Set Target for Sample Thickness

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Details

Name	Set Target for Sample Thickness
Permalink	https://serialemscripts.nexperion.net/script/64
Category	Single Particle
Language	SerialEM Scripting
Description	Allows to change the applied thresholds set by the "Measure Sample Thickness" which updates the coloring at acquire status accordingly.
Author	Jan Rheinberger

Version History

Version 1.0 (November 27, 2020; 295 download(s); SerialEM version ≥ 3.9)

Version 1.0

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Upload date	November 27, 2020
Download count	295
SerialEM version ≥	3.9

# Optimized data acquisition workflow by sample thickness determination
# Rheinberger, Oostergetel, Resch, and Paulino, submitted for publication
# (C) Nexperion e.U. - Solutions for Electron Microscopy, 2020
# https://www.nexperion.net
# Requires SerialEM >= 3.9.0
# Last update November 20, 2020

ScriptName HFIT-SetTarget
SuppressReports

EmptyString @=

# Get parameters
EnterDefaultedNumber 1 -1 First item to process
FirstItemIndex = $ReportedValue1
ReportOtherItem -1
EnterDefaultedNumber $ReportedValue1 -1 Last item to process
LastItemIndex = $ReportedValue1
EnterOneNumber Minimum thickness
MinimumThickness = $ReportedValue1
EnterOneNumber Maximum thickness
MaximumThickness = $ReportedValue1

# TODO Range checking of parameters
TotalItems = ( $LastItemIndex - $FirstItemIndex + 1 )

SuspendNavRedraw

DoLoop i $FirstItemIndex $LastItemIndex
ReportOtherItem $i
if ( $ReportedValue5 == 0 )
   CompareStrings NavNote $EmptyString
   if ( $ReportedValue1 != 0 )
      Thickness = $NavNote
      if ( $Thickness < $MinimumThickness )
         ChangeItemColor $i 4
         SetItemAcquire $i 0
       elseif ( $Thickness < $MaximumThickness )
         ChangeItemColor $i 1
         SetItemAcquire $i 1
       else 
         ChangeItemColor $i 2
         SetItemAcquire $i 0
      Endif
    Else
      SetItemAcquire $i 0
   EndIf
 Else
   SetItemAcquire $i 0 
EndIf

j = ( $i - $FirstItemIndex )
If ( ( MODULO $j 100 ) == 0 )
   echo Completed item $j of $TotalItems ...
EndIf

EndLoop

SuspendNavRedraw 0
echo Completed item $TotalItems of $TotalItems, done.

Related Scripts

The following scripts provide a similar or related functionality, but are not required to run this script:

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/)