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Python library for diffraction tomography with the Born and Rytov approximations
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README.rst

ODTbrain

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ODTbrain provides image reconstruction algorithms for Optical Diffraction Tomography with a Born and Rytov Approximation-based Inversion to compute the refractive index (n) in 2D and in 3D.

Documentation

The documentation, including the reference and examples, is available at odtbrain.readthedocs.io.

Installation

Dependencies

Mac OS X

MacPorts

Install the FFTW3 and Python libraries. For Python 3.6, run

sudo port selfupdate
sudo port install fftw-3 py36-numpy py36-scipy py36-pyfftw pip
sudo easy_install pip
sudo pip install odtbrain

Homebrew

Install the FFTW3 and Python libraries. For Python 3.6, run

sudo brew tap homebrew/python
sudo brew update && brew upgrade
sudo brew install python --framework
sudo brew install fftw numpy scipy
sudo easy_install pip
sudo pip install odtbrain

Windows

  • Install Anaconda with Python3 for your architecture (32-bit or 64-bit).

  • Run:

    pip install odtbrain
    

Debian/Ubuntu

Install the following packages:

  • Packages from the repository:

    sudo apt-get install libfftw3-3 libfftw3-dev python3-cffi python3-numpy python3-pip python3-scipy``
    
  • Install the PyFFTW package. Depending on your distribution, the package name is python3-fftw3 (old), python3-pyfftw (new), or non-existent. Attention: The package python-fftw provides a different FFTW library that is not used by ODTbrain. Alternatively, install from PyPI:

    pip install pyfftw
    
  • Finally:

    pip install odtbrain
    

Testing

After cloning into odtbrain, create a virtual environment

virtualenv --system-site-packages env
source env/bin/activate

Install all dependencies

pip install -e .

Running an example

python examples/backprop_from_fdtd_2d.py

Running tests

python setup.py test
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