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‎docs/source/api.rst‎

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API
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===
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.. autosummary::
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:toctree: generated
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.. toctree::
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:maxdepth: 4
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lumache
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pymic.io
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pymic.layer
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pymic.loss
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pymic.net
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pymic.net_run
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pymic.net_run_nll
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pymic.net_run_ssl
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pymic.net_run_wsl
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pymic.transform
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pymic.util

‎docs/source/conf.py‎

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# Configuration file for the Sphinx documentation builder.
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# -- 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 = 'PyMIC'
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copyright = '2021, HiLab'

‎docs/source/index.rst‎

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Welcome to PyMIC's documentation!
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===================================
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PyMIC is a pytorch-based toolkit for medical image computing with annotation-efficient deep learning.
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PyMIC is developed to support learning with imperfect labels, including semi-supervised and weakly supervised learning, and learning with noisy annotations.
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PyMIC is a pytorch-based toolkit for medical image computing with annotation-efficient
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deep learning. PyMIC is developed to support learning with imperfect labels, including
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semi-supervised and weakly supervised learning, and learning with noisy annotations.
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Check out the :doc:`usage` section for further information, including
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how to :ref:`installation` the project.
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Check out the :doc:`installation` section for install PyMIC, and go to the :doc:`usage`
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section for understanding modules for the segmentation pipeline designed in PyMIC.
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Please follow `PyMIC_examples <https://github.com/HiLab-git/PyMIC_examples/>`_
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to quickly start with using PyMIC.
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.. note::
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This project is under active development. It will be updated later.
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Contents
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--------
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.. toctree::
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:maxdepth: 2
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:caption: Getting Started
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installation
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usage
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api
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Citation
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--------
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If you use PyMIC for your research, please acknowledge it accordingly by citing our paper:
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`G. Wang, X. Luo, R. Gu, S. Yang, Y. Qu, S. Zhai, Q. Zhao, K. Li, S. Zhang. (2022).
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PyMIC: A deep learning toolkit for annotation-efficient medical image segmentation.
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arXiv, 2208.09350. <http://arxiv.org/abs/2208.09350>`_
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BibTeX entry:
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.. code-block:: none
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usage
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api
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@article{Wang2022pymic,
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author = {Guotai Wang and Xiangde Luo and Ran Gu and Shuojue Yang and Yijie Qu and Shuwei Zhai and Qianfei Zhao and Kang Li and Shaoting Zhang},
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title = {{PyMIC: A deep learning toolkit for annotation-efficient medical image segmentation}},
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year = {2022},
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url = {http://arxiv.org/abs/2208.09350},
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journal = {arXiv},
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volume = {2208.09350},
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pages = {1-10},
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}

‎docs/source/installation.rst‎

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Installation
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============
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Install PyMIC using pip (e.g., within a `Python virtual environment <https://www.geeksforgeeks.org/python-virtual-environment/>`_):
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.. code-block:: bash
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pip install PYMIC
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Alternatively, you can download or clone the code from `GitHub <https://github.com/HiLab-git/PyMIC>`_ and install PyMIC by
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.. code-block:: bash
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git clone https://github.com/HiLab-git/PyMIC
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cd PyMIC
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python setup.py install
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PyMIC requires Python 3.6 (or higher) and depends on the following packages:
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- `pandas <https://pandas.pydata.org/>`_
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- `h5py <https://www.h5py.org/>`_
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- `NumPy <https://numpy.org/>`_
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- `scikit-image <https://scikit-image.org/>`_
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- `SciPy <https://www.scipy.org/>`_
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- `SimpleITK <https://simpleitk.org/>`_

‎docs/source/modules.rst‎

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pymic
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=====
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.. toctree::
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:maxdepth: 4
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pymic

‎docs/source/pymic.io.rst‎

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pymic.io package
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================
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Submodules
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----------
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pymic.io.h5\_dataset module
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---------------------------
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.. automodule:: pymic.io.h5_dataset
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:members:
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:undoc-members:
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:show-inheritance:
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pymic.io.image\_read\_write module
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----------------------------------
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.. automodule:: pymic.io.image_read_write
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:members:
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:undoc-members:
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:show-inheritance:
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pymic.io.nifty\_dataset module
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------------------------------
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.. automodule:: pymic.io.nifty_dataset
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:members:
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:undoc-members:
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:show-inheritance:
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Module contents
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---------------
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.. automodule:: pymic.io
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/source/pymic.layer.rst‎

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pymic.layer package
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===================
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Submodules
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----------
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pymic.layer.activation module
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-----------------------------
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.. automodule:: pymic.layer.activation
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:members:
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:undoc-members:
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:show-inheritance:
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pymic.layer.convolution module
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------------------------------
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.. automodule:: pymic.layer.convolution
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:members:
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:undoc-members:
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:show-inheritance:
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pymic.layer.deconvolution module
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--------------------------------
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.. automodule:: pymic.layer.deconvolution
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:members:
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:undoc-members:
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:show-inheritance:
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pymic.layer.space2channel module
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--------------------------------
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.. automodule:: pymic.layer.space2channel
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:members:
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:undoc-members:
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:show-inheritance:
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Module contents
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---------------
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.. automodule:: pymic.layer
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/source/pymic.loss.cls.rst‎

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pymic.loss.cls package
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======================
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Submodules
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----------
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pymic.loss.cls.basic module
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------------------------
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.. automodule:: pymic.loss.cls.basic
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:members:
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:undoc-members:
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:show-inheritance:
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pymic.loss.cls.util module
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--------------------------
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.. automodule:: pymic.loss.cls.util
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:members:
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:undoc-members:
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:show-inheritance:
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Module contents
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---------------
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.. automodule:: pymic.loss.cls
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:show-inheritance:

‎docs/source/pymic.loss.rst‎

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pymic.loss package
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==================
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Subpackages
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-----------
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.. toctree::
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:maxdepth: 4
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pymic.loss.cls
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pymic.loss.seg
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Submodules
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----------
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pymic.loss.loss\_dict\_cls module
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---------------------------------
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.. automodule:: pymic.loss.loss_dict_cls
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:undoc-members:
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pymic.loss.loss\_dict\_seg module
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---------------------------------
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.. automodule:: pymic.loss.loss_dict_seg
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:members:
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:undoc-members:
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:show-inheritance:
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Module contents
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---------------
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.. automodule:: pymic.loss
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/source/pymic.loss.seg.rst‎

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pymic.loss.seg package
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======================
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----------
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pymic.loss.seg.abstract module
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------------------------
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.. automodule:: pymic.loss.seg.abstract
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:members:
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:show-inheritance:
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pymic.loss.seg.ce module
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------------------------
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.. automodule:: pymic.loss.seg.ce
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:members:
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pymic.loss.seg.combined module
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------------------------------
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.. automodule:: pymic.loss.seg.combined
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:members:
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:undoc-members:
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:show-inheritance:
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pymic.loss.seg.deep\_sup module
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-------------------------------
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.. automodule:: pymic.loss.seg.deep_sup
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:members:
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:undoc-members:
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:show-inheritance:
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pymic.loss.seg.dice module
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--------------------------
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.. automodule:: pymic.loss.seg.dice
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:members:
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:undoc-members:
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:show-inheritance:
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pymic.loss.seg.exp\_log module
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------------------------------
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.. automodule:: pymic.loss.seg.exp_log
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:members:
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:undoc-members:
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:show-inheritance:
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pymic.loss.seg.gatedcrf module
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------------------------------
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.. automodule:: pymic.loss.seg.gatedcrf
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:undoc-members:
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pymic.loss.seg.mse module
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-------------------------
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pymic.loss.seg.mumford\_shah module
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-----------------------------------
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:undoc-members:
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pymic.loss.seg.slsr module
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--------------------------
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pymic.loss.seg.ssl module
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-------------------------
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pymic.loss.seg.util module
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--------------------------
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.. automodule:: pymic.loss.seg.util
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Module contents
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---------------
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.. automodule:: pymic.loss.seg
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:show-inheritance:

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