def find_shortest_path(ipl, penaltypower, bounds, disttransf, locmax):
# Modify distancetransform
#
# a) Invert: the lowest values (i.e. the lowest penalty for the shortest path detection) should be at the center of
# the current process
disttransf = lib.invert_image(disttransf)
#
# b) Set all values outside the process to infinity
disttransf = lib.filter_values(disttransf, np.amax(disttransf), type='eq', setto=np.inf)
#
# c) Increase the value difference between pixels near the boundaries and pixels central within the processes
# This increases the likelihood of the paths to follow the center of processes, thus avoiding short-cuts
disttransf = lib.power(disttransf, penaltypower)
# Get local maxima
indices = np.where(locmax)
coords = zip(indices[0], indices[1], indices[2])
ipl.logging('Local maxima coordinates: {}', coords)
# Make pairwise list of coordinates that will serve as source and target
pairs = []
for i in xrange(0, len(coords)-1):
for j in xrange(i+1, len(coords)):
pairs.append((coords[i], coords[j]))
paths, pathim = lib.shortest_paths(disttransf, pairs, bounds=bounds, hfp=ipl)
# # Make sure no empty paths lists are returned
# paths = [x for x in paths if x.any()]
return paths, pathim
def find_shortest_path(ipl, penaltypower, bounds, disttransf, locmax, labels,
labelgroup):
# Modify distancetransform
#
# a) Invert: the lowest values (i.e. the lowest penalty for the shortest path detection) should be at the center of
# the current process
disttransf = lib.invert_image(disttransf)
#
# b) Set all values outside the process to infinity
disttransf = lib.filter_values(disttransf,
np.amax(disttransf),
type='eq',
setto=np.inf)
#
# c) Increase the value difference between pixels near the boundaries and pixels central within the processes
# This increases the likelihood of the paths to follow the center of processes, thus avoiding short-cuts
disttransf = lib.power(disttransf, penaltypower)
# The situation:
# We have multiple objects (n > 1) of unknown number.
# We want to extract the local maxima within each object individually and create a
# list of all possible partners (pairs)
# Each partner of a pair has to be located within a different object (label area)
#
# Approach 1:
# For each locmax iterate over all other locmaxs and write pairs, which satisfy the
# desired condition, to the pairs list
#
# Approach 2:
# For each label object iterate over all the others and append all possible locmax
# pairs to the pairs list
# Probably faster than approach 1 when implemented correctly? Someone should test that...
# Approach 2 in its implemented form
pairs = []
for i in xrange(0, len(labelgroup) - 1):
indices_i = np.where((labels == labelgroup[i]) & (locmax > 0))
indices_i = zip(indices_i[0], indices_i[1], indices_i[2])
if indices_i:
for j in xrange(i + 1, len(labelgroup)):
indices_j = np.where((labels == labelgroup[j]) & (locmax > 0))
indices_j = zip(indices_j[0], indices_j[1], indices_j[2])
if indices_j:
ipl.logging('Ind_i = {}\nInd_j = {}', indices_i, indices_j)
# Now, lets do some magic!
pairs = pairs + zip(indices_i * len(indices_j),
sorted(indices_j * len(indices_i)))
paths, pathim = lib.shortest_paths(disttransf,
pairs,
bounds=bounds,
hfp=ipl)
return paths, pathim
def find_shortest_path(ipl, penaltypower, bounds, disttransf, locmax,
labels, labelgroup):
# Modify distancetransform
#
# a) Invert: the lowest values (i.e. the lowest penalty for the shortest path detection) should be at the center of
# the current process
disttransf = lib.invert_image(disttransf)
#
# b) Set all values outside the process to infinity
disttransf = lib.filter_values(disttransf, np.amax(disttransf), type='eq', setto=np.inf)
#
# c) Increase the value difference between pixels near the boundaries and pixels central within the processes
# This increases the likelihood of the paths to follow the center of processes, thus avoiding short-cuts
disttransf = lib.power(disttransf, penaltypower)
# The situation:
# We have multiple objects (n > 1) of unknown number.
# We want to extract the local maxima within each object individually and create a
# list of all possible partners (pairs)
# Each partner of a pair has to be located within a different object (label area)
#
# Approach 1:
# For each locmax iterate over all other locmaxs and write pairs, which satisfy the
# desired condition, to the pairs list
#
# Approach 2:
# For each label object iterate over all the others and append all possible locmax
# pairs to the pairs list
# Probably faster than approach 1 when implemented correctly? Someone should test that...
# Approach 2 in its implemented form
pairs = []
for i in xrange(0, len(labelgroup)-1):
indices_i = np.where((labels == labelgroup[i]) & (locmax > 0))
indices_i = zip(indices_i[0], indices_i[1], indices_i[2])
if indices_i:
for j in xrange(i+1, len(labelgroup)):
indices_j = np.where((labels == labelgroup[j]) & (locmax > 0))
indices_j = zip(indices_j[0], indices_j[1], indices_j[2])
if indices_j:
ipl.logging('Ind_i = {}\nInd_j = {}', indices_i, indices_j)
# Now, lets do some magic!
pairs = pairs + zip(indices_i * len(indices_j), sorted(indices_j * len(indices_i)))
paths, pathim = lib.shortest_paths(disttransf, pairs, bounds=bounds, hfp=ipl)
return paths, pathim
def find_shortest_path(hfp, penaltypower, bounds, disttransf, locmax):
# Modify distancetransform
#
# a) Invert: the lowest values (i.e. the lowest penalty for the shortest path detection) should be at the center of
# the current process
disttransf = lib.invert_image(disttransf)
#
# b) Set all values outside the process to infinity
disttransf = lib.filter_values(disttransf,
np.amax(disttransf),
type='eq',
setto=np.inf)
#
# c) Increase the value difference between pixels near the boundaries and pixels central within the processes
# This increases the likelihood of the paths to follow the center of processes, thus avoiding short-cuts
disttransf = lib.power(disttransf, penaltypower)
# Get local maxima
indices = np.where(locmax)
coords = zip(indices[0], indices[1], indices[2])
hfp.logging('Local maxima coordinates: {}', coords)
# Make pairwise list of coordinates that will serve as source and target
pairs = []
for i in xrange(0, len(coords) - 1):
for j in xrange(i + 1, len(coords)):
pairs.append((coords[i], coords[j]))
paths, pathim = lib.shortest_paths(disttransf,
pairs,
bounds=bounds,
hfp=hfp)
# # Make sure no empty paths lists are returned
# paths = [x for x in paths if x.any()]
return paths, pathim
def shortest_paths(penaltypower,
bounds,
lbl,
keylist_lblim,
gt,
disttransf,
pathends,
for_class=True,
correspondence={},
avoid_duplicates=True,
max_paths_per_object=[],
max_paths_per_object_seed=[],
yield_in_bounds=False,
return_pathim=True,
minimum_alternative_label_count=0,
logger=None):
"""
:param penaltypower:
:param bounds:
:param lbl:
:param keylist_lblim: Needed for correspondence table
:param disttransf:
:param pathends:
:param for_class:
True: paths are computed for when endpoints are in the same ground truth oject
False: paths are computed for when endpoints are in different ground truth objects
:param correspondence:
:param avoid_duplicates:
:param max_paths_per_object:
:param max_paths_per_object_seed:
:param yield_in_bounds:
:param return_pathim:
:param minimum_alternative_label_count: Paths of merges (for_class=False) are removed if
too little pixels of the merged object are found
:param logger:
:return:
"""
# Pick up some statistics along the way
stats_excluded_paths = 0
statistics = Rdict()
# Determine the endpoints of the current object
indices = np.where(pathends)
coords = zip(indices[0], indices[1], indices[2])
# Make pairwise list of coordinates serving as source and target
# First determine all pairings
all_pairs = []
for i in xrange(0, len(coords) - 1):
for j in xrange(i + 1, len(coords)):
all_pairs.append((coords[i], coords[j]))
# And only use those that satisfy certain criteria:
# a) Are in either the same gt object (for_class=True)
# or in different gt objects (for_class=False)
# b) Are not in the correspondence list
pairs = []
label_pairs = []
# if avoid_duplicates:
new_correspondence = {}
for pair in all_pairs:
# Determine whether the endpoints are in different gt objects
if (gt[pair[0]] == gt[pair[1]]) == for_class:
# Check correspondence list if pairings were already computed in different image
labelpair = tuple(sorted([gt[pair[0]], gt[pair[1]]]))
if avoid_duplicates:
if labelpair not in correspondence.keys():
pairs.append(pair)
label_pairs.append(labelpair)
# new_correspondence[labelpair] = [keylist_lblim, lbl]
if logger is not None:
logger.logging('Found pairing: {}', labelpair)
else:
if logger is not None:
logger.logging(
'Pairing already in correspondence table: {}',
labelpair)
else:
pairs.append(pair)
if logger is not None:
logger.logging('Found pairing: {}', labelpair)
# if avoid_duplicates:
# correspondence.update(new_correspondence)
# Select a certain number of pairs if number is too high
if max_paths_per_object:
if len(pairs) > max_paths_per_object:
if logger is not None:
logger.logging('Reducing number of pairs to {}',
max_paths_per_object)
if max_paths_per_object_seed:
random.seed(max_paths_per_object_seed)
else:
random.seed()
pairs = random.sample(pairs, max_paths_per_object)
if logger is not None:
logger.logging('Modified pairs list: {}', pairs)
# If pairs are found that satisfy all conditions
if pairs:
if logger is not None:
logger.logging('Found {} pairings which satisfy all criteria',
len(pairs))
else:
print 'Found {} pairings which satisfy all criteria'.format(
len(pairs))
# Pre-processing of the distance transform
# a) Invert: the lowest values (i.e. the lowest penalty for the shortest path
# detection) should be at the center of the current process
disttransf = lib.invert_image(disttransf)
#
# b) Set all values outside the process to infinity
disttransf = lib.filter_values(disttransf,
np.amax(disttransf),
type='eq',
setto=np.inf)
#
# c) Increase the value difference between pixels near the boundaries and pixels
# central within the processes. This increases the likelihood of the paths to
# follow the center of processes, thus avoiding short-cuts
disttransf = lib.power(disttransf, penaltypower)
# Compute the shortest paths according to the pairs list
ps_computed, ps_in_bounds = lib.shortest_paths(
disttransf,
pairs,
bounds=bounds,
logger=logger,
return_pathim=return_pathim,
yield_in_bounds=yield_in_bounds)
# Criteria for keeping paths which can only be computed after path computation
if for_class:
# A path without merge must not switch labels on the way!
ps = []
for i in xrange(0, len(ps_computed)):
if len(
np.unique(gt[ps_in_bounds[i][:, 0],
ps_in_bounds[i][:, 1],
ps_in_bounds[i][:, 2]])) == 1:
ps.append(ps_computed[i])
if logger is not None:
logger.logging('Path label = True')
# Add entry to correspondence table
if avoid_duplicates:
new_correspondence[label_pairs[i]] = [
keylist_lblim, lbl
]
else:
# The path switched objects multiple times on the way and is not added to the list\
if logger is not None:
logger.logging(
'Path starting and ending in label = {} had multiple labels and was excluded',
gt[tuple(ps_in_bounds[i][0])])
stats_excluded_paths += 1
else:
ps = []
for i in xrange(0, len(ps_computed)):
un, counts = np.unique(gt[ps_in_bounds[i][:, 0],
ps_in_bounds[i][:, 1],
ps_in_bounds[i][:, 2]],
return_counts=True)
# At least two of the entries in counts have to be larger than the threshold
c = 0
for count in counts:
if count >= minimum_alternative_label_count:
c += 1
if c > 1:
break
if c > 1:
ps.append(ps_computed[i])
# Add entry to correspondence table
if avoid_duplicates:
new_correspondence[label_pairs[i]] = [
keylist_lblim, lbl
]
else:
if logger is not None:
logger.logging(
'Path starting in label {} and ending in {} only crossed one of the labels for {} voxels',
gt[tuple(ps_in_bounds[i][0])],
gt[tuple(ps_in_bounds[i][-1])], np.min(counts))
statistics['excluded_paths'] = stats_excluded_paths
statistics['kept_paths'] = len(ps)
return ps, new_correspondence, statistics
else:
statistics['excluded_paths'] = 0
statistics['kept_paths'] = 0
return [], new_correspondence, statistics