Algorithms for diffraction tomography
Project description
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)
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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