Metadata-Version: 1.1
Name: odtbrain
Version: 0.1.7
Summary: Algorithms for diffraction tomography
Home-page: http://RI-imaging.github.io/ODTbrain/
Author: Paul Müller
Author-email: dev@craban.de
License: BSD (3 clause)
Description-Content-Type: UNKNOWN
Description: ODTbrain
        ========
        
        |PyPI Version| |Build Status| |Coverage Status| |Docs passing|
        
        
        **ODTbrain** provides image reconstruction algorithms for **O**\ ptical **D**\ iffraction **T**\ omography with a **B**\ orn and **R**\ ytov
        **A**\ pproximation-based **I**\ nversion to compute the refractive index (**n**\ ) in 2D and in 3D.
        
        
        Documentation
        -------------
        
        The documentation, including the reference and examples, is available on `readthedocs.io <https://odtbrain.readthedocs.io/en/stable/>`__.
        
        
        Installation
        ------------
        
        Dependencies
        ~~~~~~~~~~~~
        
        - Python 2.7 or Python 3.x
        - The FFTW3 library
        - These Python packages: 
        
          - `PyFFTW <https://github.com/hgomersall/pyFFTW>`__ (not `PyFFTW3`)
          - `numpy <https://github.com/numpy/numpy>`__
          - `scipy <https://github.com/scipy/scipy>`__
          - `unwrap <https://github.com/geggo/phase-unwrap>`__
        
        
        Mac OS X
        ~~~~~~~~
        
        `MacPorts <https://www.macports.org/>`__
        ________________________________________
        
        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 <http://brew.sh/>`__
        ______________________________
        
        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 <http://continuum.io/downloads#all>`__ version matching your architecture (32-bit or 64-bit).
        - Install `PyFFTW` using the corresponding `installer at PyPI <https://pypi.python.org/pypi/pyFFTW>`__.
        - 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
        
            
        
        .. |PyPI Version| image:: http://img.shields.io/pypi/v/odtbrain.svg
           :target: https://pypi.python.org/pypi/odtbrain
        .. |Build Status| image:: http://img.shields.io/travis/RI-imaging/ODTbrain.svg
           :target: https://travis-ci.org/RI-imaging/ODTbrain
        .. |Coverage Status| image:: https://img.shields.io/coveralls/RI-imaging/ODTbrain.svg
           :target: https://coveralls.io/r/RI-imaging/ODTbrain
        .. |Docs passing| image:: https://media.readthedocs.org/static/projects/badges/passing.svg
           :target: https://readthedocs.org/projects/odtbrain/builds/
            
        
Keywords: odt,opt,diffraction,born,rytov,radon,backprojection,backpropagation,inverse problem,Fourier diffraction theorem,Fourier slice theorem
Platform: ALL
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Intended Audience :: Science/Research
