You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 46 Next »

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-2.0.20

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 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

POP example:

 ami-local -l /reg/g/psdm/tutorials/ami2/tmo/pop.fc

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 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

Example includes:

  • calculator executing based on conditional logic

 ami-local -l /reg/g/psdm/tutorials/ami2/random/calculator.fc random:///reg/g/psdm/tutorials/ami2/random/worker.json


Complex example


 Example includes:

  • binning based on conditional logic
ami-local -l /reg/g/psdm/tutorials/ami2/random/complex_example.fc random:///reg/g/psdm/tutorials/ami2/random/worker.json

 

 

 

 

  • No labels