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Bug #2988

open

tiltalign issues

Added by David Veesler almost 10 years ago. Updated almost 9 years ago.

Status:
Assigned
Priority:
Low
Assignee:
Category:
-
Target version:
-
Start date:
12/08/2014
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.1.0
Show in known bugs:
No
Workaround:

Description

On guppy:

/ami/data15/appion/14dec03c/tiltalign/autotiltrun9

tarting image 1 ( skip:23, remain:1008 ) id:3245786, file: 14dec03c_011gr_01sq_02cs_03en_00
... Pixel size: 2.05044
... processing mrc for first image
... processing mrc for second image
... Refining tilt axis angles
using slow tilt angle calculator
Traceback (most recent call last):
File "/opt/myamisnap/bin/tiltAutoAligner.py", line 346, in
imgLoop.run()
File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 90, in run
results = self.loopProcessImage(imgdata)
File "/opt/myamisnap/bin/tiltAutoAligner.py", line 124, in loopProcessImage
result = self.runTiltAligner(imgdata, tiltdata)
File "/opt/myamisnap/bin/tiltAutoAligner.py", line 310, in runTiltAligner
result = autotilter.processTiltPair(imgpath, tiltpath, picks1, picks2, theta, outfile1, pixdiam, tiltaxis)

File "/opt/myamisnap/lib/appionlib/apTilt/autotilt.py", line 348, in processTiltPair
origin, newpart, snr, bestang = apTiltShift.getTiltedCoordinates(img1, img2, tiltangle, picks1, True,
tiltaxis, msg=msg)
File "/opt/myamisnap/lib/appionlib/apTilt/apTiltShift.py", line 37, in getTiltedCoordinates
filt1 = apImage.highPassFilter(binned1, apix=1.0, radius=20.0, localbin=4/bin)
TypeError: highPassFilter() got an unexpected keyword argument 'radius'

On garibaldi:
/ami/data15/appion/14dec03c/tiltalign/autotiltrun10

Traceback (most recent call last):
File "/opt/applications/myami/trunk/bin/tiltAutoAligner.py", line 346, in <module>
imgLoop.run()
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/appionLoop2.py", line 97, in run
self.loopCommitToDatabase(imgdata)
File "/opt/applications/myami/trunk/bin/tiltAutoAligner.py", line 167, in loopCommitToDatabase
self.insertParticlePeakPairs(imgdata, tiltdata, transdata)
File "/opt/applications/myami/trunk/bin/tiltAutoAligner.py", line 181, in insertParticlePeakPairs
imgdata, tiltdata, transdata, self.params['runname'])
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apParticle.py", line 171, in insertParticlePeakPairs
apDisplay.timeString((time.time() - t0)/count*(len(peaktree1)-count)),
ZeroDivisionError: float division


Related issues 1 (1 open0 closed)

Related to Appion - Bug #2939: Appion Developers Conference Call NotesNew09/24/2014

Actions
Actions #1

Updated by Anchi Cheng almost 10 years ago

  • Status changed from New to Assigned
  • Assignee changed from Anchi Cheng to Neil Voss
  • Priority changed from Normal to Immediate

Hi, Neil,

Could you quickly fix the one show up on guppy ? It seems that you have two highPassFilter defined in apImage/imagefilter.py. One takes radius, the other one does not.

all computers goes down on Monday.

Actions #2

Updated by Anchi Cheng almost 10 years ago

For a workaround, I renamed the new highPassFilter to highPassFilter2.

Actions #3

Updated by Anchi Cheng almost 10 years ago

  • Priority changed from Immediate to High

server is about to go down. Downgrade this to be fixed after the move

Actions #4

Updated by Neil Voss almost 10 years ago

Sorry, I was away from my email. Is it fixed now?

Actions #5

Updated by Anchi Cheng almost 10 years ago

I just renamed it so that it does not duplicate. Please fix it after the server is up again in the new year.

Thanks.

Actions #6

Updated by Neil Voss almost 10 years ago

  • Related to Bug #2939: Appion Developers Conference Call Notes added
Actions #7

Updated by Neil Voss almost 9 years ago

  • Priority changed from High to Low
Actions

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