pyFAI calibration gui operations for 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