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Bug #825
closedCould not find image: error on uploadparticles.py
Status:
Won't Fix or Won't Do
Priority:
Normal
Assignee:
Amber Herold
Category:
-
Target version:
Start date:
08/18/2010
Due date:
% Done:
0%
Estimated time:
Affected Version:
Appion/Leginon 2.2.0
Show in known bugs:
No
Workaround:
Rename the box files to match the image filenames that have been saved to the database.
Description
/ami/sw/bin/appion uploadParticles --projectid=277 --session=10aug17z --runname=manual1 --files="/home/lfisher/hi_res/japan/micro_mrc/*.box" --diam=330 --rundir=/ami/data00/appion/10aug17z/extract/manual1 --bin=1 --commit
... Time stamp: 10aug17q15... Function name: uploadParticles
... Appion directory: /ami/sw/packages/myamitrunk/appion
!!! WARNING: There is more than one appion directory in your PYTHONPATH
['/ami/sw/packages/pyappion/lib', '/ami/sw/packages/myamitrunk/appion']
!!! WARNING: Using split database
Connected to database: 'ap277'
... Committing data to database
... Looking up session, 10aug17z
... Run directory: /ami/data00/appion/10aug17z/extract/manual1
!!! WARNING: directory '/ami/data00/appion/10aug17z/extract/manual1' already exists.
... Writing function log to: uploadParticles.log
... Found 4 processors on this machine
... Running Appion version 'r14669'
... Getting box files
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1433.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1441.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1448.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1405.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1410.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1420.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1455.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1456.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1385.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1430.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1426.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1429.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1444.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1413.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1440.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1432.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1408.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1391.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1443.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1401.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1397.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1400.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1454.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1449.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1416.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1424.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1393.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1398.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1396.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1428.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1403.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1445.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1414.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1457.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1434.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1402.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1404.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1459.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1407.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1411.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1439.box
... Copying file to /ami/data00/appion/10aug17z/extract/manual1/a1390.box
... Getting image data from database
Querying database for 42 specific images ...
[]
Traceback (most recent call last):
File "/ami/sw/packages/myamitrunk/appion/bin/uploadParticles.py", line 159, in ?
uploadpart.start()
File "/ami/sw/packages/myamitrunk/appion/bin/uploadParticles.py", line 141, in start
imgtree = apDatabase.getSpecificImagesFromDB(boxfiles)
File "/ami/sw/packages/myamitrunk/appion/appionlib/apDatabase.py", line 70, in getSpecificImagesFromDB
apDisplay.printError("Could not find image: "+imgname)
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 ***
Could not find image: a1433
Files
Updated by Amber Herold over 14 years ago
- Status changed from New to Assigned
- Priority changed from Normal to Urgent
Import tools->Upload Particles
Can get data files from Lauren if needed.
Updated by Amber Herold over 14 years ago
- Priority changed from Urgent to Normal
- Target version set to Appion/Leginon 2.2.0
Looks like the problem is that the images have 10aug17z_ prepended to their filenames as they appear in the database, and the box files do not. They must match for this function to work.
It would be nice to have more error checking in the db lookup and perhaps make it more clear to the user what the files should be named. It is confusing because image viewer listed the files without the session name prepended.
Updated by Amber Herold over 14 years ago
- Subject changed from error on uploadparticles.py to Could not find image: error on uploadparticles.py
Updated by Amber Herold almost 14 years ago
- Deliverable set to 2.2 Bug Reduction
Updated by Amber Herold over 12 years ago
- Target version changed from Appion/Leginon 2.2.0 to Appion/Leginon Future Version
Updated by Amber Herold over 10 years ago
- Status changed from Assigned to Won't Fix or Won't Do
- Affected Version changed from Appion/Leginon 2.0.2 to Appion/Leginon 2.2.0
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