pl-surfdisterr is a ChRIS
ds plugin which calculates the distance error of surfaces (.obj)
from masks (.mnc). It is for assessing the accuracy of surface
extraction and deformation algorithms.
pl-surfdisterr can operate on multiple data files in its
input directory. For every mask in its input directory:
for every surface in the directory of the mask, compute the
distance from every vertex of the surface to the mask.
Under the hood, pl-surfdisterr is a script which calls
mincchamfer and volume_object_evaluate.
pl-surfdisterr is a ChRIS plugin, meaning it can
run from either within ChRIS or the command-line.
To get started with local command-line usage, use Apptainer
(a.k.a. Singularity) to run pl-surfdisterr as a container:
singularity exec docker://fnndsc/pl-surfdisterr surfdisterr input/ output/To print its available options, run:
singularity exec docker://fnndsc/pl-surfdisterr surfdisterr --helpsurfdisterr requires two positional arguments: a directory containing
input data, and a directory where to create output data.
First, create the input directory and move input data into it.
mkdir incoming/ outgoing/
mv some.dat other.dat incoming/
singularity exec docker://fnndsc/pl-surfdisterr:latest surfdisterr [--args] incoming/ outgoing/Instructions for developers.
Build a local container image:
docker build -t localhost/fnndsc/pl-surfdisterr .Run chris_plugin_info
to produce a JSON description of this plugin, which can be uploaded to a ChRIS Store.
docker run --rm localhost/fnndsc/pl-surfdisterr chris_plugin_info > chris_plugin_info.jsonMount the source code app.py into a container to test changes without rebuild.
docker run --rm -it --userns=host -u $(id -u):$(id -g) \
-v $PWD/surfdisterr.py:/usr/local/lib/python3.10/site-packages/surfdisterr.py:ro \
-v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
localhost/fnndsc/pl-surfdisterr surfdisterr /incoming /outgoing