k3blackstripecheck

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Details

Name	k3blackstripecheck
Permalink	https://serialemscripts.nexperion.net/script/50
Category	High-Level Functions
Language	SerialEM Scripting
Description	Detects when K3 sector fails, pauses acquisition, sends email, close valves.
Author	Wim Hagen
Literature reference	http://NA
Website link	http://NA

Version History

Version 0.1 (November 04, 2019; 515 download(s); SerialEM version ≥ 3.8)

Version 0.1

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Upload date	November 04, 2019
Download count	515
SerialEM version ≥	3.8

Function BlackStripeCheckK3
   
   # Function to detect black stripes in K3 images, will pause script, close valves and send email.
   # Call this function anywhere in a script, with last image in buffer a.
   # 2019 Wim Hagen, EMBL Heidelberg
   
   echo BlackStripeCheckK3
   
   SuppressReports
   
   # EMBL k3 black stripe mean ~2.7, image with valves closed ~17 in bin 4 images
   BlackStripeTreshold = 5
   
   # calculate stripe size
   ImageProperties A xsize ysize binning
   StripSize = 576 / $binning
   
   # 90 degree rotation so horizontal stripes
   If $xsize < $ysize
      Loop 10 index
         x0 = 0
         x1 = $xsize - 1
         y0 = ($index - 1) * $StripSize + 10    # for a litle bit of safety margin
         y1 = $index * $StripSize - 10            # for a litle bit of safety margin
         SubareaMean $x0 $x1 $y0 $y1 mean
         If $mean < $BlackStripeTreshold 
            echo  mean =  $mean : black stripe in sector $index
            MailSubject Krios 2
            SendEmail Black stripe problem Krios 2 K3, acquisition paused, valves closed.
            #SetColumnOrGunValve 1
            Pause See EM-help/Problems/Large black stripe, then continue.
         endif
      endloop
   Endif 
   
   # 0 degree rotation so vertical stripes
   If $xsize > $ysize
      Loop 10 index
         echo $index
         x0 = ($index - 1) * $StripSize + 10    # for a litle bit of safety margin
         x1 = $index * $StripSize - 10            # for a litle bit of safety margin
         y0 = 0
         y1 = $ysize - 1 
         SubareaMean $x0 $x1 $y0 $y1 mean
         If $mean < $BlackStripeTreshold 
            echo  mean =  $mean : black stripe in sector $index
            MailSubject Krios 2
            SendEmail Black stripe problem Krios 2 K3, acquisition paused, valves closed.
            #SetColumnOrGunValve 1
            Pause See EM-help/Problems/Large black stripe, then continue.
         endif
      endloop
   Endif 
   
endfunction

Documentation

Put function in a script right after some image action=, to ensure buffer A has an image.

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/)