def find_ellipses2( dfore , bw, dofix=True ):
"""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)
if dofix:
# check if any are small, and [try to] fix those
est.fixsmall(ellipses,L,dfore)
# check if any are large, and [try to] fix those
est.fixlarge(ellipses,L,dfore)
return (ellipses,L)
def find_ellipses(dfore, L, ncc, dofix=True):
"""Fits ellipses to connected components in image.
Returns an EllipseList, each member representing
the x,y position and orientation of a single fly."""
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)))
# fit ellipses
ellipses = est.weightedregionprops(L, ncc, dfore)
if DEBUG_TRACKINGSETTINGS:
print 'initial list of ellipses:'
for i in range(len(ellipses)):
print 'ellipse[%d] = ' % i + str(ellipses[i])
#print 'time to fit ellipses: %.2f'%(time.time() - last_time)
if dofix:
# store current time to find out how long fitting ellipses takes
last_time = time.time()
# check if any are small, and [try to] fix those
est.fixsmall(ellipses, L, dfore)
#print 'after fixing small, ellipses = '
#for i in range(len(ellipses)):
# print 'ellipse[%d] = '%i + str(ellipses[i])
#print 'time to fix small ellipses: %.2f'%(time.time() - last_time)
last_time = time.time()
# check if any are large, and [try to] fix those
est.fixlarge(ellipses, L, dfore)
if DEBUG_TRACKINGSETTINGS:
print 'after fixing large, ellipses ='
for i in range(len(ellipses)):
print 'ellipse[%d] = ' % i + str(ellipses[i])
#print 'time to fix large ellipses: %.2f'%(time.time() - last_time)
#est.deleteellipses(ellipses)
return ellipses
def find_ellipses(dfore, L, ncc, dofix=True):
"""Fits ellipses to connected components in image.
Returns an EllipseList, each member representing
the x,y position and orientation of a single fly."""
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)))
# fit ellipses
ellipses = est.weightedregionprops(L, ncc, dfore)
if DEBUG_TRACKINGSETTINGS:
print "initial list of ellipses:"
for i in range(len(ellipses)):
print "ellipse[%d] = " % i + str(ellipses[i])
# print 'time to fit ellipses: %.2f'%(time.time() - last_time)
if dofix:
# store current time to find out how long fitting ellipses takes
last_time = time.time()
# check if any are small, and [try to] fix those
est.fixsmall(ellipses, L, dfore)
# print 'after fixing small, ellipses = '
# for i in range(len(ellipses)):
# print 'ellipse[%d] = '%i + str(ellipses[i])
# print 'time to fix small ellipses: %.2f'%(time.time() - last_time)
last_time = time.time()
# check if any are large, and [try to] fix those
est.fixlarge(ellipses, L, dfore)
if DEBUG_TRACKINGSETTINGS:
print "after fixing large, ellipses ="
for i in range(len(ellipses)):
print "ellipse[%d] = " % i + str(ellipses[i])
# print 'time to fix large ellipses: %.2f'%(time.time() - last_time)
# est.deleteellipses(ellipses)
return ellipses
def find_ellipses2( dfore , L, ncc, dofix=True ):
"""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
ellipses = est.weightedregionprops(L,ncc,dfore)
if dofix:
# check if any are small, and [try to] fix those
est.fixsmall(ellipses,L,dfore)
# check if any are large, and [try to] fix those
est.fixlarge(ellipses,L,dfore)
return (ellipses,L)
def find_ellipses2(dfore, L, ncc, dofix=True):
"""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
ellipses = est.weightedregionprops(L, ncc, dfore)
if dofix:
# check if any are small, and [try to] fix those
est.fixsmall(ellipses, L, dfore)
# check if any are large, and [try to] fix those
est.fixlarge(ellipses, L, dfore)
return (ellipses, L)
def find_ellipses( dfore , bw, dofix=True ):
"""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 )
# store current time to find out how long computing ccs takes
last_time = time.time()
# 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
#print 'time to compute connected components: %.2f'%(time.time()-last_time)
# store current time to find out how long fitting ellipses takes
last_time = time.time()
# fit ellipses
ellipses = est.weightedregionprops(L,ncc,dfore)
#print 'initial list of ellipses:'
#for i in range(len(ellipses)):
# print 'ellipse[%d] = '%i + str(ellipses[i])
#print 'time to fit ellipses: %.2f'%(time.time() - last_time)
if dofix:
# store current time to find out how long fitting ellipses takes
last_time = time.time()
# check if any are small, and [try to] fix those
est.fixsmall(ellipses,L,dfore)
#print 'after fixing small, ellipses = '
#for i in range(len(ellipses)):
# print 'ellipse[%d] = '%i + str(ellipses[i])
#print 'time to fix small ellipses: %.2f'%(time.time() - last_time)
last_time = time.time()
# check if any are large, and [try to] fix those
est.fixlarge(ellipses,L,dfore)
#print 'after fixing large, ellipses = \n'
#for i in range(len(ellipses)):
# print 'ellipse[%d] = '%i + str(ellipses[i])
#print 'time to fix large ellipses: %.2f'%(time.time() - last_time)
#est.deleteellipses(ellipses)
return ellipses
def find_ellipses(dfore, L, ncc, dofix=True, return_vals=False):
"""Fits ellipses to connected components in image.
Returns a list of ellipses, each item representing
the x,y position and orientation of a single fly."""
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)))
# fit ellipses
ellipses = est.weightedregionprops(L, ncc, dfore)
if return_vals:
ellipsescopy = [ell.copy() for ell in ellipses]
if DEBUG_TRACKINGSETTINGS:
print 'initial list of ellipses:'
for i in range(len(ellipses)):
print 'ellipse[%d] = ' % i + str(ellipses[i])
if dofix or return_vals:
# check if any are small, and [try to] fix those
(ellsmall, didlowerthresh, didmerge,
diddelete) = est.fixsmall(ellipses, L, dfore, return_vals)
# "ellipses" are fixed in place
# check if any are large, and [try to] fix those
(elllarge, didsplit) = est.fixlarge(ellipses, L, dfore, return_vals)
if DEBUG_TRACKINGSETTINGS:
print 'after fixing large, ellipses ='
for i in range(len(ellipses)):
print 'ellipse[%d] = ' % i + str(ellipses[i])
if params.enforce_minmax_shape:
# enforce shape parameters on remaining ellipses
for ell in ellipses:
if ell.area() < params.minshape.area or \
ell.area() > params.maxshape.area or \
ell.size.height < params.minshape.major or \
ell.size.height > params.maxshape.major or \
ell.size.width < params.minshape.minor or \
ell.size.width > params.maxshape.minor or \
ell.eccentricity() < params.minshape.ecc or \
ell.eccentricity() > params.maxshape.ecc:
# compare ell.eccentricity() to params.minshape.ecc because
# the .ecc was calculated from the distribution of eccentricity(),
# whereas params.minshape.eccentricity() would just be the
# eccentricity of params.minshape alone
if DEBUG_TRACKINGSETTINGS and False:
print params.minshape.area, ell.area(
), params.maxshape.area, (
ell.area() < params.minshape.area
or ell.area() > params.maxshape.area)
print params.minshape.major, ell.size.height, params.maxshape.major, (
ell.size.height < params.minshape.major
or ell.size.height > params.maxshape.major)
print params.minshape.minor, ell.size.width, params.maxshape.minor, (
ell.size.width < params.minshape.minor
or ell.size.width > params.maxshape.minor)
print params.minshape.ecc, ell.eccentricity(
), params.maxshape.ecc, (
ell.eccentricity() < params.minshape.ecc
or ell.eccentricity() > params.maxshape.ecc)
ell.size.height = 0
est.deleteellipses(ellipses, L)
if DEBUG_TRACKINGSETTINGS:
print "minshape:", params.minshape
print "maxshape:", params.maxshape
print 'after enforcing min/max shapes, ellipses ='
for i in range(len(ellipses)):
print 'ellipse[%d] = ' % i + str(ellipses[i])
if return_vals:
return (ellipsescopy, ellsmall, elllarge, didlowerthresh, didmerge,
diddelete, didsplit)
else:
return ellipses