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Bug #4204

closed

catch error in validation and commit and move on

Added by Anchi Cheng over 8 years ago. Updated almost 7 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Anchi Cheng
Category:
-
Target version:
Appion/Leginon 3.3
Start date:
05/24/2016
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.2
Show in known bugs:
No
Workaround:

Description

ctf estimation is used in live data collection and it makes stopping appionLoop when validation has problem a bad place to stop.

Here are examples of them which I will use a try-except to bypass.
16may23b_00131fcn.mrc

Traceback (most recent call last):
  File "/home/acheng/myami/appion/bin/ctffind4.py", line 353, in <module>
    imgLoop.run()
  File "/home/acheng/myami/appion/appionlib/appionLoop2.py", line 95, in run
    self.loopCommitToDatabase(imgdata)
  File "/home/acheng/myami/appion/appionlib/appionLoop2.py", line 153, in loopCommitToDatabase
    return self.commitToDatabase(imgdata)
  File "/home/acheng/myami/appion/bin/ctffind4.py", line 306, in commitToDatabase
    ctfinsert.validateAndInsertCTFData(imgdata, self.ctfvalues, self.ctfrun, self.params['rundir'])
  File "/home/acheng/myami/appion/appionlib/apCtf/ctfinsert.py", line 45, in validateAndInsertCTFData
    ctfvalues = runCTFdisplayTools(imgdata, ctfvalues, opimagedir, fftpath, fftfreq)
  File "/home/acheng/myami/appion/appionlib/apCtf/ctfinsert.py", line 80, in runCTFdisplayTools
    ctfdisplaydict = ctfdisplay.makeCtfImages(imgdata, ctfvalues, fftpath, fftfreq)
  File "/home/acheng/myami/appion/appionlib/apCtf/ctfdisplay.py", line 1436, in makeCtfImages
    ctfdisplaydict = a.CTFpowerspec(imgdata, ctfdata, fftpath, fftfreq, twod=twod)
  File "/home/acheng/myami/appion/appionlib/apCtf/ctfdisplay.py", line 1318, in CTFpowerspec
    normpowerspec = self.normalizeCtf(powerspec, twod=twod)
  File "/home/acheng/myami/appion/appionlib/apCtf/ctfdisplay.py", line 588, in normalizeCtf
    ind5peak2 = numpy.searchsorted(raddata, peakradii[5])
IndexError: index out of bounds

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