def rag_solidity(labels, connectivity=2):
graph = RAG()
# The footprint is constructed in such a way that the first
# element in the array being passed to _add_edge_filter is
# the central value.
fp = ndi.generate_binary_structure(labels.ndim, connectivity)
for d in range(fp.ndim):
fp = fp.swapaxes(0, d)
fp[0, ...] = 0
fp = fp.swapaxes(0, d)
# For example
# if labels.ndim = 2 and connectivity = 1
# fp = [[0,0,0],
# [0,1,1],
# [0,1,0]]
#
# if labels.ndim = 2 and connectivity = 2
# fp = [[0,0,0],
# [0,1,1],
# [0,1,1]]
ndi.generic_filter(labels,
function=_add_edge_filter,
footprint=fp,
mode='nearest',
output=np.zeros(labels.shape, dtype=np.uint8),
extra_arguments=(graph, ))
# remove bg_label
# graph.remove_node(-1)
graph.remove_node(0)
for n in graph:
mask = (labels == n)
solidity = 1. * mask.sum() / convex_hull_image(mask).sum()
graph.node[n].update({
'labels': [n],
'solidity': solidity,
'mask': mask
})
if LooseVersion(networkx.__version__) >= '2':
edges_iter = graph.edges(data=True)
else:
edges_iter = graph.edges_iter(data=True)
for x, y, d in edges_iter:
new_mask = np.logical_or(graph.node[x]['mask'], graph.node[y]['mask'])
new_solidity = 1. * new_mask.sum() / convex_hull_image(new_mask).sum()
org_solidity = np.mean(
[graph.node[x]['solidity'], graph.node[y]['solidity']])
d['weight'] = org_solidity / new_solidity
return graph
def _solidity_weight_func(graph, src, dst, n):
"""Callback to handle merging nodes by recomputing solidity."""
org_solidity = np.mean([graph.node[src]['solidity'],
graph.node[dst]['solidity']])
new_mask1 = np.logical_or(graph.node[src]['mask'], graph.node[n]['mask'])
new_mask2 = np.logical_or(graph.node[dst]['mask'], graph.node[n]['mask'])
new_solidity1 = 1. * new_mask1.sum() / convex_hull_image(new_mask1).sum()
new_solidity2 = 1. * new_mask2.sum() / convex_hull_image(new_mask2).sum()
weight1 = org_solidity / new_solidity1
weight2 = org_solidity / new_solidity2
return min([weight1, weight2])
def _solidity_weight_func(graph, src, dst, n):
"""Callback to handle merging nodes by recomputing solidity."""
org_solidity = np.mean(
[graph.node[src]['solidity'], graph.node[dst]['solidity']])
new_mask1 = np.logical_or(graph.node[src]['mask'], graph.node[n]['mask'])
new_mask2 = np.logical_or(graph.node[dst]['mask'], graph.node[n]['mask'])
new_solidity1 = 1. * new_mask1.sum() / convex_hull_image(new_mask1).sum()
new_solidity2 = 1. * new_mask2.sum() / convex_hull_image(new_mask2).sum()
weight1 = org_solidity / new_solidity1
weight2 = org_solidity / new_solidity2
return {'weight': min([weight1, weight2])}
def rag_solidity(labels, connectivity=2):
graph = RAG()
# The footprint is constructed in such a way that the first
# element in the array being passed to _add_edge_filter is
# the central value.
fp = ndi.generate_binary_structure(labels.ndim, connectivity)
for d in range(fp.ndim):
fp = fp.swapaxes(0, d)
fp[0, ...] = 0
fp = fp.swapaxes(0, d)
# For example
# if labels.ndim = 2 and connectivity = 1
# fp = [[0,0,0],
# [0,1,1],
# [0,1,0]]
#
# if labels.ndim = 2 and connectivity = 2
# fp = [[0,0,0],
# [0,1,1],
# [0,1,1]]
ndi.generic_filter(
labels,
function=_add_edge_filter,
footprint=fp,
mode='nearest',
output=np.zeros(labels.shape, dtype=np.uint8),
extra_arguments=(graph,))
# remove bg_label
# graph.remove_node(-1)
graph.remove_node(0)
for n in graph:
mask = (labels == n)
solidity = 1. * mask.sum() / convex_hull_image(mask).sum()
graph.node[n].update({'labels': [n],
'solidity': solidity,
'mask': mask})
for x, y, d in graph.edges_iter(data=True):
new_mask = np.logical_or(graph.node[x]['mask'], graph.node[y]['mask'])
new_solidity = 1. * new_mask.sum() / convex_hull_image(new_mask).sum()
org_solidity = np.mean([graph.node[x]['solidity'],
graph.node[y]['solidity']])
d['weight'] = org_solidity / new_solidity
return graph
def convex_image(self):
# TODO: grlee77: avoid host/device transfers
# from ..morphology.convex_hull import convex_hull_image
from skimage.morphology.convex_hull import convex_hull_image
# CuPy Backend: copy required here to avoid unexpected behavior
# reported in https://github.com/cupy/cupy/issues/4354
return cp.asarray(convex_hull_image(cp.asnumpy(self.image))).copy()
def infer_order_hull(inmodal):
num = inmodal.shape[0]
order_matrix = np.zeros((num, num), dtype=np.int)
occ_value_matrix = np.zeros((num, num), dtype=np.float32)
for i in range(num):
for j in range(i + 1, num):
if bordering(inmodal[i], inmodal[j]):
amodal_i = convex_hull.convex_hull_image(inmodal[i])
amodal_j = convex_hull.convex_hull_image(inmodal[j])
occ_value_matrix[i, j] = ((amodal_i > inmodal[i]) &
(inmodal[j] == 1)).sum()
occ_value_matrix[j, i] = ((amodal_j > inmodal[j]) &
(inmodal[i] == 1)).sum()
order_matrix[occ_value_matrix > occ_value_matrix.transpose()] = -1
order_matrix[occ_value_matrix < occ_value_matrix.transpose()] = 1
order_matrix[(occ_value_matrix == 0)
& (occ_value_matrix == 0).transpose()] = 0
return order_matrix
def infer_amodal_hull(inmodal, bboxes, order_matrix, order_grounded=True):
amodal = []
num = inmodal.shape[0]
for i in range(num):
m = inmodal[i]
hull = convex_hull.convex_hull_image(m).astype(np.uint8)
if order_grounded:
assert order_matrix is not None
ancestors = get_ancestors(order_matrix, i)
eraser = (inmodal[ancestors, ...].sum(axis=0) > 0).astype(
np.uint8) # union
hull[(eraser == 0) & (m == 0)] = 0
amodal.append(hull)
return amodal
def _rotate_tooth_image(image, mt_masks):
"""
Rotate the tooth image by using the gravity centers of mineralized tissues.
Parameters
----------
image: PIL.Image
The initial tooth image
mt_masks: [np.array]
List of masks of mineralized tissues
Returns
-------
(angle, angle deg, rotated image)
angle: float
The rotation angle in radiangs
angle deg: float
The rotation angle in degrees
rotated image: PIL.Image
The tooth image, rotated
rotated mt masks: [np.array]
A list of rotated masks
"""
from skimage.morphology.convex_hull import convex_hull_image
mt_merged_mask = np.zeros(mt_masks[0].shape)
for mask in mt_masks:
mt_merged_mask[mask > 0] = 1
hull_mask = convex_hull_image(mt_merged_mask)
hull_gc = _mask_gravity_center(hull_mask)
hull_gc = (int(hull_gc[1]), int(hull_gc[0]))
mt_merged_gc = _mask_gravity_center(mt_merged_mask)
mt_merged_gc = (int(mt_merged_gc[1]), int(mt_merged_gc[0]))
angle = math.atan2(mt_merged_gc[1] - hull_gc[1], mt_merged_gc[0] - hull_gc[0]) + math.pi / 2
angle_deg = angle * 180 / math.pi
rotated_image = image.rotate(angle_deg, expand=True)
rotated_mt_masks = [ _pillow_image_to_np_binary(_np_binary_to_pillow_image(mt_mask).rotate(angle_deg, expand=True)) for mt_mask in mt_masks]
return (angle, angle_deg, rotated_image, rotated_mt_masks)
def star(a, dtype=np.uint8):
"""Generates a star shaped structuring element.
Much faster than skimage.morphology version
"""
if a == 1:
bfilter = np.zeros((3, 3), dtype)
bfilter[:] = 1
return bfilter
m = 2 * a + 1
n = a // 2
selem_square = np.zeros((m + 2 * n, m + 2 * n), dtype=np.uint8)
selem_square[n:m + n, n:m + n] = 1
c = (m + 2 * n - 1) // 2
if True:
# We can do this much faster with opencv
b = (m + 2 * n) - 1
vertices = np.array([
[0, c],
[c, 0],
[b, c],
[c, b],
[0, c],
])
pts = vertices.astype(int)[:, None, :]
mask = np.zeros_like(selem_square)
mask = cv2.fillConvexPoly(mask, pts, color=1)
selem_rotated = mask
else:
from skimage.morphology.convex_hull import convex_hull_image
selem_rotated = np.zeros((m + 2 * n, m + 2 * n), dtype=np.float32)
selem_rotated[0, c] = selem_rotated[-1, c] = 1
selem_rotated[c, 0] = selem_rotated[c, -1] = 1
selem_rotated = convex_hull_image(selem_rotated).astype(int)
selem = np.add(selem_square, selem_rotated, out=selem_square)
selem[selem > 0] = 1
return selem.astype(dtype)
def _solidity_merge_func(graph, src, dst):
"""Callback called before merging two nodes of a solidity graph."""
new_mask = np.logical_or(graph.node[src]['mask'], graph.node[dst]['mask'])
graph.node[dst]['mask'] = new_mask
graph.node[dst]['solidity'] = \
1. * np.sum(new_mask) / np.sum(convex_hull_image(new_mask))
def calculate_df(event_path,oi_stage):
# initialize lists to hold data across events
mask_array = []
time_array = []
perimeter_array = []
area_array = []
circ_array = []
deform_array = []
r_um_array = []
xcm_pix_array, ycm_pix_array = [],[]
xcm_um_array, ycm_um_array = [],[]
tf_array = []
event = []
perimeter_array_cx = []
area_array_cx = []
circ_array_cx = []
deform_array_cx = []
r_um_array_cx = []
ellipse_xc_um_array = []
ellipse_yc_um_array = []
ellipse_a_array, ellipse_b_array = [],[]
aspect_array = []
r_um_elps_array = []
df_raw = pd.read_pickle(event_path)
for j in df_raw.keys():
num = len(df_raw[j]['mask'])
xcm_pix = np.empty(num)
ycm_pix = np.empty(num)
xcm_um = np.empty(num)
ycm_um = np.empty(num)
area = np.empty(num)
per = np.empty(num)
circ = np.empty(num)
deform = np.empty(num)
r_um = np.empty(num)
tf = np.empty(num)
masks = []
area_cx = np.empty(num)
per_cx = np.empty(num)
circ_cx = np.empty(num)
deform_cx = np.empty(num)
r_um_cx = np.empty(num)
ellipse_xc_um = np.empty(num)
ellipse_yc_um = np.empty(num)
ellipse_a = np.empty(num)
ellipse_b = np.empty(num)
aspect = np.empty(num)
r_um_elps = np.empty(num)
for i in range(num):
frame = np.reshape(df_raw[j]['mask'][i],(140,880))
masks.append(frame)
hull = convex_hull.convex_hull_image(frame)
xpix = np.where(frame==1)[1]
ypix = np.where(frame==1)[0]
xc_pix ,yc_pix = oi_stage.get_channel_coordinates(xpix, ypix)
xc_um = oi_stage.pixels_to_meters(xc_pix)
yc_um = oi_stage.pixels_to_meters(yc_pix)
xcm_pix = np.mean(xc_pix)
ycm_pix = np.mean(yc_pix)
xcm_um[i] = np.mean(xc_um)
ycm_um[i] = np.mean(yc_um)
area[i] = np.sum(frame)
per[i] = measure.perimeter(frame)
circ[i] = 2*np.sqrt(np.pi)*np.sqrt(area[i])/per[i]
deform[i] = 1 - circ[i]
r_um[i] = (oi_stage.pixels_to_meters(np.sqrt(area[i]/np.pi))+oi_stage.pixels_to_meters(per[i]/(2*np.pi)))/2
tf[i] = df_raw[j]['time'][i]
area_cx[i] = np.sum(hull)
per_cx[i] = measure.perimeter(hull)
circ_cx[i] = 2*np.sqrt(np.pi)*np.sqrt(area[i])/per[i]
deform_cx[i] = 1 - circ[i]
r_um_cx[i] = (oi_stage.pixels_to_meters(np.sqrt(area[i]/np.pi))+oi_stage.pixels_to_meters(per[i]/(2*np.pi)))/2
#ellipse_pixels = np.where(processed_frame == 1)
ellipse = oi.fit_ellipse_image_aligned(xpix, ypix)
ellipse_x, ellipse_y = oi.get_ellipse_center(ellipse)
ellipse_xc,ellipse_yc = oi_stage.get_channel_coordinates(ellipse_x,ellipse_y)
ellipse_xc_um[i] = oi_stage.pixels_to_meters(ellipse_xc)
ellipse_yc_um[i] = oi_stage.pixels_to_meters(ellipse_yc)
ellipse_a[i], ellipse_b[i] = oi.get_ellipse_axes_lengths(ellipse)
aspect[i] = ellipse_a[i]/ellipse_b[i]
r_um_elps[i] = np.sqrt(ellipse_a[i]*ellipse_b[i])
event.append(j)
mask_array.append(masks)
time_array.append(tf)
perimeter_array.append(per)
area_array.append(area)
circ_array.append(circ)
deform_array.append(deform)
r_um_array.append(r_um)
xcm_um_array.append(xcm_um)
ycm_um_array.append(ycm_um)
perimeter_array_cx.append(per_cx)
area_array_cx.append(area_cx)
circ_array_cx.append(circ_cx)
deform_array_cx.append(deform_cx)
r_um_array_cx.append(r_um_cx)
ellipse_xc_um_array.append(ellipse_xc_um)
ellipse_yc_um_array.append(ellipse_yc_um)
ellipse_a_array.append(ellipse_a)
ellipse_b_array.append(ellipse_b)
aspect_array.append(aspect)
r_um_elps_array.append(r_um_elps)
d = {'event':event,'tf':time_array,'mask':mask_array,'perimeter':perimeter_array,'area':area_array,
'circ':circ_array,'deform':deform_array,'r_um':r_um_array,'xcm_um':xcm_um_array,'yc_um':ycm_um_array,
'perimeter_cx':perimeter_array_cx,'area_cx':area_array_cx,'circ_cx':circ_array_cx,'deform_cx':deform_array_cx,
'r_um_cx':r_um_array_cx,'xc_um_el':ellipse_xc_um_array,'yc_um_el':ellipse_yc_um_array,'a':ellipse_a_array,
'b':ellipse_b_array,'aspect':aspect_array,'r_um_el':r_um_elps_array}
df = pd.DataFrame(data=d)
df['cell'] = particle_type
df['date'] = date
df['run'] = file_index
#Remove events with empty time series. Artifact of event detection
df = df[df.tf.map(lambda a: a.size!=0)]
return df
def convex_image(self):
# from ..morphology.convex_hull import convex_hull_image
# TODO: grlee77: avoid host/device transfers
from skimage.morphology.convex_hull import convex_hull_image
return cp.asarray(convex_hull_image(cp.asnumpy(self.image)))
def bug_tertiary():
rp = regionprops(SAMPLE)[0]
img = rp.image
conv_img = convex_hull_image(img)
return
def _solidity_merge_func(graph, src, dst):
"""Callback called before merging two nodes of a solidity graph."""
new_mask = np.logical_or(graph.node[src]['mask'], graph.node[dst]['mask'])
graph.node[dst]['mask'] = new_mask
graph.node[dst]['solidity'] = \
1. * np.sum(new_mask) / np.sum(convex_hull_image(new_mask))
def localize_apices_engine(image,
mt_masks,
debug=False,
output_dir='.',
image_name=''):
# load the masks
# check the mask length
if len(mt_masks) < 2:
raise ValueError('2 MT masks are needed to infer')
mt_masks = utils._find_greatest_mt_masks(mt_masks)
angle, _, rotated_image, mt_masks = utils._rotate_tooth_image(
image, mt_masks)
width, height = rotated_image.size
apical_mt_mask, coronal_mt_mask = mt_masks
mt_merged_mask = apical_mt_mask | coronal_mt_mask
# gradient cancel masks
coronal_distance = ndi.distance_transform_edt(
np.where(coronal_mt_mask > 0, 0, 1))
apical_distance = ndi.distance_transform_edt(
np.where(apical_mt_mask > 0, 0, 1))
hull = convex_hull_image(apical_mt_mask | coronal_mt_mask)
cancel_mask = np.where(
np.abs(coronal_distance - apical_distance) < 2, 1, 0)
thin_cancel_mask = skeletonize(cancel_mask) & hull
apical_hull = convex_hull_image(apical_mt_mask)
utils._apply_mask_to_image(rotated_image, cancel_mask, (0, 255, 0))
utils._apply_mask_to_image(rotated_image,
thin_cancel_mask, (255, 255, 0),
alpha=1)
utils._apply_mask_to_image(rotated_image,
coronal_mt_mask, (255, 0, 0),
alpha=0.2)
utils._apply_mask_to_image(rotated_image,
apical_hull, (0, 0, 255),
alpha=0.2)
# display outlines
coronal_outline, apical_outline, coronal_outline_mask, apical_outline_mask = display_outlines(
rotated_image, coronal_mt_mask, apical_mt_mask)
# display hull
utils._apply_mask_to_image(rotated_image, hull, (255, 0, 255), alpha=0.05)
# temporary endpoints
temporary_endpoints = get_temporary_endpoints(rotated_image,
thin_cancel_mask, hull)
if len(temporary_endpoints) < 2:
_logger.error(
'can not find endpoints if less than 2 potential endpoints')
return
coronal_dp_points, apical_dp_points = get_dp_points(
width, height, rotated_image, thin_cancel_mask, apical_outline_mask,
apical_mt_mask, coronal_outline_mask, coronal_mt_mask)
# get the split points
apical_split_point, coronal_split_point = get_dentin_pulp_split_points(
rotated_image, coronal_mt_mask, apical_mt_mask, coronal_outline,
apical_outline, coronal_outline_mask, apical_outline_mask)
utils._add_mark(rotated_image, apical_split_point, (255, 128, 0))
utils._add_mark(rotated_image, coronal_split_point, (255, 128, 0))
apical_dp_points.append(apical_split_point)
coronal_dp_points.append(coronal_split_point)
# reorder the points
ordered_apical_dp_points = reorder_dentin_pulp_points(
apical_dp_points, apical_outline)
ordered_coronal_dp_points = reorder_dentin_pulp_points(
coronal_dp_points, coronal_outline)
for point in ordered_apical_dp_points + ordered_coronal_dp_points:
rotated_image.putpixel(point, (255, 128, 0))
# clean the dp points
left_middle_endpoint, right_middle_endpoint = temporary_endpoints[
0], temporary_endpoints[1]
if left_middle_endpoint[0] > right_middle_endpoint[0]:
left_middle_endpoint, right_middle_endpoint = right_middle_endpoint, left_middle_endpoint
left_coronal_points, left_apical_points, right_apical_points, right_coronal_points = clean_dp_points(
rotated_image, temporary_endpoints, apical_split_point,
coronal_split_point, ordered_apical_dp_points,
ordered_coronal_dp_points, mt_merged_mask)
# find the new endpoints
draw = ImageDraw.Draw(rotated_image)
endpoint_pairs = select_endpoint_pairs(
left_middle_endpoint, right_middle_endpoint, left_coronal_points,
left_apical_points, right_apical_points, right_coronal_points)
for endpoint_pair in endpoint_pairs:
for point in endpoint_pair:
utils._add_mark(rotated_image, point, (255, 0, 0))
draw.line(endpoint_pair, (255, 0, 0))
(tooth_height, min_y,
max_y) = utils._get_tooth_height(apical_mt_mask | coronal_mt_mask)
draw.line((width // 2, min_y, width // 2, max_y), (0, 0, 255))
(i3m, min_apex_opening,
max_apex_opening) = utils._compute_i3m(endpoint_pairs, tooth_height)
result = {
'output_image': rotated_image,
'I3M': i3m,
'min_apex_opening': min_apex_opening,
'max_apex_opening': max_apex_opening,
'height': tooth_height
}
# draw the rotated image if debug
if debug:
image_path = os.path.join(output_dir, f'{image_name}-debug.png')
rotated_image.save(image_path)
return result
def segment_lesion(image, mode="KMeans"):
## Unsupervised Segmentation
# K-Means Clustering
if (mode == "KMeans"):
# K-Means Clustering
deim = denoise(cv2.cvtColor(image, cv2.COLOR_RGB2GRAY), weight=150)
kmeans = KMeans(n_clusters=2, random_state=0,
n_jobs=-1).fit(deim.reshape(-1, 1))
mask = (kmeans.labels_).reshape(deim.shape[0],
deim.shape[1]).astype('uint8')
# Expectation-Maximization Gaussian Mixture Model
elif (mode == "EM"):
# K-Means Clustering
feature_vector = (denoise(cv2.cvtColor(image, cv2.COLOR_RGB2GRAY),
weight=150)).reshape(-1, 1)
kmeans = KMeans(n_clusters=2, random_state=0,
n_jobs=-1).fit(feature_vector)
KMpredict = kmeans.predict(feature_vector)
# Expectation Step: Initialization with K-Means
KM_BG = feature_vector[KMpredict == 0]
KM_FG = feature_vector[KMpredict == 1]
# Expectation Step: Mean and Covariance
mean_BG = np.mean(KM_BG, axis=0)
mean_FG = np.mean(KM_FG, axis=0)
covar_BG = np.cov(KM_BG, rowvar=False)
covar_FG = np.cov(KM_FG, rowvar=False)
# Expectation Step: Prior Probabilities
prob_BG = KM_BG.shape[0] / feature_vector.shape[0]
prob_FG = KM_FG.shape[0] / feature_vector.shape[0]
# Iterative Update
min_change = 0.01
max_steps = 5
for i in range(max_steps):
# Expectation Step: Probability Density Function
PDF_BG = multivariate_normal.pdf(feature_vector,
mean=mean_BG,
cov=covar_BG)
PDF_FG = multivariate_normal.pdf(feature_vector,
mean=mean_FG,
cov=covar_FG)
weights_BG = (prob_BG * PDF_BG) / ((prob_FG * PDF_FG) +
(prob_BG * PDF_BG))
weights_FG = (prob_FG * PDF_FG) / ((prob_FG * PDF_FG) +
(prob_BG * PDF_BG))
weights = np.concatenate(
(weights_BG.reshape(-1, 1), weights_FG.reshape(-1, 1)), axis=1)
log_B = sum((np.log(sum(weights))))
# Maximization Step: New Probabilities
_, counts = np.unique(np.argmax(weights, axis=1),
return_counts=True)
prob_BG = counts[0] / feature_vector.shape[0]
prob_FG = counts[1] / feature_vector.shape[0]
# Maximization Step: New Mean and Covariance
mean_BG = (1 / counts[0]) * (weights[:, 0] @ feature_vector)
mean_FG = (1 / counts[1]) * (weights[:, 1] @ feature_vector)
covar_BG = (1 / counts[0]) * (
weights[:, 0] * np.transpose(feature_vector - mean_BG)) @ (
feature_vector - mean_BG)
covar_FG = (1 / counts[1]) * (
weights[:, 1] * np.transpose(feature_vector - mean_FG)) @ (
feature_vector - mean_FG)
# Maximization Step: Probability Density Function
PDF_BG = multivariate_normal.pdf(feature_vector,
mean=mean_BG,
cov=covar_BG)
PDF_FG = multivariate_normal.pdf(feature_vector,
mean=mean_FG,
cov=covar_FG)
weights_BG = (prob_BG * PDF_BG) / ((prob_FG * PDF_FG) +
(prob_BG * PDF_BG))
weights_FG = (prob_FG * PDF_FG) / ((prob_FG * PDF_FG) +
(prob_BG * PDF_BG))
weights = np.concatenate(
(weights_BG.reshape(-1, 1), weights_FG.reshape(-1, 1)), axis=1)
log_N = sum((np.log(sum(weights))))
# Update Trackers, Verify Conditions
change_log = np.linalg.norm(log_N - log_B)
if (change_log <= min_change):
continue
else:
break
# Output Image Reconstruction
mask = (np.argmax(weights, axis=1)).reshape(-1, 1)
mask = np.reshape(mask,
(image.shape[0], image.shape[1])).astype('uint8')
# Chan-Vese Active Contours
elif (mode == "active_contours"):
# Morphological ACWE
image = img_as_float(cv2.cvtColor(image, cv2.COLOR_RGB2GRAY))
# Initial level Set
init_ls = checkerboard_level_set(image.shape, 6)
# List with Intermediate Results for Plotting the Evolution
evolution = []
callback = store_evolution_in(evolution)
mask = morphological_chan_vese(image,
5,
init_level_set=init_ls,
smoothing=10,
iter_callback=callback).astype(np.uint8)
# Watershed
elif (mode == "mod_watershed"):
ret, thresh = cv2.threshold(cv2.cvtColor(image,
cv2.COLOR_RGB2GRAY), 0, 255,
cv2.THRESH_BINARY_INV + cv2.THRESH_OTSU)
kernel = np.ones((3, 3), np.uint8)
opening = cv2.morphologyEx(thresh,
cv2.MORPH_OPEN,
kernel,
iterations=2)
sure_bg = cv2.dilate(opening, kernel, iterations=3)
dist_transform = cv2.distanceTransform(opening, cv2.DIST_L2, 5)
ret, sure_fg = cv2.threshold(dist_transform,
0.01 * dist_transform.max(), 255, 0)
ls = np.uint8(sure_fg) / 255
circle_mask = create_circular_mask(image.shape[0],
image.shape[1],
radius=220)
ls = ls * circle_mask
# Discard Edge-to-Edge Connected Component
large = getLargestCC(ls).astype(np.uint8)
if (corner_mean(large) > 1):
large = getLargestCC(ls - large).astype(np.uint8)
# Post-Process Masks
post = ndimage.binary_fill_holes(large, structure=np.ones(
(5, 5))).astype(bool)
else:
print("ERROR: Undefined Segmentation Mode")
## Segmentation Label Selection
# Define Target Scope
candidate_mask_1 = mask.copy() * create_circular_mask(
image.shape[0], image.shape[1], radius=230)
candidate_mask_2 = (np.invert(mask.copy()) + 2) * create_circular_mask(
image.shape[0], image.shape[1], radius=230)
# Compute Area of Convex Hulls
convex_hull_1 = convex_hull_image(candidate_mask_1)
convex_hull_2 = convex_hull_image(candidate_mask_2)
# Set Segmentation Component Labels
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (10, 10))
if (np.sum(convex_hull_1) < np.sum(convex_hull_2)):
dilation = cv2.dilate(candidate_mask_1, kernel, iterations=1)
mask = ndimage.binary_fill_holes(dilation, structure=np.ones((5, 5)))
else:
dilation = cv2.dilate(candidate_mask_2, kernel, iterations=1)
mask = ndimage.binary_fill_holes(dilation, structure=np.ones((5, 5)))
if (np.sum(mask) < 5000):
mask = create_circular_mask(image.shape[0], image.shape[1], radius=230)
return mask
def bug_quaternary():
img = SAMPLE.astype(np.bool)
conv_img = convex_hull_image(img)
return