BTandSTIGvsISmeasure CryoARM300

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Name	BTandSTIGvsISmeasure CryoARM300
Permalink	https://serialemscripts.nexperion.net/script/72
Category	Calibrations
Language	SerialEM Scripting
Description	Measures tilt and stig in a circular pattern and at varying distances. Can be used to characterise the microscope
Author	Marcus Fislage

Version History

Version 1 (April 02, 2021; 261 download(s); SerialEM version ≥ 3.8)

Version 1

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Upload date	April 02, 2021
Download count	261
SerialEM version ≥	3.8

ScriptName BTandSTIGvsISmeasure

###################################
#
# Script to acquire SPA data
#
# R. Efremov & M.Fislage Jan 2021
#
# Script modified version of https://sphinx-emdocs.readthedocs.io/en/latest/serialEM-note-tackle-coma.html
# The goal is to measure BT and STIG vs IS in cicular pattern with defined radius
#   
# STATUS: functional
#
###################################

IS_RAD = {6.0 8.0 10.0} # radii for IS cirular pattern
point_number = 16 # number of eqiuanglular points 
SetImageShift 0 0 
SetProperty AstigBTBacklashDelay 2

echo *********************************************************************************************************************
echo STARTING SCRIPT  BTandSTIGvsIS measure
echo *********************************************************************************************************************
echo RUN COMA and ASTIGMATISM MEASUREMENTS FOR RADIUS $IS_RAD and $point_number POINTS 
echo DO STIG AND COMA CORRECTION AT IS 0

#FixAstigmatismByCTF
#FixComaByCTF
#FixAstigmatismByCTF

# main program

ReportImageShift xbase ybase
ReportBeamTilt   txbase tybase

loop $IS_RAD ind
   echo *********** MEASURE FOR RADIUS $IS_RAD[$ind] ********************
   loop $point_number  icount  
      IS_ANGLE = ( $icount - 1 ) * 360 / $point_number
      IS_X = $IS_RAD[$ind] * cos ( $IS_ANGLE)
      IS_Y = $IS_RAD[$ind] * sin ( $IS_ANGLE)
      
      ImageShiftbyMicrons $IS_X $IS_Y 0 0
      ReportImageShift IS_Xunits IS_Yunits 
      
      Delay 1 sec
      FixComaByCTF 1 1 0   
      ReportComaTiltNeeded xt yt
      SetBeamTilt ( $txbase + $xt ) ( $tybase + $yt )
      Delay 1 sec
      FixAstigmatismByCTF 1 1
      ReportStigmatorNeeded  xs ys    
      R
      SetBeamTilt $txbase $tybase
      
      echo RADIUS  $IS_RAD[$ind]    ANGLE $IS_ANGLE  IS in units  IS_X $IS_Xunits  IS_Y $IS_Yunits  BEAMTILT   $xt $yt ASTIGMATISM  $xs $ys
      
      
      
      #SetImageShift $xbase $ybase
      ImageShiftbyMicrons ( - $IS_X ) (- $IS_Y ) 0 0
      
   EndLoop
EndLoop

SetProperty AstigBTBacklashDelay 0
echo *********************************************************************************************************************
echo END SCRIPT BTandSTIGvsIS measure
echo *********************************************************************************************************************
EndMacro
Macro	23
ScriptName IR_residual_drift

IS_RAD = {2.0 4.0} # radii for IS cirular pattern
point_number = 16 # number of eqiuanglular points 
SetImageShift 0 0 
SetProperty AstigBTBacklashDelay 0

echo *********************************************************************************************************************
echo STARTING SCRIPT IR_residual_drift
echo *********************************************************************************************************************
echo RUN COMA and ASTIGMATISM MEASUREMENTS FOR RADIUS $IS_RAD and $point_number POINTS 
echo DO STIG AND COMA CORRECTION AT IS 0

# main program

ReportImageShift xbase ybase
ReportBeamTilt   txbase tybase
ReportObjectiveStigmator stig_x stig_y
loop $IS_RAD ind
   echo *********** MEASURE FOR RADIUS $IS_RAD[$ind] ********************
   loop $point_number  icount  
      ResetClock 
      IS_ANGLE = ( $icount - 1 ) * 360 / $point_number
      IS_X = $IS_RAD[$ind] * cos ( $IS_ANGLE)
      IS_Y = $IS_RAD[$ind] * sin ( $IS_ANGLE)
      
      ImageShiftbyMicrons $IS_X $IS_Y 0 0
      SetBeamTilt ( $txbase + 1 ) ( $tybase + 1 )
      SetObjectiveStigmator ($stig_x+0.001)  ($stig_y+0.001)
      R
      ReportClock
      echo RADIUS  $IS_RAD[$ind]    ANGLE $IS_ANGLE required Time  $reportedValue1 sec
      SetBeamTilt $txbase $tybase
      SetBeamTilt $txbase $tybase
      SetObjectiveStigmator $stig_x  $stig_y
      
      
      #ResetImageShift
      ImageShiftbyMicrons ( - $IS_X ) (- $IS_Y ) 0 0
      
   EndLoop
EndLoop

SetProperty AstigBTBacklashDelay 0
echo *********************************************************************************************************************
echo END SCRIPT IR_residual_drift
echo *********************************************************************************************************************
EndMacro

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/)