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1. First, if you haven't already done so, check out a local copy of the F2_LAA directory in your home folder (in my case /home/fphysics/cemma/git_work/matlabTNG/F2_LAA). 
   
   
2. In your local directory do a git pull to confirm you have the most up to date version of the GUI checked out
   
   
3. 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
   
   
4. 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
   
   
5. 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
   
   
6. 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 pull