fixed docs

.readthedocs.yaml

@@ -0,0 +1,27 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+    # You can also specify other tool versions:
+    # nodejs: "16"
+    # rust: "1.55"
+    # golang: "1.17"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   builder: html
+   configuration: docs/source/conf.py
+   fail_on_warning: true
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: requirements/requirements.txt

README.md

@@ -14,7 +14,7 @@
 **MRIDC is a toolbox for applying AI methods on MR imaging. A collection of tools for data consistency and data quality
 is provided for MRI data analysis. Primarily it focuses on the following tasks:**
 
-### **Reconstruction**: 
+### **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),
@@ -33,15 +33,15 @@ 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).
 
-### **Segmentation**: 
+### **Segmentation**:
 _Coming soon..._
 
-### **Acknowledgements** 
+### **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. 
+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: 
+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).
 
@@ -103,5 +103,5 @@ Please cite MRIDC using the "_Cite this repository_" button or as
 
 The following papers use the MRIDC repo:
 
-[1] [Karkalousos, D. et al. (2021) ‘Assessment of Data Consistency through Cascades of Independently Recurrent 
+[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)

docs/make.bat

@@ -10,8 +10,6 @@ if "%SPHINXBUILD%" == "" (
 set SOURCEDIR=source
 set BUILDDIR=build
 
-if "%1" == "" goto help
-
 %SPHINXBUILD% >NUL 2>NUL
 if errorlevel 9009 (
 	echo.
@@ -25,6 +23,8 @@ if errorlevel 9009 (
 	exit /b 1
 )
 
+if "%1" == "" goto help
+
 %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
 goto end
 

docs/source/conf.py

@@ -10,19 +10,23 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
+import os
+import sys
+
+from typing import List
+
+sys.path.insert(0, os.path.abspath("."))
+sys.path.insert(0, os.path.abspath("../.."))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'mridc'
-copyright = '2022, Dimitrios Karkalousos'
-author = 'Dimitrios Karkalousos'
+project = "mridc"
+copyright = "2022, Dimitrios Karkalousos"
+author = "Dimitrios Karkalousos"
 
 # The full version, including alpha/beta/rc tags
-release = 'v.0.0.1'
+release = "v.0.0.1"
 
 
 # -- General configuration ---------------------------------------------------
@@ -31,25 +35,28 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    "myst_parser",
+    "sphinx.ext.napoleon",
 ]
 
+
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
+exclude_patterns: List = []
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path: List = []

docs/source/index.rst

@@ -1,16 +1,16 @@
 .. mridc documentation master file, created by
-   sphinx-quickstart on Thu May  5 13:52:11 2022.
+   sphinx-quickstart on Mon May 23 12:30:03 2022.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to mridc's documentation!
-=================================
-
+MRI Data Consistency Documentation
+==================================
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
-
+   :caption: Getting started:
 
+.. include:: ../../README.md
+   :parser: myst_parser.sphinx_
 
 Indices and tables
 ==================

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 +1,53 @@
+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.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.reconstruction.data.rst

@@ -0,0 +1,29 @@
+mridc.collections.reconstruction.data package
+=============================================
+
+Submodules
+----------
+
+mridc.collections.reconstruction.data.mri\_data module
+------------------------------------------------------
+
+.. automodule:: mridc.collections.reconstruction.data.mri_data
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mridc.collections.reconstruction.data.subsample module
+------------------------------------------------------
+
+.. automodule:: mridc.collections.reconstruction.data.subsample
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mridc.collections.reconstruction.data
+   :members:
+   :undoc-members:
+   :show-inheritance: