API Reference

The toolbox map. imatools is stateless and contract-driven: core holds pure workflows, io reads/writes formats and returns typed contracts, and contracts defines what passes between layers. For the design rationale and the canonical command flow, start with Architecture.

Import name

The package is imported as imatools (e.g. from imatools.core import mesh). To browse a symbol's signature, use imatools-<tool> --help or read the source under src/imatools/.

Core — pure workflows (imatools.core)

Module	What it does
geometry	Geometric primitives and calculations on points/cells.
image	Image-array workflows (indexing, sampling, coordinate conversion).
io	In-memory helpers shared across the core workflows.
label	Label-map operations (binarise, relabel, merge, dtype-safe combine).
mesh	Mesh workflows — mapping, scalar projection, fibrosis_score, quality metrics.
mesh_topology	Connectivity / topology utilities extracted during the refactor.
metrics	Characterization and comparison metrics for meshes and fields.
parfile	In-memory parfile (pot) construction and manipulation.
scar	Scar thresholding (get_threshold), CEMRGAPP_IGNORE, scar-score logic.
segmentation	Segmentation workflows behind the imatools-segmentation subcommands.
spatial	Spatial transforms and coordinate math.

IO — format load/save (imatools.io)

Module	What it does
carp_io	CARP .pts/.elem read/write (incl. triangle-mesh element detection).
image_io	NIfTI / medical-image load and save (SimpleITK-backed).
mesh_io	VTK polydata load/save and mesh export.
parfile_io	Parfile (pot) read/write, e.g. get_empty_pot.
paths	Path helpers used by the IO layer.
scar_io	Scar-specific inputs/outputs (stats files, corridors).

Contracts — data passed between layers (imatools.contracts)

Module	What it does
image	Image contract (array + metadata).
mesh	Mesh contract (points, cells, scalar arrays).
operations	Operation-parameter contracts shared across workflows.
report	Inputs/parameters for the report and render pipeline.

Supporting packages

Module	What it does
parsers.dotmesh	Parser for .mesh (dotmesh) files → CARP.
render.mesh_views / render.plots / render.report_views / render.vtk_png	VTK-to-PNG rendering and report views used by imatools-report.

Looking for the orchestration pattern?

The high-level command flow and the core types are documented on the Architecture page.