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Bug #2437
closedautomasker.py shape mismatch?
Start date:
07/24/2013
Due date:
% Done:
0%
Estimated time:
Affected Version:
Appion/Leginon 3.0.0
Show in known bugs:
No
Workaround:
Description
I'm trying to run the automasker on data collected on the T2 DD. I'm using /opt/myamisnap/bin appion. I get this error on the first image:
Beginning Main Loop
Starting image 1 ( skip:1201, remain:1672 ) id:1970578, file: 12oct30b_021hl_03ed
... Pixel size: 1.424
... Converting mrc image to jpg.
... running em hole finder Wed Jul 24 09:14:31 2013
source /opt/em_hole_finder/env/bin/activate; python /opt/em_hole_finder/find_mask_amber_dev.py --ifile=/ami/data15/appion/glander/12oct30b/mask/maskauto1/jpgs/12oct30b_00021hl_v02_00003ed.jpg --ofile=/ami/data15/appion/glander/12oct30b/mask/maskauto1/masks/12oct30b_00021hl_v02_00003ed_mask.jpg --downsample=20 --compsizethresh=50 --adapthresh=500 --blur=10 --dilation=10 --erosion=1
==== Committing data to database ====
... Writing results to database: Wed Jul 24 09:14:49 2013
... MRC Image Shape:
[3072 4096]
... MRC Image Size:
12582912
... Mask Image Shape:
(124, 175)
... resizing mask image.
24.7741935484
... Mask Image Shape:
(3072, 4335)
... getting mask region info.
getting region info
Getting real perimeter length
Getting real mean and stdev
Traceback (most recent call last):
File "/ami/sw/packages/myamitrunk/appion/bin/automasker.py", line 317, in <module>
function.run()
File "/ami/sw/packages/myamitrunk/appion/appionlib/appionLoop2.py", line 97, in run
self.loopCommitToDatabase(imgdata)
File "/ami/sw/packages/myamitrunk/appion/appionlib/appionLoop2.py", line 146, in loopCommitToDatabase
return self.commitToDatabase(imgdata)
File "/ami/sw/packages/myamitrunk/appion/bin/automasker.py", line 167, in commitToDatabase
infos,testlog = apCrud.getLabeledInfo( imgdata['image'], img3, labeled_regions, range(1,clabels+1), False, infos, testlog)
File "/ami/sw/packages/myamitrunk/appion/appionlib/apCrud.py", line 349, in getLabeledInfo
info=getRealLabeledMeanStdev(image,labeled_image,indices,info)
File "/ami/sw/packages/myamitrunk/appion/appionlib/apCrud.py", line 232, in getRealLabeledMeanStdev
mean=nd.mean(image,labels=labeled_image,index=indices)
File "/usr/lib64/python2.6/site-packages/scipy/ndimage/measurements.py", line 141, in mean
labels = _broadcast(labels, input.shape)
File "/usr/lib64/python2.6/site-packages/scipy/ndimage/measurements.py", line 417, in _broadcast
return_value[sslices] = arr[aslices]
ValueError: shape mismatch: objects cannot be broadcast to a single shape
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