# Ptychography analysis using a command-line script¶

The simplest way to analys a ptychography dataset using PyNX is to use a command-line script.

The generic pynx-cxipty.py script reads data from a CXI file (see http://cxidb.org, see below how to create such a file) including data for a two-dimensional projection. A simple data analysis can be done using:

pynx-cxipty.py data=data.cxi algorithm=analysis,ML**100,DM**200,nbprobe=3,probe=1 \
probe=gaussian,200e-9x200e-9 liveplot saveplot


This will import the data from the data.cxi, which includes all information (observed frames, motor positions, detector distance, wavelength, mask…), and then optimise the object and probe.

The algorithm string is interpreted right-to-left (without any space):

• probe=1 activates the probe optimisation (by default only the object is optimised)
• nbprobe=3 activates 3 probe modes
• ML**100,DM**200: run 200 cycles of Difference Map, followed by 100 cycles of conjugate gradient Maximum Likelihood.
• analysis: analyse the final probe, determining the position of the focus and plotting it, and the probe modes.

The initial shape for the probe (probe=gaussian,200e-9x200e-9) will be a Gaussian with a horizontal x vertical width of 200 x 200 nm**2.

The liveplot and saveplot keywords will trigger the display of plots during the optimisation (Note that unless the dataset is quite large, this will significantly slow down the optimisation), and the saving of the final object and probe.

ALl results (CXI output and plots) are saved in a subdirectory ResultsScanNNNN, where NNNN is the scan number.

You can try this using an example dataset. On a Linux or macOS computer:

# If necessary, activate your python environment with PyNX
source /path/to/my/python/environment/bin activate

curl -O http://ftp.esrf.fr/pub/scisoft/PyNX/data/ptycho-siemens-star-id01.cxi

# View the CXI file using the silx viewer:
silx view ptycho-siemens-star-id01.cxi

# Run the PyNX analysis script
pynx-cxipty.py data=ptycho-siemens-star-id01.cxi\
algorithm=analysis,ML**100,DM**200,nbprobe=3,probe=1 \
probe=focus,60e-6x200e-6,0.09 defocus=200e-6 defocus=200e-6 liveplot saveplot

# View the result from the output CXI file using the silx viewer
silx view ResultsScan0013/latest.cxi

# You can also open latest.png, latest-probe-modes.png and latest-probe-z.png in ResultsScan0013.


In this script, the initial probe is simulated from a 60x200 microns aperture, focused 9 cm, and then defocused 200 microns

Example output images:

Object and probe: .. image:: http://ftp.esrf.fr/pub/scisoft/PyNX/data/ptycho-siemens-star-id01.png

Probe focus analysis: .. image:: http://ftp.esrf.fr/pub/scisoft/PyNX/data/ptycho-siemens-star-id01-probe-z.png

Probe modes analysis: .. image:: http://ftp.esrf.fr/pub/scisoft/PyNX/data/ptycho-siemens-star-id01-probe-modes.png

## Creating a CXI file¶

To create a CXI file from data (see http://cxidb.org), the save_ptycho_data_cxi() function can be used:

from pynx.ptycho import save_ptycho_data_cxi
save_ptycho_data_cxi(file_name, iobs, pixel_size, wavelength, detector_distance, x, y)


See the corresponding API documentation at pynx.ptycho.ptycho.save_ptycho_data_cxi()

Note that it is critical to get the motor and detector orientation right. The detector origin should be at the top, left corner, as seen from the sample. The X sample position coordinate should be horizontal, towards the left as seen from the X-ray source, and the Y coordinate should be vertical, looking towards the ceiling. This corresponds to the CXI convention (see http://cxidb.org), itself deriving from the NeXus and McStas ones.

To test all possible orientations (motor and image axes orientation and exchange), you can also try to use the orientation_round_robin command-line keyword, which will test a grand total of 64 possibilities (a number being equivalent), with 8 motor axes and 8 image flip/transpose combinations. This can be unstable, so using a stabilising algorithm such as AP**1000 is recommended. This approach works best with a standard target such as a Siemens star.