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python AnalyzeH5.py -r 123 -f $OUTPUT_ROOT/lowFlux/SimpleClusters__c0_r123_n666.h5 -p $OUTPUT_ROOT/lowFlux

python runAnalyzeH5.py /sdf/data/lcls/ds/rix/rixx1003721/results/lowFlux 384 SimpleClusters 384,385,386,387,388,389
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

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python analyze_npy.py $OUTPUT_ROOT/scan/LinearityPlotsParallel_r84_sliceFits_testforSept_raw.npy 3 for e.g. asic 3:

display ../scan/LinearityPlotsParallel_r325_sliceFits_residualTest2_raw_g1slope_g0slope_ratio_map_and_histo.png

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python AnalyzeH5.py -r 470 -f /sdf/data/lcls/ds/rix/rixx1003721/results/lowFlux/SimpleClusters_c0_r468_n1.h5,/sdf/data/lcls/ds/rix/rixx1003721/results/lowFlux/SimpleClusters_c0_r469_n1.h5,/sdf/data/lcls/ds/rix/rixx1003721/results/lowFlux/SimpleClusters_c0_r470_n1.h5 -p $OUTPUT_ROOT/lowFlux