# These CXI datasets were taken on id16 with a Siemens star target at 17 keV
# The two datasets where taken with different trajectories for the sample to ensure they are independent

# 0) Set the GPU number in the PYNX_PU if not already done (replace '1' by your trainne number):
export PYNX_PU=.1

# 1) analyse it using

pynx-cxipty.py siemens_star_00118_defoc500um_step150nm_dt125ms.cxi probe=focus,120e-6x120e-6,0.1 defocus=500e-6 algorithm=analysis,ML**100,AP**200,positions=1,AP**50,DM**200,nbprobe=3,probe=1 saveplot=object_phase save=all liveplot

pynx-cxipty.py siemens_star_00119_defoc500um_step150nm_dt125ms_sym.cxi probe=focus,120e-6x120e-6,0.1 defocus=500e-6 algorithm=analysis,ML**100,AP**200,positions=1,AP**50,DM**200,nbprobe=3,probe=1 saveplot=object_phase save=all liveplot

# 2) You can look at the results of the analysis using:

eog ResultsScan*/lat*.png

or:
 silx view ResultsScan*/latest.cxi
(with silx, use the 'image' viewer and see the amplitude, phase or mixed phase/amplitude view)


# 3) Analysis of the resolution using Fourier Shell Correlation
pynx-resolution-FSC.py ResultsScan0118/latest.cxi ResultsScan0119/latest.cxi save_plot

