meshmash

Mesh analysis tools.

Usage:

meshmash [OPTIONS] COMMAND [ARGS]...

Options:

  --install-completion  Install completion for the current shell.
  --show-completion     Show completion for the current shell, to copy it or
                        customize the installation.

datasets

Fetch and cache sample datasets.

Usage:

meshmash datasets [OPTIONS] [NAME]

Options:

  [NAME]  Dataset name to fetch (without file extension), or 'all' to fetch
          every available dataset. Available: microns_neuron_sample,
          microns_dendrite_sample.  [default: all]

hks

Compute condensed Heat Kernel Signature features on a mesh.

Usage:

meshmash hks [OPTIONS] MESH_PATH

Options:

  MESH_PATH                       Path to the input mesh file (any format
                                  supported by meshio).  [required]
  -o, --output PATH               Path to write the output .npz file.
                                  [required]
  -c, --config PATH               Path to a TOML config file. Parameter values
                                  from the file act as defaults and can be
                                  overridden by CLI flags.
  --simplify-agg INTEGER          Aggressiveness of mesh decimation (0=best
                                  quality, 10=fastest).  [default: 7]
  --simplify-target-reduction FLOAT
                                  Fraction of triangles to remove during
                                  simplification. Set to None to skip
                                  simplification.  [default: 0.7]
  --overlap-distance FLOAT        Geodesic distance to overlap mesh chunks.
                                  [default: 20000]
  --max-vertex-threshold INTEGER  Maximum number of vertices per mesh chunk
                                  before overlapping.  [default: 20000]
  --min-vertex-threshold INTEGER  Minimum number of vertices for a chunk to be
                                  included.  [default: 200]
  --max-overlap-neighbors INTEGER
                                  Maximum neighbors to consider when
                                  overlapping chunks; overrules
                                  overlap_distance.  [default: 40000]
  --n-components INTEGER          Number of HKS timescales (= number of HKS
                                  features).  [default: 32]
  --t-min FLOAT                   Minimum timescale for the HKS computation.
                                  [default: 50000.0]
  --t-max FLOAT                   Maximum timescale for the HKS computation.
                                  [default: 20000000.0]
  --max-eigenvalue FLOAT          Maximum eigenvalue for the HKS computation.
                                  [default: 5e-06]
  --robust / --no-robust          Use the robust Laplacian.  [default: robust]
  --mollify-factor FLOAT          Mollification factor for the robust
                                  Laplacian.  [default: 1e-05]
  --truncate-extra / --no-truncate-extra
                                  Truncate extra eigenpairs computed past
                                  max_eigenvalue.  [default: truncate-extra]
  --drop-first / --no-drop-first  Drop the first eigenpair (proportional to
                                  vertex areas).  [default: drop-first]
  --decomposition-dtype TEXT      Dtype for the decomposition: 'float32' or
                                  'float64'.  [default: float32]
  --distance-threshold FLOAT      Distance threshold for agglomerating the
                                  mesh into domains.  [default: 3.0]
  --auxiliary-features / --no-auxiliary-features
                                  Compute and include auxiliary features (e.g.
                                  component size).  [default: auxiliary-
                                  features]
  --n-jobs INTEGER                Number of parallel jobs. -1 uses all
                                  available cores.  [default: -1]
  --verbose / --no-verbose        Print progress messages.  [default: no-
                                  verbose]