
image-info
Usage:
shapeworks image-info [args]...
Description: prints requested image dimensions, spacing, size, origin, direction (coordinate system), center, center of mass and bounding box [default: prints everything]
Options:
-h, --help: show this help message and exit
--dims: Whether to display image dimensions [default: true].
--spacing: Whether to display physical spacing [default: true].
--size: Whether to display size [default: true].
--origin: Whether to display physical origin [default: true].
--direction: Whether to display direction [default: true].
--center: Whether to display center. [default: true]
--centerofmass: Whether to display center of mass. [default: true]
--boundingbox: Whether to display bounding box. [default: true]
image-to-mesh
Usage:
shapeworks image-to-mesh [args]...
Description: converts the current image to a mesh
Options:
-h, --help: show this help message and exit
-v DOUBLE, --isovalue=DOUBLE: Isovalue to determine mesh boundary [default: 1].
intensity
Usage:
shapeworks intensity [args]...
Description: applies intensity windowing image filter
Options:
-h, --help: show this help message and exit
--min=DOUBLE: Minimum value of window [default: 0].
--max=DOUBLE: Maximum value of window [default: 0].
isolate
Usage:
shapeworks isolate [args]...
Description: finds the largest object in a binary segmentation and removes all other objects
Options:
-h, --help: show this help message and exit
multiply
Usage:
shapeworks multiply [args]...
Description: multiply an image by a constant
Options:
-h, --help: show this help message and exit
-x DOUBLE, --value=DOUBLE: Value with which to multiply [default: 1.0]
negate
Usage:
shapeworks negate [args]...
Description: negate the values in the given image
Options:
-h, --help: show this help message and exit
pad
Usage:
shapeworks pad [args]...
Description: pads an image with specified value by specified number of voxels in the x-, y-, and/or z- directions; origin remains at the same location (note: negative padding to shrink an image is permitted)
Options:
-h, --help: show this help message and exit
--padding=INT: Pad this many voxels in ALL directions (used if set) [default: 0].
-x INT, --padx=INT: Pad this many voxels in the x-direction [default: 0].
-y INT, --pady=INT: Pad this many voxels in the y-direction [default: 0].
-z INT, --padz=INT: Pad this many voxels in the z-direction [default: 0].
--value=DOUBLE: Value used to fill padded voxels [default: 0].
read-image
Usage:
shapeworks read-image [args]...
Description: reads an image
Options:
-h, --help: show this help message and exit
--name=STRING: Name of file to read.
recenter
Usage:
shapeworks recenter [args]...
Description: recenters an image by changing its origin in the image header to the physical coordinates of the center of the image
Options:
-h, --help: show this help message and exit
reflect-image
Usage:
shapeworks reflect-image [args]...
Description: reflect image with respect to logical image center and the specified axis
Options:
-h, --help: show this help message and exit
--axis=STRING: Axis along which to reflect (X, Y, or Z).
resample
Usage:
shapeworks resample [args]...
Description: resamples an image using new physical spacing (computes new dims)
Options:
-h, --help: show this help message and exit
--isospacing=DOUBLE: Use this spacing in all dimensions.
--spacex=DOUBLE: Pixel spacing in x-direction [default: 1].
--spacey=DOUBLE: Pixel spacing in y-direction [default: 1].
--spacez=DOUBLE: Pixel spacing in z-direction [default: 1].
--sizex=UNSIGNED: Output size in x-direction [default: current size].
--sizey=UNSIGNED: Output size in y-direction [default: current size].
--sizez=UNSIGNED: Output size in z-direction [default: current size].
--originx=DOUBLE: Output origin in x-direction [default: current origin].
--originy=DOUBLE: Output origin in y-direction [default: current origin].
--originz=DOUBLE: Output origin in z-direction [default: current origin].
--interp=CHOICE: Interpolation method to use [default: linear]. (choose from 'linear', 'nearest')
resize
Usage:
shapeworks resize [args]...
Description: resizes an image (computes new physical spacing)
Options:
-h, --help: show this help message and exit
-x UNSIGNED, --sizex=UNSIGNED: Output size in x-direction [default: current size].
-y UNSIGNED, --sizey=UNSIGNED: Output size in y-direction [default: current size].
-z UNSIGNED, --sizez=UNSIGNED: Output size in z-direction [default: current size].
rotate
Usage:
shapeworks rotate [args]...
Description: rotates image by specified value
Options:
-h, --help: show this help message and exit
-x DOUBLE, --rx=DOUBLE: Physical axis around which to rotate [default: z-axis].
-y DOUBLE, --ry=DOUBLE: Physical axis around which to rotate [default: z-axis].
-z DOUBLE, --rz=DOUBLE: Physical axis around which to rotate [default: z-axis].
--radians=DOUBLE: Angle in radians.
--degrees=DOUBLE: Angle in degrees.
scale-image
Usage:
shapeworks scale-image [args]...
Description: scales image by specified value
Options:
-h, --help: show this help message and exit
-x DOUBLE, --sx=DOUBLE: X scale.
-y DOUBLE, --sy=DOUBLE: Y scale.
-z DOUBLE, --sz=DOUBLE: Z scale.
set-origin
Usage:
shapeworks set-origin [args]...
Description: set origin
Options:
-h, --help: show this help message and exit
-x DOUBLE, --x=DOUBLE: X value of origin [default: 0].
-y DOUBLE, --y=DOUBLE: Y value of origin [default: 0].
-z DOUBLE, --z=DOUBLE: Z value of origin [default: 0].
set-region
Usage:
shapeworks set-region [args]...
Description: set the current (physical) region to the specified min/max in each direction, for use with downstreams commands such as crop (note: could instead use the image-bounds command with an isovalue)
Options:
-h, --help: show this help message and exit
--xmin=DOUBLE: Minimum X.
--xmax=DOUBLE: Maximum X.
--ymin=DOUBLE: Minimum Y.
--ymax=DOUBLE: Maximum Y.
--zmin=DOUBLE: Minimum Z.
--zmax=DOUBLE: Maximum Z.
set-spacing
Usage:
shapeworks set-spacing [args]...
Description: set spacing
Options:
-h, --help: show this help message and exit
-x DOUBLE, --x=DOUBLE: x value of spacing [default: 1].
-y DOUBLE, --y=DOUBLE: y value of spacing [default: 1].
-z DOUBLE, --z=DOUBLE: z value of spacing [default: 1].
sigmoid
Usage:
shapeworks sigmoid [args]...
Description: computes sigmoid function pixel-wise using sigmoid image filter
Options:
-h, --help: show this help message and exit
--alpha=DOUBLE: Value of alpha [default: 10].
--beta=DOUBLE: Value of beta [default: 10].
subtract
Usage:
shapeworks subtract [args]...
Description: subtract a value from each pixel in this image and/or subtract another image in a pixelwise manner
Options:
-h, --help: show this help message and exit
-x DOUBLE, --value=DOUBLE: Value to subtract from each pixel [default: 0.0].
--name=STRING: Name of image to subtract pixelwise.
topo-preserving-smooth
Usage:
shapeworks topo-preserving-smooth [args]...
Description: helper command that applies gradient and sigmoid filters to create a feature image for the TPLevelSet filter; note that a curvature flow filter is sometimes applied to the image before this
Options:
-h, --help: show this help message and exit
--scaling=DOUBLE: Scale for TPLevelSet level set filter [default: 20].
--alpha=DOUBLE: Value of alpha for sigmoid fitler [default: 10].
--beta=DOUBLE: Value of beta for sigmoid fitler [default: 10].
tp-levelset
Usage:
shapeworks tp-levelset [args]...
Description: segments structures in image using topology preserving geodesic active contour level set filter
Options:
-h, --help: show this help message and exit
--featureimage=STRING: Path of feature image for filter
--scaling=DOUBLE: Value of scale [default: 20].
translate-image
Usage:
shapeworks translate-image [args]...
Description: translates image by specified physical (image space) distance
Options:
-h, --help: show this help message and exit
--centerofmass: Use center of mass [default: false].
-x DOUBLE, --tx=DOUBLE: X distance.
-y DOUBLE, --ty=DOUBLE: Y distance.
-z DOUBLE, --tz=DOUBLE: Z distance.
warp-image
Usage:
shapeworks warp-image [args]...
Description: finds the warp between the source and target landmarks and transforms image by this warp
Options:
-h, --help: show this help message and exit
--source=STRING: Path to source landmarks.
--target=STRING: Path to target landmarks.
--stride=INT: Every stride points will be used for warping [default: 1].
write-image
Usage:
shapeworks write-image [args]...
Description: writes the current image (determines type by its extension)
Options:
-h, --help: show this help message and exit
--name=STRING: Name of file to write.
--compressed=BOOL: Whether to compress file [default: true].
Mesh Commands
bounding-box-mesh
Usage:
shapeworks bounding-box-mesh [args]...
Description: compute bounding box of mesh
Options:
-h, --help: show this help message and exit
--names :
Paths to meshes (must be followed by --), ex: "bounding-box-mesh --names *.vtk -- --center 1")
clip-closed-surface
Usage:
shapeworks clip-closed-surface [args]...
Description: clips mesh resulting in a closed surface
Options:
-h, --help: show this help message and exit
--px=DOUBLE: Value of point.x for cutting plane [default: 0].
--py=DOUBLE: Value of point.y for cutting plane [default: 0].
--pz=DOUBLE: Value of point.z for cutting plane [default: 0].
--nx=DOUBLE: Value of normal.x for cutting plane [default: 0].
--ny=DOUBLE: Value of normal.y for cutting plane [default: 0].
--nz=DOUBLE: Value of normal.z for cutting plane [default: 0].
clip-mesh
Usage:
shapeworks clip-mesh [args]...
Description: clips mesh
Options:
-h, --help: show this help message and exit
--px=DOUBLE: Value of point.x for cutting plane [default: 0].
--py=DOUBLE: Value of point.y for cutting plane [default: 0].
--pz=DOUBLE: Value of point.z for cutting plane [default: 0].
--nx=DOUBLE: Value of normal.x for cutting plane [default: 0].
--ny=DOUBLE: Value of normal.y for cutting plane [default: 0].
--nz=DOUBLE: Value of normal.z for cutting plane [default: 0].
closest-point
Usage:
shapeworks closest-point [args]...
Description: returns closest point to given point on mesh
Options:
-h, --help: show this help message and exit
--x=DOUBLE: Value of x for point.
--y=DOUBLE: Value of y for point.
--z=DOUBLE: Value of z for point.
compare-mesh
Usage:
shapeworks compare-mesh [args]...
Description: compare two meshes
Options:
-h, --help: show this help message and exit
--name=STRING: Compare this mesh with another.
--epsilon=DOUBLE: Epsilon [default: -1].
compute-normals
Usage:
shapeworks compute-normals [args]...
Description: computes and adds oriented point and cell normals
Options:
-h, --help: show this help message and exit
coverage
Usage:
shapeworks coverage [args]...
Description: creates mesh of coverage between two meshes
Options:
-h, --help: show this help message and exit
--name=STRING: Path to other mesh with which to create coverage.
--allowbackintersections=BOOL: Allow back-intersections in coverage calculation [default: true].
--anglethreshold=DOUBLE: This checks the cosine between the ray’s direction vector (e1) and the normal at the intersection point (e2) [default: 0].
--backsearchradius=DOUBLE: Max distance of a back-intersection [default: 0].
distance
Usage:
shapeworks distance [args]...
Description: computes the distance between two meshes, printing the largest distance between any point from source to target, target to source, and the Hausdorff distance (the largest of these two)
Options:
-h, --help: show this help message and exit
--name=STRING: Filename of other mesh.
--method=CHOICE: Method used to compute distance (point-to-point or point-to-cell) [default: point-to-cell]. (choose from 'point-to-point', 'point-to-cell')
--ids=BOOL: Set shared field to the ids of the closest points/cells instead of the distances [default: false].
--summary=BOOL: Print largest distance of any point in mesh to target [default: true].
field-mean
Usage:
shapeworks field-mean [args]...
Description: prints the mean of the given field
Options:
-h, --help: show this help message and exit
--name=STRING: Name of scalar field.
--type=CHOICE: Type of field to fetch (point or face). (choose from 'point', 'face')
field-names
Usage:
shapeworks field-names [args]...
Description: prints all the field names present in mesh
Options:
-h, --help: show this help message and exit
field-range
Usage:
shapeworks field-range [args]...
Description: prints the range of the given field
Options:
-h, --help: show this help message and exit
--name=STRING: Name of scalar field.
--type=CHOICE: Type of field to fetch (point or face). (choose from 'point', 'face')
field-std
Usage:
shapeworks field-std [args]...
Description: prints the standard deviation of the given field
Options:
-h, --help: show this help message and exit
--name=STRING: Name of scalar field.
--type=CHOICE: Type of field to fetch (point or face). (choose from 'point', 'face')
fill-holes
Usage:
shapeworks fill-holes [args]...
Description: finds holes in a mesh and closes them
Options:
-h, --help: show this help message and exit
fix-element
Usage:
shapeworks fix-element [args]...
Description: fix element winding of mesh
Options:
-h, --help: show this help message and exit
geodesic-distance
Usage:
shapeworks geodesic-distance [args]...
Description: computes geodesic distance between two vertices on mesh
Options:
-h, --help: show this help message and exit
--v1=INT: Index of first point in mesh.
--v2=INT: Index of second point in mesh.
geodesic-distance-landmark
Usage:
shapeworks geodesic-distance-landmark [args]...
Description: computes geodesic distance between a point (landmark) and each vertex on mesh
Options:
-h, --help: show this help message and exit
--x=DOUBLE: Value of x for landmark point.
--y=DOUBLE: Value of y for landmark point.
--z=DOUBLE: Value of z for landmark point.
get-field
Usage:
shapeworks get-field [args]...
Description: gets field of mesh with given name
Options:
-h, --help: show this help message and exit
--name=STRING: Name of scalar field.
--type=CHOICE: Type of field to get (point or face). (choose from 'point', 'face')
get-field-value
Usage:
shapeworks get-field-value [args]...
Description: prints value of element at index in given field of mesh
Options:
-h, --help: show this help message and exit
--name=STRING: Name of scalar field.
-i INT, --index=INT: index of value to return [default: 0].
invert-normal
Usage:
shapeworks invert-normal [args]...
Description: flips the normal
Options:
-h, --help: show this help message and exit
mean-normals
Usage:
shapeworks mean-normals [args]...
Description: computes average normals for each point in given set of meshes
Options:
-h, --help: show this help message and exit
--names :
Paths to meshes (must be followed by --), ex: "mean-normals --names *.vtk --")
--generatenormals=BOOL: Auto generate normals if the mesh does not have normals [default: true].
mesh-bounds
Usage:
shapeworks mesh-bounds [args]...
Description: return physical bounds of mesh
Options:
-h, --help: show this help message and exit
mesh-curvature
Usage:
shapeworks mesh-curvature [args]...
Description: computes and adds curvature
Options:
-h, --help: show this help message and exit
--type=CHOICE: Curvature type to use [default: principal]. (choose from 'principal', 'gaussian', 'mean')
mesh-info
Usage:
shapeworks mesh-info [args]...
Description: prints requested mesh center, center of mass, number of vertices, number of faces and bounding box [default: prints everything]
Options:
-h, --help: show this help message and exit
--vertices: Whether to display number of vertices [default: true].
--faces: Whether to display number of faces [default: true].
--center: Whether to display center [default: true].
--centerofmass: Whether to display center of mass [default: true].
--boundingbox: Whether to display bounding box [default: true].
--fieldnames: Whether to display field names [default: true].
mesh-to-dt
Usage:
shapeworks mesh-to-dt [args]...
Description: converts mesh to a distance transform, using unit spacing by default
Options:
-h, --help: show this help message and exit
--sx=DOUBLE: Spacing of output image in x-direction [default: unit spacing].
--sy=DOUBLE: Spacing of output image in y-direction [default: unit spacing].
--sz=DOUBLE: Spacing of output image in z-direction [default: unit spacing].
--pad=INT: Number of pixels to pad the output region [default: 1].
mesh-to-image
Usage:
shapeworks mesh-to-image [args]...
Description: converts mesh to a binary segmentation image, using unit spacing by default
Options:
-h, --help: show this help message and exit
--sx=DOUBLE: Spacing of output image in x-direction [default: unit spacing].
--sy=DOUBLE: Spacing of output image in y-direction [default: unit spacing].
--sz=DOUBLE: Spacing of output image in z-direction [default: unit spacing].
--pad=DOUBLE: Pad the region to extract [default: 0.0].
probe-volume
Usage:
shapeworks probe-volume [args]...
Description: probe feature volumes at each mesh vertex and output vtk meshes with scalar field defined based on such probing process
Options:
-h, --help: show this help message and exit
--image=STRING: Path of image.
read-mesh
Usage:
shapeworks read-mesh [args]...
Description: reads a mesh
Options:
-h, --help: show this help message and exit
--name=STRING: Name of file to read.
reflect-mesh
Usage:
shapeworks reflect-mesh [args]...
Description: reflect meshes with respect to a specified center and specific axis
Options:
-h, --help: show this help message and exit
--axis=STRING: Axis along which to reflect (X, Y, or Z).
-x DOUBLE, --originx=DOUBLE: Origin about which reflection occurs in x-direction [default: 0].
-y DOUBLE, --originy=DOUBLE: Origin about which reflection occurs in y-direction [default: 0].
-z DOUBLE, --originz=DOUBLE: Origin about which reflection occurs in z-direction [default: 0].
remesh
Usage:
shapeworks remesh [args]...
Description: applies remeshing using approximated centroidal voronoi diagrams for a given number of vertices and adaptivity
Options:
-h, --help: show this help message and exit
--target=DOUBLE: Target number of vertices.
--adaptivity=DOUBLE: 0-2, low adaptivity to high adaptivity
remesh-percent
Usage:
shapeworks remesh-percent [args]...
Description: applies remeshing using approximated centroidal voronoi diagrams for a given percentage of vertices and adaptivity
Options:
-h, --help: show this help message and exit
--percentage=DOUBLE: Target percentage number of vertices
--adaptivity=DOUBLE: 0-2, low adaptivity to high adaptivity
scale-mesh
Usage:
shapeworks scale-mesh [args]...
Description: scales mesh
Options:
-h, --help: show this help message and exit
-x DOUBLE, --sx=DOUBLE: X scale.
-y DOUBLE, --sy=DOUBLE: Y scale.
-z DOUBLE, --sz=DOUBLE: Z scale.
set-field
Usage:
shapeworks set-field [args]...
Description: adds the current field to the current mesh with the given name.
Options:
-h, --help: show this help message and exit
--name=STRING: Name of scalar field.
--type=CHOICE: Type of field to set (point or face). (choose from 'point', 'face')
set-field-value
Usage:
shapeworks set-field-value [args]...
Description: sets value of element at index in given field of mesh
Options:
-h, --help: show this help message and exit
--name=STRING: Name of scalar field.
-i INT, --index=INT: index of value to return [default: 0].
--value=DOUBLE: value to be set [default: 0].
smooth
Usage:
shapeworks smooth [args]...
Description: applies laplacian smoothing
Options:
-h, --help: show this help message and exit
--iterations=INT: Number of iterations [default: 0].
--relaxation=DOUBLE: Amount of displacement for a vertex to move in each iteration [default: 0].
smooth-sinc
Usage:
shapeworks smooth-sinc [args]...
Description: applies windowed sinc smoothing
Options:
-h, --help: show this help message and exit
--iterations=INT: Number of iterations [default: 0].
--passband=DOUBLE: Set the passband value for the windowed sinc filter [default: 0].
transform-mesh
Usage:
shapeworks transform-mesh [args]...
Description: transform mesh to target mesh using iterative closest point (ICP) using specified landmark transform (rigid, similarity, or affine)
Options:
-h, --help: show this help message and exit
--target=STRING: Filename of target mesh.
--type=CHOICE: Alignment type to use [default: similarity]. (choose from 'rigid', 'similarity', 'affine')
--iterations=UNSIGNED: Number of iterations run [default: 10].
translate-mesh
Usage:
shapeworks translate-mesh [args]...
Description: translates mesh
Options:
-h, --help: show this help message and exit
-x DOUBLE, --tx=DOUBLE: X distance.
-y DOUBLE, --ty=DOUBLE: Y distance.
-z DOUBLE, --tz=DOUBLE: Z distance.
warp-mesh
Usage:
shapeworks warp-mesh [args]...
Description: warps a mesh given reference and target particles
Options:
-h, --help: show this help message and exit
--reference_mesh=STRING: Name of reference mesh.
--reference_points=STRING: Name of reference points.
--landmark_file=STRING: Optional Argument to specify the name of Landmark file, if landmarks are available for warping
--target_points :
Names of target points (must be followed by --), ex: "... --target_points *.particles -- ...
--save_dir=STRING: Optional: Path to the directory where the mesh files will be saved
write-mesh
Usage:
shapeworks write-mesh [args]...
Description: writes the current mesh
Options:
-h, --help: show this help message and exit
--name=STRING: Name of file to write.
--binary=BOOL: Whether to write file as binary.
Optimize Commands
optimize
Usage:
shapeworks optimize [args]...
Description: generate a particle system
Options:
-h, --help: show this help message and exit
--name=STRING: Path to parameter file.
ParticleSystem Commands
compactness
Usage:
shapeworks compactness [args]...
Description: Compute compactness of a loaded particle system
Options:
-h, --help: show this help message and exit
--nmodes=INT: Number of modes to use [default: 1].
--saveto=STRING: Save the scree plots for all modes to a file.
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generalization
Usage:
shapeworks generalization [args]...
Description: compute generalization of a loaded particle system
Options:
-h, --help: show this help message and exit
--nmodes=INT: Number of modes to use [default: 1].
--saveto=STRING: Save the reconstructions sorted by generalization along with the mapping to the original shape.
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read-particle-system
Usage:
shapeworks read-particle-system [args]...
Description: reads a particle system
Options:
-h, --help: show this help message and exit
--names :
Paths to .particle files (must be followed by --), ex: "--names *.particle -- next-command...")
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specificity
Usage:
shapeworks specificity [args]...
Description: compute specificity of a loaded particle system
Options:
-h, --help: show this help message and exit
--nmodes=INT: Number of modes to use [default: 1].
--saveto=STRING: Save the reconstructions sorted by specificity along with the mapping to the original shape.
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Shapeworks Commands
seed
Usage:
shapeworks seed [args]...
Description: sets the seed for random number generation (useful for debugging)
Options:
-h, --help: show this help message and exit
--value=INT: Value of seed.