working lld analysis checker

.github/workflows/ci.yml

@@ -41,8 +41,7 @@ jobs:
 
   build:
     name: Build
-    if: false  # delete this line and uncomment the line below to enable automatic builds
-    # if: github.event_name == 'push' || github.event_name == 'release'
+    if: github.event_name == 'push' || github.event_name == 'release'
     # needs: [ test ]  # uncomment to require passing tests
     runs-on: ubuntu-22.04
 

Dockerfile

@@ -1,22 +1,23 @@
 # Python version can be changed, e.g.
 # FROM python:3.8
 # FROM ghcr.io/mamba-org/micromamba:1.5.1-focal-cuda-11.3.1
-FROM docker.io/python:3.12.1-slim-bookworm
+FROM docker.io/python:latest
 
 LABEL org.opencontainers.image.authors="FNNDSC <dev@babyMRI.org>" \
-      org.opencontainers.image.title="ChRIS Plugin Title" \
-      org.opencontainers.image.description="A ChRIS plugin that..."
+      org.opencontainers.image.title="A ChRIS plugin to analyze the result produced by an LLD analysis " \
+      org.opencontainers.image.description="A ChRIS plugin to analyze the result produced by an LLD analysis "
 
-ARG SRCDIR=/usr/local/src/app
+ARG SRCDIR=/usr/local/src/pl-lld_chxr
 WORKDIR ${SRCDIR}
 
 COPY requirements.txt .
 RUN --mount=type=cache,sharing=private,target=/root/.cache/pip pip install -r requirements.txt
+RUN apt-get update ; apt-get install docker.io -y ; bash
 
 COPY . .
 ARG extras_require=none
 RUN pip install ".[${extras_require}]" \
     && cd / && rm -rf ${SRCDIR}
 WORKDIR /
 
-CMD ["commandname"]
+CMD ["lld_chxr"]

README.md

@@ -1,76 +1,10 @@
-# _ChRIS_ Plugin Template
+# A ChRIS plugin to analyze the result produced by an LLD analysis 
 
-[![test status](https://github.com/FNNDSC/python-chrisapp-template/actions/workflows/src.yml/badge.svg)](https://github.com/FNNDSC/python-chrisapp-template/actions/workflows/src.yml)
-[![MIT License](https://img.shields.io/github/license/FNNDSC/python-chrisapp-template)](LICENSE)
+[![Version](https://img.shields.io/docker/v/fnndsc/pl-lld_chxr?sort=semver)](https://hub.docker.com/r/fnndsc/pl-lld_chxr)
+[![MIT License](https://img.shields.io/github/license/fnndsc/pl-lld_chxr)](https://github.com/FNNDSC/pl-lld_chxr/blob/main/LICENSE)
+[![ci](https://github.com/FNNDSC/pl-lld_chxr/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-lld_chxr/actions/workflows/ci.yml)
 
-This is a minimal template repository for _ChRIS_ plugin applications in Python.
-
-## About _ChRIS_ Plugins
-
-A _ChRIS_ plugin is a scientific data-processing software which can run anywhere all-the-same:
-in the cloud via a [web app](https://github.com/FNNDSC/ChRIS_ui/), or on your own laptop
-from the terminal. They are easy to build and easy to understand: most simply, a
-_ChRIS_ plugin is a command-line program which processes data from an input directory
-and creates data to an output directory with the usage
-`commandname [options...] inputdir/ outputdir/`.
-
-For more information, visit our website https://chrisproject.org
-
-## How to Use This Template
-
-Go to https://github.com/FNNDSC/python-chrisapp-template and click "Use this template".
-The newly created repository is ready to use right away.
-
-A script `bootstrap.sh` is provided to help fill in and rename values for your new project.
-It is optional to use.
-
-1. Edit the variables in `bootstrap.sh`
-2. Run `./bootstrap.sh`
-3. Follow the instructions it will print out
-
-## Example Plugins
-
-Here are some good, complete examples of _ChRIS_ plugins created from this template.
-
-- https://github.com/FNNDSC/pl-dcm2niix (basic command wrapper example)
-- <https://github.com/FNNDSC/pl-adapt_object_mesh> (parallelizes a command)
-- https://github.com/FNNDSC/pl-mri-preview (uses [NiBabel](https://nipy.org/nibabel/))
-- https://github.com/FNNDSC/pl-pyvista-volume (example using Python package project structure and pytest)
-- https://github.com/FNNDSC/pl-fetal-cp-surface-extract (has a good README.md)
-
-## What's Inside
-
-| Path                       | Purpose                                                                                                                                                                                                  |
-|----------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| `app.py`                   | Main script: start editing here!                                                                                                                                                                         |
-| `tests/`                   | Unit tests                                                                                                                                                                                               |
-| `setup.py`                 | [Python project metadata and installation script](https://packaging.python.org/en/latest/guides/distributing-packages-using-setuptools/#setup-py)                                                        |
-| `requirements.txt`         | List of Python dependencies                                                                                                                                                                              |
-| `Dockerfile`               | [Container image build recipe](https://docs.docker.com/engine/reference/builder/)                                                                                                                        |
-| `.github/workflows/ci.yml` | "continuous integration" using [Github Actions](https://docs.github.com/en/actions/learn-github-actions/understanding-github-actions): automatic testing, building, and uploads to https://chrisstore.co |
-
-## Contributing
-
-The source code for the `main` branch of this repository is on the
-[src](https://github.com/fnndsc/python-chrisapp-template/tree/src)
-branch, which has an additional file
-[`.github/workflows/src.yml`](https://github.com/FNNDSC/python-chrisapp-template/blob/src/.github/workflows/src.yml)
-When tests pass, changes are automatically merged into `main`.
-Developers should commit to or make pull requests targeting `src`.
-Do not push directly to `main`.
-
-This is a workaround in order to do automatic testing of this template
-without including the `.github/workflows/src.yml` file in the template itself.
-
-<!-- BEGIN README TEMPLATE
-
-# ChRIS Plugin Title
-
-[![Version](https://img.shields.io/docker/v/fnndsc/pl-appname?sort=semver)](https://hub.docker.com/r/fnndsc/pl-appname)
-[![MIT License](https://img.shields.io/github/license/fnndsc/pl-appname)](https://github.com/FNNDSC/pl-appname/blob/main/LICENSE)
-[![ci](https://github.com/FNNDSC/pl-appname/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-appname/actions/workflows/ci.yml)
-
-`pl-appname` is a [_ChRIS_](https://chrisproject.org/)
+`pl-lld_chxr` is a [_ChRIS_](https://chrisproject.org/)
 _ds_ plugin which takes in ...  as input files and
 creates ... as output files.
 
@@ -80,34 +14,34 @@ creates ... as output files.
 
 ## Installation
 
-`pl-appname` is a _[ChRIS](https://chrisproject.org/) plugin_, meaning it can
+`pl-lld_chxr` is a _[ChRIS](https://chrisproject.org/) 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](https://apptainer.org/)
-(a.k.a. Singularity) to run `pl-appname` as a container:
+(a.k.a. Singularity) to run `pl-lld_chxr` as a container:
 
 ```shell
-apptainer exec docker://fnndsc/pl-appname commandname [--args values...] input/ output/
+apptainer exec docker://fnndsc/pl-lld_chxr lld_chxr [--args values...] input/ output/
 ```
 
 To print its available options, run:
 
 ```shell
-apptainer exec docker://fnndsc/pl-appname commandname --help
+apptainer exec docker://fnndsc/pl-lld_chxr lld_chxr --help
 ```
 
 ## Examples
 
-`commandname` requires two positional arguments: a directory containing
+`lld_chxr` 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.
 
 ```shell
 mkdir incoming/ outgoing/
 mv some.dat other.dat incoming/
-apptainer exec docker://fnndsc/pl-appname:latest commandname [--args] incoming/ outgoing/
+apptainer exec docker://fnndsc/pl-lld_chxr:latest lld_chxr [--args] incoming/ outgoing/
 ```
 
 ## Development
@@ -119,18 +53,18 @@ Instructions for developers.
 Build a local container image:
 
 ```shell
-docker build -t localhost/fnndsc/pl-appname .
+docker build -t localhost/fnndsc/pl-lld_chxr .
 ```
 
 ### Running
 
-Mount the source code `app.py` into a container to try out changes without rebuild.
+Mount the source code `lld_chxr.py` into a container to try out changes without rebuild.
 
 ```shell
 docker run --rm -it --userns=host -u $(id -u):$(id -g) \
-    -v $PWD/app.py:/usr/local/lib/python3.12/site-packages/app.py:ro \
+    -v $PWD/lld_chxr.py:/usr/local/lib/python3.12/site-packages/lld_chxr.py:ro \
     -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
-    localhost/fnndsc/pl-appname commandname /incoming /outgoing
+    localhost/fnndsc/pl-lld_chxr lld_chxr /incoming /outgoing
 ```
 
 ### Testing
@@ -140,8 +74,8 @@ It's recommended to rebuild the image to ensure that sources are up-to-date.
 Use the option `--build-arg extras_require=dev` to install extra dependencies for testing.
 
 ```shell
-docker build -t localhost/fnndsc/pl-appname:dev --build-arg extras_require=dev .
-docker run --rm -it localhost/fnndsc/pl-appname:dev pytest
+docker build -t localhost/fnndsc/pl-lld_chxr:dev --build-arg extras_require=dev .
+docker run --rm -it localhost/fnndsc/pl-lld_chxr:dev pytest
 ```
 
 ## Release
@@ -158,8 +92,8 @@ Increase the version number in `setup.py` and commit this file.
 Build and push an image tagged by the version. For example, for version `1.2.3`:
 
 ```
-docker build -t docker.io/fnndsc/pl-appname:1.2.3 .
-docker push docker.io/fnndsc/pl-appname:1.2.3
+docker build -t docker.io/fnndsc/pl-lld_chxr:1.2.3 .
+docker push docker.io/fnndsc/pl-lld_chxr:1.2.3
 ```
 
 ### Get JSON Representation
@@ -168,10 +102,9 @@ Run [`chris_plugin_info`](https://github.com/FNNDSC/chris_plugin#usage)
 to produce a JSON description of this plugin, which can be uploaded to _ChRIS_.
 
 ```shell
-docker run --rm docker.io/fnndsc/pl-appname:1.2.3 chris_plugin_info -d docker.io/fnndsc/pl-appname:1.2.3 > chris_plugin_info.json
+docker run --rm docker.io/fnndsc/pl-lld_chxr:1.2.3 chris_plugin_info -d docker.io/fnndsc/pl-lld_chxr:1.2.3 > chris_plugin_info.json
 ```
 
 Intructions on how to upload the plugin to _ChRIS_ can be found here:
 https://chrisproject.org/docs/tutorials/upload_plugin
 
-END README TEMPLATE -->

app.py → lld_chxr.py

@@ -2,24 +2,30 @@
 
 from pathlib import Path
 from argparse import ArgumentParser, Namespace, ArgumentDefaultsHelpFormatter
-
+import json
 from chris_plugin import chris_plugin, PathMapper
+import subprocess
 
 __version__ = '1.0.0'
 
 DISPLAY_TITLE = r"""
-ChRIS Plugin Template Title
+       _        _ _     _       _               
+      | |      | | |   | |     | |              
+ _ __ | |______| | | __| |  ___| |__ __  ___ __ 
+| '_ \| |______| | |/ _` | / __| '_ \\ \/ / '__|
+| |_) | |      | | | (_| || (__| | | |>  <| |   
+| .__/|_|      |_|_|\__,_| \___|_| |_/_/\_\_|   
+| |                    ______                   
+|_|                   |______|                  
 """
 
 
-parser = ArgumentParser(description='!!!CHANGE ME!!! An example ChRIS plugin which '
-                                    'counts the number of occurrences of a given '
-                                    'word in text files.',
+parser = ArgumentParser(description='A ChRIS plugin to analyze the result produced by an LLD analysis ',
                         formatter_class=ArgumentDefaultsHelpFormatter)
-parser.add_argument('-w', '--word', required=True, type=str,
-                    help='word to count')
-parser.add_argument('-p', '--pattern', default='**/*.txt', type=str,
+parser.add_argument('-f', '--fileFilter', default='json', type=str,
                     help='input file filter glob')
+parser.add_argument('-e', '--marginOfError', default=0.02, type=float,
+                    help='Accepted margin of error in tibia to femur ratio')
 parser.add_argument('-V', '--version', action='version',
                     version=f'%(prog)s {__version__}')
 
@@ -30,7 +36,7 @@
 # documentation: https://fnndsc.github.io/chris_plugin/chris_plugin.html#chris_plugin
 @chris_plugin(
     parser=parser,
-    title='My ChRIS plugin',
+    title='A ChRIS plugin to analyze the result produced by an LLD analysis',
     category='',                 # ref. https://chrisstore.co/plugins
     min_memory_limit='100Mi',    # supported units: Mi, Gi
     min_cpu_limit='1000m',       # millicores, e.g. "1000m" = 1 CPU core
@@ -56,14 +62,29 @@ def main(options: Namespace, inputdir: Path, outputdir: Path):
     #
     # Refer to the documentation for more options, examples, and advanced uses e.g.
     # adding a progress bar and parallelism.
-    mapper = PathMapper.file_mapper(inputdir, outputdir, glob=options.pattern, suffix='.count.txt')
+    mapper = PathMapper.file_mapper(inputdir, outputdir, glob=f"**/*.{options.fileFilter}",fail_if_empty=False)
     for input_file, output_file in mapper:
-        # The code block below is a small and easy example of how to use a ``PathMapper``.
-        # It is recommended that you put your functionality in a helper function, so that
-        # it is more legible and can be unit tested.
-        data = input_file.read_text()
-        frequency = data.count(options.word)
-        output_file.write_text(str(frequency))
+        with open(input_file) as f:
+            data = json.load(f)
+            analyze_measurements(data,options.marginOfError)
+
+
+def analyze_measurements(data, margin_error):
+    """
+    Analyze the measurements of lower limbs and verify
+    if the measurements are correct.
+    """
+    AVG_RATIO = 0.8
+    for row in data:
+        rt = data[row]["pixel_distance"]["Right tibia"]
+        rf = data[row]["pixel_distance"]["Right femur"]
+        ratio = round(rt / rf, 2)
+        print(f"Calculated tibia to femur ratio: {ratio} [Average ratio: {AVG_RATIO} ± {margin_error}]")
+        if ratio > AVG_RATIO + margin_error or ratio < AVG_RATIO - margin_error:
+            print("Measurements are incorrect.")
+        else:
+            print("Measurements are correct.")
+
 
 
 if __name__ == '__main__':

requirements.txt

@@ -1 +1,3 @@
 chris_plugin==0.4.0
+plugin2cube
+python-chrisclient==2.9.1

setup.py

@@ -19,18 +19,18 @@ def get_version(rel_path: str) -> str:
 
 
 setup(
-    name='chris-plugin-template',
-    version=get_version('app.py'),
-    description='A ChRIS DS plugin template',
+    name='lld_chxr',
+    version=get_version('lld_chxr.py'),
+    description='A ChRIS plugin to analyze the result produced by an LLD analysis ',
     author='FNNDSC',
     author_email='dev@babyMRI.org',
-    url='https://github.com/FNNDSC/python-chrisapp-template',
-    py_modules=['app'],
+    url='https://github.com/FNNDSC/pl-lld_',
+    py_modules=['lld_chxr'],
     install_requires=['chris_plugin'],
     license='MIT',
     entry_points={
         'console_scripts': [
-            'commandname = app:main'
+            'lld_chxr = lld_chxr:main'
         ]
     },
     classifiers=[