pyFAI calibration gui operations for InstantPlot

InstantPlot documentation is here: https://wiki.classe.cornell.edu/CHESS/FMB/InstantPlot

Running the pyFAI calibration gui

  • 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' )

  • In terminal, run:

    • pyFAI-calib2

  • The gui window will open to the “Experiment settings” screen. Enter beam energy, choose calibrant, choose detector name

    • Navigate to data file. 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

      • data is located in /nfs/chess/raw/current/id3b/[username-BTR-ID]/

    • Make sure to choose “orient Y-axis downward”

  • 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.

    • You can save the mask (as a .tif) from this screen for use in InstantPlot later

  • 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. 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. If it looks good, use “Save as PONI file” to save a .poni file for this detector

    • File names typically: Calibrant_PIL#_date.poni or something similar

    • You can switch the x-axis unit under the “radial unit” drop down menu

Official documentation

Official documention for the GUI is here: pyFAI-calib2

-- LouisaSmieska - 23 Feb 2022
Topic revision: r2 - 24 Oct 2022, LouisaSmieska
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