bump to 0.2.0 (#101)

.pre-commit-config.yaml

@@ -14,6 +14,6 @@ repos:
     hooks:
       - id: black
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.961
+    rev: v0.971
     hooks:
       - id: mypy

CITATION.cff

@@ -4,10 +4,13 @@ authors:
   - family-names: Karkalousos
     given-names: Dimitrios
     orcid: https://orcid.org/0000-0001-5983-0322
+ - family-names: Zhang
+    given-names: Chaoping
+    orcid: https://orcid.org/0000-0002-6004-983X
   - family-names: Caan
     given-names: Matthan
     orcid: https://orcid.org/0000-0002-5162-8880
 title: "MRI Data Consistency"
 url: "https://github.com/wdika/mridc"
-version: 0.1.1
-date-released: 2022-25-05
+version: 0.2.0
+date-released: 2022-12-09

Dockerfile

@@ -29,7 +29,7 @@ COPY . .
 
 # start building the final container
 FROM mridc-deps as mridc
-ARG MRIDC_VERSION=0.1.1
+ARG MRIDC_VERSION=0.2.0
 
 # Check that MRIDC_VERSION is set. Build will fail without this. Expose MRIDC and base container
 # version information as runtime environment variable for introspection purposes

README.md

@@ -1,8 +1,8 @@
 # Data Consistency for Magnetic Resonance Imaging
 
 [![CodeQL](https://github.com/wdika/mridc/actions/workflows/codeql-analysis.yml/badge.svg)](https://github.com/wdika/mridc/actions/workflows/codeql-analysis.yml)
-[![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)
+[![Tox](https://github.com/wdika/mridc/actions/workflows/tox.yml/badge.svg)](https://github.com/wdika/mridc/actions/workflows/tox.yml)
 <a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg"></a>
 
 ---
@@ -12,6 +12,7 @@
 is provided for MRI data analysis. Primarily it focuses on the following tasks:**
 
 ### **Reconstruction**:
+The following models are implemented for accelerated MRI reconstruction:
 1.[Cascades of Independently Recurrent Inference Machines (CIRIM)](https://iopscience.iop.org/article/10.1088/1361-6560/ac6cc2),
 2.[Compressed Sensing (CS)](https://ieeexplore.ieee.org/document/4472246),
 3.[Convolutional Recurrent Neural Networks (CRNN)](https://ieeexplore.ieee.org/document/8425639),
@@ -30,17 +31,22 @@ is provided for MRI data analysis. Primarily it focuses on the following tasks:*
 16.[XPDNet](https://arxiv.org/abs/2010.07290),
 17.and Zero-Filled reconstruction (ZF).
 
+### **Quantitative Imaging**:
+The following models are implemented for quantitative imaging:
+1.[quantitative Cascades of Independently Recurrent Inference Machines (qCIRIM)](https://iopscience.iop.org/article/10.1088/1361-6560/ac6cc2),
+2.[quantitative End-to-End Variational Network (qE2EVN)](https://link.springer.com/chapter/10.1007/978-3-030-59713-9_7),
+3.[quantitative Independently Recurrent Inference Machines (qIRIM)](http://arxiv.org/abs/2012.07819),
+4.[quantitative Recurrent Inference Machines (qRIM)](https://www.sciencedirect.com/science/article/abs/pii/S1361841518306078?via%3Dihub).
+
+_Note: Currently only the above models are implemented. More models can be added by extending the reconstruction models
+for quantitative imaging. If you wish to extend the toolbox, please open an issue._
+
 ### **Segmentation**:
 _Coming soon..._
 
-### **Acknowledgements**
-
-MRIDC is based on the [NeMo](https://github.com/NVIDIA/NeMo) framework, using PyTorch Lightning for feasible
-high-performance multi-GPU/multi-node mixed-precision training.
+## Usage
 
-For the reconstruction methods:
-- the implementations of 6 and 14 are thanks to and based on the [fastMRI repo](https://github.com/facebookresearch/fastMRI).
-- The implementations of 7, 9, 10, 11, 13, and 16 are thanks to and based on the [DIRECT repo](https://github.com/NKI-AI/direct).
+Check the [projects](https://github.com/wdika/mridc/blob/main/projects/README.md) page for more information of how to use **mridc**.
 
 ## Installation
 
@@ -66,17 +72,6 @@ cd mridc
 ./reinstall.sh
 ```
 
-## Usage
-
-Check the [projects](https://github.com/wdika/mridc/blob/main/projects/README.md) page for more information of how to use **mridc**.
-
-### Datasets
-
-Recommended public datasets to use with this repo:
-
-- [fastMRI](http://arxiv.org/abs/1811.08839),
-- [Fully Sampled Knees](http://old.mridata.org/fullysampled/knees/).
-
 ## API Documentation
 
 [![Documentation Status](https://readthedocs.org/projects/mridc/badge/?version=latest)](https://mridc.readthedocs.io/en/latest/?badge=latest)
@@ -87,15 +82,24 @@ Access the API Documentation [here](https://mridc.readthedocs.io/en/latest/modul
 
 [![License: Apache 2.0](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 
+## Acknowledgements
+
+MRIDC is based on the [NeMo](https://github.com/NVIDIA/NeMo) framework, using PyTorch Lightning for feasible
+high-performance multi-GPU/multi-node mixed-precision training.
+
+For the reconstruction methods:
+- the implementations of 6 and 14 are thanks to and based on the [fastMRI repo](https://github.com/facebookresearch/fastMRI).
+- The implementations of 7, 9, 10, 11, 13, and 16 are thanks to and based on the [DIRECT repo](https://github.com/NKI-AI/direct).
+
 ## Citation
 
 Please cite MRIDC using the "_Cite this repository_" button or as
 
 ```BibTeX
 @misc{mridc,
-    author = {Karkalousos, Dimitrios and Caan, Matthan},
+    author = {Karkalousos Dimitrios, Zhang Chaoping, and Caan Matthan},
     title = {MRIDC: Data Consistency for Magnetic Resonance Imaging},
-    year = {2021},
+    year = {2022},
     url = {https://github.com/wdika/mridc},
 }
 ```
@@ -106,3 +110,5 @@ The following papers use the MRIDC repo:
 
 [1] [Karkalousos, D. et al. (2021) ‘Assessment of Data Consistency through Cascades of Independently Recurrent
 Inference Machines for fast and robust accelerated MRI reconstruction’](https://iopscience.iop.org/article/10.1088/1361-6560/ac6cc2)
+
+[2] Zhang, C. et al. (2022) 'A unified model for reconstruction and R2* mapping of accelerated 7T data using the quantitative Recurrent Inference Machine'

codecov.yml

@@ -13,6 +13,12 @@ coverage:
 # --------------
 # which folders/files to ignore
 ignore:
+  - mridc/launch.py
+  - mridc/core/utils/*
+  - mridc/utils/arguments.py
+  - mridc/utils/distributed.py
+  - mridc/utils/export_utils.py
+  - mridc/utils/decorators/*
   - projects/*
   - setup.py
 

docs/source/modules.rst

@@ -0,0 +1,7 @@
+mridc
+=====
+
+.. toctree::
+   :maxdepth: 4
+
+   mridc

docs/source/mridc.collections.common.callbacks.rst

@@ -0,0 +1,21 @@
+mridc.collections.common.callbacks package
+==========================================
+
+Submodules
+----------
+
+mridc.collections.common.callbacks.callbacks module
+---------------------------------------------------
+
+.. automodule:: mridc.collections.common.callbacks.callbacks
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mridc.collections.common.callbacks
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/mridc.collections.common.data.rst

@@ -0,0 +1,21 @@
+mridc.collections.common.data package
+=====================================
+
+Submodules
+----------
+
+mridc.collections.common.data.dataset module
+--------------------------------------------
+
+.. automodule:: mridc.collections.common.data.dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mridc.collections.common.data
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/mridc.collections.common.losses.rst

@@ -0,0 +1,29 @@
+mridc.collections.common.losses package
+=======================================
+
+Submodules
+----------
+
+mridc.collections.common.losses.aggregator module
+-------------------------------------------------
+
+.. automodule:: mridc.collections.common.losses.aggregator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mridc.collections.common.losses.ssim module
+-------------------------------------------
+
+.. automodule:: mridc.collections.common.losses.ssim
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mridc.collections.common.losses
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/mridc.collections.common.metrics.rst

@@ -0,0 +1,21 @@
+mridc.collections.common.metrics package
+========================================
+
+Submodules
+----------
+
+mridc.collections.common.metrics.global\_average\_loss\_metric module
+---------------------------------------------------------------------
+
+.. automodule:: mridc.collections.common.metrics.global_average_loss_metric
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mridc.collections.common.metrics
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/mridc.collections.common.parts.rst

@@ -0,0 +1,61 @@
+mridc.collections.common.parts package
+======================================
+
+Submodules
+----------
+
+mridc.collections.common.parts.fft module
+-----------------------------------------
+
+.. automodule:: mridc.collections.common.parts.fft
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mridc.collections.common.parts.patch\_utils module
+--------------------------------------------------
+
+.. automodule:: mridc.collections.common.parts.patch_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mridc.collections.common.parts.ptl\_overrides module
+----------------------------------------------------
+
+.. automodule:: mridc.collections.common.parts.ptl_overrides
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mridc.collections.common.parts.rnn\_utils module
+------------------------------------------------
+
+.. automodule:: mridc.collections.common.parts.rnn_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mridc.collections.common.parts.training\_utils module
+-----------------------------------------------------
+
+.. automodule:: mridc.collections.common.parts.training_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mridc.collections.common.parts.utils module
+-------------------------------------------
+
+.. automodule:: mridc.collections.common.parts.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mridc.collections.common.parts
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/mridc.collections.common.rst

@@ -0,0 +1,22 @@
+mridc.collections.common package
+================================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   mridc.collections.common.callbacks
+   mridc.collections.common.data
+   mridc.collections.common.losses
+   mridc.collections.common.metrics
+   mridc.collections.common.parts
+
+Module contents
+---------------
+
+.. automodule:: mridc.collections.common
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/mridc.collections.quantitative.data.rst

@@ -0,0 +1,21 @@
+mridc.collections.quantitative.data package
+===========================================
+
+Submodules
+----------
+
+mridc.collections.quantitative.data.qmri\_data module
+-----------------------------------------------------
+
+.. automodule:: mridc.collections.quantitative.data.qmri_data
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mridc.collections.quantitative.data
+   :members:
+   :undoc-members:
+   :show-inheritance: