Install directions

NOTE: pyPhase is under development is currently not available for download/install.

To run pyPhase during this period, the source code files need to be in the machine. Make sure to add their path to the system.

Here you can find install directions for pyPhase.

Conda

Install pyPhase in your conda enviornment with

conda install pyphase 

Pip

With pip

pip install pyphase

Using the source code

Obtain a copy or download pyPhase source code from a git repository. Make sure to had the code's path to your system. This can be done in python with

import os
import sys

pyphase_path = os.path.abspath('~/path/to/pyphase')
sys.path.append(pyphase_path)

or in your system. In bash do

PATH=$PATH:~/path/to/pyphase

Requeriments

pyPhase has the following packages dependencies: - numpy - pyelastix - EDFfile - PIL - yaml - pickle - sortedcontainers - parallelizer

TODO: add versions.

Elastix

To use shift and motions correction in pyPhase, elastix needs to be installed in the machine. By default, pyelastix will look for elastix's executables in '/user/bin/', '/user/local/bin' and '/opt/local/bin'. If your binaries are elswhere add their path to pyelastix.py under the _find_executables() method.