odtbrain 0.2.2

Algorithms for diffraction tomography

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

• Python 3.4 or higher

• The FFTW3 library

• These Python packages:

  • PyFFTW (not PyFFTW3)

  • numpy

  • scikit-image

  • scipy

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