def find_ellipses_display( dfore , bw ):
"""Fits ellipses to connected components in image.
Returns an EllipseList, each member representing
the x,y position and orientation of a single fly."""
# check number of above-threshold pixels
rows, cols = num.nonzero( bw )
# find connected components
(L,ncc) = meas.label(bw)
# make sure there aren't too many connected components
if ncc > params.max_n_clusters:
warn( "too many objects found (>%d); truncating object search"%(params.max_n_clusters) )
# for now, just throw out the last connected components.
# in the future, we can sort based on area and keep those
# with the largest area. hopefully, this never actually
# happens.
ncc = params.max_n_clusters
L[L >= ncc] = 0
# fit ellipses
ellipses = est.weightedregionprops(L,ncc,dfore)
# check if any are small, and [try to] fix those
(issmall,didlowerthresh,didmerge,diddelete) = est.fixsmalldisplay(ellipses,L,dfore)
# check if any are large, and [try to] fix those
(islarge,didsplit) = est.fixlargedisplay(ellipses,L,dfore)
return (ellipses,issmall,islarge,didlowerthresh,didmerge,diddelete,didsplit)
def find_ellipses_display( dfore , L, ncc ):
"""Fits ellipses to connected components in image.
Returns an EllipseList, each member representing
the x,y position and orientation of a single fly."""
# fit ellipses
if DEBUG_TRACKINGSETTINGS: print 'ncc = ' + str(ncc) + ', max(L) = ' + str(num.max(L)) + ', nnz(L) = ' + str(num.flatnonzero(L).shape) + ', sum(dfore) = ' + str(num.sum(num.sum(dfore)))
ellipses = est.weightedregionprops(L,ncc,dfore)
ellipsescopy = []
for ell in ellipses:
ellipsescopy.append(ell.copy())
if DEBUG_TRACKINGSETTINGS: print 'before fixing, ellipses = ' + str(ellipses) + ', len = ' + str(len(ellipses))
if DEBUG_TRACKINGSETTINGS:
areasum = 0
for ell in ellipses:
areasum += ell.area
print 'summed area of ellipses = ' + str(areasum)
# check if any are small, and [try to] fix those
(ellsmall,didlowerthresh,didmerge,diddelete) = est.fixsmalldisplay(ellipses,L,dfore)
if DEBUG_TRACKINGSETTINGS: print 'after fixing small ellipses, ellipses = ' + str(ellipses) + ', len = ' + str(len(ellipses))
if DEBUG_TRACKINGSETTINGS: print 'ellsmall = ' + str(ellsmall)
if DEBUG_TRACKINGSETTINGS: print 'didlowerthresh = ' + str(didlowerthresh)
if DEBUG_TRACKINGSETTINGS: print 'didmerge = ' + str(didmerge)
if DEBUG_TRACKINGSETTINGS: print 'diddelete = ' + str(diddelete)
# check if any are large, and [try to] fix those
(elllarge,didsplit) = est.fixlargedisplay(ellipses,L,dfore)
if DEBUG_TRACKINGSETTINGS: print 'after fixing large ellipses, ellipses = ' + str(ellipses) + ', len = ' + str(len(ellipses))
if DEBUG_TRACKINGSETTINGS: print 'elllarge = ' + str(elllarge)
if DEBUG_TRACKINGSETTINGS: print 'didsplit = ' + str(didsplit)
if DEBUG_TRACKINGSETTINGS: print 'ellsmall = ' + str(ellsmall)
if DEBUG_TRACKINGSETTINGS: print 'didlowerthresh = ' + str(didlowerthresh)
if DEBUG_TRACKINGSETTINGS: print 'didmerge = ' + str(didmerge)
if DEBUG_TRACKINGSETTINGS: print 'diddelete = ' + str(diddelete)
if DEBUG_TRACKINGSETTINGS: print 'returning ellipsescopy = ' + str(ellipsescopy) + ', len = ' + str(len(ellipsescopy))
if DEBUG_TRACKINGSETTINGS:
areasum = 0
for ell in ellipsescopy:
areasum += ell.area
print 'summed area of ellipses = ' + str(areasum)
return (ellipsescopy,ellsmall,elllarge,didlowerthresh,didmerge,diddelete,didsplit)
def find_ellipses_display( dfore , L, ncc ):
"""Fits ellipses to connected components in image.
Returns an EllipseList, each member representing
the x,y position and orientation of a single fly."""
# fit ellipses
if DEBUG_TRACKINGSETTINGS: print 'ncc = ' + str(ncc) + ', max(L) = ' + str(num.max(L)) + ', nnz(L) = ' + str(num.flatnonzero(L).shape) + ', sum(dfore) = ' + str(num.sum(num.sum(dfore)))
ellipses = est.weightedregionprops(L,ncc,dfore)
ellipsescopy = []
for ell in ellipses:
ellipsescopy.append(ell.copy())
if DEBUG_TRACKINGSETTINGS: print 'before fixing, ellipses = ' + str(ellipses) + ', len = ' + str(len(ellipses))
if DEBUG_TRACKINGSETTINGS:
areasum = 0
for ell in ellipses:
areasum += ell.area
print 'summed area of ellipses = ' + str(areasum)
# check if any are small, and [try to] fix those
(ellsmall,didlowerthresh,didmerge,diddelete) = est.fixsmalldisplay(ellipses,L,dfore)
if DEBUG_TRACKINGSETTINGS: print 'after fixing small ellipses, ellipses = ' + str(ellipses) + ', len = ' + str(len(ellipses))
if DEBUG_TRACKINGSETTINGS: print 'ellsmall = ' + str(ellsmall)
if DEBUG_TRACKINGSETTINGS: print 'didlowerthresh = ' + str(didlowerthresh)
if DEBUG_TRACKINGSETTINGS: print 'didmerge = ' + str(didmerge)
if DEBUG_TRACKINGSETTINGS: print 'diddelete = ' + str(diddelete)
# check if any are large, and [try to] fix those
(elllarge,didsplit) = est.fixlargedisplay(ellipses,L,dfore)
if DEBUG_TRACKINGSETTINGS: print 'after fixing large ellipses, ellipses = ' + str(ellipses) + ', len = ' + str(len(ellipses))
if DEBUG_TRACKINGSETTINGS: print 'elllarge = ' + str(elllarge)
if DEBUG_TRACKINGSETTINGS: print 'didsplit = ' + str(didsplit)
if DEBUG_TRACKINGSETTINGS: print 'ellsmall = ' + str(ellsmall)
if DEBUG_TRACKINGSETTINGS: print 'didlowerthresh = ' + str(didlowerthresh)
if DEBUG_TRACKINGSETTINGS: print 'didmerge = ' + str(didmerge)
if DEBUG_TRACKINGSETTINGS: print 'diddelete = ' + str(diddelete)
if DEBUG_TRACKINGSETTINGS: print 'returning ellipsescopy = ' + str(ellipsescopy) + ', len = ' + str(len(ellipsescopy))
if DEBUG_TRACKINGSETTINGS:
areasum = 0
for ell in ellipsescopy:
areasum += ell.area
print 'summed area of ellipses = ' + str(areasum)
return (ellipsescopy,ellsmall,elllarge,didlowerthresh,didmerge,diddelete,didsplit)
