molecular-moviemaker

Scripts and functions for processing LCLS data using MATLAB to make Molecular Movies

The schema of the data analysis is as follows:

LargeRun

IS CALLED BY: none CALLS: GetExpFina, fetch_timepoints, rdCSPADTS, goodshotsonly, getXRayWavelength, generatePedestal, image2rad, AnalysisFunc, universalmaskmaker

• the big boss function that organizes everything
• "photonimg_xxxx_unbinned_tot" summed from "photonimg_xxxx_unbinned", taken from AnalysisFunc (output as "photon_img")
• then creates "photonimg_xxxx_unbinned_avg" by: "photonimg_xxxx_unbinned_tot" / "N_xxxxshots_counter" * "goodPixels" then subtracting a weighted vacuum

image2rad

IS CALLED BY: LargeRun CALLS: radialAverage

• provides additional experimental parameters to radialAverage
• takes "photonimg_xxxx_unbinned_avg" (from LargeRun) as input, provides "I_xxxx_unbinned" (output as I_q from radialAverage) as output

radialAverage

IS CALLED BY: image2rad CALLS: physicalQ, constructIq

• uses "images" (photon counts at each pixel, input as "photon_avg") to create a radial average I_q (output from constructIq)

physicalQ

IS CALLED BY: radialAverage CALLS: none

• uses detector geometry to convert physical space to q space

constructIq

IS CALLED BY: radialAverage CALLS: none

• uses "image", aka "iFlat", which is an array of photon counts at each pixel
• then applies corrections to provide I_q to radialAverage

AnalysisFunc

IS CALLED BY: LargeRun CALLS: rdCSPADdataXPP, CSPADtoMS, photon_map_hybrid

• only input is from "in_struc"
• applies common mode and gain corrections (to masks)

photon_map_hybrid

IS CALLED BY: AnalysisFunc CALLS: none

• uses hybrid photon counting method (a minimum ADU threshold)
• then time bins data to produce "binned_img"