Appion

Note: we are using highPassFilter2() not highPassFilter()

current bug in templateCorrelator:

dlyumkis@bpho-bladerunner-1 jpgs] templateCorrelator.py --runname=tmplrun5_220heter --rundir=/data2/log-l/appion/15sep15a/extract/tmplrun5_220heter --projectid=2 --session=15sep15a --no-rejects --no-wait --no-commit --no-continue --mrclist=15sep15a_00022sq_00036hl_00002ed-a.mrc --overlapmult=1.25 --peaktype=centerofmass --maxpeaks=200 --thresh=0.48 --invert --median=2 --lowpass=22 --planereg --bin=4 --diam=220 --pixlimit=4.0 --template-list=57,55,53,51,49,47,45,43,41,39,37 --range-list=0,10,20x0,10,20x0,10,20x0,10,20x0,10,20x0,10,20x0,10,20x0,10,20x0,10,20x0,10,20x0,10,20 --thread-findem --use-mirrors 
 ... Time stamp: 15sep16l55
 ... Function name: templateCorrelator
 ... Appion directory: /data2/log-l/progs/myami/appion
!!! WARNING: There is more than one appion directory in your PYTHONPATH
['/usr/local/appion/EMAN2/bin', '/data2/log-l/progs/myami/appion', '/usr/local/appion/EMAN2/lib']
 ... Using split database
Connected to database: 'ap2'
!!! WARNING: Not committing data to database
 ... Found 40 processors on this machine
 ... Found project id=2 for session 15sep15a in 8.28 msec
 ... Run directory: /data2/log-l/appion/15sep15a/extract/tmplrun5_220heter
!!! WARNING: directory '/data2/log-l/appion/15sep15a/extract/tmplrun5_220heter' already exists.
 ... Writing function log to: templateCorrelator.log
 ... Uploading ScriptData....
 ... Found 40 processors on this machine
 ... Running Appion version 'trunk-r19170M'
 ... Creating new done dictionary: templateCorrelator.donedict
Querying database for 1 specific images ... 
 ... Looking up session, 15sep15a
 ... Found 1 images in 5.35 msec
 ... Remove processed images
 ... finished skipping in 16.13 msec
 ... Process images old to new
 ... getting templates
 ... getting template: /data2/log-l/appion/15sep15a/templates/template15sep16d14/IKK2_tetramer_box_64_apix_3.93_image_43-15sep16k36.mrc
 ... reading MRC: origTemplate1.mrc size:(64, 64) dtype:float32
 ... rescaling template 1: 3.93->1.31
 ... scaling template by a factor of 3.0
Traceback (most recent call last):
  File "/data2/log-l/progs/myami/appion/bin/templateCorrelator.py", line 8, in <module>
    imgLoop.run()
  File "/data2/log-l/progs/myami/appion/appionlib/appionLoop2.py", line 63, in run
    self.preLoopFunctions()
  File "/data2/log-l/progs/myami/appion/appionlib/apTemplateCorrelator.py", line 139, in preLoopFunctions
    apTemplate.getTemplates(self.params)
  File "/data2/log-l/progs/myami/appion/appionlib/apTemplate.py", line 73, in getTemplates
    templatearray = apImage.preProcessImage(templatearray, params=params, highpass=0, planeReg=False, invert=False)
  File "/data2/log-l/progs/myami/appion/appionlib/apImage/imagefilter.py", line 121, in preProcessImage
    result = _processImage(imgarray, bin, apix, lowpass, highpass, planeReg, median, invert, pixlimit, msg)
  File "/data2/log-l/progs/myami/appion/appionlib/apImage/imagefilter.py", line 43, in _processImage
    simgarray = highPassFilter2(simgarray, highpass, apix)
  File "/data2/log-l/progs/myami/appion/appionlib/apImage/imagefilter.py", line 549, in highPassFilter2
    filter = tanhFilter(hpFilterSize, data.shape)
  File "/data2/log-l/progs/myami/appion/appionlib/apImage/imagefilter.py", line 572, in tanhFilter
    filter = numpy.tanh(radial/fuzzyEdge - 1.01*(max(shape))/float(pixelradius)/fuzzyEdge)/2.0 + 0.5
ZeroDivisionError: float division

Well, one of these values must be zero:

radial, fuzzyEdge, max(shape), pixelradius

my guess is pixelradius

this looks ok now, I'm actually not sure what exactly the issue was, I will have to backtrack to see what exactly was done ...

I am going a different direction with this, see #3970 in future.