CINAAutoFocus

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Name	CINAAutoFocus
Permalink	https://serialemscripts.nexperion.net/script/19
Category	Function Libraries
Language	SerialEM Scripting
Description	Macro CINAAutoFocus # # This macro will focus the specimen. To do so, it # - Centers the beam # - Meausres current defocus # - If measurement gave a reasonable value, it will correct the focus on the microscope # # The entire focussing routin is only happening every so often, as defined by "focusEachHole"
Author	Henning Stahlberg
Website link	http://c-cina.org

Version History

Version 1.0 (February 24, 2017; 593 download(s); SerialEM version ≥ 3.7)

Version 1.0

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Upload date	February 24, 2017
Download count	593
SerialEM version ≥	3.7

################################################################################
#
#   Macro CINAAutoFocus
#
#   This macro will focus the specimen. To do so, it 
#   - Centers the beam
#   - Meausres current defocus 
#   - If measurement gave a reasonable value, it will correct the focus on the microscope
#
#   The entire focussing routin is only happening every so often, as defined by "focusEachHole"
#
# Daniel Caujolle-Bert, Henning Stahlberg, C-CINA, Biozentrum, University of Basel
# Feb. 25, 2017
#
################################################################################
MacroName CINAAutoFocus

# Check if the stage moved to a different grid square at a different Z height:
ReportStageXYZ
NEWX = $reportedValue1
NEWY = $reportedValue2
NEWZ = $reportedValue3
If ABS ($NEWX - $LASTX) > 15.0 
   echo Large X change detected. LASTX = $LASTX,  NEWX = $NEWX.  Requires new focussing.
   FOCUSCOUNTER := 0
endif
If ABS ($NEWY - $LASTY) > 15.0
   echo Large Y change detected. LASTY = $LASTY,  NEWY = $NEWY.  Requires new focussing.
   FOCUSCOUNTER := 0
endif
If ABS ($NEWZ - $LASTZ) > 0.1 
   echo Z change detected. LASTZ = $LASTZ,  NEWZ = $NEWZ.  Requires new focussing.
   FOCUSCOUNTER := 0
endif

# Check, if it is already time to focus:
If $FOCUSCOUNTER < 2
   Echo Focussing on this one..., Focus Counter = $FOCUSCOUNTER
   
   LASTX := $NEWX
   LASTY := $NEWY
   LASTZ := $NEWZ
   
   ## Center Beam, assume AutoCenterBeam policy has been set up
   # AutoCenterBeam
   
   ## Center beam in Focus mode 
   F
   ReportMeanCounts 
   if $repVal1 > 10
      CenterBeamFromImage
   endif
   
   if  $repVal1 < 1 
      Echo FOCUS image is black. MeanCounts was $repVal1.
      focus_problem_counter := $focus_problem_counter + 1
      echo FOCUS problem counter = $focus_problem_counter
    else
      focus_problem_counter := 0
   endif
   
   if $focus_problem_counter > 3
      Echo Trying to save the beam:
      SetEucentricFocus
      ChangeFocus -2
      SetBeamShift $good_beamshift_x $good_beamshift_y
      ## Center beam in Focus mode 
      F
      CenterBeamFromImage
      focus_problem_counter := 0
      FOCUSCOUNTER := 0
   endif
   
   ReportNumNavAcquire
   
   ## CycleTargetFocus, range is set in macro "Parameters".
   Call CycleTargetDefocus
   
   FocusChangeLimits -70 70
   Echo Now focussing:
   Loop 1
      CallFunction FocusOnce
   EndLoop
   if $GridType == 2
      # Use TRIAL mode with a small focussed beam to center the beam
      GoToLowDoseArea T
      Delay 1
      T
      CenterBeamFromImage
      T
   endif
   DISPLAYCOUNTER := 0
 Else
   Echo Skipping focussing, Focus Counter = $FOCUSCOUNTER
   GoToLowDoseArea F
   ChangeFocus -0.1
   delay 1
   # F
   # ReportMeanCounts 
   # if $repVal1 > 10
   #     CenterBeamFromImage
   # endif
   FOCUSCOUNTER := $FOCUSCOUNTER - 1
Endif

Function FocusOnce
   # Get current defocus
   ReportDefocus 
   curDefocus = $repVal1
   # Get and store measured value
   if $GridType == 2
      ChangeFocus -4
      G -1
      ChangeFocus +4
      ReportAutofocus 
      repAutoFocus = $repVal1 + 4
    else  
      G -1
      ReportAutofocus 
      repAutoFocus = $repVal1
   endif
   If ( ABS ($repAutoFocus) <= 0.1 ) OR ( ABS ($repAutoFocus) >= 200.0 )
      # Autofocusing has failed, restore previous defocus value
      Echo Autofocus has failed, restore previous defocus value
      SetDefocus $curDefocus
      FOCUSCOUNTER := 0
    Else
      # Autofocusing has worked well
      # Apply measured defocus
      ReportTargetDefocus
      newDefocus = $curDefocus  -  $repAutoFocus + $repVal1 
      Echo Autofocus has succeeded, Target defocus: $repVal1 , new defocus: $newDefocus
      SetDefocus $newDefocus
      F
      ReportMeanCounts 
      if $repVal1 > 10
         CenterBeamFromImage
      endif
      FOCUSCOUNTER := $focusEachHole
      ReportBeamShift 
      good_beamshift_x := $repVal1 
      good_beamshift_y := $repVal2
      focus_problem_counter := 0
      echo good beamshift = $good_beamshift_x, $good_beamshift_y
   Endif
EndFunction

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License

This code can be shared and adapted under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) License (https://creativecommons.org/licenses/by-nc-sa/4.0/)