u-net_Segmentation/HighResnet

==========
highresnet
==========


.. image:: https://img.shields.io/pypi/v/highresnet.svg
        :target: https://pypi.python.org/pypi/highresnet

.. image:: https://img.shields.io/travis/fepegar/highresnet.svg
        :target: https://travis-ci.org/fepegar/highresnet

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3349989.svg
   :target: https://doi.org/10.5281/zenodo.3349989

.. image:: https://readthedocs.org/projects/highresnet/badge/?version=latest
        :target: https://highresnet.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status

.. image:: https://pyup.io/repos/github/fepegar/highresnet/shield.svg
     :target: https://pyup.io/repos/github/fepegar/highresnet/
     :alt: Updates

::

   $ NII_FILE=`download_oasis`
   $ deepgif $NII_FILE


.. image:: https://raw.githubusercontent.com/fepegar/highresnet/master/images/slicer_screenshot.png
     :alt: 3D Slicer screenshot

PyTorch implementation of HighRes3DNet from `Li et al. 2017,
*On the Compactness, Efficiency, and Representation of
3D Convolutional Networks: Brain Parcellation as a
Pretext Task* <https://arxiv.org/pdf/1707.01992.pdf>`_.

All the information about how the weights were ported from NiftyNet can be found
in `my submission to the MICCAI Educational Challenge
2019 <https://nbviewer.jupyter.org/github/fepegar/miccai-educational-challenge-2019/blob/master/Combining_the_power_of_PyTorch_and_NiftyNet.ipynb?flush_cache=true>`_.


Usage
-----

Command line interface
^^^^^^^^^^^^^^^^^^^^^^

.. code-block:: shell

   (deepgif) $ deepgif t1_mri.nii.gz
   Using cache found in /home/fernando/.cache/torch/hub/fepegar_highresnet_master
   100%|███████████████████████████████████████████| 36/36 [01:13<00:00,  2.05s/it]


`PyTorch Hub <https://pytorch.org/hub>`_
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

If you are using `pytorch>=1.1.0`, you can import the model
directly from this repository using
`PyTorch Hub <https://pytorch.org/hub>`_.

.. code-block:: python

   import torch
   repo = 'fepegar/highresnet'
   model_name = 'highres3dnet'
   print(torch.hub.help(repo, model_name))
   "HighRes3DNet by Li et al. 2017 for T1-MRI brain parcellation"
   "pretrained (bool): load parameters from pretrained model"
   model = torch.hub.load(repo, model_name, pretrained=True)
   
Installation
------------

1. Create a `conda <https://docs.conda.io/en/latest/>`_ environment (recommended)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. code-block:: shell

   ENVNAME="gifenv"  # for example
   conda create -n $ENVNAME python -y
   conda activate $ENVNAME

2. Install PyTorch and `highresnet`
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Within the `conda` environment:

.. code-block:: shell

   pip install light-the-torch  # to get the best PyTorch
   ltt install torch  # to get the best PyTorch
   pip install highresnet

Now you can do

.. code-block:: python

   from highresnet import HighRes3DNet
   model = HighRes3DNet(in_channels=1, out_channels=160)