pyFAI calibration gui operations for InstantPlot

Running the pyFAI calibration gui

• On NoMachine, open a terminal window and connect to a node that is not lnx201 or the station computer.
  • Run qrsh -q chess_fmb.q for FMB node; or
  • qrsh -q interactive.q -pe sge_pe 32 for a paralle processing node
• Run source /nfs/chess/sw/miniconda3_msnc/envs/saxswaxs-viewer/bin/activate
  • (alternative: run source /nfs/chess/sw/miniconda3_msnc/bin/activate then run conda activate saxswaxs-viewer)
• Run pyFAI-calib2 to open the gui. It will open to the “Experiment settings” screen.
• Enter beam energy, choose calibrant, choose detector name
• Navigate to data file (/nfs/chess/raw/current/id3b/[username-BTR-ID]/). Be sure to match the “PIL#” string in the filename to the detector you want to calibrate.
  • PIL5 = SAXS detector, pilatus 300K
  • PIL9, PIL11 = WAXS detectors, pilatus 200Ks
  • Make sure to choose "orient Y-axis downard"

• Click Next for mask tab.
  • Dead pixels between panels should automatically show up magenta (masked).
  • Also good to hit “mask below” with a threshold of 0 to remove any other dead pixels
  • Use the polygon under “draw tools” to exclude other regions (like the beamstop). click once on the start point to close the shape.
  • Save the mask (as a .tif) from this screen for use in InstantPlot and SAXSWAXS automation later. The recommended location to save the mask file is /nfs/chess/auxiliary/reduced_data/cycles/[YYYY-X]/id3b/[BTR-ID]/setup.
    • YYYY-X is the year and cycle number, e.g. 2025-1.
    • BTR-ID is PI name and project number, e.g. smieska-3222-A.
    • File names typically: PIL#_mask_date.tif or similar.

• Click Next for peak picking.
  • Use multiple or single point selection tools to select points on the rings in your image. ring number corresponds to first, second, third peak etc.

• Click Next to see fitting results. If something looks off, go back to the peak picking tab and make sure there aren’t outlier points or misnumbered rings; make sure you get points on rings close to the edges of the detector when possible.
  • PIL11 is above the beam and rotated on its side 90 degrees. You need to manually change rot3 = 1.57 rad and fit again before continuing on.

• Click Next to see cake plot and 1D I vs q.
  • You can switch the x-axis unit under the “radial unit” drop down menu
• If it looks good, use “Save as PONI file” to save a .poni file for this detector. The recommended location to save the mask file is /nfs/chess/auxiliary/reduced_data/cycles/[YYYY-X]/id3b/[BTR-ID]/setup.
  • YYYY-X is the year and cycle number, e.g. 2025-1.
  • BTR-ID is PI name and project number, e.g. smieska-3222-A.
  • File names typically: Calibrant_PIL#_date.poni or something similar.

Official documentation