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Bug #3660

open

Mean/StdDev filtering of stack not working with virtual stack

Added by Priyamvada Acharya about 9 years ago. Updated about 9 years ago.

Status:
Assigned
Priority:
Normal
Assignee:
Gabriel Lander
Category:
-
Target version:
-
Start date:
10/14/2015
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.2
Show in known bugs:
Workaround:

click the "*generate some missing information*" in stack summary table to generate the real stack before running this

Description

Error message:

subStack.start()
File "/opt/myamisnap/bin/stackFilter.py", line 88, in start
apStack.makeNewStack(oldstack, newstack, self.params['keepfile'], bad=True)
File "/opt/myamisnap/lib/appionlib/apStack.py", line 55, in makeNewStack
a.run()
File "/opt/myamisnap/lib/appionlib/proc2dLib.py", line 45, in run
self.approc2d.checkConflicts()
File "/opt/myamisnap/lib/appionlib/proc2dLib.py", line 112, in checkConflicts
self.inputNumParticles = self.inheader['nz']
TypeError: 'NoneType' object is unsubscriptable

Session ID: 15oct05d
Path: /gpfs/appion/pacharya/15oct05d/stacks/alignsub53/

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 #1

Updated by Anchi Cheng about 9 years ago

  • Project changed from 138 to Appion
  • Assignee set to Priyamvada Acharya
  • Affected Version set to Appion/Leginon 3.2

The error in /gpfs/appion/pacharya/15oct05d/stacks/meanfilt103

!!! WARNING: could not find old stack: /gpfs/appion/pacharya/15oct05d/stac
ks/alignsub53/start.hed

alignsub53 Ended at Wed, 14 Oct 2015 11:17:50 but
the stack modified time was Oct 14 15:00

It seems that the stack in question was not generated until 15:00. The stackFilter.py ran after that worked fine.

Any comment on why the stack was modified after the run ended ? Is this a virtual stack ? Could this be related to virtual stack function ?

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 #2

Updated by Venkata Dandey about 9 years ago

I had the same issue... Actually some times the stack created shows like "*generate some missing information*" in the place of size of the stack in MB.

So, when I tried to click the "*generate some missing information*" it shows a command which as I remember starts with something like "generate information". I copied the command and run over the terminal in cluster and then size of the stack showed up.

After this any stack operation worked. Don't know what causing this issue... But there is work around for now. I hope this info helps to debug.

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 #3

Updated by Gabriel Lander about 9 years ago

the Mean/STDdev function hasn't been fixed to work with virtual stacks yet. Nor has xmipp projection matching. Unfortunately I haven't had the time to dedicate to this, in the meantime continue with the workaround of generating the stack.
Alternatively, when you make a substack, there's a checkbox to make the actual file instead of a virtual stack.

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 #4

Updated by Anchi Cheng about 9 years ago

  • Subject changed from Mean/StdDev filtering of stack not working to Mean/StdDev filtering of stack not working with virtual stack
  • Status changed from New to Assigned
  • Assignee changed from Priyamvada Acharya to Gabriel Lander
  • Workaround updated (diff)
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