bilateralfilter 0.0.15
Trainable Bilateral Filter Layer (PyTorch)

Trainable Bilateral Filter Layer (PyTorch)
==========================================

This repository contains our GPU-accelerated trainable bilateral filter
layer (three spatial and one range filter dimension) that can be
directly included in any Pytorch graph, just as any conventional layer
(FCL, CNN, …). By calculating the analytical derivative of the bilateral
filter with respect to its parameters and its input, the (so far)
hyperparameters can be automatically optimized via backpropagation for a
calculated loss.

Our corresponding paper `Ultra low-parameter denoising: Trainable
bilateral filter layers in computed
tomography <https://doi.org/10.1002/mp.15718>`__ can be found on
`Medical Physics <https://doi.org/10.1002/mp.15718>`__ (open access) and
`arXiv <https://arxiv.org/pdf/2201.10345.pdf>`__ (pre-print).

Citation:
~~~~~~~~~

If you find our code useful, please cite our work

::

   @article{wagner2022ultra,
     title={Ultra low-parameter denoising: Trainable bilateral filter layers in computed tomography},
     author={Wagner, Fabian and Thies, Mareike and Gu, Mingxuan and Huang, Yixing and Pechmann, Sabrina and Patwari, Mayank and Ploner, Stefan and Aust, Oliver and Uderhardt, Stefan and Schett, Georg and Christiansen, Silke and Maier, Andreas},
     journal={Medical Physics},
     year={2022},
     doi={https://doi.org/10.1002/mp.15718}
   }

Implementation:
~~~~~~~~~~~~~~~

The general structure of the implementation follows the PyTorch
documentation for `creating custom C++ and CUDA
extensions <https://pytorch.org/tutorials/advanced/cpp_extension.html>`__.
The forward pass implementation of the layer is based on code from the
`Project MONAI <https://docs.monai.io/en/latest/networks.html>`__
framework, originally published under the `Apache License, Version
2.0 <https://www.apache.org/licenses/LICENSE-2.0>`__. The correct
implementation of the analytical forward and backward pass can be
verified by running the gradcheck.py script, comparing numerical
gradients with the derived analytical gradient using the PyTorch
built-in `gradcheck
function <https://pytorch.org/docs/stable/generated/torch.autograd.gradcheck.html>`__.

Setup:
~~~~~~

The C++/CUDA implemented forward and backward functions are compiled via
the setup.py script using setuptools:

1. Create and activate a python environment (python>=3.7).
2. Install `Torch <https://pytorch.org/get-started/locally/>`__ (tested versions: 1.7.1, 1.9.0).
3. Install the bilateral filter layer via pip:

.. code:: bash

   pip install bilateralfilter

In case you encounter problems with 3. install the layer directly from our
`GitHub repository <https://github.com/faebstn96/trainable-bilateral-filter-source>`__:

3. Download the repository.
4. Navigate into the extracted repo.
5. Compile/install the bilateral filter layer by calling

.. code:: bash

   python setup.py install

Example scripts:
~~~~~~~~~~~~~~~~
-  Can be found in our `GitHub repository <https://github.com/faebstn96/trainable-bilateral-filter-source>`__
-  Try out the forward pass by running the example_filter.py (requires
   `Matplotlib <https://matplotlib.org/stable/users/installing.html>`__
   and
   `scikit-image <https://scikit-image.org/docs/stable/install.html>`__).
-  Run the gradcheck.py script to verify the correct gradient
   implementation.
-  Run example_optimization.py to optimize the parameters of a bilateral
   filter layer to automatically denoise an image.

Optimized bilateral filter prediction:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

|image0|

Troubleshooting
~~~~~~~~~~~~~~~

nvcc-related errors:
^^^^^^^^^^^^^^^^^^^^

1. Compiling the filter layers requires the Nvidia CUDA toolkit. Check
   its version

   .. code:: bash

      nvcc --version

   or install it via, e.g.,

   .. code:: bash

      sudo apt update
      sudo apt install nvidia-cuda-toolkit

2. The NVIDIA CUDA toolkit 11.6 made some problems on a Windows machine
   in combination with pybind. Downgrading the toolkit to version 11.3
   fixed the problem (see
   `this <https://discuss.pytorch.org/t/cuda-11-6-extension-problem/145830>`__
   discussion). #### Windows-related problems: Make sure the
   `cl.exe <https://docs.microsoft.com/en-us/cpp/build/reference/compiler-options?view=msvc-170>`__
   environment variable is correctly set.

.. |image0| image:: out/example_optimization.png