(alternative: run 'source /nfs/chess/sw/miniconda3_msnc/bin/activate' then run 'conda activate saxswaxs-viewer' )
In terminal, run:
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