This is a pre-production deployment of Warehouse, however changes made here WILL affect the production instance of PyPI.
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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
Release History

Release History

0.1.5

This version

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Changelog content for this version goes here.

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0.1.4

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0.1.3

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0.1.2

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0.1.1

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0.1.0

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Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
odtbrain-0.1.5.tar.gz (268.2 kB) Copy SHA256 Checksum SHA256 Source Jul 12, 2016

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