Hole Pattern Directions CryoARM300

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Name	Hole Pattern Directions CryoARM300
Permalink	https://serialemscripts.nexperion.net/script/69
Category	High-Level Functions
Language	SerialEM Scripting
Description	Define the vectors for multio hole collection. Resulting vectors 1 and 2 will be used in the parameters script version 2
Author	Marcus Fislage
Literature reference	https://journals.iucr.org/m/issues/2020/04/00/pw5013/index.html
Website link	http://www.becm.be

Version History

Version 1 (April 02, 2021; 292 download(s); SerialEM version ≥ 3.8)

Version 1

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Upload date	April 02, 2021
Download count	292
SerialEM version ≥	3.8

MacroName HolePatternDirections
###################################
#
# Script to define Vector1 and 2 for the multi hole acquisition defined in the Parameters script
#
# M.Fislage & R. Efremov Jan 2021
#   
# STATUS: functional
#
###################################

GoToLowDoseArea R
OKBox 1) Lower the screen 2) Remove CL

OKBox Center stage on a hole using stage shift and/or  IS

ReportImageShift
shift0_x = $reportedValue1
shift0_y = $reportedValue2
echo ---------------START PROCEDURE TO DEFINE VECTORS ------------
echo Starting values $shift0_x  $shift0_y

OKBox Center on nearest hole using IS
ReportImageShift
shift1_x = $reportedValue1
shift1_y = $reportedValue2
VECTOR1 = { ($shift1_x - $shift0_x)  ($shift1_y - $shift0_y)  }

echo VECTOR1 $VECTOR1
SetImageShift -1 * $VECTOR1[2] + $shift0_x $VECTOR1[1] + $shift0_y
OKBox Roughly centered on perpenducilar hole. Center carefully with IS and press ok.  
ReportImageShift
shift2_x = $reportedValue1
shift2_y = $reportedValue2
VECTOR2 = { ($shift2_x - $shift0_x)  ($shift2_y - $shift0_y)  }
echo VECTOR2 $VECTOR2

EnterDefaultedNumber 3 -1 ENTER NUMBER OF HOLES TO SHIFT FOR FINE ADJUSTMENT
Nholes = $reportedValue1

SetImageShift $VECTOR1[1] * $Nholes + $shift0_x $VECTOR1[2] * $Nholes + $shift0_y
OKBox ADJUST CENTER USING IS and press OK

ReportImageShift
shift1_x = $reportedValue1
shift1_y = $reportedValue2
VECTOR1 = { ( ($shift1_x - $shift0_x) / $Nholes )  ( ($shift1_y - $shift0_y) / $Nholes ) }
echo REFINED VECTOR1 $VECTOR1

SetImageShift $VECTOR2[1] * $Nholes + $shift0_x $VECTOR2[2] * $Nholes + $shift0_y
OKBox ADJUST CENTER USING IS and press OK

ReportImageShift
shift2_x = $reportedValue1
shift2_y = $reportedValue2
VECTOR2 = { ( ($shift2_x - $shift0_x) / $Nholes )  ( ($shift2_y - $shift0_y) / $Nholes) }
echo REFINED VECTOR2 $VECTOR2
SetImageShift  0 0 
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/)