Updates for release

.codecov.yml

@@ -0,0 +1,31 @@
+# For more configuration details:
+# https://docs.codecov.io/docs/codecov-yaml
+
+# Check if this file is valid by running in bash:
+# curl -X POST --data-binary @.codecov.yml https://codecov.io/validate
+
+# Coverage configuration
+# ----------------------
+coverage:
+  status:
+    patch: false
+
+  range: 70..90     # First number represents red, and second represents green
+  # (default is 70..100)
+  round: down       # up, down, or nearest
+  precision: 2      # Number of decimal places, between 0 and 5
+
+# Ignoring Paths
+# --------------
+# which folders/files to ignore
+ignore:
+  - scripts/*
+  - tools/*
+  - setup.py
+
+# Pull request comments:
+# ----------------------
+# Diff is the Coverage Diff of the pull request.
+# Files are the files impacted by the pull request
+comment:
+  layout: diff, files  # accepted in any order: reach, diff, flags, and/or files

.deepsource.toml

@@ -14,9 +14,9 @@ enabled = true
 name = "python"
 enabled = true
 
-  [analyzers.meta]
-  runtime_version = "3.x.x"
-  max_line_length = 119
+[analyzers.meta]
+runtime_version = "3.x.x"
+max_line_length = 119
 
 [[transformers]]
 name = "black"

.github/workflows/codecov.yml

@@ -0,0 +1,37 @@
+name: Upload report on Codecov
+
+on: [ push ]
+
+jobs:
+  run:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [ ubuntu-latest ]
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: '3.9'
+
+    steps:
+      - uses: actions/checkout@master
+
+      - name: Setup Python
+        uses: actions/setup-python@master
+        with:
+          python-version: 3.9
+
+      - name: Generate coverage report
+        run: |
+          pip install -r requirements.txt
+          pip install pytest-cov
+          pytest --cov=./ --cov-report=xml
+
+      - name: "Upload coverage to Codecov"
+        uses: codecov/codecov-action@v2
+        with:
+          fail_ci_if_error: true
+          flags: pytests # optional
+          name: codecov-umbrella # optional
+          verbose: true # optional (default = false)

.github/workflows/codeql-analysis.yml

@@ -37,34 +37,34 @@ jobs:
         # Learn more about CodeQL language support at https://git.io/codeql-language-support
 
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v2
+      - name: Checkout repository
+        uses: actions/checkout@v2
 
-    # Initializes the CodeQL tools for scanning.
-    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v1
-      with:
-        languages: ${{ matrix.language }}
-        # If you wish to specify custom queries, you can do so here or in a config file.
-        # By default, queries listed here will override any specified in a config file.
-        # Prefix the list here with "+" to use these queries and those in the config file.
-        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v1
+        with:
+          languages: ${{ matrix.language }}
+          # If you wish to specify custom queries, you can do so here or in a config file.
+          # By default, queries listed here will override any specified in a config file.
+          # Prefix the list here with "+" to use these queries and those in the config file.
+          # queries: ./path/to/local/query, your-org/your-repo/queries@main
 
-    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
-    # If this step fails, then you should remove it and run the build manually (see below)
-    - name: Autobuild
-      uses: github/codeql-action/autobuild@v1
+      # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+      # If this step fails, then you should remove it and run the build manually (see below)
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v1
 
-    # ℹ️ Command-line programs to run using the OS shell.
-    # 📚 https://git.io/JvXDl
+      # ℹ️ Command-line programs to run using the OS shell.
+      # 📚 https://git.io/JvXDl
 
-    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
-    #    and modify them (or add more) to build your code if your project
-    #    uses a compiled language
+      # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+      #    and modify them (or add more) to build your code if your project
+      #    uses a compiled language
 
-    #- run: |
-    #   make bootstrap
-    #   make release
+      #- run: |
+      #   make bootstrap
+      #   make release
 
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v1
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v1

README.md

@@ -1,20 +1,80 @@
-# Magnetic Resonance Imaging Data Consistency
+# Data Consistency for Magnetic Resonance Imaging
 
+[![Build Status](https://app.travis-ci.com/wdika/mridc.svg?branch=main)](https://app.travis-ci.com/wdika/mridc)
+[![CircleCI](https://circleci.com/gh/wdika/mridc/tree/main.svg?style=svg)](https://circleci.com/gh/wdika/mridc/tree/main)
+[![codecov](https://codecov.io/gh/wdika/mridc/branch/main/graph/badge.svg?token=KPPQ33DOTF)](https://codecov.io/gh/wdika/mridc)
+[![DeepSource](https://deepsource.io/gh/wdika/mridc.svg/?label=active+issues&show_trend=true&token=txj87v43GA6vhpbSwPEUTQtX)](https://deepsource.io/gh/wdika/mridc/?ref=repository-badge)
+[![DeepSource](https://deepsource.io/gh/wdika/mridc.svg/?label=resolved+issues&show_trend=true&token=txj87v43GA6vhpbSwPEUTQtX)](https://deepsource.io/gh/wdika/mridc/?ref=repository-badge)
 
+---
+
+**Data Consistency (DC) is crucial for generalization in multi-modal MRI data and robustness in detecting pathology.**
+
+This repo implements the following reconstruction methods:
+
+- Cascades of Independently Recurrent Inference Machines (CIRIM) [1],
+- Independently Recurrent Inference Machines (IRIM) [2, 3],
+- End-to-End Variational Network (E2EVN), [4, 5]
+- the UNet [5, 6],
+- Compressed Sensing (CS) [7], and
+- zero-filled reconstruction (ZF).
+
+The CIRIM, the RIM, and the E2EVN target unrolled optimization by gradient descent. Thus, DC is implicitly enforced.
+Through cascades DC can be explicitly enforced by a designed term [1, 4].
+
+## Usage
+
+Check on [scripts](scripts) how to train models and run a method for reconstruction.
+
+Check on [tools](tools) for preprocessing and evaluation tools.
+
+Recommended public datasets to use with this repo:
+
+- [fastMRI](https://fastmri.org/) [5].
+
+## Documentation
+
+[![Documentation Status](https://readthedocs.org/projects/mridc/badge/?version=latest)](https://mridc.readthedocs.io/en/latest/?badge=latest)
+
+Read the docs [here](https://mridc.readthedocs.io/en/latest/index.html)
 
 ## License
 
-This repo is released under the [Apache 2.0 License](LICENSE).
+[![License: Apache 2.0](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 
 ## Citation
 
-Check CITATION.cff file or cite this repository widget. Alternatively cite as
+Check CITATION.cff file or cite using the widget. Alternatively cite as
 
 ```BibTeX
-@misc{MRIDC,
-  author =       {Karkalousos, Dimitrios and Caan, Matthan},
-  title =        {MRI Data Consistency},
-  howpublished = {\url{https://github.com/wdika/mridc}},
-  year =         {2021}
+@misc{mridc,
+  author={Karkalousos, Dimitrios and Caan, Matthan},
+  title={MRIDC: Data Consistency for Magnetic Resonance Imaging},
+  year={2021},
+  url = {https://github.com/wdika/mridc},
 }
 ```
+
+## Bibliography
+
+[1] CIRIM
+
+[2] Lønning, K. et al. (2019) ‘Recurrent inference machines for reconstructing heterogeneous MRI data’, Medical Image
+Analysis, 53, pp. 64–78. doi: 10.1016/j.media.2019.01.005.
+
+[3] Karkalousos, D. et al. (2020) ‘Reconstructing unseen modalities and pathology with an efficient Recurrent Inference
+Machine’, pp. 1–31. Available at: http://arxiv.org/abs/2012.07819.
+
+[4] Sriram, A. et al. (2020) ‘End-to-End Variational Networks for Accelerated MRI Reconstruction’, Lecture Notes in
+Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics),
+12262 LNCS, pp. 64–73. doi: 10.1007/978-3-030-59713-9_7.
+
+[5] Zbontar, J. et al. (2018) ‘fastMRI: An Open Dataset and Benchmarks for Accelerated MRI’, arXiv, pp. 1–35. Available
+at: http://arxiv.org/abs/1811.08839.
+
+[6] Ronneberger, O., Fischer, P. and Brox, T. (2015) ‘U-Net: Convolutional Networks for Biomedical Image Segmentation’,
+in Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image
+Computing and Computer-Assisted Intervention, pp. 234–241. doi: 10.1007/978-3-319-24574-4_28.
+
+[7] Lustig, M. et al. (2008) ‘Compressed Sensing MRI’, IEEE Signal Processing Magazine, 25(2), pp. 72–82. doi:
+10.1109/MSP.2007.914728.

SECURITY.md

@@ -2,8 +2,8 @@
 
 ## Supported Versions
 
-Use this section to tell people about which versions of your project are
-currently being supported with security updates.
+Use this section to tell people about which versions of your project are currently being supported with security
+updates.
 
 | Version | Supported          |
 | ------- | ------------------ |
@@ -16,6 +16,5 @@ currently being supported with security updates.
 
 Use this section to tell people how to report a vulnerability.
 
-Tell them where to go, how often they can expect to get an update on a
-reported vulnerability, what to expect if the vulnerability is accepted or
-declined, etc.
+Tell them where to go, how often they can expect to get an update on a reported vulnerability, what to expect if the
+vulnerability is accepted or declined, etc.

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     = source
+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/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd