Leginon

Hello,

While we have appion running on a single machine here at Harard, I'm trying to start extend our Appion use to other machines in our lab. We are using an SBGrid computer setup, where they provide an appion installation for our use, where all of the /myami/appion/bin files are installed already. When I try to run a simple commend (e.g. ApDogPicker.py) on a single micrograph, this is the output that I get:

$ ApDogPicker.py  -i /labdata/allab/leginondata/13feb27l/rawdata/13feb27l_00005hl_00002en.mrc -a 2.19 -t 0.3 -o test --diam=200
/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/pyami/tifffile.py:903: UserWarning: Failed to import _tifffile.decodepackbits
  warnings.warn("Failed to import %s" % module_function)
/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/pyami/tifffile.py:903: UserWarning: Failed to import _tifffile.decodelzw
  warnings.warn("Failed to import %s" % module_function)
 ... Time stamp: 13feb28s29
 ... Function name: ApDogPicker
 ... Writing function log to: ApDogPicker.log
particle pixel sizes= [ 45.09493544  46.23639879]
diameter list= [ 197.51600647  202.51499939]
Traceback (most recent call last):
  File "/programs/x/appion/2.2/ApDogPicker.py", line 148, in <module>
    dogpicker.start()
  File "/programs/x/appion/2.2/ApDogPicker.py", line 109, in start
    msg=True, bin=1)
  File "/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/appionlib/apPeaks.py", line 94, in findPeaksInMap
    varyThreshold(imgmap, thresh, maxsize)
  File "/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/appionlib/apPeaks.py", line 330, in varyThreshold
    blobtree, percentcov = findBlobs(ccmap, thresh, maxsize=maxsize)
  File "/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/appionlib/apPeaks.py", line 396, in findBlobs
    maxsize, minsize, maxmoment, elim, summary)
  File "/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/pyami/imagefun.py", line 357, in find_blobs
    blobs = scipyblobs(image,tmpmask)
  File "/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/pyami/imagefun.py", line 286, in scipyblobs
    stds = scipy.ndimage.standard_deviation(im,labels,range(1,n+1))
  File "/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/scipy/ndimage/measurements.py", line 642, in standard_deviation
    return numpy.sqrt(variance(input, labels, index))
  File "/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/scipy/ndimage/measurements.py", line 589, in variance
    count, sum, sum_c_sq = _stats(input, labels, index, centered=True)
  File "/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/scipy/ndimage/measurements.py", line 432, in _stats
    sums_c = _sum_centered(labels.ravel())
  File "/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/scipy/ndimage/measurements.py", line 406, in _sum_centered
    centered_input = input - means[labels]
ValueError: operands could not be broadcast together with shapes (4096,4096) (16777216) 

It looks like it gets tripped up on the python libraries that SBGrid has installed. I'd like to know how to approach SBGrid to have them help me get these scripts running.

If anyone has use Appion through SBGrid, I'd be glad to hear your experience.

Thanks!
Mike