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Bug #2080

open

templateCorrelator crash

Added by Scott Stagg about 12 years ago. Updated about 11 years ago.

Status:
In Test
Priority:
Normal
Assignee:
Natalia de Val
Category:
Image Processing
Target version:
Appion/Leginon 2.2.0
Start date:
10/04/2012
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.2.0
Show in known bugs:
No
Workaround:

Description

I am getting a bug where templateCorrelator (from trunk) crashes when the program finds just 1 particle. Zero particles is OK, and >1 particles is OK, just not 1 particle. The exception is below:

Traceback (most recent call last):
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/bin/templateCorrelator.py", line 190, in <module>
    imgLoop.run()
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/appionlib/appionLoop2.py", line 70, in run
    results = self.loopProcessImage(imgdata)
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/appionlib/particleLoop2.py", line 104, in loopProcessImage
    self.peaktree = filterLoop.FilterLoop.loopProcessImage(self, imgdata)
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/appionlib/filterLoop.py", line 87, in loopProcessImage
    peaktree = self.processImage(imgdata, self.filtarray)
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/bin/templateCorrelator.py", line 163, in processImage
    peaktree  = apPeaks.findPeaks(imgdata, ccmaplist, self.params)
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/appionlib/apPeaks.py", line 51, in findPeaks
    maxpeaks, maxsizemult, msg, tmpldbid, mapdiam, bin=bin, peaktype=peaktype)
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/appionlib/apPeaks.py", line 101, in findPeaksInMap
    peaktree = convertBlobsToPeaks(blobtree, bin, tmpldbid, count, mapdiam, peaktype)
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/appionlib/apPeaks.py", line 365, in convertBlobsToPeaks
    peakdict['ycoord']      = int(round( float(blobclass.stats['center'][0])*float(bin) ))
TypeError: float() argument must be a string or a number

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 #1

Updated by Anchi Cheng about 12 years ago

  • Status changed from New to In Code Review
  • Assignee set to Jim Pulokas

Looks like scipy now return array instead of single value when statistics functions give one result. r17166 detects this.
Will merge to 2.2-redux if test is passed.

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 #2

Updated by Anchi Cheng about 11 years ago

  • Status changed from In Code Review to In Test
  • Assignee changed from Jim Pulokas to Natalia de Val

Natalia,

Once you've tested with trunk, update this issue and assign it back to me. This fix should be added to 2.2 version.

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 #3

Updated by Natalia de Val about 11 years ago

  • Category set to Image Processing
  • Target version set to Appion/Leginon 2.2.0
  • Deliverable set to 2.2 Bug Reduction

Traceback (most recent call last):
File "/opt/applications/myami/trunk/bin/templateCorrelator.py", line 8, in <module>
imgLoop.run()
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/appionLoop2.py", line 90, in run
results = self.loopProcessImage(imgdata)
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/particleLoop2.py", line 104, in loopProcessImage
self.peaktree = filterLoop.FilterLoop.loopProcessImage(self, imgdata)
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/filterLoop.py", line 87, in loopProcessImage
peaktree = self.processImage(imgdata, self.filtarray)
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apTemplateCorrelator.py", line 169, in processImage
cclist = self.runTemplateCorrelator(imgdata)
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apTemplateCorrelator.py", line 141, in runTemplateCorrelator
ccmaplist = apFindEM.runFindEM(imgdata, self.params, thread=self.params['threadfindem'])
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apFindEM.py", line 171, in runFindEM
apDisplay.printError("findem.exe did not run or crashed.\n")
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apDisplay.py", line 61, in printError
raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
Exception: * FATAL ERROR *
findem.exe did not run or crashed.

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