How to use pyPhase

pyPhase may be used in python, or using a terminal.

Note: For the moment being pyPhase is supported for Linux only.

Conda and source code

Create a new Conda environment

# load Anaconda module (optional, required on Aurora)
module purge
module load Anaconda3/5.2.0

# create new environment
conda create -n myenv python=3.6 numpy tifffile

# activate the enviornment
source activate myenv

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 the terminal

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

Import pyphase into your python script with:

import pyphase

Usage examples can be found here.

Using Terminal

After installing run:

:~$ pyphase -h

pyphase.py [-h] [-p start end] [--parameter alpha] [--algorithm alg]
                  [--reconstruct_delta | --reconstruct_beta | --project_delta | --project_beta | --propagate | --difference | --retrieve_difference | --reconstruct_delta_update | --reconstruct_beta_update | --update_delta | --update_beta]
                  name


PyPhase phase retrieval

positional arguments:
  name                  name of the data set

optional arguments:
  -h, --help            show this help message and exit
  -p start end, --projections start end
                        projections to reconstruct
  --parameter alpha     regularisation parameter
  --algorithm alg       algorithm for phase retrieval or propagation
  --reconstruct_delta   tomographic reconstruction of delta from phase maps
  --reconstruct_beta    tomographic reconstruction of beta from attenuation
                        maps
  --project_delta       create projections of delta
  --project_beta        create projections of beta
  --propagate           propagate projections
  --difference          calculate difference between measurement and current
                        solution in contrast plane
  --retrieve_difference
                        retrieve phase from difference images
  --reconstruct_delta_update
                        reconstruct delta update from retrieved difference
                        image
  --reconstruct_beta_update
                        reconstruct beta update from retrieved difference
                        image
  --update_delta        update current solution for delta with calculated
                        update
  --update_beta         update current solution for beta with calculated
                        update

Usage examples can be found here.