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Bug #5044

closed

as of last night can no longer create stack using myami/3.2

Added by Elizabeth Wilson-Kubalek over 7 years ago. Updated over 7 years ago.

Status:
Closed
Priority:
Urgent
Assignee:
-
Category:
-
Target version:
-
Start date:
06/23/2017
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.2
Show in known bugs:
No
Workaround:

Description

using myami/3.2 allowed me to obtain stacks with correct particle number but now I can't get any stack using myami/3.2 the error reads

!!! WARNING: skipped 9 of 1269 images
... [[ 0 no reprocess | 9 rejected | 0 wrong tilt | 0 in donedict ]]
... Process images old to new
!!! WARNING: Checking for dd
... Stack pixelsize = 1.310 A
... Looking up session, 17may30d
... missing acecutoff
Inserting stack parameters into database
... querying stack particles from stackid=41 at Fri Jun 23 10:22:47 2017
!!! WARNING: failed to get particles of stackid=41
... sorting particles
... received 0 stack particles in 3.11 msec
!!! WARNING: file exists but no particles in database, deleting stack file
... Starting at particle number: 0

2.0
Traceback (most recent call last):
File "/opt/applications/myami/3.2/bin/makestack2.py", line 1320, in <module>
makeStack.run()
File "/opt/applications/myami/3.2/lib/python2.7/site-packages/appionlib/appionLoop2.py", line 65, in r
un
self.preLoopFunctions()
File "/opt/applications/myami/3.2/bin/makestack2.py", line 1206, in preLoopFunctions
self.summedParticles = numpy.zeros((binbox, binbox))
TypeError: 'float' object cannot be interpreted as an index


Related issues 2 (2 open0 closed)

Related to Appion - Feature #4932: Should we add scaling (as opposed to binning) in makestack: box size divided by bin size is a float in makestackAssignedNeil Voss04/26/2017

Actions
Related to Appion - Bug #4994: CTFdisplayTool errorAssignedScott Stagg05/31/2017

Actions
Actions #1

Updated by Neil Voss over 7 years ago

Liz: I would try again on an older machine. I think the software version is too new and we have some fixes to make before it works again.

Group: I think this is another instance of bug #4994, because the version of numpy is too new. We are going to have several fixes needed to deal all of the float being using as shape variables.

Actions #2

Updated by Neil Voss over 7 years ago

  • Related to Feature #4932: Should we add scaling (as opposed to binning) in makestack: box size divided by bin size is a float in makestack added
Actions #3

Updated by Neil Voss over 7 years ago

  • Related to Bug #4994: CTFdisplayTool error added
Actions #4

Updated by Neil Voss over 7 years ago

Actually, this may be related to bug #4932, where we have not made a decision on handling bin as a float.

Actions #5

Updated by Elizabeth Wilson-Kubalek over 7 years ago

Neil Voss wrote:

Actually, this may be related to bug #4932, where we have not made a decision on handling bin as a float.

Thanks Niel, you are correct our computer manager for Scripps has fixed something on numpy at it running now. I am hoping the stack will run to completion.

Actions #6

Updated by Anchi Cheng over 7 years ago

  • Status changed from New to Closed
Actions

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