fnndsc/pl-bichamfer repository overview

⁠Radial Distance Map

pl-bichamfer is a ChRIS⁠ ds plugin wrapper around a bi-directional mincchamfer program. It creates a radial distance map for every MINC mask image inside a given input directory.

⁠Installation

pl-bichamfer is a ChRIS⁠ plugin, meaning it can run from either within ChRIS or the command-line.

⁠Local Usage

To get started with local command-line usage, use Apptainer⁠ (a.k.a. Singularity) to run pl-bichamfer as a container. To print its available options, run:

apptainer exec docker://fnndsc/pl-bichamfer bichamfer --help

⁠Examples

Convert a directory containing .mnc mask images to distance map volumes, where output files use the same file names as their corresponding files:

apptainer exec docker://fnndsc/pl-bichamfer bichamfer input_masks/ output_chamfers/

If the input directory is the same as the output directory, then output file names are renamed to have the suffix .chamfer.mnc. This is useful for running pl-bichamfer "in-place" on all masks in the current working directory:

apptainer exec docker://fnndsc/pl-bichamfer bichamfer . .