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Bug #4055

closed

eman whole image phase flipping does not take non-square image

Added by Zhening Zhang over 8 years ago. Updated almost 7 years ago.

Status:
Won't Fix or Won't Do
Priority:
Normal
Assignee:
Anchi Cheng
Category:
-
Target version:
Appion/Leginon 3.3
Start date:
03/23/2016
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.2.0
Show in known bugs:
Yes
Workaround:

Description

Session id: 16mar07f run name: stack4.appionsub.job

Traceback (most recent call last):
File "/opt/myamisnap/bin/makestack2.py", line 1213, in
makeStack.run()
File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 87, in run
results = self.loopProcessImage(imgdata)
File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 137, in loopProcessImage
return self.processImage(imgdata)
File "/opt/myamisnap/lib/appionlib/apParticleExtractor.py", line 510, in processImage
total_processed_particles = self.processParticles(imgdata,partdatas,shiftdata)
File "/opt/myamisnap/bin/makestack2.py", line 76, in processParticles
self.boxedpartdatas, self.imgstackfile, self.partmeantree = self.boxParticlesFromImage(imgdata, partdatas,
shiftdata)
File "/opt/myamisnap/bin/makestack2.py", line 234, in boxParticlesFromImage
partmeantree = self.calculateParticleStackStats(imgstackfile, boxedpartdatas)
File "/opt/myamisnap/bin/makestack2.py", line 303, in calculateParticleStackStats
apDisplay.printError("Standard deviation for particle d in image %s"(i,self.shortname))
File "/opt/myamisnap/lib/appionlib/apDisplay.py", line 65, in printError
raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
Exception:
  • FATAL ERROR ***
    Standard deviation for particle in image 16mar07f_Ribosome_manual_024gr_01sq_02hl_03en-a
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 #1

Updated by Anchi Cheng over 8 years ago

  • Project changed from 138 to Appion
  • Subject changed from error msg from stack making to eman whole image phase flipping does not take non-square image
  • Status changed from New to In Test
  • Target version set to Appion/Leginon 3.3
  • Affected Version set to Appion/Leginon 2.2.0
  • Show in known bugs set to Yes

r19632 does not allow the method to be used in myamiweb if image is not square.
r19633 gives error message and stop in the python script

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 #2

Updated by Anchi Cheng almost 7 years ago

  • Status changed from In Test to Won't Fix or Won't Do
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