CLI Reference

pycemrg-meshing installs a single console entry point, a Click group with three subcommands:

pycemrg-meshing [-v/--verbose] {init-par | run | laplace} ...

The top-level -v/--verbose flag enables INFO logging. Use -h/--help on the group or any subcommand for the full, authoritative option list.

---

init-par — write a default parameter file

Generates a meshtools3d .par file seeded with the core defaults.

pycemrg-meshing init-par -o heart.par \
  --set segmentation.seg_dir=/data/case01 \
  --set meshing.facet_angle=30

Option	Description
-o, --output PATH	Path for the generated parameter file (default: heart.par).
--set SECTION.KEY=VALUE	Override a default parameter. Repeatable. Keys are validated against the schema and a typo raises.

---

run — run meshtools3d

Builds a MeshingJob from an existing .par file and runs the meshtools3d binary. The .par file is never modified; per-run overrides are passed to the binary as its native flags.

pycemrg-meshing run heart.par --seg-dir /data/case01 --out-dir /data/case01/mesh

Argument / Option	Description
PARFILE	Path to an existing .par file (required).
--binary PATH	Explicit binary path; otherwise resolved via pycemrg's asset manager.
--cwd PATH	Working directory for the binary (default: derived from seg_dir).
--seg-dir	Override [segmentation] seg_dir (binary -seg_dir).
--seg-name	Override [segmentation] seg_name (binary -seg_name).
--out-dir	Override [output] outdir (binary -out_dir).
--out-name	Override [output] name (binary -out_name).

---

laplace — run laplace_solver

Runs the laplace_solver binary over a CARP mesh. Unlike run, laplace carries its mesh/output/BC paths directly as flags (there is no .par to override); the optional -f/--parfile only supplies [laplacesolver] parameters.

pycemrg-meshing laplace \
  --mesh-dir /data/case01/mesh --mesh-name myo \
  --out-dir /data/case01/laplace --out-name thickness \
  --zero-bc endo.vtx --one-bc epi.vtx --vtk

Option	Description
--mesh-dir	Directory containing the CARP mesh (required, -mesh_dir).
--mesh-name	CARP mesh basename (required, -mesh_name).
--out-dir	Output directory (required, -out_dir).
--out-name	Output basename (required, -out_name).
--zero-bc PATH	vtx node-set assigned value 0.0. Repeatable.
--one-bc PATH	vtx node-set assigned value 1.0. Repeatable.
-f, --parfile PATH	Optional GetPot file for [laplacesolver] params.
--binary PATH	Explicit binary path; otherwise resolved via pycemrg's asset manager.
--vtk	Write VTK output.
--vtk-binary	Binary VTK; requires --vtk.
--potential	Write potential output.
--no-thickness	Solve only, skip thickness.
--swap-regions	Swap endo/epi direction.
--thickness-algo	Select the thickness algorithm.
--solver-verbose	Verbose solver output.