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Bug #2796

open

makestack2.py

Added by David Veesler over 10 years ago. Updated over 10 years ago.

Status:
New
Priority:
Normal
Assignee:
Anchi Cheng
Category:
-
Target version:
-
Start date:
05/28/2014
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.1.0
Show in known bugs:
No
Workaround:

Description

I am getting the following error message when trying to create a stack.

  • FATAL ERROR ***
    Standard deviation == 0 for particle 0 in image 14apr04c_045gr_03sq_02hl_02ed

Here is the command I used.

/opt/myamisnap/bin/appion makestack2.py --single=start.hed --selectionid=37 --invert --normalized --phaseflip --flip-type=emanimage --boxsize=560 --ctfcutoff=0.8 --description="test 10 images" --runname=stack15 --rundir=/ami/data15/appion/14apr04c/stacks/stack15 --limit=10 --commit --preset=ed --projectid=416 --session=14apr04c --no-rejects --no-wait --continue --expid=13243 --jobtype=makestack2

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 #1

Updated by David Veesler over 10 years ago

Traceback (most recent call last):
File "/opt/myamisnap/bin/makestack2.py", line 1205, in <module>
makeStack.run()
File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 90, in run
results = self.loopProcessImage(imgdata)
File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 139, in loopProcessImage
return self.processImage(imgdata)
File "/opt/myamisnap/lib/appionlib/apParticleExtractor.py", line 494, in processImage
total_processed_particles = self.processParticles(imgdata,partdatas,shiftdata)
File "/opt/myamisnap/bin/makestack2.py", line 77, in processParticles
self.boxedpartdatas, self.imgstackfile, self.partmeantree = self.boxParticlesFromImage(imgdata,partdatas,shiftdata)
File "/opt/myamisnap/bin/makestack2.py", line 236, in boxParticlesFromImage
partmeantree = self.calculateParticleStackStats(imgstackfile,boxedpartdatas)
File "/opt/myamisnap/bin/makestack2.py", line 305, in calculateParticleStackStats
apDisplay.printError("Standard deviation 0 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 0 for particle 0 in image 14apr04c_045gr_03sq_02hl_02ed

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