...
Else do --fakePedestals ... after doing CalcNoiseAndMean
where you'll want FM for FM and AML-M. Eventually we'll want to have specialized cluster cuts for all modes, but for now check that the seedCut in SimpleClustersParallelSlice.py is about 0.5 photons.
When all the runs are done, you can go to the rix directory and run e.g.
python runAnalyzeH5.py /sdf/data/lcls/ds/rix/rixx1003721/results/lowFlux 384 SimpleClusters 384,385,386,387,388,389
Cut and paste the command this prints.
This makes plots and .npy labelled run 384 using the SimpleClusters analysis for the listed runs.
Let me know if this makes sense and works for you. At the end you can do e.g.
display ../lowFlux/*384*285*62*png
display ../lowFlux/*384*gain*png
...