Bug #906: manual tilt picker crashes after first image - Appion - Electron Microscopy Group

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Bug #906

closed

manual tilt picker crashes after first image

Added by Arne Moeller over 13 years ago. Updated over 8 years ago.

Status:

Closed

Priority:

High

Assignee:

Arne Moeller

Category:

Python scripting

Target version:

Appion/Leginon 3.1.0

Start date:

10/11/2010

Due date:

% Done:

Estimated time:

Affected Version:

Appion/Leginon 2.0.2

Show in known bugs:

Workaround:

Description

manual tilt picker crashes after first image pair. You can transfer the coordinates of the picks from one image to the next but the images don't get "optimized". after clicking the forward button the viewer crashes. I've tested it on different machines and with different datasets, as well as different binning factors.

ERROR MESSAGE:

... 24 of 25 good (1 bad) particles; min worst error=4.598
... writing peak JPEG: /ami/data07/appion/10jun25a/tiltalign/tiltrun9-ends/jpgs/10jun25a_c_00014gr_00017sq_v01_00002cs_v01_00002en_00.prtl.jpg
... writing peak JPEG: /ami/data07/appion/10jun25a/tiltalign/tiltrun9-ends/jpgs/10jun25a_c_00014gr_00017sq_v01_00002cs_v02_00002en_01.prtl.jpg ==== Committing data to database ====
... Final image assessment: keep (10jun25a_c_014gr_017sq_02cs_02en_00)
... Final image assessment: keep (10jun25a_c_014gr_017sq_02cs_02en_01)
Traceback (most recent call last):
File "/ami/sw/packages/myamitrunk/appion/bin/tiltaligner.py", line 386, in ?
imgLoop.run()
File "/ami/sw/packages/myamitrunk/appion/appionlib/appionLoop2.py", line 77, in run
self.loopCommitToDatabase(imgdata)
File "/ami/sw/packages/myamitrunk/appion/bin/tiltaligner.py", line 155, in loopCommitToDatabase
transdata = apTiltPair.insertTiltTransform(imgdata, tiltdata, self.tiltparams, self.params)
File "/ami/sw/packages/myamitrunk/appion/appionlib/apTilt/apTiltPair.py", line 181, in insertTiltTransform
apDisplay.printError("Key: "+key+" was not found in transformation data")
File "/ami/sw/packages/myamitrunk/appion/appionlib/apDisplay.py", line 56, in printError
raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
Exception:

FATAL ERROR ***
Key: overlap was not found in transformation data

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Updated by Neil Voss over 13 years ago

The crash is happening because the images are not getting optimized. The Pipeline TiltPicker requires an optimization step to insert. I need to ask more about that. Why are the images not getting optimized?

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Updated by Arne Moeller over 13 years ago

Hi Neil,
I do not know why.... If you run it it does not do the cutting of the image after clicking auto-optimize. However the coordinates are transferred correctly from one image to the other. I suspected that this issue might be related to the fact that the data is deposited on data07 and not on data00 - I asked Christopher about that and he said that this cannot be the case.

how can I find out why the images are not optimized?

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Updated by Arne Moeller over 13 years ago

Category set to Image Processing

Hi Neil, I ran into the same issue with a brand new dataset... I think it is a real bug... Let me know what I can check to provide you with the data you need....

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Updated by Neil Voss over 13 years ago

Hi Arne, provide me with the exact command that you run and make sure that I can read and write to the processing directory. I will try to login to amibox and run the command remotely.

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Updated by Arne Moeller over 13 years ago

/ami/sw/bin/appion tiltaligner.py --projectid=249 --preset=en --session=10nov04f --runname=tiltrun6-man --rundir=/ami/data00/appion/10nov04f/tiltalign/tiltrun6-man --no-rejects --no-wait --commit --continue --median=2 --lowpass=15 --highpass=0 --planereg --bin=4 --diam=100 --pixlimit=4.0 --outtype=spider

I ran this command from amibox02

Thanks

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Updated by Neil Voss over 13 years ago

Category changed from Image Processing to Python scripting
Status changed from New to In Code Review
Assignee changed from Neil Voss to Amber Herold

Arne I've committed a fix to the trunk. There was a typo in the code that always crashed when reaching that line. See if this fixes the problem.

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Updated by Arne Moeller over 13 years ago

Hi Neil,
The tilt picker window pops up and crashes within the next second producing this error message:

... 3 of 5 good (2 bad) particles; min worst error=52.194
Traceback (most recent call last):
  File "/ami/sw/packages/myami-2.1/appion/bin/tiltaligner.py", line 386, in ?
    imgLoop.run()
  File "/ami/sw/leginon/myami-trunk/appion/appionlib/appionLoop2.py", line 70, in run
    results = self.loopProcessImage(imgdata)
  File "/ami/sw/packages/myami-2.1/appion/bin/tiltaligner.py", line 106, in loopProcessImage
    self.runTiltAligner(imgdata, tiltdata)
  File "/ami/sw/packages/myami-2.1/appion/bin/tiltaligner.py", line 363, in runTiltAligner
    self.app.onAutoOptim(None)
  File "/ami/sw/packages/myami-2.1/appion/bin/ApTiltPicker.py", line 1335, in onAutoOptim
    self.onMaskRegion(None)
  File "/ami/sw/packages/myami-2.1/appion/bin/ApTiltPicker.py", line 651, in onMaskRegion
    if self.data[''] is False:
KeyError: ''