def learn_flat(self, gts, feature_map, ws_is_gt, *args, **kwargs):
if type(gts) != list:
gts = [gts] # allow using single ground truth as input
ctables = [contingency_table(self.get_segmentation(), gt) for gt in gts]
assignments = [(ct == ct.max(axis=1)[:,newaxis]) for ct in ctables]
return map(array, zip(*[
self.learn_edge(e, ctables, assignments, feature_map, ws_is_gt)
for e in self.real_edges()]))
def best_possible_segmentation(ws, gt):
"""Build the best possible segmentation given a superpixel map."""
cnt = contingency_table(ws, gt)
assignment = cnt == cnt.max(axis=1)[:, newaxis]
hard_assignment = where(assignment.sum(axis=1) > 1)[0]
# currently ignoring hard assignment nodes
assignment[hard_assignment, :] = 0
ws = Rag(ws)
for gt_node in range(1, cnt.shape[1]):
ws.merge_subgraph(where(assignment[:, gt_node])[0])
return ws.get_segmentation()
def best_possible_segmentation(ws, gt):
"""Build the best possible segmentation given a superpixel map."""
cnt = contingency_table(ws, gt)
assignment = cnt == cnt.max(axis=1)[:,newaxis]
hard_assignment = where(assignment.sum(axis=1) > 1)[0]
# currently ignoring hard assignment nodes
assignment[hard_assignment,:] = 0
ws = Rag(ws)
for gt_node in range(1,cnt.shape[1]):
ws.merge_subgraph(where(assignment[:,gt_node])[0])
return ws.get_segmentation()
def learn_flat(self, gts, feature_map, ws_is_gt, *args, **kwargs):
if type(gts) != list:
gts = [gts] # allow using single ground truth as input
ctables = [
contingency_table(self.get_segmentation(), gt) for gt in gts
]
assignments = [(ct == ct.max(axis=1)[:, newaxis]) for ct in ctables]
return map(
array,
zip(*[
self.learn_edge(e, ctables, assignments, feature_map, ws_is_gt)
for e in self.real_edges()
]))
def set_ground_truth(self, gt=None):
if gt is not None:
gtm = gt.max() + 1
gt_ignore = [0, gtm] if (gt == 0).any() else [gtm]
seg_ignore = [0, self.boundary_body] if \
(self.segmentation==0).any() else [self.boundary_body]
self.gt = morpho.pad(gt, gt_ignore)
self.rig = contingency_table(self.segmentation, self.gt)
self.rig[:, gt_ignore] = 0
self.rig[seg_ignore, :] = 0
else:
self.gt = None
# null pattern to transparently allow merging of nodes.
# Bonus feature: counts how many sp's went into a single node.
try:
self.rig = ones(self.watershed.max() + 1)
except ValueError:
self.rig = ones(self.number_of_nodes() + 1)
def set_ground_truth(self, gt=None):
if gt is not None:
gtm = gt.max()+1
gt_ignore = [0, gtm] if (gt==0).any() else [gtm]
seg_ignore = [0, self.boundary_body] if \
(self.segmentation==0).any() else [self.boundary_body]
self.gt = morpho.pad(gt, gt_ignore)
self.rig = contingency_table(self.segmentation, self.gt)
self.rig[:, gt_ignore] = 0
self.rig[seg_ignore, :] = 0
else:
self.gt = None
# null pattern to transparently allow merging of nodes.
# Bonus feature: counts how many sp's went into a single node.
try:
self.rig = ones(self.watershed.max()+1)
except ValueError:
self.rig = ones(self.number_of_nodes()+1)
plt.scatter(x16, y16, c='purple')
plt.scatter(x17, y17, c='navy')
plt.scatter(x18, y18, c='violet')
plt.scatter(x19, y19, c='purple')
plt.scatter(x20, y20, c='coral')
plt.show()
#result2 is the predicted class of every sample
#label is the autual class of samples
label = []
result2 = []
for i in range(len(result[1])):
label.append(int(result[1][i].category))
for j in range(len(clf.labels_)):
result2.append(clf.labels_[j])
import evaluate as A
purity = A.purity(result2, label)
NMI = A.NMI(result2, label)
TP, TN, FP, FN = A.contingency_table(result2, label)
rand_index = A.rand_index(result2, label)
precision = A.precision(result2, label)
recall = A.recall(result2, label)
F_measure = A.F_measure(result2, label)
print("Purity:" + str(purity))
print("Precision:" + str(precision))
print("Recall:" + str(recall))
print("F_measue:" + str(F_measure))
def learn_agglomerate(self,
gts,
feature_map,
min_num_samples=1,
*args,
**kwargs):
"""Agglomerate while comparing to ground truth & classifying merges."""
learn_flat = kwargs.get('learn_flat', True)
learning_mode = kwargs.get('learning_mode', 'strict').lower()
labeling_mode = kwargs.get('labeling_mode', 'assignment').lower()
priority_mode = kwargs.get('priority_mode', 'random').lower()
memory = kwargs.get('memory', True)
unique = kwargs.get('unique', True)
max_numepochs = kwargs.get('max_numepochs', 10)
if priority_mode == 'mean' and unique:
max_numepochs = 2 if learn_flat else 1
if priority_mode in ['random', 'mean'] and not memory:
max_numepochs = 1
label_type_keys = {
'assignment': 0,
'vi-sign': 1,
'rand-sign': 2,
'boundary': 3
}
if type(gts) != list:
gts = [gts] # allow using single ground truth as input
master_ctables = \
[contingency_table(self.get_segmentation(), gt) for gt in gts]
# Match the watershed to the ground truths
ws_is_gt = zeros_like(self.watershed).astype(float)
for gt in gts:
ws_is_gt += self.assign_gt_to_ws(gt)
ws_is_gt /= float(len(gts))
ws_is_gt = ws_is_gt > 0.5
alldata = []
data = [[], [], [], []]
for numepochs in range(max_numepochs):
ctables = deepcopy(master_ctables)
if len(data[0]) > min_num_samples:
break
if learn_flat and numepochs == 0:
alldata.append(self.learn_flat(gts, feature_map, ws_is_gt))
data = unique_learning_data_elements(alldata) if unique else \
alldata[-1]
continue
g = self.copy()
if priority_mode == 'mean':
g.merge_priority_function = boundary_mean
elif numepochs > 0 and priority_mode == 'active' or \
numepochs % 2 == 1 and priority_mode == 'mixed':
cl = kwargs.get('classifier', RandomForest())
cl = cl.fit(data[0], data[1][:,
label_type_keys[labeling_mode]])
if type(cl) == RandomForest:
logging.info('classifier oob error: %.2f' % cl.oob)
g.merge_priority_function = \
classifier_probability(feature_map, cl)
elif priority_mode == 'random' or \
(priority_mode == 'active' and numepochs == 0):
g.merge_priority_function = random_priority
elif priority_mode == 'custom':
g.merge_priority_function = kwargs.get('mpf', boundary_mean)
g.show_progress = False # bug in MergeQueue usage causes
# progressbar crash.
g.rebuild_merge_queue()
alldata.append(
g._learn_agglomerate(ctables, feature_map, ws_is_gt,
learning_mode, labeling_mode))
if memory:
if unique:
data = unique_learning_data_elements(alldata)
else:
data = concatenate_data_elements(alldata)
else:
data = alldata[-1]
logging.debug('data size %d at epoch %d' %
(len(data[0]), numepochs))
return data, alldata
def learn_agglomerate(self, gts, feature_map, min_num_samples=1,
*args, **kwargs):
"""Agglomerate while comparing to ground truth & classifying merges."""
learn_flat = kwargs.get('learn_flat', True)
learning_mode = kwargs.get('learning_mode', 'strict').lower()
labeling_mode = kwargs.get('labeling_mode', 'assignment').lower()
priority_mode = kwargs.get('priority_mode', 'random').lower()
memory = kwargs.get('memory', True)
unique = kwargs.get('unique', True)
max_numepochs = kwargs.get('max_numepochs', 10)
if priority_mode == 'mean' and unique:
max_numepochs = 2 if learn_flat else 1
if priority_mode in ['random', 'mean'] and not memory:
max_numepochs = 1
label_type_keys = {'assignment':0, 'vi-sign':1,
'rand-sign':2, 'boundary':3}
if type(gts) != list:
gts = [gts] # allow using single ground truth as input
master_ctables = \
[contingency_table(self.get_segmentation(), gt) for gt in gts]
# Match the watershed to the ground truths
ws_is_gt = zeros_like(self.watershed).astype(float)
for gt in gts:
ws_is_gt += self.assign_gt_to_ws(gt)
ws_is_gt /= float(len(gts))
ws_is_gt = ws_is_gt>0.5
alldata = []
data = [[],[],[],[]]
for numepochs in range(max_numepochs):
ctables = deepcopy(master_ctables)
if len(data[0]) > min_num_samples:
break
if learn_flat and numepochs == 0:
alldata.append(self.learn_flat(gts, feature_map, ws_is_gt))
data = unique_learning_data_elements(alldata) if unique else \
alldata[-1]
continue
g = self.copy()
if priority_mode == 'mean':
g.merge_priority_function = boundary_mean
elif numepochs > 0 and priority_mode == 'active' or \
numepochs % 2 == 1 and priority_mode == 'mixed':
cl = kwargs.get('classifier', RandomForest())
cl = cl.fit(data[0], data[1][:,label_type_keys[labeling_mode]])
if type(cl) == RandomForest:
logging.info('classifier oob error: %.2f'%cl.oob)
g.merge_priority_function = \
classifier_probability(feature_map, cl)
elif priority_mode == 'random' or \
(priority_mode == 'active' and numepochs == 0):
g.merge_priority_function = random_priority
elif priority_mode == 'custom':
g.merge_priority_function = kwargs.get('mpf', boundary_mean)
g.show_progress = False # bug in MergeQueue usage causes
# progressbar crash.
g.rebuild_merge_queue()
alldata.append(g._learn_agglomerate(ctables, feature_map, ws_is_gt,
learning_mode, labeling_mode))
if memory:
if unique:
data = unique_learning_data_elements(alldata)
else:
data = concatenate_data_elements(alldata)
else:
data = alldata[-1]
logging.debug('data size %d at epoch %d'%(len(data[0]), numepochs))
return data, alldata