def fit(self, X, Y, w=None, w_asymmetric=None, depth=1, T=100, **kwargs):
self.X = X.copy()
self.Y = Y.copy()
N = len(self.Y)
if w is None:
w = (1.0/float(N))*numpy.ones(N)
if w_asymmetric is None:
w_asymmetric = (1.0/float(N))*numpy.ones(N)
self.weights = w.copy()
self.weights_asymmetric = numpy.array([i**(1.0/float(T))
for i in w_asymmetric])
self.weights /= float(sum(self.weights))
self.weak_classifier_ensemble = []
self.alpha = []
for t in with_progress(range(T), pbar=self.progressbar):
# Apply asymmetric weights
self.weights *= self.weights_asymmetric
weak_learner = DecisionTree().fit(self.X,self.Y,self.weights, depth=depth)
Y_pred = weak_learner.predict(self.X)
e = sum(0.5*self.weights*abs(self.Y-Y_pred))/sum(self.weights)
if e > 0.5:
logging.warning(' ending training, no good weak classifiers.')
break
ee = (1.0-e)/float(e)
alpha = 0.5*math.log(ee)
# increase weights for wrongly classified:
self.weights *= numpy.exp(-alpha*self.Y*Y_pred)
self.weights /= sum(self.weights)
self.weak_classifier_ensemble.append(weak_learner)
self.alpha.append(alpha)
return self
def watershed(a, seeds=None, smooth_thresh=0.0, smooth_seeds=False,
minimum_seed_size=0, dams=True, show_progress=False, connectivity=1):
seeded = seeds is not None
sel = generate_binary_structure(a.ndim, connectivity)
if smooth_thresh > 0.0:
b = hminima(a, smooth_thresh)
if seeded:
if smooth_seeds:
seeds = binary_opening(seeds, sel)
b = impose_minima(a, seeds.astype(bool), connectivity)
else:
seeds = regional_minima(a, connectivity)
b = a
if seeds.dtype == bool:
ws = label(seeds, sel)[0]
else:
ws = seeds
levels = unique(a)
a = pad(a, a.max()+1)
b = pad(b, b.max()+1)
ar = a.ravel()
br = b.ravel()
ws = pad(ws, 0)
wsr = ws.ravel()
maxlabel = iinfo(ws.dtype).max
current_label = 0
neighbors = build_neighbors_array(a, connectivity)
level_pixels = build_levels_dict(a)
if show_progress: wspbar = ip.StandardProgressBar('Watershed...')
else: wspbar = ip.NoProgressBar()
for i, level in ip.with_progress(enumerate(levels),
pbar=wspbar, length=len(levels)):
idxs_adjacent_to_labels = queue([idx for idx in level_pixels[level] if
any(wsr[neighbors[idx]])])
while len(idxs_adjacent_to_labels) > 0:
idx = idxs_adjacent_to_labels.popleft()
if wsr[idx]> 0: continue # in case we already processed it
nidxs = neighbors[idx] # neighbors
lnidxs = nidxs[
((wsr[nidxs] != 0) * (wsr[nidxs] != maxlabel)).astype(bool)
] # labeled neighbors
adj_labels = unique(wsr[lnidxs])
if len(adj_labels) > 1 and dams: # build a dam
wsr[idx] = maxlabel
elif len(adj_labels) >= 1: # assign a label
wsr[idx] = wsr[lnidxs][ar[lnidxs].argmin()]
idxs_adjacent_to_labels.extend(nidxs[((wsr[nidxs] == 0) *
(br[nidxs] == level)).astype(bool) ])
if dams:
ws[ws==maxlabel] = 0
return juicy_center(ws)
def label_merges(g, merge_history, feature_map_function, gt, loss_function):
"""Replay an agglomeration history and label the loss of each merge."""
labels = np.zeros(len(merge_history))
number_of_features = feature_map_function(g, *g.edges_iter().next()).size
features = np.zeros((len(merge_history), number_of_features))
labeled_image = np.zeros(gt.shape, np.double)
for i, nodes in enumerate(ip.with_progress(
merge_history, title='Replaying merge history...',
pbar=ip.StandardProgressBar())):
n1, n2 = nodes
features[i,:] = feature_map_function(g, n1, n2)
labels[i] = loss_function(g, n1, n2, gt)
labeled_image.ravel()[list(g[n1][n2]['boundary'])] = 2+labels[i]
g.merge_nodes(n1,n2)
return features, labels, labeled_image
def label_merges(g, merge_history, feature_map_function, gt, loss_function):
"""Replay an agglomeration history and label the loss of each merge."""
labels = np.zeros(len(merge_history))
number_of_features = feature_map_function(g, *g.edges_iter().next()).size
features = np.zeros((len(merge_history), number_of_features))
labeled_image = np.zeros(gt.shape, np.double)
for i, nodes in enumerate(
ip.with_progress(merge_history,
title='Replaying merge history...',
pbar=ip.StandardProgressBar())):
n1, n2 = nodes
features[i, :] = feature_map_function(g, n1, n2)
labels[i] = loss_function(g, n1, n2, gt)
labeled_image.ravel()[list(g[n1][n2]['boundary'])] = 2 + labels[i]
g.merge_nodes(n1, n2)
return features, labels, labeled_image
def build_graph_from_watershed(self,
allow_shared_boundaries=True,
idxs=None):
if self.watershed.size == 0: return # stop processing for empty graphs
if not allow_shared_boundaries:
self.ignored_boundary = zeros(self.watershed.shape, bool)
if idxs is None:
idxs = arange(self.watershed.size)
self.add_node(
self.boundary_body,
extent=set(flatnonzero(self.watershed == self.boundary_body)))
inner_idxs = idxs[self.watershed_r[idxs] != self.boundary_body]
pbar = ip.StandardProgressBar() if self.show_progress \
else ip.NoProgressBar()
for idx in ip.with_progress(inner_idxs, title='Graph... ', pbar=pbar):
ns = self.neighbor_idxs(idx)
adj_labels = self.watershed_r[ns]
adj_labels = unique(adj_labels)
adj_labels = adj_labels[adj_labels.nonzero()]
nodeid = self.watershed_r[idx]
if nodeid != 0:
adj_labels = adj_labels[adj_labels != nodeid]
edges = zip(repeat(nodeid), adj_labels)
if not self.has_node(nodeid):
self.add_node(nodeid, extent=set())
try:
self.node[nodeid]['extent'].add(idx)
except KeyError:
self.node[nodeid]['extent'] = set([idx])
else:
if len(adj_labels) == 0: continue
if adj_labels[-1] != self.boundary_body:
edges = list(combinations(adj_labels, 2))
else:
edges = list(product([self.boundary_body],
adj_labels[:-1]))
if allow_shared_boundaries or len(edges) == 1:
for l1, l2 in edges:
if self.has_edge(l1, l2):
self[l1][l2]['boundary'].add(idx)
else:
self.add_edge(l1, l2, boundary=set([idx]))
elif len(edges) > 1:
self.ignored_boundary.ravel()[idx] = True
def build_graph_from_watershed(self,
allow_shared_boundaries=True, idxs=None):
if self.watershed.size == 0: return # stop processing for empty graphs
if not allow_shared_boundaries:
self.ignored_boundary = zeros(self.watershed.shape, bool)
if idxs is None:
idxs = arange(self.watershed.size)
self.add_node(self.boundary_body,
extent=set(flatnonzero(self.watershed==self.boundary_body)))
inner_idxs = idxs[self.watershed_r[idxs] != self.boundary_body]
pbar = ip.StandardProgressBar() if self.show_progress \
else ip.NoProgressBar()
for idx in ip.with_progress(inner_idxs, title='Graph... ', pbar=pbar):
ns = self.neighbor_idxs(idx)
adj_labels = self.watershed_r[ns]
adj_labels = unique(adj_labels)
adj_labels = adj_labels[adj_labels.nonzero()]
nodeid = self.watershed_r[idx]
if nodeid != 0:
adj_labels = adj_labels[adj_labels != nodeid]
edges = zip(repeat(nodeid), adj_labels)
if not self.has_node(nodeid):
self.add_node(nodeid, extent=set())
try:
self.node[nodeid]['extent'].add(idx)
except KeyError:
self.node[nodeid]['extent'] = set([idx])
else:
if len(adj_labels) == 0: continue
if adj_labels[-1] != self.boundary_body:
edges = list(combinations(adj_labels, 2))
else:
edges = list(product([self.boundary_body], adj_labels[:-1]))
if allow_shared_boundaries or len(edges) == 1:
for l1,l2 in edges:
if self.has_edge(l1, l2):
self[l1][l2]['boundary'].add(idx)
else:
self.add_edge(l1, l2, boundary=set([idx]))
elif len(edges) > 1:
self.ignored_boundary.ravel()[idx] = True
def watershed(a,
seeds=None,
connectivity=1,
mask=None,
smooth_thresh=0.0,
smooth_seeds=False,
minimum_seed_size=0,
dams=False,
override_skimage=False,
show_progress=False):
"""Perform the watershed algorithm of Vincent & Soille (1991).
Parameters
----------
a : np.ndarray, arbitrary shape and type
The input image on which to perform the watershed transform.
seeds : np.ndarray, int or bool type, same shape as `a` (optional)
The seeds for the watershed. If provided, these are the only basins
allowed, and the algorithm proceeds by flooding from the seeds.
Otherwise, every local minimum is used as a seed.
connectivity : int, {1, ..., a.ndim} (optional, default 1)
The neighborhood of each pixel, defined as in `scipy.ndimage`.
mask : np.ndarray, type bool, same shape as `a`. (optional)
If provided, perform watershed only in the parts of `a` that are set
to `True` in `mask`.
smooth_thresh : float (optional, default 0.0)
Local minima that are less deep than this threshold are suppressed,
using `hminima`.
smooth_seeds : bool (optional, default False)
Perform binary opening on the seeds, using the same connectivity as
the watershed.
minimum_seed_size : int (optional, default 0)
Remove seed regions smaller than this size.
dams : bool (optional, default False)
Place a dam where two basins meet. Set this to True if you require
0-labeled boundaries between different regions.
override_skimage : bool (optional, default False)
skimage.morphology.watershed is used to implement the main part of the
algorithm when `dams=False`. Use this flag to use the separate pure
Python implementation instead.
show_progress : bool (optional, default False)
Show a cute little ASCII progress bar (using the progressbar package)
Returns
-------
ws : np.ndarray, same shape as `a`, int type.
The watershed transform of the input image.
"""
seeded = seeds is not None
sel = generate_binary_structure(a.ndim, connectivity)
# various keyword arguments operate by modifying the input image `a`.
# However, we operate on a copy of it called `b`, so that `a` can be used
# to break ties.
b = a
if smooth_thresh > 0.0:
b = hminima(a, smooth_thresh)
if not seeded:
seeds = regional_minima(b, connectivity)
if minimum_seed_size > 0:
seeds = remove_small_connected_components(seeds,
minimum_seed_size,
in_place=True)
seeds = relabel_from_one(seeds)[0]
if smooth_seeds:
seeds = binary_opening(seeds, sel)
if seeds.dtype == bool:
seeds = label(seeds, sel)[0]
if skimage_available and not override_skimage and not dams:
return skimage.morphology.watershed(b, seeds, sel, None, mask)
elif seeded:
b = impose_minima(a, seeds.astype(bool), connectivity)
levels = unique(b)
a = pad(a, a.max() + 1)
b = pad(b, b.max() + 1)
ar = a.ravel()
br = b.ravel()
ws = pad(seeds, 0)
wsr = ws.ravel()
neighbors = build_neighbors_array(a, connectivity)
level_pixels = build_levels_dict(b)
if show_progress: wspbar = ip.StandardProgressBar('Watershed...')
else: wspbar = ip.NoProgressBar()
for i, level in ip.with_progress(enumerate(levels),
pbar=wspbar,
length=len(levels)):
idxs_adjacent_to_labels = queue(
[idx for idx in level_pixels[level] if any(wsr[neighbors[idx]])])
while len(idxs_adjacent_to_labels) > 0:
idx = idxs_adjacent_to_labels.popleft()
if wsr[idx] > 0: continue # in case we already processed it
nidxs = neighbors[idx] # neighbors
lnidxs = nidxs[(wsr[nidxs] != 0).astype(bool)] # labeled neighbors
adj_labels = unique(wsr[lnidxs])
if len(adj_labels) == 1 or len(adj_labels) > 1 and not dams:
# assign a label
wsr[idx] = wsr[lnidxs][ar[lnidxs].argmin()]
idxs_adjacent_to_labels.extend(
nidxs[((wsr[nidxs] == 0) *
(br[nidxs] == level)).astype(bool)])
return juicy_center(ws)
def watershed(a, seeds=None, connectivity=1, mask=None, smooth_thresh=0.0,
smooth_seeds=False, minimum_seed_size=0, dams=False,
override_skimage=False, show_progress=False):
"""Perform the watershed algorithm of Vincent & Soille (1991).
Parameters
----------
a : np.ndarray, arbitrary shape and type
The input image on which to perform the watershed transform.
seeds : np.ndarray, int or bool type, same shape as `a` (optional)
The seeds for the watershed. If provided, these are the only basins
allowed, and the algorithm proceeds by flooding from the seeds.
Otherwise, every local minimum is used as a seed.
connectivity : int, {1, ..., a.ndim} (optional, default 1)
The neighborhood of each pixel, defined as in `scipy.ndimage`.
mask : np.ndarray, type bool, same shape as `a`. (optional)
If provided, perform watershed only in the parts of `a` that are set
to `True` in `mask`.
smooth_thresh : float (optional, default 0.0)
Local minima that are less deep than this threshold are suppressed,
using `hminima`.
smooth_seeds : bool (optional, default False)
Perform binary opening on the seeds, using the same connectivity as
the watershed.
minimum_seed_size : int (optional, default 0)
Remove seed regions smaller than this size.
dams : bool (optional, default False)
Place a dam where two basins meet. Set this to True if you require
0-labeled boundaries between different regions.
override_skimage : bool (optional, default False)
skimage.morphology.watershed is used to implement the main part of the
algorithm when `dams=False`. Use this flag to use the separate pure
Python implementation instead.
show_progress : bool (optional, default False)
Show a cute little ASCII progress bar (using the progressbar package)
Returns
-------
ws : np.ndarray, same shape as `a`, int type.
The watershed transform of the input image.
"""
seeded = seeds is not None
sel = generate_binary_structure(a.ndim, connectivity)
# various keyword arguments operate by modifying the input image `a`.
# However, we operate on a copy of it called `b`, so that `a` can be used
# to break ties.
b = a
if smooth_thresh > 0.0:
b = hminima(a, smooth_thresh)
if not seeded:
seeds = regional_minima(b, connectivity)
if minimum_seed_size > 0:
seeds = remove_small_connected_components(seeds, minimum_seed_size,
in_place=True)
seeds = relabel_from_one(seeds)[0]
if smooth_seeds:
seeds = binary_opening(seeds, sel)
if seeds.dtype == bool:
seeds = label(seeds, sel)[0]
if skimage_available and not override_skimage and not dams:
return skimage.morphology.watershed(b, seeds, sel, None, mask)
elif seeded:
b = impose_minima(a, seeds.astype(bool), connectivity)
levels = unique(b)
a = pad(a, a.max()+1)
b = pad(b, b.max()+1)
ar = a.ravel()
br = b.ravel()
ws = pad(seeds, 0)
wsr = ws.ravel()
neighbors = build_neighbors_array(a, connectivity)
level_pixels = build_levels_dict(b)
if show_progress: wspbar = ip.StandardProgressBar('Watershed...')
else: wspbar = ip.NoProgressBar()
for i, level in ip.with_progress(enumerate(levels),
pbar=wspbar, length=len(levels)):
idxs_adjacent_to_labels = queue([idx for idx in level_pixels[level] if
any(wsr[neighbors[idx]])])
while len(idxs_adjacent_to_labels) > 0:
idx = idxs_adjacent_to_labels.popleft()
if wsr[idx] > 0: continue # in case we already processed it
nidxs = neighbors[idx] # neighbors
lnidxs = nidxs[(wsr[nidxs] != 0).astype(bool)] # labeled neighbors
adj_labels = unique(wsr[lnidxs])
if len(adj_labels) == 1 or len(adj_labels) > 1 and not dams:
# assign a label
wsr[idx] = wsr[lnidxs][ar[lnidxs].argmin()]
idxs_adjacent_to_labels.extend(nidxs[((wsr[nidxs] == 0) *
(br[nidxs] == level)).astype(bool) ])
return juicy_center(ws)