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

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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.

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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.

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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].

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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].

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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].

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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].

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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].

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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].

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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].

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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].

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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

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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].

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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].

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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].

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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

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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].

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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].

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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]

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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].

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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].

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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]

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negate

Usage:

shapeworks  negate [args]...

Description: negate the values in the given image

Options:

-h, --help: show this help message and exit

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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].

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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.

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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

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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).

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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')

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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].

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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.

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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.

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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].

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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.

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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].

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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].

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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.

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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].

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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].

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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.

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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].

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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].

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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")

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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].

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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].

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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.

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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].

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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

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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].

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cvd-decimate

Usage:

shapeworks  cvd-decimate [args]...

Description: applies cvd (centroidal voronoi diagram) decimation filter

Options:

-h, --help: show this help message and exit

--percentage=DOUBLE: Percentage of target number of clusters/vertices [default: 0.5].

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decimate

Usage:

shapeworks  decimate [args]...

Description: applies filter to reduce number of triangles in mesh

Options:

-h, --help: show this help message and exit

--reduction=DOUBLE: Percent reduction of total number of polygons [default: 0.5].

--angle=DOUBLE: Necessary angle (in degrees) between two trianges to warrant keeping them separate [default: 15].

--preservetopology=BOOL: Whether to preserve topology [default: true].

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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 [default: point-to-point]. (choose from 'point-to-point', 'point-to-cell')

--summary=BOOL: Print largest distance of any point in mesh to target [default: true].

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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.

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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

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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.

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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.

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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

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fix-element

Usage:

shapeworks  fix-element [args]...

Description: fix element winding of mesh

Options:

-h, --help: show this help message and exit

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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

--x1=DOUBLE: Value of x for source point.

--y1=DOUBLE: Value of y for source point.

--z1=DOUBLE: Value of z for source point.

--x2=DOUBLE: Value of x for target point.

--y2=DOUBLE: Value of y for target point.

--z2=DOUBLE: Value of z for target point.

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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.

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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].

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invert-normal

Usage:

shapeworks  invert-normal [args]...

Description: flips the normal

Options:

-h, --help: show this help message and exit

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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].

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mesh-bounds

Usage:

shapeworks  mesh-bounds [args]...

Description: return physical bounds of mesh

Options:

-h, --help: show this help message and exit

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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')

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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].

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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=DOUBLE: Pad the region to extract [default: 0.0].

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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].

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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.

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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.

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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].

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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.

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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.

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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].

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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].

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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].

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transform-mesh

Usage:

shapeworks  transform-mesh [args]...

Description: point (ICP) 3D rigid registration)

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')

--method=CHOICE: Method used to compute transform [default: icp]. (choose from 'icp')

--iterations=UNSIGNED: Number of iterations run [default: 10].

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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.

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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.

--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

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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.

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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.

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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.

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