Metadata-Version: 2.1
Name: pyphase
Version: 1.0.1
Summary: An open source phase retrieval code
Home-page: https://gitlab.in2p3.fr/mlanger/pyPhase/
Author: Max Langer
Author-email: max.langer@creatis.insa-lyon.fr
License: CeCILL FREE SOFTWARE LICENSE AGREEMENT
Platform: UNKNOWN
Description-Content-Type: text/x-rst
Requires-Dist: alabaster (==0.7.12)
Requires-Dist: attrs (==20.1.0)
Requires-Dist: Babel (==2.8.0)
Requires-Dist: bleach (==3.1.5)
Requires-Dist: certifi (==2020.6.20)
Requires-Dist: chardet (==3.0.4)
Requires-Dist: cycler (==0.10.0)
Requires-Dist: defusedxml (==0.6.0)
Requires-Dist: docutils (==0.16)
Requires-Dist: entrypoints (==0.3)
Requires-Dist: h5py (==2.10.0)
Requires-Dist: idna (==2.10)
Requires-Dist: imagesize (==1.2.0)
Requires-Dist: importlib-metadata (==1.7.0)
Requires-Dist: ipython-genutils (==0.2.0)
Requires-Dist: Jinja2 (==2.11.2)
Requires-Dist: jsonschema (==3.2.0)
Requires-Dist: jupyter-core (==4.6.3)
Requires-Dist: kiwisolver (==1.2.0)
Requires-Dist: MarkupSafe (==1.1.1)
Requires-Dist: matplotlib (==3.3.1)
Requires-Dist: mistune (==0.8.4)
Requires-Dist: nbconvert (==5.6.1)
Requires-Dist: nbformat (==5.0.7)
Requires-Dist: nbsphinx (==0.7.1)
Requires-Dist: numpy (==1.19.1)
Requires-Dist: packaging (==20.4)
Requires-Dist: pandocfilters (==1.4.2)
Requires-Dist: Pillow (==7.2.0)
Requires-Dist: pockets (==0.9.1)
Requires-Dist: Pygments (==2.6.1)
Requires-Dist: pyparsing (==2.4.7)
Requires-Dist: pyrsistent (==0.16.0)
Requires-Dist: python-dateutil (==2.8.1)
Requires-Dist: pytz (==2020.1)
Requires-Dist: PyYAML (==5.3.1)
Requires-Dist: requests (==2.24.0)
Requires-Dist: scipy (==1.5.2)
Requires-Dist: six (==1.15.0)
Requires-Dist: snowballstemmer (==2.0.0)
Requires-Dist: sortedcontainers (==2.2.2)
Requires-Dist: Sphinx (==3.2.1)
Requires-Dist: sphinx-rtd-theme (==0.5.0)
Requires-Dist: sphinxcontrib-applehelp (==1.0.2)
Requires-Dist: sphinxcontrib-devhelp (==1.0.2)
Requires-Dist: sphinxcontrib-htmlhelp (==1.0.3)
Requires-Dist: sphinxcontrib-jsmath (==1.0.1)
Requires-Dist: sphinxcontrib-napoleon (==0.7)
Requires-Dist: sphinxcontrib-qthelp (==1.0.3)
Requires-Dist: sphinxcontrib-serializinghtml (==1.1.4)
Requires-Dist: testpath (==0.4.4)
Requires-Dist: traitlets (==5.0.3)
Requires-Dist: urllib3 (==1.25.10)
Requires-Dist: webencodings (==0.5.1)
Requires-Dist: zipp (==3.1.0)

**pyPhase** is an open-source Python package for phase retrieval from phase contrast images in the Fresnel regime. For an overview, check out the pyPhase manuscript: https://arxiv.org/abs/2012.07942

Features
========

* Phase retrieval algorithms
* Wave propagation.
* Handling of different image sources and formats
* Tools for pre-processing such as registration of phase contrast images and motion estimation

Installation
============

Installation is currently through PyPI. Create a virtual environment using your favourite virtual environment manager, verify that pip is installed, then:

.. code-block::

   pip install pyphase


PyPhase currently requires Elastix 4.9 installed for registration. 
To manually install elastix 4.9 go to https://elastix.lumc.nl/download.php

* Unzip the archive.
* Add the path for elastix/bin to your .bashrc: add YOUR_PATH_TO_elastix/bin to your environment variable PATH.
* Add the path for elastix/lib to your .bashrc: add YOUR_PATH_TO_elastix/lib to your environment variable LD_LIBRARY_PATH.

Test your installation:

.. code-block::

    python3 import pyphase









