Ptychography

ptychography toolbox module for python

To install as the local user on Linux

$ git clone https://github.com/andyofmelbourne/Ptychography.git ~/.local/lib/python2.7/site-packages/Ptychography

Done!

Requires

• python (probably >= 2.7)
• scipy
• numpy

And for display and testing routines:

• h5py
• pyqtgraph

Examples

command line usage

This will perform reconstructions updating just the object, the probe or both with and without background correction using the difference map, and the error reduction algorithm.

$ cp ~/.local/lib/python2.7/site-packages/Ptychography/test.py .
$ python test.py

or with 2 cpu cores

$ mpirun -n 2 python test.py

Now you should have a file your local directory "output_method1.cxi". To have a look at the retrievals run:

$ python ~/.local/lib/python2.7/site-packages/Ptychography/ptychography/display.py output_method1.cxi

ERA on a single cpu, within python

>>> import Ptychography as pty
>>> I, R, M, P, O, B = pty.forward_sim()
>>> O_ret, info      = pty.ERA(I, R, P, None, iters=100, mask=M, method=1)

To run on the max-cfel machines

$ ssh -X max-cfel
$ source /nfs/cfel/cxi/common/cfelsoft-rh7/anaconda-py2/anaconda-setup-bash.sh 
$ cd ~/.local/lib/python2.7/site-packages/Ptychography
$ mpirun -n 2 python ptychography/era.py