Rename to pl-gifit

.github/workflows/ci.yml

@@ -30,12 +30,12 @@ jobs:
           context: .
           load: true
           push: false
-          tags: "localhost/fnndsc/pl-innerspfit:latest"
+          tags: "localhost/fnndsc/pl-gifit:latest"
           cache-from: type=gha
           cache-to: type=gha,mode=max
       - name: Run pytest
         run: |
-          docker run -v "$GITHUB_WORKSPACE:/app:ro" -w /app localhost/fnndsc/pl-innerspfit:latest \
+          docker run -v "$GITHUB_WORKSPACE:/app:ro" -w /app localhost/fnndsc/pl-gifit:latest \
             pytest -o cache_dir=/tmp/pytest
 
   build:

Dockerfile

@@ -1,15 +1,15 @@
-FROM docker.io/fnndsc/pl-innerspfit:base-1
+FROM docker.io/fnndsc/pl-gifit:base-1
 
 LABEL org.opencontainers.image.authors="FNNDSC <[email protected]>" \
-      org.opencontainers.image.title="Inner Subplate Surface Fit" \
-      org.opencontainers.image.description="Outer to inner surface mesh deformation using a radial distance map for human fetal MRI"
+      org.opencontainers.image.title="pl-gifit" \
+      org.opencontainers.image.description="A ChRIS plugin for surface mesh deformation using different parameters depending on gyrification index"
 
 RUN \
     --mount=type=cache,sharing=private,target=/home/mambauser/.mamba/pkgs,uid=57439,gid=57439 \
     --mount=type=cache,sharing=private,target=/opt/conda/pkgs,uid=57439,gid=57439 \
     micromamba install -y -n base -c conda-forge python=3.11.5 pandas=2.1.1
 
-ARG SRCDIR=/home/mambauser/pl-innerspfit
+ARG SRCDIR=/home/mambauser/pl-gifit
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
 WORKDIR ${SRCDIR}
 

README.md

@@ -1,18 +1,28 @@
 # Inner Subplate Surface Fit
 
-[![Version](https://img.shields.io/docker/v/fnndsc/pl-innerspfit?sort=semver)](https://hub.docker.com/r/fnndsc/pl-innerspfit)
-[![MIT License](https://img.shields.io/github/license/fnndsc/pl-innerspfit)](https://github.com/FNNDSC/pl-innerspfit/blob/main/LICENSE)
-[![ci](https://github.com/FNNDSC/pl-innerspfit/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-innerspfit/actions/workflows/ci.yml)
+[![Version](https://img.shields.io/docker/v/fnndsc/pl-gifit?sort=semver)](https://hub.docker.com/r/fnndsc/pl-gifit)
+[![MIT License](https://img.shields.io/github/license/fnndsc/pl-gifit)](https://github.com/FNNDSC/pl-gifit/blob/main/LICENSE)
+[![ci](https://github.com/FNNDSC/pl-gifit/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-gifit/actions/workflows/ci.yml)
 
-`pl-innerspfit` is a [_ChRIS_](https://chrisproject.org/)
-_ds_ plugin which takes in ...  as input files and
-creates ... as output files.
+`pl-gifit` is a [_ChRIS_](https://chrisproject.org/) _ds_ plugin which
+performs mesh deformation. Different deformation parameters are used depending
+on the gyrification index of the input surface. Similar to the CIVET function
+`expand_from_white`, `pl-gifit` is a wrapper around `surface_fit`.
 
-## Abstract
+## Models
 
-...
+The primary goal of `pl-gifit` is to deform inwards mesh deformation from the outer
+subplate surface to the inner subplate surface for _in-vivo_ human brain MRI.
 
-## Installation
+A "model" for `pl-gifit` refers to a CSV file containing parameters for `surface_fit`.
+A model CSV file optimized for inner subplate fitting is provided as the default.
 
-`pl-innerspfit` is a _[ChRIS](https://chrisproject.org/) plugin_, meaning it can
+One "schedule" of parameters is run per brain hemisphere. A "schedule" is one or more
+runs of `surface_fit`. Sometimes, it is ideal to run `surface_fit` multiple times with
+different paremeters. Each run with different parameters is called a "stage."
+One row of a model CSV file corresponds to one "stage" of a "schedule."
+
+## Usage
+
+`pl-gifit` is a _[ChRIS](https://chrisproject.org/) plugin_, meaning it can
 run from either within _ChRIS_ or the command-line.

base/README.md

@@ -1,5 +1,5 @@
 Uses [microminc](https://github.com/FNNDSC/microminc)
-to create a minimized base image for `pl-innerspfit`,
+to create a minimized base image for `pl-gifit`,
 which copies the necessary minc-tool binaries to a multi-arch micromamba image.
 
 This image is built and pushed manually.

base/build.sh

@@ -2,4 +2,4 @@
 
 exec docker buildx build --push \
     --platform linux/amd64,linux/arm64,linux/ppc64le \
-    -t docker.io/fnndsc/pl-innerspfit:base-1 .
+    -t docker.io/fnndsc/pl-gifit:base-1 .

innerspfit/__main__.py

@@ -32,7 +32,7 @@
 
 @chris_plugin(
     parser=parser,
-    title='Inner subplate surface mesh deformation',
+    title='Surface mesh deformation',
     category='Surfaces',
     min_memory_limit='1Gi',
     min_cpu_limit='1000m',

innerspfit/gi.py

@@ -21,7 +21,7 @@ def _run_adapt_object_mesh(surface: str | os.PathLike, output: str | os.PathLike
     """
     Run ``adapt_object_mesh``. Doing this before ``gyrification_index`` can work around some bugs.
 
-    See https://github.com/FNNDSC/pl-innerspfit/issues/1
+    See https://github.com/FNNDSC/pl-gifit/issues/1
 
     If ``adapt_object_mesh`` fails, as a fallback ``output`` is created as a symlink to ``surface``.
     """

setup.py

@@ -31,7 +31,7 @@ def get_version(rel_path: str) -> str:
     description='Outer to inner surface mesh deformation using a radial distance map for human fetal MRI',
     author='FNNDSC',
     author_email='[email protected]',
-    url='https://github.com/FNNDSC/pl-innerspfit',
+    url='https://github.com/FNNDSC/pl-gifit',
     packages=['innerspfit'],
     install_requires=['chris_plugin', 'pandas', 'loguru'],
     license='MIT',