Calibrating Monochromator

Every time a component of the monochromator (MC) is adjusted (light source, input slit, output position, etc), the feed from the MC requires calibration anew. 

The Python scripts used in this calibration are included in the InstrumentScripts repository of the Stubbs lab: 
https://github.com/stubbslab/InstrumentScripts/tree/main/sampleMonochromitorCalData 

Calibrating MC requires three steps

1. Calibrate spectrograph (not necessary if spectrograph is already calibrated)
2. Take MC data on spectrograph
3. Use gathered data to calibrate spectrograph

We detail an example below.  In this example, we use the StellarNet Inc Black Comet spectrograph, which we calibrate with the Ocean Optics KR-1 calibration light source.  Future re-calibrations of MC can use the same calibration of the StellarNet spectrograph, which we include in sampleMonochromatorCalData directory. 

Here are the steps in our example:

STEP 0: If running this analysis on a new computer, you must download the StellarNet drivers for the black comet spectrograph. See the Black Comet Instrument Page here: 

StellarNet Black Comet Spectrograph

STEP 1: Calibrating Spectrograph with KR-1 Light Source

1. You need to determine your wavelength solution (reported wavelength vs true wavelength) of your calibrating spectrograph.  
   
   1. This step does not need to be repeated every time MC requires new calibration, provided the old spectrograph calibration data is available.
2. Pick a very small optical fiber to connect your calibration light and the spectrograph
   1. Very small as the raw KR-1 source is too bright for the spectrograph if not attenuated
3. Take an image of KR1 lamp with spectrograph

STEP 2: Take monochromator data with spectrograph

1. Plug optical fiber from monochromator output into Black Comet spectrograph
   
   1. MC end of fiber SHOULD NOT BE moved 
2. Move monochromator to 700 nm, and set spectrograph exposure time to ~10ms
3. Place an ND filter in spectrograph input path, selected to make Black Comet peak intensity at this exposure time and wavelength ~10-20k
   1. The spectrograph sensitivity with the ThorLabs halogen light peaks around 700nm.  So we make a minimal exposure time give good S/N at that wavelength.
4. Take a data series, starting from ~350 nm and ending at ~1050 nm. 
   1. Use Python to step MC forward
   2. Use Black Comet to save the data. 
   3. This requires manually saving the black comet files, and so cannot be easily automated. 
   4. Here is an example of the run python scripts:
      

      $ cd Documents/PythonScripts/CBP
      $ python
      >>> import monochromator as mono 
      >>> my_mono = mono.CornerStone260('COM3') #Need to check which COM port mono is read at 
      >>> waves = list(range(350, 1051, 52)) 
      >>> for wave in waves: 
          my_mono.GoWave(wave) 
          input('Monochromator  at wavelength ' + str(wave) + ' nm.  Press any key to move to next wavelength (SAVE THE FILE FIRST THOUGH!!!!)') 

      *** Save the file, such as BC_mono_XXXnm_XXXms.SSM.  Then press a button ****
   5. You will need to adjust the exposure time to keep the number of counts in a good range (~5k-40k).

STEP 3: Run the wavelength solution

1. Run the XXX script.