The File stack_script.dat

When you set up a stack (see 2.11.1) you create a file called stack_script.dat, that lists all commands, which sm_script is supposed to work through. The sm_script command structure is the following:

  command[,param1[,param2[,param3[,...]]]]

Available commands and parameters are:

• moveto_micron
  • motor (XPZT,YPZT,XSTG,YSTG,ZSTG,XDET,YDET,ZDET)
  • micron position (float) of where to move to
  example: moveto_micron,XSTG,30.5
• moveby_micron
  • motor (XPZT,YPZT,XSTG,YSTG,ZSTG,XDET,YDET,ZDET)
  • micron position (float) by how much to move
  example: moveby_micron,XSTG,2.0
• moveto_ev
  • energy in eV (float) to which to move SGM (ZSTG, ZOSA and ZDET tracking)
  example: moveto_ev,520.0
• shutter
  • instruction (open,close,automatic)
  example: shutter,open
• helium
  • on,off
  example: helium,on
• wait
  • wait time in seconds (float)
  example: wait,2.5
• data_channels
  • names of the data channels to record
  example: data_channels,Sidet01,Sidet02,...,Counter,Clock
• scan
  • fast motor (XPZT,YPZT,XSTG,YSTG,ZSTG,XDET,YDET,ZDET)
  • fast pixel size in microns (float)
  • number of fast pixels (integer)
  • slow motor (XPZT,YPZT,XSTG,YSTG,ZSTG,XDET,YDET,ZDET)
  • slow pixel size in microns (float)
  • number of slow pixels (integer)
  • dwell time in msec (float)
  • bidirectional flag (0,1)
  example: scan,XPZT,0.1,200,YPZT,0.1,200,5.,0
• spectrum
  • start energy in eV (float)
  • stop energy in eV (float)
  • delta eV (float)
  • dwell in msec (float)
  example: spectrum,500.,530.,0.5,5.
• calibrate_sidet
• scientist
  • name of scientist (string in double quotes)
  example: scientist,"Zaphod Beeblebrox"
• sample
  • name of sample (string in double quotes)
  example: sample,"Gill cell of Babel Fish"
• comments1
  • first comment (string in double quotes)
  example: comments1,"Mostly Harmless"
• comments2
  • second comment (string in double quotes)
  example: comments2,"Don't Panic"
• disp_name
  • default display name (string in double quotes)
  example: disp_name,"Predefined Combinations::BF total"
• beamstatus
  • instruction (check,ignore,heed) ^2.2
  example: beamstatus,check
• laser_positions
  • axis (X,Y,Z)
  • instruction (ON,OFF)
  example: laser_positions,X,OFF

The structure of a stack script created by stack_setup.pro (used in SM_GUI) is as follows:

• header instructions:
  Commands, that prepare your microscope for scanning. They should not be removed are altered, unless you really know, what you are doing.
• #End of Header #################################
  Indicates the end of header instructions.
• stack instructions:
  The actual stack commands (scans, energy changes, sidet calibrations etc.). You may edit those to your liking.

Lines starting with a pound sign (#) are ignored in microscope control. The same goes for lines starting with an exclamation mark (!), but they be followed by instructions to sm_script. Currently the only implemented instruction is !GOTO, which allows you to jump forward to a certain command in the script.
example: !GOTO moveto_ev,535.000
The command has to exactly match the line, that you want to jump to. If the stack was manually interrupted, such lines will be placed directly after the header.