Merge branch 'created_repostatus/statistics' of https://github.com/ab…

…hicodes369/TF2.4_IVIM-MRI_CodeCollection into created_repostatus/statistics

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

@@ -0,0 +1,39 @@
+---
+name: Download Artifact
+description: Download artifact from the same or different workflow
+
+inputs:
+    name:
+        description: Artifact to be downloaded
+        required: true
+        type: string
+
+runs:
+    using: composite
+    steps:
+      - name: Download Artifact
+        uses: actions/github-script@v6
+        with:
+          script: |
+            var inputs = ${{ toJSON(inputs) }}
+            var artifactName = inputs['name']
+            let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({
+               owner: context.repo.owner,
+               repo: context.repo.repo,
+               run_id: context.payload.workflow_run.id,
+            });
+            let matchArtifact = allArtifacts.data.artifacts.filter((artifact) => {
+              return artifact.name == artifactName
+            })[0];
+            let download = await github.rest.actions.downloadArtifact({
+               owner: context.repo.owner,
+               repo: context.repo.repo,
+               artifact_id: matchArtifact.id,
+               archive_format: 'zip',
+            });
+            let fs = require('fs');
+            fs.writeFileSync(`${process.env.GITHUB_WORKSPACE}/${artifactName}.zip`, Buffer.from(download.data));
+
+      - name: 'Unzip artifact'
+        run: unzip ${{ inputs.name }}.zip
+        shell: bash

.github/workflows/analysis.yml

@@ -18,18 +18,18 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: "3.11"
-          cache: 'pip'
-      # - name: Cache virtualenv
-      #   uses: actions/cache@v3
-      #   with:
-      #     key: venv-${{ runner.os }}-${{ steps.setup_python.outputs.python-version}}-${{ hashFiles('requirements.txt') }}
-      #     path: .venv
+      - name: Cache pip
+        uses: actions/cache@v3
+        id: pip-cache
+        with:
+          key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }}
+          path: ${{ env.pythonLocation }}
+        if: steps.pip-cache.outputs.cache-hit != 'true'
+
       - name: Install dependencies
         run: |
-          python -m venv .venv
-          source .venv/bin/activate
-          python -m pip install -r requirements.txt
-          python -m pip install pytest
+          pip install -r requirements.txt
+
       - name: Read algorithms
         id: algorithms
         run: |
@@ -58,21 +58,16 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: "3.11"
-          cache: 'pip'
-      # - name: Cache virtualenv
-      #   uses: actions/cache@v3
-      #   with:
-      #     key: venv-${{ runner.os }}-${{ steps.setup_python.outputs.python-version}}-${{ hashFiles('requirements.txt') }}
-      #     path: .venv
-      - name: Install dependencies
-        run: |
-          python -m venv .venv
-          source .venv/bin/activate
-          python -m pip install -r requirements.txt
-          python -m pip install pytest
+        if: steps.pip-cache.outputs.cache-hit != 'true'
+      - name: Restore cache
+        id: python-cache
+        uses: actions/cache@v3
+        with:
+          key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }}
+          path: ${{ env.pythonLocation }}
+
       - name: Generate fitting data
         run: |
-          source .venv/bin/activate
           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
       - name: Upload raw data
         uses: actions/upload-artifact@v3

.github/workflows/documentation.yml

@@ -0,0 +1,66 @@
+name: Build & Deploy Documentation
+
+on:
+  workflow_run:
+    workflows: [Algorithm Analysis]
+    types:
+      - completed
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+      - name: Set up Python
+        id: setup_python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Cache pip
+        uses: actions/cache@v3
+        id: pip-cache
+        with:
+          key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }}
+          path: ${{ env.pythonLocation }}
+        if: steps.pip-cache.outputs.cache-hit != 'true'
+
+      - name: Install dependencies
+        run: |
+          pip install -r requirements.txt
+
+      # Action to download artifacts from a different workflow (analysis.yml)
+      - name: 'Download artifact'
+        if: ${{ github.event.workflow_run.conclusion == 'success' }}
+        uses: ./.github/actions/download-artifact
+        with:
+          name: 'Figures'
+
+      - name: Build html
+        run: |
+          mkdir docs/_static
+          mv *.pdf docs/_static/
+          sphinx-apidoc -o docs src
+          cd docs/
+          make html
+
+      - name: Upload docs artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: 'docs/_build/html'
+
+  deploy:
+    needs: build
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -9,6 +9,12 @@ __pycache__/
 *.mat
 *.raw
 bvals.txt
+download
+md5sums.txt
+*.gz
+*.zip
+*.tmp
+
 # Unit test / coverage reports
 .tox/
 .coverage

README.md

@@ -31,4 +31,5 @@ The **utils** folder contains various helpful tools.
 
 ## View Testing Reports
 [![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)
-[![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)
+[![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)
+[![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

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,36 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath(".."))
+
+project = 'TF2.4 IVIM MRI Code Collection'
+copyright = '2024, OSIPI'
+author = 'OSIPI team'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["sphinx.ext.todo", "sphinx.ext.viewcode", "sphinx.ext.autodoc"]
+
+templates_path = ['_templates']
+exclude_patterns = ['Thumbs.db', '.DS_Store']
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+html_show_sphinx = False
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+html_show_copyright = False
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']

docs/figures.rst

@@ -0,0 +1,45 @@
+Algorithm Analysis Figures
+===========
+
+.. raw:: html
+
+   <!DOCTYPE html>
+   <html lang="en">
+   <head>
+       <meta charset="UTF-8">
+       <meta name="viewport" content="width=device-width, initial-scale=1.0">
+       <title>Algorithm Analysis Figures</title>
+       <style>
+ 
+           embed {
+               width: 90%;
+               margin-bottom: 4rem;
+               height: 100vh;
+           }
+       </style>
+   </head>
+   <body>
+        <h4>Diffusion grid for limited algorithms:</h4>
+       <embed src="_static/D_limited.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+       <h4>Diffusion grid for all algorithms:</h4>
+       <embed src="_static/D.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+
+       <h4>Perfusion grid for limited algorithms:</h4>
+       <embed src="_static/Dp_limited.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+       <h4>Perfusion grid for all algorithms:</h4>
+       <embed src="_static/Dp.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+
+       <h4>Perfusion fraction grid for limited algorithms:</h4>
+       <embed src="_static/f_limited.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+       <h4>Perfusion fraction grid for all algorithms:</h4>
+       <embed src="_static/f.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+
+      <h4>Fitted curves:</h4>
+       <embed src="_static/fitted_curves.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+      <h4>Curve plot:</h4>
+      <embed src="_static/curve_plot.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+      <h4>Algorithm Fitting duration:</h4>
+      <embed src="_static/durations.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+
+   </body>
+   </html>

docs/index.rst

@@ -0,0 +1,19 @@
+.. TF2.4 IVIM MRI Code Collection documentation master file, created by
+   sphinx-quickstart on Wed Mar  6 00:06:13 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to TF2.4 IVIM MRI Code Collection's documentation!
+==========================================================
+
+.. toctree::
+   :maxdepth: 4
+   :caption: Contents:
+
+   figures
+   modules
+
+Indices and tables
+==================
+
+* :ref:`modindex`

phantoms/MR_XCAT_qMRI/README.md

@@ -1 +1,61 @@
-# MR_XCAT_qMRI
+# 4D IVIM Phantom Generator
+
+A command-line tool for generating a 4D IVIM (Intravoxel Incoherent Motion) phantom as a NIfTI file.
+
+## Usage
+
+```sh
+python sim_vim_sig.py  [-h] [-b BVALUE [BVALUE ...] | -f FILE] [-n NOISE] [-m] [-i]
+```
+
+## Arguments
+
+- `-b`, `--bvalue` : B values (list of numbers)
+- `-f`, `--bvalues-file` : JSON file containing the B values (default: b_values.json)
+- `-n`, `--noise` : Noise level (default: 0.0005)
+- `-m`, `--motion` : Enable motion flag (default: False)
+- `-i`, `--interleaved` : Enable interleaved flag (default: False)
+
+**Note:** Either provide `--bvalue` or `--bvalues-file`, not both.
+
+If neither `--bvalues-file` nor `--bvalue` is provided, the script will use the default `b_values.json` file.
+
+## Customizing B Values
+
+You can customize the B values by editing the `b_values.json` file. Here's an example of the default format:
+
+```json
+{
+    "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],
+    "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],
+    "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],
+    "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],
+    "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]
+}
+```
+
+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`):
+
+The default `generic_<custom_name>.json` file can be found in the following location:
+
+```
+TF2.4_IVIM-MRI_CodeCollection/tests/IVIMmodels/unit_tests
+```
+
+## Running the Script
+
+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`:
+
+```sh
+export PYTHONPATH=$PYTHONPATH:~/TF2.4_IVIM-MRI_CodeCollection
+```
+
+Replace `~/TF2.4_IVIM-MRI_CodeCollection` with the actual path to the directory containing the script.
+
+## Example
+
+```sh
+python sim_ivim_sig.py -n 0.0001 -m
+```
+
+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.

phantoms/MR_XCAT_qMRI/b_values.json

@@ -0,0 +1,7 @@
+{
+    "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],
+    "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],
+    "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],
+    "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],
+    "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]
+}