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The auto-aligner references are stored in a .mat structure named s20LaserTargetPositionswMPA.mat located in the same directory as the auto aligner GUI: /usr/local/facet/matlabTNG/F2_LAA/the S20 Laser config file located on the control system at $TOOLS/pydm/display/user-facet/config/S20LaserConfig.toml.

Steps

1. First, if you haven't already done so, check out a local copy of the F2_LAA pydm displays directory in your home folder (in my case /home/fphysics/cemmarariniel/git_work/matlabTNG/F2_LAA). pydm/user-facet). See Git at FACET for details.
2. In your local directory do a git pull to confirm you have the most up to date version of the GUI config file checked out
   Load the reference structure.references = importdata('s20LaserTargetPositionswMPA.mat');
   the references structure has 15 elements, one for each camera in the auto-aligner. Each element has the fields cameraPV, cameraName, XmeanTarget, YmeanTarget. The XmeanTarget and YmeanTarget are the reference X and Y positions that the auto-aligner will align to. If for example you want to change the references for the first camera to the type:
   newreferences = references;
   newreferences(1).XmeanTarget = NewXReference;
   newreferences(1).YmeanTarget = NewYReference;
   where NewXReference and NewYReference are your new X and Y references. Repeat this for every camera you want to change the reference for
   Save the new references: save('s20LaserTargetPositionswMPA','newreferences'); Note: this will over-write the old reference structure in your local directory. If you want to, save a local copy of the old references somewhere else so you can undo the changes if they don't work out for some reason
   Test the auto-aligner with the new references in your local directory:
   launch F2_LAA 
   Use the GUI to align the laser to your new references
   If step 5 is successful push the new references to the production Note: this will change the references for everyone who is using the auto aligner going forward. Do not do this until you have tested that the laser can be aligned to these references in step 5 above.
   git add s20LaserTargetPositionswMPA.mat
   git commit -m "changed the reference positions for the S20 laser auto aligner"
   git push 
   cd /usr/local/facet/tools/matlabTNG/F2_LAA/
   git
3. Determine the new reference positions on each of the cameras you are planning to change them for. Use stats in the profile monitor, make sure Method is set to 1 to match the algorithm used by the auto-aligner.
   1. Alternatively, use the pointing jitter GUI to average over many shots. The center finding algorithm is slightly different so this isn't always a good option.
4. Edit the config file located at in your git repository at config/config/S20LaserConfig.toml.
   1. Find the section for the camera that needs to be be updated and change the value of "target" to the new coordinates.
5. Save the file.
6. Now save the changes to the git repo and pull them into production. The aligner cannot be tested in development, it must be tested in production.

git add config/config/S20LaserConfig.toml
git commit -m "Changed the target positions for the S20 laser auto aligner"
git push 

cd $TOOLS/pydm/display/user-facet/
git pull