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-2.0.12
Run the appropriate command from the "examples" sections below (you should see a window similar to this) 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
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 -t -n 1 hdf5:///reg/g/psdm/tutorials/ami2/tmo/amoi0314_run167.json ami-local -t -n 1 hdf5:///reg/g/psdm/tutorials/ami2/tmo/amoi0314_run171.json ami-local -t -n 1 hdf5:///reg/g/psdm/tutorials/ami2/tmo/amoi0314_run172.json ami-local -t -n 1 hdf5:///reg/g/psdm/tutorials/ami2/tmo/amo86815_run37.json ami-local -t -n 1 hdf5:///reg/g/psdm/tutorials/ami2/tmo/amo86815_run71.json ami-local -t -n 1 hdf5:///reg/g/psdm/tutorials/ami2/tmo/amo86815_run72.json
Quadanode example:
ami-local -l /reg/g/psdm/tutorials/ami2/tmo/amox27716-r0100.fc -t -n 1 psana:///reg/g/psdm/tutorials/ami2/tmo/amox27716-r0100.json ami-local -t -n 1 hdf5:///reg/g/psdm/tutorials/ami2/tmo/amox27716_run78.json ami-local -t -n 1 hdf5:///reg/g/psdm/tutorials/ami2/tmo/amox27716_run100.json
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
Overview
Content Tools