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Procedure to start up and align the IR laser in the laser room.

Assumption is that the oscillator and Regen are running, and that the auto aligner is being used as much as possible.

The auto aligner uses the references recorded here Laser cameras and alignment references. If those change, the values have to be changed in the code as well.

A) Preparations

1. Check status of chillers and refill if necessary:
   1. Outside: Regen
   2. Inside: MPA crystal, Oscillator etc.
   3. Chiller load for SAGAs: https://docs.google.com/document/d/1tVj5wvT-RQI_wx3ykWPv121MkaEuvCQ05LFtRqwuRRc/
2. Check for any other alarms. Regen and oscillator running.
3. Check beam out of MPA is blocked with power meter.
4. Make sure the LSS-2 key is out in the laser room LSS-2 control panel.
5. Ensure the EPS shutter is in (FACETHOME→Laser→LI20, green means the EPS shutter is in).

B) Start up/warm up

1. Turn on PreAmp (Flashlamp and Q-Switch).
2. Turn on both SAGAs (shutters closed): https://docs.google.com/document/d/1tVj5wvT-RQI_wx3ykWPv121MkaEuvCQ05LFtRqwuRRc/

C) PreAmp and MPA alignment

1. Open S20 Laser Room Multi Profile Monitor (FACETHOME→Matlab GUIs→S20 Laser Tools→S20 Laser Room Multi Profile Monitor).
2. Start display and check profiles look fine (cameras are running), and laser is visible.
3. Make sure ROIs are set somewhat tightly, set Zoom ROI in Profile Monitor GUI if needed.
   
4. Open auto align GUI (FACETHOME→Matlab GUIs→S20 Laser Tools→S20 Laser Auto Alignment), see Figure 1.
5. Press 'Stop Alignment' (red button). This will stop any scripts running on other machines.
6. Set camera exposure time for laser room cameras by pressing 'Amp cameras' (see Figure 1, 3.).
7. Click the 'Expert...' button. This opens a new window (see Figure 2).
8. Check the gain settings. No value should be above 0.2000. Higher values tend to overshoot too much and affect pointing.
9. Check maximum tolerances on the same panel: Global value around 5 pixels, MPA Near/Far in the end ~20 but initially >100.
   1. Note: The auto-aligner won't do anything if it measures an offset larger than the tolerance. It will print a warning in the log.
10. Tick boxes for first three sets of laser cameras: 'Pulse Picker and Regen Out', 'Preamp Near and Far', 'MPA Near and Far'.
11. Click 'Clear References', then 'Grab References'. This might take a few seconds.
12. Click 'Start Alignment'. The software will loop through the list of cameras (top to bottom), calculate offsets and then move motors.
    1. Note: For MPA Near and Far the offset is calculated using a 20-shot average. This step takes a bit longer than for the other motors. 
13. Monitor the log to make sure that the offset tolerances were set appropriately and that the auto aligner does its job.
14. Reduce max offset tolerance in expert panel once alignment is close.
15. Open SAGA shutters.

D) DMNear and DMFar alignment

1. Check if RP attenuator is at "in" position. If not:
   1. Flip the full power laser ND filter into the common beam path of DMNear and DMFar cameras.
   2. Install the full power ND filter before the lens in the InjNear and InjFar camera line.
   3. Install the full power ND filter in the wavefront sensor and MO beam path.
   4. Flip the ND filters in front of both the wavefront sensor and MO camera to the in position. 
2. Unblock the laser after the MPA so that the Ti:Sapph laser can propagate to the DMNear and Far beam path.
3. Open two profile monitors (FACETHOME→Matlab GUIs→Profile Monitor), one for DMNear, one for DMFar. The laser beam should appear on both cameras. If not, increase their exposure time to at least 100ms.
4. Select "Show Stats" for both profile monitors.
   1. For DMFar: If the ROI isn't set correctly, the burn spot on the camera may be visible. If this is the case, do the following:
   2. Click the zoom check box and select the half of the image that does not include the burned spot.
   3. Select the "Stats (Zoom)" checkbox so the stats panel only looks at the zoomed in region of the camera.
5. In FACETHOME, follow Laser→LI20→Infrastructure→MOC-LI20-MC06→DM Near. Use Ch1 and Ch2 to adjust the beam pointing to the reference position on DMNear, and use Ch3 and Ch4 to adjust to the reference position on DMFar. Please use the latest reference positions from Laser cameras and alignment references.
6. Repeat step 5 as needed until the alignment converges.
7. In general, the alignment on DMFar is more important. The stats position of DMNear is sensitive to the laser beam profile, so offsets of ~10 pixels in each direction are acceptable.