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 here.
Installation
Dependencies
Mac OS X
MacPorts
Install the FFTW3 and Python libraries. For Python 2.7, run
sudo port selfupdate sudo port install fftw-3 py27-numpy py27-scipy py27-pyfftw pip sudo easy_install pip sudo pip install odtbrain
Homebrew
Install the FFTW3 and Python libraries. For Python 2.7, 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 the Anaconda version matching your architecture (32-bit or 64-bit).
Install PyFFTW using the corresponding installer at PyPI.
Finally:
pip install odtbrain
Debian/Ubuntu
Install the following packages:
for Python 2.7:
sudo apt-get install libfftw3-3 libfftw3-dev python-cffi python-numpy python-pip python-scipy`
for Python 3.4:
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 either python-fftw3, python3-fftw3 (old) or python-pyfftw, python3-pyfftw (new). 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
Known Problems
For older versions of Ubuntu, the C foreign function interface``python-cffi`` is not available. Install the following packages
sudo apt-get install python-dev libffi-dev
and install cffi and numpy > 1.7.0 via pip, e.g.
pip install cffi pip install numpy==1.7.0
Testing
Note: The tests may fail for some Python installations. Please check the algorithms by running the examples or update your distribution to the latest version.
After cloning into odtbrain, create a virtual environment
virtualenv --system-site-packages ve source ve/bin/activate
Install all dependencies
python setup.py develop
Running an example
python examples/backprop_from_fdtd_2d.py
Running tests
python setup.py test
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.