Bug #906
closedmanual tilt picker crashes after first image
0%
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
Updated by Neil Voss about 14 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?
Updated by Arne Moeller about 14 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?
Updated by Arne Moeller about 14 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....
Updated by Neil Voss about 14 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.
Updated by Arne Moeller about 14 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
Updated by Neil Voss about 14 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.
Updated by Arne Moeller about 14 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: ''Updated by Neil Voss about 14 years ago
Hi Arne, that is the bug I just fixed you are using the old version, you need to find a way to use the trunk version of myami.
Updated by Amber Herold almost 14 years ago
- Status changed from In Code Review to In Test
- Assignee changed from Amber Herold to Arne Moeller
I reviewed the fix, looks good. Arne, can you test this now? You should be able to use cronus3/betamyamiweb now.
Updated by Anchi Cheng almost 14 years ago
r15130 committed the fix to branch 2.1
Updated by Anchi Cheng almost 9 years ago
- Status changed from In Test to Closed
- Target version changed from Appion/Leginon 2.0.2 to Appion/Leginon 3.1.0