NOTE: if you want to run ami2 on LCLS1 data, you can do it by generating an h5 file with the LCLS1 MPIDataSource.
To get the ami2 environment on the psana cluster:
ssh psana source /reg/g/psdm/sw/conda2/manage/bin/psconda.sh conda activate ps-2.0.19
Run the appropriate command from the "examples" sections below and do (for example) the following:
- click on "apply" (menu item near the top left) to activate the analysis "graph"
- click on one of the green boxes to open a plot
For examples that load a predefined graph (.fc file, for "flow chart") you should see a window like this, while examples with no .fc file will have an empty area in the upper right:
TMO Examples
Example includes:
- waveform viewing, ROI, integration and normalization of peak area
- waveform peak finding, histogramming, and scaling of axes using a polynomial "calibration"
ami-local -l /reg/g/psdm/tutorials/ami2/tmo/run43.fc -t -n 1 hdf5:///reg/g/psdm/tutorials/ami2/tmo/run43.json
Cookiebox example:
ami-local hdf5:///reg/g/psdm/tutorials/ami2/tmo/amoi0314_run167.json ami-local hdf5:///reg/g/psdm/tutorials/ami2/tmo/amoi0314_run171.json ami-local hdf5:///reg/g/psdm/tutorials/ami2/tmo/amoi0314_run172.json ami-local hdf5:///reg/g/psdm/tutorials/ami2/tmo/amo86815_run37.json ami-local hdf5:///reg/g/psdm/tutorials/ami2/tmo/amo86815_run70.json ami-local hdf5:///reg/g/psdm/tutorials/ami2/tmo/amo86815_run71.json ami-local hdf5:///reg/g/psdm/tutorials/ami2/tmo/amo86815_run72.json
Quadanode example:
ami-local -l /reg/g/psdm/tutorials/ami2/tmo/amox27716-r0100.fc ami-local hdf5:///reg/g/psdm/tutorials/ami2/tmo/amox27716_run78.json ami-local hdf5:///reg/g/psdm/tutorials/ami2/tmo/amox27716_run100.json
Peakfinder example:
ami-local -l /reg/g/psdm/tutorials/ami2/tmo/amox-27716_run100.fc
NEH2.2 Example
Example includes:
- photon centroid finding on vertically binned Andor camera
- linearity check of normalization (andor camera intensity vs. acqiris waveform intensity) with pearson-R calculation as a function of time
ami-local -l /reg/g/psdm/tutorials/ami2/neh2.2/run22.fc -t -n 1 hdf5:///reg/g/psdm/tutorials/ami2/neh2.2/worker.json
XPP Example
ami-local hdf5:///reg/g/psdm/tutorials/ami2/xpp/xpp.json
Random Data Example
Calculator example includes:
- calculator executing based on conditional logic
Complex example includes:
- binning based on conditional logic
ami-local -l /reg/g/psdm/tutorials/ami2/random/calculator.fc random:///reg/g/psdm/tutorials/ami2/random/worker.json ami-local -l /reg/g/psdm/tutorials/ami2/random/complex_example.fc random:///reg/g/psdm/tutorials/ami2/random/worker.json
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