try:
thesemice[os.path.basename(k)] = mice[os.path.join(mkbase,os.path.basename(k))]
except KeyError:
print >>sys.stderr, 'key %s not found; skip' % os.path.join(mkbase,os.path.basename(k))
#print >> sys.stderr, 'write %s mice to %s' % (len(thesemice),new_base+'.mice')
open(new_base+'.mice','w').write(thesemice.__repr__())
#if we need to link ground:
if not os.path.exists(new_base+'.ground'):
#print >> sys.stderr, 'link %s from %s' % (new_base+'.ground',source_base+'.ground')
os.system('ln -s %s %s' % (os.path.join(os.getcwd(),source_base+'.ground'), os.path.join(os.getcwd(),new_base+'.ground') ) )
#if we need to compute frame avg:
if not os.path.exists(new_base+'.frame'):
frameav = vidtools.average_frames(vidtools.load_normed_arrays(new_ims[i:i+segment_step],pixav))
frameav.tofile(new_base+'.frame')
frameavs = sorted(glob(new_outroot+'/*.frame'))
print >> sys.stderr, 'compute activity matrices from frame averages (%s frame averages found)' % len(frameavs)
for i,f in enumerate(frameavs):
actmatf = os.path.splitext(f)[0]+'.actmat'
if not os.path.exists(actmatf) and i>0 and i<len(frameavs)-1:
actmat = Util.zscore(numpy.fromfile(frameavs[i-1]).reshape(shape) - numpy.fromfile(frameavs[i+1]).reshape(shape))
actmat.tofile(actmatf)
# switches cumulative activity calc to activity below an artificial "lowest ground" - should fix squirrely groundfinding
if not images:
raise ValueError, 'no images found in '+imagedir
if mask == 'None':
try:
mask = Util.file_in_path('mask',imagedir)
print >> sys.stderr, 'mask in path (%s) exists; using' % mask
except ValueError:
print >> sys.stderr, 'no mask in path'
else:
print >> sys.stderr, 'mask found? %s\n' % os.path.exists(mask)
SHAPE=vidtools.load_normed_arrays(images[:1])[0].shape
#print >> sys.stderr, opts
print >> sys.stderr,'xybounds: %s\nburrow entrance at: %s\nground anchors at: %s\nhill_bounds: %s' \
% (opts['xybounds'],opts['burrow_entrance_xy'],opts['ground_anchors'],opts['hill_bounds'])
match = re.search('([\d\.]+)fps',imagedir)
if match:
fps = float(match.groups()[0])
segment_step = int(seglen)* fps
print >> sys.stderr, 'segment length will be %s frames (%s seconds, %s fps)\n' % (segment_step,seglen,fps)
unit = 'sec'
else:
fps = 1.0
segment_step = int(seglen)
mkbase, os.path.basename(k))
#print >> sys.stderr, 'write %s mice to %s' % (len(thesemice),new_base+'.mice')
open(new_base + '.mice', 'w').write(thesemice.__repr__())
#if we need to link ground:
if not os.path.exists(new_base + '.ground'):
#print >> sys.stderr, 'link %s from %s' % (new_base+'.ground',source_base+'.ground')
os.system('ln -s %s %s' %
(os.path.join(os.getcwd(), source_base + '.ground'),
os.path.join(os.getcwd(), new_base + '.ground')))
#if we need to compute frame avg:
if not os.path.exists(new_base + '.frame'):
frameav = vidtools.average_frames(
vidtools.load_normed_arrays(new_ims[i:i + segment_step], pixav))
frameav.tofile(new_base + '.frame')
frameavs = sorted(glob(new_outroot + '/*.frame'))
print >> sys.stderr, 'compute activity matrices from frame averages (%s frame averages found)' % len(
frameavs)
for i, f in enumerate(frameavs):
actmatf = os.path.splitext(f)[0] + '.actmat'
if not os.path.exists(actmatf) and i > 0 and i < len(frameavs) - 1:
actmat = Util.zscore(
numpy.fromfile(frameavs[i - 1]).reshape(shape) -
numpy.fromfile(frameavs[i + 1]).reshape(shape))
actmat.tofile(actmatf)
# switches cumulative activity calc to activity below an artificial "lowest ground" - should fix squirrely groundfinding
if not images:
raise ValueError, "no images found in " + imagedir
if mask == "None":
try:
mask = Util.file_in_path("mask", imagedir)
print >>sys.stderr, "mask in path (%s) exists; using" % mask
except ValueError:
print >>sys.stderr, "no mask in path"
else:
print >>sys.stderr, "mask found? %s\n" % os.path.exists(mask)
SHAPE = vidtools.load_normed_arrays(images[:1])[0].shape
# print >> sys.stderr, opts
print >>sys.stderr, "xybounds: %s\nburrow entrance at: %s\nground anchors at: %s\nhill_bounds: %s" % (
opts["xybounds"],
opts["burrow_entrance_xy"],
opts["ground_anchors"],
opts["hill_bounds"],
)
match = re.search("([\d\.]+)fps", imagedir)
if match:
fps = float(match.groups()[0])
segment_step = int(seglen) * fps
print >>sys.stderr, "segment length will be %s frames (%s seconds, %s fps)\n" % (segment_step, seglen, fps)