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Bug #1401
closeddogpicker fails with scipy 0.9.0
Status:
Won't Fix or Won't Do
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Start date:
08/18/2011
Due date:
% Done:
0%
Estimated time:
Affected Version:
Appion/Leginon 2.1.0
Show in known bugs:
No
Workaround:
Description
This was from Ben Eisenbraun at Harvard:
ApDogPicker.py --image=groel-stain.mrc --outfile=picks.txt --invert --thresh=0.7 --diam=10
... Time stamp: 11aug18m18
... Function name: ApDogPicker
... Appion directory: /nfs/programs/x86_64-linux/dogpicker/0.2
!!! WARNING: Not committing data to database
... Writing function log to: ApDogPicker.log
particle pixel sizes= [ 3.93075689 6.36009825]
diameter list= [ 7.86199999 12.72000027]
Traceback (most recent call last):
File "/programs/x/dogpicker/0.2/ApDogPicker.py", line 164, in <module>
dogpicker.start()
File "/programs/x/dogpicker/0.2/ApDogPicker.py", line 125, in start
msg=True, bin=1)
File "/nfs/programs/x86_64-linux/dogpicker/0.2/appionlib/apPeaks.py", line 95,
in findPeaksInMap
varyThreshold(imgmap, thresh, maxsize)
File "/nfs/programs/x86_64-linux/dogpicker/0.2/appionlib/apPeaks.py", line 331
, in varyThreshold
blobtree, percentcov = findBlobs(ccmap, thresh, maxsize=maxsize)
File "/nfs/programs/x86_64-linux/dogpicker/0.2/appionlib/apPeaks.py", line 397
, in findBlobs
maxsize, minsize, maxmoment, elim, summary)
File "/nfs/programs/x86_64-linux/dogpicker/0.2/pyami/imagefun.py", line 338, i
+n find_blobs
File "/nfs/programs/x86_64-linux/dogpicker/0.2/pyami/imagefun.py", line 267, i
+n scipyblobs
stds = scipy.ndimage.standard_deviation(im,labels,range(1,n+1))
File "/programs/x/python/2.7/lib/python2.7/site-packages/scipy/ndimage/measure
+ments.py", line 649, in standard_deviation
return numpy.sqrt(variance(input, labels, index))
File "/programs/x/python/2.7/lib/python2.7/site-packages/scipy/ndimage/measure
+ments.py", line 596, in variance
count, sum, sum_c_sq = _stats(input, labels, index, centered=True)
File "/programs/x/python/2.7/lib/python2.7/site-packages/scipy/ndimage/measure
+ments.py", line 434, in _stats
sums_c = _sum_centered(labels.ravel())
File "/programs/x/python/2.7/lib/python2.7/site-packages/scipy/ndimage/measure
+ments.py", line 408, in _sum_centered
centered_input = input - means[labels]
ValueError: operands could not be broadcast together with shapes (512,512)
(262144)
$ python --version
Python 2.7
$ python -c "import scipy; print scipy.version.version"
0.9.0rc1Files
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