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‎.github/actions/download-artifact/action.yml

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---
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name: Download Artifact
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description: Download artifact from the same or different workflow
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inputs:
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name:
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description: Artifact to be downloaded
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required: true
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type: string
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runs:
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using: composite
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steps:
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- name: Download Artifact
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uses: actions/github-script@v6
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with:
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script: |
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var inputs = ${{ toJSON(inputs) }}
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var artifactName = inputs['name']
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let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({
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owner: context.repo.owner,
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repo: context.repo.repo,
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run_id: context.payload.workflow_run.id,
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});
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let matchArtifact = allArtifacts.data.artifacts.filter((artifact) => {
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return artifact.name == artifactName
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})[0];
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let download = await github.rest.actions.downloadArtifact({
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owner: context.repo.owner,
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repo: context.repo.repo,
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artifact_id: matchArtifact.id,
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archive_format: 'zip',
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});
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let fs = require('fs');
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fs.writeFileSync(`${process.env.GITHUB_WORKSPACE}/${artifactName}.zip`, Buffer.from(download.data));
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- name: 'Unzip artifact'
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run: unzip ${{ inputs.name }}.zip
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shell: bash

‎.github/workflows/analysis.yml

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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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cache: 'pip'
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# - name: Cache virtualenv
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# uses: actions/cache@v3
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# with:
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# key: venv-${{ runner.os }}-${{ steps.setup_python.outputs.python-version}}-${{ hashFiles('requirements.txt') }}
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# path: .venv
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- name: Cache pip
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uses: actions/cache@v3
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id: pip-cache
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with:
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key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }}
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path: ${{ env.pythonLocation }}
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if: steps.pip-cache.outputs.cache-hit != 'true'
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- name: Install dependencies
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run: |
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python -m venv .venv
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source .venv/bin/activate
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python -m pip install -r requirements.txt
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python -m pip install pytest
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pip install -r requirements.txt
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- name: Read algorithms
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id: algorithms
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run: |
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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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cache: 'pip'
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# - name: Cache virtualenv
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# uses: actions/cache@v3
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# with:
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# key: venv-${{ runner.os }}-${{ steps.setup_python.outputs.python-version}}-${{ hashFiles('requirements.txt') }}
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# path: .venv
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- name: Install dependencies
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run: |
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python -m venv .venv
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source .venv/bin/activate
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python -m pip install -r requirements.txt
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python -m pip install pytest
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if: steps.pip-cache.outputs.cache-hit != 'true'
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- name: Restore cache
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id: python-cache
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uses: actions/cache@v3
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with:
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key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }}
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path: ${{ env.pythonLocation }}
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- name: Generate fitting data
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run: |
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source .venv/bin/activate
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python -m pytest -m slow --selectAlgorithm ${{ matrix.algorithm }} --saveFileName test_output_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv --SNR ${{ matrix.SNR }} --fitCount 300 --saveDurationFileName test_duration_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv
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- name: Upload raw data
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uses: actions/upload-artifact@v3

‎.github/workflows/documentation.yml

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name: Build & Deploy Documentation
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on:
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workflow_run:
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workflows: [Algorithm Analysis]
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types:
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- completed
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permissions:
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contents: read
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pages: write
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id-token: write
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Setup Pages
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uses: actions/configure-pages@v4
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- name: Set up Python
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id: setup_python
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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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- name: Cache pip
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uses: actions/cache@v3
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id: pip-cache
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with:
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key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }}
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path: ${{ env.pythonLocation }}
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if: steps.pip-cache.outputs.cache-hit != 'true'
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- name: Install dependencies
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run: |
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pip install -r requirements.txt
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# Action to download artifacts from a different workflow (analysis.yml)
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- name: 'Download artifact'
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if: ${{ github.event.workflow_run.conclusion == 'success' }}
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uses: ./.github/actions/download-artifact
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with:
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name: 'Figures'
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- name: Build html
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run: |
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mkdir docs/_static
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mv *.pdf docs/_static/
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sphinx-apidoc -o docs src
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cd docs/
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make html
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- name: Upload docs artifact
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uses: actions/upload-pages-artifact@v3
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with:
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path: 'docs/_build/html'
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deploy:
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needs: build
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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runs-on: ubuntu-latest
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v4

‎.gitignore

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*.mat
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*.raw
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bvals.txt
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download
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md5sums.txt
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*.gz
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*.zip
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*.tmp
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# Unit test / coverage reports
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.tox/
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.coverage

‎README.md

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## View Testing Reports
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[![Unit tests](https://github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection/actions/workflows/unit_test.yml/badge.svg?branch=main)](https://github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection/actions/workflows/unit_test.yml)
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[![Algorithm Analysis](https://github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection/actions/workflows/analysis.yml/badge.svg?branch=main)](https://github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection/actions/workflows/analysis.yml)
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[![Algorithm Analysis](https://github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection/actions/workflows/analysis.yml/badge.svg?branch=main)](https://github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection/actions/workflows/analysis.yml)
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[![Build & Deploy Documentation](https://github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection/actions/workflows/documentation.yml/badge.svg?branch=main)](https://github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection/actions/workflows/documentation.yml)

‎docs/Makefile

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line, and also
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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = .
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BUILDDIR = _build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

‎docs/conf.py

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# Configuration file for the Sphinx documentation builder.
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#
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# For the full list of built-in configuration values, see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Project information -----------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
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import os
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import sys
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sys.path.insert(0, os.path.abspath(".."))
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project = 'TF2.4 IVIM MRI Code Collection'
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copyright = '2024, OSIPI'
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author = 'OSIPI team'
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# -- General configuration ---------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
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extensions = ["sphinx.ext.todo", "sphinx.ext.viewcode", "sphinx.ext.autodoc"]
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templates_path = ['_templates']
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exclude_patterns = ['Thumbs.db', '.DS_Store']
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# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
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html_show_sphinx = False
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# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
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html_show_copyright = False
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# -- Options for HTML output -------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
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html_theme = 'sphinx_rtd_theme'
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html_static_path = ['_static']

‎docs/figures.rst

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Algorithm Analysis Figures
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===========
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.. raw:: html
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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="UTF-8">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<title>Algorithm Analysis Figures</title>
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<style>
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embed {
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width: 90%;
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margin-bottom: 4rem;
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height: 100vh;
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}
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</style>
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</head>
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<body>
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<h4>Diffusion grid for limited algorithms:</h4>
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<embed src="_static/D_limited.pdf" type="application/pdf" frameborder="0" scrolling="auto">
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<h4>Diffusion grid for all algorithms:</h4>
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<embed src="_static/D.pdf" type="application/pdf" frameborder="0" scrolling="auto">
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<h4>Perfusion grid for limited algorithms:</h4>
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<embed src="_static/Dp_limited.pdf" type="application/pdf" frameborder="0" scrolling="auto">
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<h4>Perfusion grid for all algorithms:</h4>
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<embed src="_static/Dp.pdf" type="application/pdf" frameborder="0" scrolling="auto">
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<h4>Perfusion fraction grid for limited algorithms:</h4>
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<embed src="_static/f_limited.pdf" type="application/pdf" frameborder="0" scrolling="auto">
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<h4>Perfusion fraction grid for all algorithms:</h4>
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<embed src="_static/f.pdf" type="application/pdf" frameborder="0" scrolling="auto">
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<h4>Fitted curves:</h4>
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<embed src="_static/fitted_curves.pdf" type="application/pdf" frameborder="0" scrolling="auto">
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<h4>Curve plot:</h4>
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<embed src="_static/curve_plot.pdf" type="application/pdf" frameborder="0" scrolling="auto">
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<h4>Algorithm Fitting duration:</h4>
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<embed src="_static/durations.pdf" type="application/pdf" frameborder="0" scrolling="auto">
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</body>
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</html>

‎docs/index.rst

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.. TF2.4 IVIM MRI Code Collection documentation master file, created by
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sphinx-quickstart on Wed Mar 6 00:06:13 2024.
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You can adapt this file completely to your liking, but it should at least
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contain the root `toctree` directive.
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Welcome to TF2.4 IVIM MRI Code Collection's documentation!
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==========================================================
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.. toctree::
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:maxdepth: 4
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:caption: Contents:
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figures
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modules
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Indices and tables
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==================
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* :ref:`modindex`

‎phantoms/MR_XCAT_qMRI/README.md

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# MR_XCAT_qMRI
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# 4D IVIM Phantom Generator
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A command-line tool for generating a 4D IVIM (Intravoxel Incoherent Motion) phantom as a NIfTI file.
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## Usage
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```sh
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python sim_vim_sig.py [-h] [-b BVALUE [BVALUE ...] | -f FILE] [-n NOISE] [-m] [-i]
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```
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## Arguments
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- `-b`, `--bvalue` : B values (list of numbers)
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- `-f`, `--bvalues-file` : JSON file containing the B values (default: b_values.json)
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- `-n`, `--noise` : Noise level (default: 0.0005)
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- `-m`, `--motion` : Enable motion flag (default: False)
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- `-i`, `--interleaved` : Enable interleaved flag (default: False)
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**Note:** Either provide `--bvalue` or `--bvalues-file`, not both.
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If neither `--bvalues-file` nor `--bvalue` is provided, the script will use the default `b_values.json` file.
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## Customizing B Values
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You can customize the B values by editing the `b_values.json` file. Here's an example of the default format:
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```json
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{
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"original": [0.0, 1.0, 2.0, 5.0, 10.0, 20.0, 30.0, 50.0, 75.0, 100.0, 150.0, 250.0, 350.0, 400.0, 550.0, 700.0, 850.0, 1000.0],
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"one": [0.0, 1.0, 2.0, 5.0, 10.0, 20.0, 30.0, 50.0, 75.0, 100.0, 150.0, 250.0, 350.0, 400.0, 550.0, 700.0, 850.0, 1000.0, 1100.0, 1200.0],
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"two": [0.0, 1.0, 2.0, 5.0, 10.0, 20.0, 30.0, 50.0, 75.0, 100.0, 150.0, 250.0, 350.0, 400.0, 500.0, 700.0, 800.0, 1000.0, 1100.0, 1200.0],
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"three": [0.0, 1.0, 2.0, 5.0, 10.0, 20.0, 30.0, 50.0, 75.0, 100.0, 150.0, 250.0, 350.0, 450.0, 550.0, 675.0, 800.0],
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"four": [0.0, 1.0, 2.0, 5.0, 10.0, 20.0, 30.0, 50.0, 75.0, 100.0, 150.0, 250.0, 300.0, 400.0, 500.0, 600.0, 700.0, 800.0]
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}
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```
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You can add or remove values as needed for your simulation. Here are the effects of customizing the B values for each of the generic profiles (`generic.json`, `generic_one.json`, `generic_two.json`, `generic_three.json`, `generic_four.json`):
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The default `generic_<custom_name>.json` file can be found in the following location:
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```
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TF2.4_IVIM-MRI_CodeCollection/tests/IVIMmodels/unit_tests
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```
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## Running the Script
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To run the script, you can add the following line to your shell configuration file (e.g., `.bashrc` or `.zshrc`) to include the necessary directory in your `PYTHONPATH`:
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```sh
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export PYTHONPATH=$PYTHONPATH:~/TF2.4_IVIM-MRI_CodeCollection
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```
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Replace `~/TF2.4_IVIM-MRI_CodeCollection` with the actual path to the directory containing the script.
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## Example
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```sh
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python sim_ivim_sig.py -n 0.0001 -m
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```
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This command will generate a 4D IVIM phantom using B values from the default `b_values.json` file, with a noise level of 0.0001 and motion enabled.

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