def get_features(paths, featureimage, featurelist, max_paths_per_label, hfp=None):
newfeats = IPL()
keylist = range(0, max_paths_per_label)
keylist = [str(x) for x in keylist]
for i, keys, vals in paths.simultaneous_iterator(max_count_per_item=max_paths_per_label, keylist=keylist):
if hfp is not None:
hfp.logging("Working in iteration = {}", i)
image = np.zeros(featureimage.shape, dtype=np.uint32)
c = 1
for curk, curv in (dict(zip(keys, vals))).iteritems():
curv = lib.swapaxes(curv, 0, 1)
lib.positions2value(image, curv, c)
c += 1
newnewfeats = IPL(
data=vigra.analysis.extractRegionFeatures(featureimage, image, ignoreLabel=0, features=featurelist)
)
for k, v in newnewfeats.iteritems():
newnewfeats[k] = newnewfeats[k][1:]
if k in newfeats:
try:
newfeats[k] = np.concatenate((newfeats[k], newnewfeats[k]))
except ValueError:
pass
else:
newfeats[k] = newnewfeats[k]
return newfeats
def get_features(paths, featureimages, featurelist, max_paths_per_label, ipl=None):
newfeats = IPL()
keylist = range(0, max_paths_per_label)
keylist = [str(x) for x in keylist]
# Iterate over all paths, yielding a list of one path per label object until no paths are left
for i, keys, vals in paths.simultaneous_iterator(
max_count_per_item=max_paths_per_label,
keylist=keylist):
if ipl is not None:
ipl.logging('Working in iteration = {}', i)
ipl.logging('Keys: {}', keys)
if not keys:
continue
# Create a working image
image = np.zeros(np.array(featureimages.yield_an_item()).shape, dtype=np.uint32)
# And fill it with one path per label object
c = 1
for curk, curv in (dict(zip(keys, vals))).iteritems():
curv = np.array(curv)
curv = lib.swapaxes(curv, 0, 1)
lib.positions2value(image, curv, c)
c += 1
# TODO: If this loop iterated over the parameter list it would be more broadly applicable
for d, k, v, kl in featureimages.data_iterator():
if type(v) is not IPL:
# Extract the region features of the working image
# TODO: Extract feature 'Count' manually due to anisotropy
newnewfeats = IPL(
data=vigra.analysis.extractRegionFeatures(
np.array(v).astype(np.float32),
image, ignoreLabel=0,
features=featurelist
)
)
# Append to the recently computed list of features
for nk, nv in newnewfeats.iteritems():
nv = nv[1:]
if newfeats.inkeys(kl+[nk]):
try:
newfeats[kl + [nk]] = np.concatenate((newfeats[kl + [nk]], nv))
except ValueError:
pass
else:
newfeats[kl + [nk]] = nv
return newfeats
def get_features(paths, featureimage, featurelist, max_paths_per_label, ipl=None):
newfeats = IPL()
# TODO: Selection of a limited amount of paths should be random
keylist = range(0, max_paths_per_label)
keylist = [str(x) for x in keylist]
# Iterate over all paths, yielding a list of one path per label object until no paths are left
for i, keys, vals in paths.simultaneous_iterator(
max_count_per_item=max_paths_per_label,
keylist=keylist):
if ipl is not None:
ipl.logging('Working in iteration = {}', i)
# Create a working image
image = np.zeros(featureimage.shape, dtype=np.uint32)
# And fill it with one path per label object
c = 1
for curk, curv in (dict(zip(keys, vals))).iteritems():
curv = lib.swapaxes(curv, 0, 1)
lib.positions2value(image, curv, c)
c += 1
# Extract the region features of the working image
newnewfeats = IPL(
data=vigra.analysis.extractRegionFeatures(
featureimage,
image, ignoreLabel=0,
features=featurelist
)
)
for k, v in newnewfeats.iteritems():
newnewfeats[k] = newnewfeats[k][1:]
if k in newfeats:
try:
newfeats[k] = np.concatenate((newfeats[k], newnewfeats[k]))
except ValueError:
pass
else:
newfeats[k] = newnewfeats[k]
return newfeats
def get_features(paths,
featureimage,
featurelist,
max_paths_per_label,
hfp=None):
newfeats = IPL()
keylist = range(0, max_paths_per_label)
keylist = [str(x) for x in keylist]
for i, keys, vals in paths.simultaneous_iterator(
max_count_per_item=max_paths_per_label, keylist=keylist):
if hfp is not None:
hfp.logging('Working in iteration = {}', i)
image = np.zeros(featureimage.shape, dtype=np.uint32)
c = 1
for curk, curv in (dict(zip(keys, vals))).iteritems():
curv = lib.swapaxes(curv, 0, 1)
lib.positions2value(image, curv, c)
c += 1
newnewfeats = IPL(data=vigra.analysis.extractRegionFeatures(
featureimage, image, ignoreLabel=0, features=featurelist))
for k, v in newnewfeats.iteritems():
newnewfeats[k] = newnewfeats[k][1:]
if k in newfeats:
try:
newfeats[k] = np.concatenate((newfeats[k], newnewfeats[k]))
except ValueError:
pass
else:
newfeats[k] = newnewfeats[k]
return newfeats
def merge_adjacent_objects(hfp):
params = hfp.get_params()
thisparams = params['merge_adjacent_objects']
numberbysize = thisparams['numberbysize']
numberbyrandom = thisparams['numberbyrandom']
targetnames = params['largeobjmnames']
# Get only the relevant labels
labels = lib.unique(hfp['largeobj'])
hfp.logging('labels = {}', labels)
# Seed the randomize function
random.seed(thisparams['seed'])
hfp.astype(np.uint32, keys='largeobj')
(grag, rag) = graphs.gridRegionAdjacencyGraph(hfp['largeobj'], ignoreLabel=0)
edge_ids = rag.edgeIds()
# hfp.logging('Edge ids: {}', edge_ids)
# Type 1:
# Select edges by size (smallest edges)
hfp.logging('Number of edgeLengths = {}', len(rag.edgeLengths()))
edgelen_ids = dict(zip(edge_ids, rag.edgeLengths()))
# ifp.logging('edgelen_ids = {}', edgelen_ids)
sorted_edgelens = np.sort(rag.edgeLengths())
#
smallest_merge_lens = sorted_edgelens[0:numberbysize]
hfp.logging('Lengths selected for merging: {}', smallest_merge_lens)
#
smallest_merge_ids = []
for x in smallest_merge_lens:
edge_id = edgelen_ids.keys()[edgelen_ids.values().index(x)]
smallest_merge_ids.append(edge_id)
edgelen_ids.pop(edge_id)
#
edge_ids = edgelen_ids.keys()
hfp.logging('Edge IDs selected for merging due to size: {}', smallest_merge_ids)
# Type 2:
# Randomly choose edges
random_merge_ids = random.sample(edge_ids, numberbyrandom)
hfp.logging('Edge IDs randomly selected for merging: {}', random_merge_ids)
# Now get the label ids
smallest_merge_labelids_u = [rag.uId(rag.edgeFromId(x)) for x in smallest_merge_ids]
smallest_merge_labelids_v = [rag.vId(rag.edgeFromId(x)) for x in smallest_merge_ids]
smallest_merge_labelids = list(zip(smallest_merge_labelids_u, smallest_merge_labelids_v))
random_merge_labelids_u = [rag.uId(rag.edgeFromId(x)) for x in random_merge_ids]
random_merge_labelids_v = [rag.vId(rag.edgeFromId(x)) for x in random_merge_ids]
random_merge_labelids = list(zip(random_merge_labelids_u, random_merge_labelids_v))
hfp.logging('Label IDs selected for merging by size: {}', smallest_merge_labelids)
hfp.logging('Label IDs randomly selected for merging: {}', random_merge_labelids)
# Concatenate
all_merge_labelids = smallest_merge_labelids + random_merge_labelids
# Sort
hfp.logging('all_merge_labelids = {}', all_merge_labelids)
all_merge_labelids = [sorted(x) for x in all_merge_labelids]
all_merge_labelids = sorted(all_merge_labelids)
hfp.logging('all_merge_labelids = {}', all_merge_labelids)
# Store this for later use
hfp[targetnames[1]] = smallest_merge_labelids
hfp[targetnames[2]] = random_merge_labelids
hfp[targetnames[3]] = all_merge_labelids
# Create change hash list
change_hash = IPL(data=dict(zip(np.unique(all_merge_labelids), [[x,] for x in np.unique(all_merge_labelids)])))
for i in xrange(0, 3):
prev_change_hash = IPL(data=change_hash)
for x in all_merge_labelids:
hfp.logging('Adding {} and {}', *x)
change_hash[x[0]] += change_hash[x[1]]
change_hash[x[0]] = list(np.unique(change_hash[x[0]]))
change_hash[x[1]] += change_hash[x[0]]
change_hash[x[1]] = list(np.unique(change_hash[x[1]]))
# This removes the redundancy from the hash
def reduce(hash):
br = False
for k, v in hash.iteritems():
for x in v:
if x != k:
if x in hash.keys():
del hash[x]
reduce(hash)
br = True
break
else:
br = False
if br:
break
reduce(change_hash)
# And now we have a perfect change list which we just need to iterate over and change the labels in the image
hfp.logging('change_hash after change:')
hfp.logging(change_hash)
hfp[targetnames[4]] = change_hash
# Create the merged image
# hfp.deepcopy_entry('largeobj', targetnames[0])
hfp.rename_entry('largeobj', targetnames[0])
for k, v in change_hash.iteritems():
for x in v:
if x != k:
hfp.logging('Setting {} to {}!', x, k)
hfp.filter_values(x, type='eq', setto=k, keys=targetnames[0])
# tkeys='{}.{}.{}'.format('result_true', k, k2))
hfp.pop('disttransf')
hfp.pop('disttransfm')
hfp.pop('result_false')
# hfp.pop('result_true')
hfp.pop('true')
hfp.pop('false')
hfp.logging('hfp datastructure:\n---\n{}---',
hfp.datastructure2string(maxdepth=2))
print hfp['result.6720_13067.8']
y = []
for k, v in hfp.iteritems():
if v:
try:
y.append(v)
x = range(0, len(v))
plt.plot(x, v)
# plt.show()
lab.savefig(params['intermedfolder'] + 'plots/' + k +
'.png')
plt.clf()
except ValueError:
pass
def merge_adjacent_objects(
ipl, key, numberbysize=0, numberbyrandom=0, seed=None,
targetnames=('largeobjm', 'mergeids_small', 'mergeids_random', 'change_hash'),
algorithm='standard'
):
"""
:param ipl:
ipl.get_params():
merge_adjacent_objects
seed
numberbysize
numberbyrandom
largeobjmnames
- 'largeobj_merged'
- 'mergeids_small'
- 'mergeids_random'
- 'mergeids_all'
- 'change_hash'
:param key: the source key for calculation
"""
# This removes the redundancy from the hash
def reduce_hash(hash):
br = False
for k, v in hash.iteritems():
for x in v:
if x != k:
if x in hash.keys():
del hash[x]
reduce_hash(hash)
br = True
break
else:
br = False
if br:
break
if algorithm == 'pairs':
# Get only the relevant labels
labels = lib.unique(ipl[key])
ipl.logging('labels = {}', labels)
# Seed the randomize function
if seed:
random.seed(seed)
else:
random.seed()
ipl.astype(np.uint32, keys=key)
(grag, rag) = graphs.gridRegionAdjacencyGraph(ipl[key], ignoreLabel=0)
edge_ids = rag.edgeIds()
merge_ids = []
used_ids = ()
# Calculate the merges such that only pairs are found
for i in xrange(0, numberbyrandom):
c = 0
finished = False
while not finished:
edge_id = random.choice(edge_ids)
uid = rag.uId(rag.edgeFromId(edge_id))
vid = rag.vId(rag.edgeFromId(edge_id))
c += 1
if c > 50:
ipl.logging('merge_adjacent_objects: Warning: Not finding any more pairs!')
finished = True
elif uid not in used_ids and vid not in used_ids:
finished = True
used_ids += (uid, vid)
merge_ids.append((uid, vid))
ipl.logging('Label IDs randomly selected for merging: {}', merge_ids)
# Sort
merge_ids = [sorted(x) for x in merge_ids]
merge_ids = sorted(merge_ids)
ipl.logging('merge_ids = {}', merge_ids)
# Store this for later use
ipl[targetnames[2]] = merge_ids
ipl[targetnames[3]] = merge_ids
# # Create change hash list
# change_hash = IPL(data=dict(zip(np.unique(merge_ids), [[x, ] for x in np.unique(merge_ids)])))
# for i in xrange(0, 3):
# prev_change_hash = IPL(data=change_hash)
# for x in merge_ids:
# ipl.logging('Adding {} and {}', *x)
# change_hash[x[0]] += change_hash[x[1]]
# change_hash[x[0]] = list(np.unique(change_hash[x[0]]))
# change_hash[x[1]] += change_hash[x[0]]
# change_hash[x[1]] = list(np.unique(change_hash[x[1]]))
#
# reduce_hash(change_hash)
# # Change the list in the hash to np-arrays for better storage in h5 files
# for k, v in change_hash.iteritems():
# change_hash[k] = np.array(v)
# # And now we have a perfect change list which we just need to iterate over and change the labels in the image
# ipl.logging('change_hash after change:')
us = [x[0] for x in merge_ids]
change_hash = IPL(data=dict(zip(us, merge_ids)))
ipl.logging('change_hash: {}', change_hash)
ipl[targetnames[4]] = change_hash
elif algorithm == 'standard':
# Get only the relevant labels
labels = lib.unique(ipl[key])
ipl.logging('labels = {}', labels)
# Seed the randomize function
random.seed(seed)
ipl.astype(np.uint32, keys=key)
(grag, rag) = graphs.gridRegionAdjacencyGraph(ipl[key], ignoreLabel=0)
edge_ids = rag.edgeIds()
# ipl.logging('Edge ids: {}', edge_ids)
# Type 1:
# Select edges by size (smallest edges)
ipl.logging('Number of edgeLengths = {}', len(rag.edgeLengths()))
edgelen_ids = dict(zip(edge_ids, rag.edgeLengths()))
# ifp.logging('edgelen_ids = {}', edgelen_ids)
sorted_edgelens = np.sort(rag.edgeLengths())
#
smallest_merge_lens = sorted_edgelens[0:numberbysize]
ipl.logging('Lengths selected for merging: {}', smallest_merge_lens)
#
smallest_merge_ids = []
for x in smallest_merge_lens:
edge_id = edgelen_ids.keys()[edgelen_ids.values().index(x)]
smallest_merge_ids.append(edge_id)
edgelen_ids.pop(edge_id)
#
edge_ids = edgelen_ids.keys()
ipl.logging('Edge IDs selected for merging due to size: {}', smallest_merge_ids)
# Type 2:
# Randomly choose edges
random_merge_ids = random.sample(edge_ids, numberbyrandom)
ipl.logging('Edge IDs randomly selected for merging: {}', random_merge_ids)
# Now get the label ids
smallest_merge_labelids_u = [rag.uId(rag.edgeFromId(x)) for x in smallest_merge_ids]
smallest_merge_labelids_v = [rag.vId(rag.edgeFromId(x)) for x in smallest_merge_ids]
smallest_merge_labelids = list(zip(smallest_merge_labelids_u, smallest_merge_labelids_v))
random_merge_labelids_u = [rag.uId(rag.edgeFromId(x)) for x in random_merge_ids]
random_merge_labelids_v = [rag.vId(rag.edgeFromId(x)) for x in random_merge_ids]
random_merge_labelids = list(zip(random_merge_labelids_u, random_merge_labelids_v))
ipl.logging('Label IDs selected for merging by size: {}', smallest_merge_labelids)
ipl.logging('Label IDs randomly selected for merging: {}', random_merge_labelids)
# Concatenate
all_merge_labelids = smallest_merge_labelids + random_merge_labelids
# Sort
ipl.logging('all_merge_labelids = {}', all_merge_labelids)
all_merge_labelids = [sorted(x) for x in all_merge_labelids]
all_merge_labelids = sorted(all_merge_labelids)
ipl.logging('all_merge_labelids = {}', all_merge_labelids)
# Store this for later use
ipl[targetnames[1]] = smallest_merge_labelids
ipl[targetnames[2]] = random_merge_labelids
ipl[targetnames[3]] = all_merge_labelids
# Create change hash list
change_hash = IPL(data=dict(zip(np.unique(all_merge_labelids), [[x,] for x in np.unique(all_merge_labelids)])))
for i in xrange(0, 3):
prev_change_hash = IPL(data=change_hash)
for x in all_merge_labelids:
ipl.logging('Adding {} and {}', *x)
change_hash[x[0]] += change_hash[x[1]]
change_hash[x[0]] = list(np.unique(change_hash[x[0]]))
change_hash[x[1]] += change_hash[x[0]]
change_hash[x[1]] = list(np.unique(change_hash[x[1]]))
# This removes the redundancy from the hash
reduce_hash(change_hash)
# Change the list in the hash to np-arrays for better storage in h5 files
for k, v in change_hash.iteritems():
change_hash[k] = np.array(v)
# And now we have a perfect change list which we just need to iterate over and change the labels in the image
ipl.logging('change_hash after change:')
ipl.logging(change_hash)
ipl[targetnames[4]] = change_hash
# Create the merged image
# ipl.deepcopy_entry('largeobj', targetnames[0])
ipl.rename_entry(key, targetnames[0])
for k, v in change_hash.iteritems():
for x in v:
if x != k:
ipl.logging('Setting {} to {}!', x, k)
ipl.filter_values(x, type='eq', setto=k, keys=targetnames[0])
return ipl
def merge_adjacent_objects(ipl, key, thisparams):
"""
:param ipl:
ipl.get_params():
merge_adjacent_objects
seed
numberbysize
numberbyrandom
largeobjmnames
- 'largeobj_merged'
- 'mergeids_small'
- 'mergeids_random'
- 'mergeids_all'
- 'change_hash'
:param key: the source key for calculation
"""
numberbysize = thisparams['numberbysize']
numberbyrandom = thisparams['numberbyrandom']
targetnames = params['largeobjmnames']
# Get only the relevant labels
labels = lib.unique(ipl[key])
ipl.logging('labels = {}', labels)
# Seed the randomize function
random.seed(thisparams['seed'])
ipl.astype(np.uint32, keys=key)
(grag, rag) = graphs.gridRegionAdjacencyGraph(ipl[key], ignoreLabel=0)
edge_ids = rag.edgeIds()
# ipl.logging('Edge ids: {}', edge_ids)
# Type 1:
# Select edges by size (smallest edges)
ipl.logging('Number of edgeLengths = {}', len(rag.edgeLengths()))
edgelen_ids = dict(zip(edge_ids, rag.edgeLengths()))
# ifp.logging('edgelen_ids = {}', edgelen_ids)
sorted_edgelens = np.sort(rag.edgeLengths())
#
smallest_merge_lens = sorted_edgelens[0:numberbysize]
ipl.logging('Lengths selected for merging: {}', smallest_merge_lens)
#
smallest_merge_ids = []
for x in smallest_merge_lens:
edge_id = edgelen_ids.keys()[edgelen_ids.values().index(x)]
smallest_merge_ids.append(edge_id)
edgelen_ids.pop(edge_id)
#
edge_ids = edgelen_ids.keys()
ipl.logging('Edge IDs selected for merging due to size: {}',
smallest_merge_ids)
# Type 2:
# Randomly choose edges
random_merge_ids = random.sample(edge_ids, numberbyrandom)
ipl.logging('Edge IDs randomly selected for merging: {}', random_merge_ids)
# Now get the label ids
smallest_merge_labelids_u = [
rag.uId(rag.edgeFromId(x)) for x in smallest_merge_ids
]
smallest_merge_labelids_v = [
rag.vId(rag.edgeFromId(x)) for x in smallest_merge_ids
]
smallest_merge_labelids = list(
zip(smallest_merge_labelids_u, smallest_merge_labelids_v))
random_merge_labelids_u = [
rag.uId(rag.edgeFromId(x)) for x in random_merge_ids
]
random_merge_labelids_v = [
rag.vId(rag.edgeFromId(x)) for x in random_merge_ids
]
random_merge_labelids = list(
zip(random_merge_labelids_u, random_merge_labelids_v))
ipl.logging('Label IDs selected for merging by size: {}',
smallest_merge_labelids)
ipl.logging('Label IDs randomly selected for merging: {}',
random_merge_labelids)
# Concatenate
all_merge_labelids = smallest_merge_labelids + random_merge_labelids
# Sort
ipl.logging('all_merge_labelids = {}', all_merge_labelids)
all_merge_labelids = [sorted(x) for x in all_merge_labelids]
all_merge_labelids = sorted(all_merge_labelids)
ipl.logging('all_merge_labelids = {}', all_merge_labelids)
# Store this for later use
ipl[targetnames[1]] = smallest_merge_labelids
ipl[targetnames[2]] = random_merge_labelids
ipl[targetnames[3]] = all_merge_labelids
# Create change hash list
change_hash = IPL(data=dict(
zip(np.unique(all_merge_labelids), [[
x,
] for x in np.unique(all_merge_labelids)])))
for i in xrange(0, 3):
prev_change_hash = IPL(data=change_hash)
for x in all_merge_labelids:
ipl.logging('Adding {} and {}', *x)
change_hash[x[0]] += change_hash[x[1]]
change_hash[x[0]] = list(np.unique(change_hash[x[0]]))
change_hash[x[1]] += change_hash[x[0]]
change_hash[x[1]] = list(np.unique(change_hash[x[1]]))
# This removes the redundancy from the hash
def reduce(hash):
br = False
for k, v in hash.iteritems():
for x in v:
if x != k:
if x in hash.keys():
del hash[x]
reduce(hash)
br = True
break
else:
br = False
if br:
break
reduce(change_hash)
# Change the list in the hash to np-arrays for better storage in h5 files
for k, v in change_hash.iteritems():
change_hash[k] = np.array(v)
# And now we have a perfect change list which we just need to iterate over and change the labels in the image
ipl.logging('change_hash after change:')
ipl.logging(change_hash)
ipl[targetnames[4]] = change_hash
# Create the merged image
# ipl.deepcopy_entry('largeobj', targetnames[0])
ipl.rename_entry(key, targetnames[0])
for k, v in change_hash.iteritems():
for x in v:
if x != k:
ipl.logging('Setting {} to {}!', x, k)
ipl.filter_values(x, type='eq', setto=k, keys=targetnames[0])
return ipl
tkeys='{}.{}.{}'.format('result_false', k, k2))
hfp.pop('disttransf')
hfp.pop('disttransfm')
# hfp.pop('result_false')
# hfp.pop('result_true')
hfp.pop('true')
hfp.pop('false')
hfp.pop('raw')
hfp.logging('hfp datastructure:\n---\n{}---', hfp.datastructure2string(maxdepth=2))
# print hfp['result.6720_13067.8']
y = []
for k, v in hfp.iteritems():
if v.values()[0]:
try:
# y.append(v)
x = range(0, len(v.values()[0]))
y = np.swapaxes(np.array(v.values()), 0, 1)
plt.plot(x, y)
# plt.show()
lab.savefig(params['intermedfolder'] + 'plots/' + k + '.png')
plt.clf()
except ValueError:
pass