marysalvana / cpabdiffeo

CPAB Transformations: finite-dimensional spaces of simple, fast, and highly-expressive diffeomorphisms derived from parametric, continuously-defined, velocity fields. Based on [Freifeld et al., ICCV '15] and [Freifeld et al. TPAMI '17]

cpabDiffeo

CPAB transformations are simple, fast, and highly-expressive finite-dimensional diffeomorphisms. They are derived from parametric, continuously-defined, velocity fields.

This implementation is based on our Journal paper, [Freifeld et al., TPAMI '17] and its earlier conference version [Freifeld et al., ICCV '15].

The current implementation is written in Python+CUDA. We will soon release a Tensorflow implementation. We plan to release a Matlab version as well. You may also want to try a partial implementation in Julia written by my student, Angel Yu. Note, however, that Angel's CPU-based implementation has fewer options than the one that is (and will be) maintained here (e.g, his code is only in 1D or 2D, has less options for the prior, doesn't have image/signal registration, etc.)

Author of this software

Oren Freifeld (email: [email protected])

License

This software is released under the MIT License (included with the software). Note, however, if you use this code (and/or the results of running it) to support any form of publication (e.g.,a book, a journal paper, a conference paper, a patent application, etc.), then we ask you to cite the following papers:

@article{freifeld2017transformations,
  title={Transformations Based on Continuous Piecewise-Affine Velocity Fields},
  author={Freifeld, Oren and Hauberg, Soren and Batmanghelich, Kayhan and Fisher, John W},
  journal={IEEE Transactions on Pattern Analysis and Machine Intelligence},
  year={2017},
  publisher={IEEE}
}
@inproceedings{freifeld2015transform,
    title = {Highly-Expressive Spaces of Well-Behaved Transformations: Keeping It Simple},
    author = {Oren Freifeld and S{\o}ren Hauberg and Kayhan Batmanghelich and John W. Fisher III},
    booktitle = {International Conference on Computer Vision (ICCV)},
    address = {Santiago, Chile},
    month = Dec,
    year = {2015}
}

Versions

• 03/28/2016, Version 0.0.5 -- Basic support for dim > 3; monotonic regression (in 1D)
• 03/24/2016, Version 0.0.4 -- Simple Landmark-based inference in 2D.
• 03/21/2016, Version 0.0.3 -- Synthesis in 3D.
• 03/16/2016, Version 0.0.2 -- 1) synthesis in 1D; 2) simple 2D image registration (intensity-based Gaussian likelihood + MCMC inference)
• 03/15/2016, Version 0.0.1 -- First release (synthsis in 2D).

Coming soon:

More options for inference, more options for the prior, handling landmarks and registration in all dimensions, more applications, etc.

Requirements

• generic python packages: numpy; scipy; matplotlib
• opencv with python's bindings
• CUDA
• pycuda
• My of and pyimg packages:

# Using https:
git clone https://github.com/freifeld/of
git clone https://github.com/freifeld/pyimg
# Using ssh:
git clone [email protected]:freifeld/of.git
git clone [email protected]:freifeld/pyimg.git

OS

The code was tested on Linux and Windows. It should work on Mac, but I didn't get a chance to test it.

Installation

(todo: add instructions for Windows users) First, get this repository:

# Using https:
git clone https://github.com/freifeld/cpabDiffeo.git
# Using ssh:
git clone [email protected]:freifeld/cpabDiffeo.git

Second, assuming you cloned this repository as well the of and pyimg repositories in your home directory (marked as ~), you will need to adjust your PYTHONPATH accordingly:

# To enable importing of both the "of" and "pyimg" packages which are in ~
export PYTHONPATH=$PYTHONPATH:$~    
# To enable  improting of the "cpab" package which is inside ~/cpabDiffeo
export PYTHONPATH=$PYTHONPATH:$~/cpabDiffeo/  

How to run the code

We provide quick demos that show synthesis in 1d, 2d, or 3d and have several possible configurations that the user can modify. To run the demos, first neviagate into the cpab directory. Then:

python cpa1d/TransformWrapper_example.py  # 1d 
python cpa2d/TransformWrapper_example.py  # 2d 
python cpa3d/TransformWrapper_example.py  # 3d 

The example function in each of these scripts takes several input arguments whose values you can change. You can do it either directly from python, as is done in the commented-out examples at the end of each of these scripts, or (in the 2D case) from the terminal using the following script:

python cpa2d/TransformWrapper_example_cmdline.py   # This will just use default parameters

Details about how to pass user-defined arguments using the terminal can be found here.

To run an example of landmark-based inference:

 python cpa2d/apps/landmarks/inference_example_LFW.py

To visualize the inference results:

python cpa2d/apps/landmarks/visualize_results_LFW.py

TODO: add instructions for how to run the example for image registration.

To run a monotonic-regression example:

python cpa1d/inference/transformation/MonotonicRegression_example.py