Bug #5044
closedas of last night can no longer create stack using myami/3.2
0%
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
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.
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
Updated by Neil Voss over 7 years ago
- Related to Bug #4994: CTFdisplayTool error added
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.
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.