fcopy = frameav.copy() print >>sys.stderr,'finalize mouse calls' for i,f in enumerate(frames): #print i #get xy coords, outlines of above-cut regions, and mean z-scores in each outline xy,ol,zsc = vidtools.find_mouse(f,fcopy,zcut=mousezcut,outline_zcut=mousezcut/2.0,grow_by=mouse_grow_by,preshrink=mouse_preshrink) if opts['ground_anchors'] is None and opts['burrowz'] is None: pass else: for p in ol: try: vidtools.subtract_outline(p,frameav) except: print >> sys.stderr, 'failure in frame %s' % i size = [len(filter(None,vidtools.shrink_mask(vidtools.mask_from_outline(p,f.shape),mouse_grow_by).flat)) for p in ol] mlen = [max([vidtools.hypotenuse(p1,p2) for p1 in p for p2 in p]) for p in ol] miceli.append( (images[i],xy) ) miceoutli.append( (images[i],ol) ) micez.append( (images[i],zsc) ) micesize.append( (images[i],size) ) micelen.append( (images[i],mlen) ) if i % tick == 0: print >> sys.stderr, 'frame %s done' % i mice = dict(miceli) miceout = dict(miceoutli) micez = dict(micez) micesize = dict(micesize) micelen = dict(micelen) try:
Util.merge_dictlist([objs_fols,to_retire_objs_fols]), \
size_h, size_bins, fol_h, fol_bins,SHAPE)
prelast_masked = prelast_avg.copy()
prelast_masked[prelast_mm] = numpy.mean(prelast_avg[:50, :50])
last_masked = last_avg.copy()
last_masked[last_mm] = numpy.mean(last_avg[:50, :50])
this_masked = this_avg.copy()
this_masked[this_mm] = numpy.mean(this_avg[:50, :50])
if opts.antfarm_config: #antfarm-specific analysis steps
digdiffs.append(prelast_masked - this_masked)
if len(digdiffs) > 3:
nll = digdiffs.pop(0)
if newactols and newactols[-1]:
prevactmask += reduce(lambda x, y: x + y, [
vidtools.shrink_mask(
vidtools.mask_from_outline(ol, this_masked.shape), 1)
for ol in newactols[-1]
])
if len(digdiffs) > 1:
m = digdiffs[-2] > 0.2 #ARBITRARY
m[last_mm] = True #add mousemask to burrow area
m[vidtools.grow_mask(vidtools.shrink_mask(prevactmask, 1),
1)] = False #MASK PREVIOUS DIGGING
m[groundmask] = False #AND EVERYTHING ABOVE FIRST GROUND
if opts.outline_engine == 'homebrew':
newactols.append(
vidtools.chain_outlines_from_mask(m,
preshrink=1,
grow_by=1,
debug=False,
return_termini=False,
Util.merge_dictlist([objs_sizes,to_retire_objs_sizes]), \
Util.merge_dictlist([objs_fols,to_retire_objs_fols]), \
size_h, size_bins, fol_h, fol_bins,SHAPE)
prelast_masked = prelast_avg.copy()
prelast_masked[prelast_mm] = numpy.mean(prelast_avg[:50,:50])
last_masked = last_avg.copy()
last_masked[last_mm] = numpy.mean(last_avg[:50,:50])
this_masked = this_avg.copy()
this_masked[this_mm] = numpy.mean(this_avg[:50,:50])
if opts.antfarm_config: #antfarm-specific analysis steps
digdiffs.append(prelast_masked-this_masked)
if len(digdiffs) > 3:
nll = digdiffs.pop(0)
if newactols and newactols[-1]:
prevactmask += reduce(lambda x,y:x+y, [vidtools.shrink_mask(vidtools.mask_from_outline(ol,this_masked.shape),1) for ol in newactols[-1]])
if len(digdiffs) > 1:
m = digdiffs[-2] > 0.2 #ARBITRARY
m[last_mm] = True #add mousemask to burrow area
m[vidtools.grow_mask(vidtools.shrink_mask(prevactmask,1),1)] = False #MASK PREVIOUS DIGGING
m[groundmask] = False #AND EVERYTHING ABOVE FIRST GROUND
if opts.outline_engine == 'homebrew':
newactols.append(vidtools.chain_outlines_from_mask(m,preshrink=1,grow_by=1,debug=False,return_termini=False,order_points=True,sort_outlines=False))
prevol = vidtools.chain_outlines_from_mask(prevactmask,preshrink=1,grow_by=1,debug=False,return_termini=False,order_points=True,sort_outlines=False)
elif opts.outline_engine == 'shapely':
newactols.append(vidtools.chain_outlines_from_mask_shapely(m,preshrink=1,grow_by=1))
prevol = vidtools.chain_outlines_from_mask_shapely(prevactmask,preshrink=1,grow_by=1)
else:
print >> sys.stderr, 'outline_engine must be one of %s' % (['homebrew','shapely'])
raise ValueError
digol = newactols[-1]
grow_by=mouse_grow_by,
preshrink=mouse_preshrink)
if opts['ground_anchors'] is None and opts['burrowz'] is None:
pass
else:
for p in ol:
try:
vidtools.subtract_outline(p, frameav)
except:
print >> sys.stderr, 'failure in frame %s' % i
size = [
len(
filter(
None,
vidtools.shrink_mask(
vidtools.mask_from_outline(p, f.shape),
mouse_grow_by).flat)) for p in ol
]
mlen = [
max([vidtools.hypotenuse(p1, p2) for p1 in p for p2 in p])
for p in ol
]
miceli.append((images[i], xy))
miceoutli.append((images[i], ol))
micez.append((images[i], zsc))
micesize.append((images[i], size))
micelen.append((images[i], mlen))
if i % tick == 0:
print >> sys.stderr, 'frame %s done' % i
mice = dict(miceli)
miceout = dict(miceoutli)
