def run_on_objects(self, object_name, workspace):
"""Run, computing the area measurements for a single map of objects"""
objects = workspace.get_objects(object_name)
if len(objects.shape) == 2:
#
# Do the ellipse-related measurements
#
i, j, l = objects.ijv.transpose()
centers, eccentricity, major_axis_length, minor_axis_length, \
theta, compactness = \
ellipse_from_second_moments_ijv(i, j, 1, l, objects.indices, True)
del i
del j
del l
self.record_measurement(workspace, object_name, F_ECCENTRICITY,
eccentricity)
self.record_measurement(workspace, object_name,
F_MAJOR_AXIS_LENGTH, major_axis_length)
self.record_measurement(workspace, object_name,
F_MINOR_AXIS_LENGTH, minor_axis_length)
self.record_measurement(workspace, object_name, F_ORIENTATION,
theta * 180 / np.pi)
self.record_measurement(workspace, object_name, F_COMPACTNESS,
compactness)
is_first = False
if len(objects.indices) == 0:
nobjects = 0
else:
nobjects = np.max(objects.indices)
mcenter_x = np.zeros(nobjects)
mcenter_y = np.zeros(nobjects)
mextent = np.zeros(nobjects)
mperimeters = np.zeros(nobjects)
msolidity = np.zeros(nobjects)
euler = np.zeros(nobjects)
max_radius = np.zeros(nobjects)
median_radius = np.zeros(nobjects)
mean_radius = np.zeros(nobjects)
min_feret_diameter = np.zeros(nobjects)
max_feret_diameter = np.zeros(nobjects)
zernike_numbers = self.get_zernike_numbers()
zf = {}
for n, m in zernike_numbers:
zf[(n, m)] = np.zeros(nobjects)
if nobjects > 0:
chulls, chull_counts = convex_hull_ijv(objects.ijv,
objects.indices)
for labels, indices in objects.get_labels():
to_indices = indices - 1
distances = distance_to_edge(labels)
mcenter_y[to_indices], mcenter_x[to_indices] = \
maximum_position_of_labels(distances, labels, indices)
max_radius[to_indices] = fix(
scind.maximum(distances, labels, indices))
mean_radius[to_indices] = fix(
scind.mean(distances, labels, indices))
median_radius[to_indices] = median_of_labels(
distances, labels, indices)
#
# The extent (area / bounding box area)
#
mextent[to_indices] = calculate_extents(labels, indices)
#
# The perimeter distance
#
mperimeters[to_indices] = calculate_perimeters(
labels, indices)
#
# Solidity
#
msolidity[to_indices] = calculate_solidity(labels, indices)
#
# Euler number
#
euler[to_indices] = euler_number(labels, indices)
#
# Zernike features
#
if self.calculate_zernikes.value:
zf_l = cpmz.zernike(zernike_numbers, labels, indices)
for (n, m), z in zip(zernike_numbers,
zf_l.transpose()):
zf[(n, m)][to_indices] = z
#
# Form factor
#
ff = 4.0 * np.pi * objects.areas / mperimeters**2
#
# Feret diameter
#
min_feret_diameter, max_feret_diameter = \
feret_diameter(chulls, chull_counts, objects.indices)
else:
ff = np.zeros(0)
for f, m in ([(F_AREA, objects.areas), (F_CENTER_X, mcenter_x),
(F_CENTER_Y, mcenter_y),
(F_CENTER_Z, np.ones_like(mcenter_x)),
(F_EXTENT, mextent), (F_PERIMETER, mperimeters),
(F_SOLIDITY, msolidity), (F_FORM_FACTOR, ff),
(F_EULER_NUMBER, euler),
(F_MAXIMUM_RADIUS, max_radius),
(F_MEAN_RADIUS, mean_radius),
(F_MEDIAN_RADIUS, median_radius),
(F_MIN_FERET_DIAMETER, min_feret_diameter),
(F_MAX_FERET_DIAMETER, max_feret_diameter)] +
[(self.get_zernike_name((n, m)), zf[(n, m)])
for n, m in zernike_numbers]):
self.record_measurement(workspace, object_name, f, m)
else:
labels = objects.segmented
props = skimage.measure.regionprops(labels)
# Area
areas = [prop.area for prop in props]
self.record_measurement(workspace, object_name, F_AREA, areas)
# Extent
extents = [prop.extent for prop in props]
self.record_measurement(workspace, object_name, F_EXTENT, extents)
# Centers of mass
centers = objects.center_of_mass()
center_z, center_y, center_x = centers.transpose()
self.record_measurement(workspace, object_name, F_CENTER_X,
center_x)
self.record_measurement(workspace, object_name, F_CENTER_Y,
center_y)
self.record_measurement(workspace, object_name, F_CENTER_Z,
center_z)
# Perimeters
perimeters = []
for label in np.unique(labels):
if label == 0:
continue
volume = np.zeros_like(labels, dtype='bool')
volume[labels == label] = True
verts, faces, _, _ = skimage.measure.marching_cubes(
volume,
spacing=objects.parent_image.spacing
if objects.has_parent_image else (1.0, ) * labels.ndim,
level=0)
perimeters += [skimage.measure.mesh_surface_area(verts, faces)]
if len(perimeters) == 0:
self.record_measurement(workspace, object_name, F_PERIMETER,
[0])
else:
self.record_measurement(workspace, object_name, F_PERIMETER,
perimeters)
for feature in self.get_feature_names():
if feature in [
F_AREA, F_EXTENT, F_CENTER_X, F_CENTER_Y, F_CENTER_Z,
F_PERIMETER
]:
continue
self.record_measurement(workspace, object_name, feature,
[np.nan])
def run_on_objects(self, object_name, workspace):
"""Run, computing the area measurements for a single map of objects"""
objects = workspace.get_objects(object_name)
assert isinstance(objects, cpo.Objects)
#
# Do the ellipse-related measurements
#
i, j, l = objects.ijv.transpose()
centers, eccentricity, major_axis_length, minor_axis_length, \
theta, compactness =\
ellipse_from_second_moments_ijv(i, j, 1, l, objects.indices, True)
del i
del j
del l
self.record_measurement(workspace, object_name, F_ECCENTRICITY,
eccentricity)
self.record_measurement(workspace, object_name, F_MAJOR_AXIS_LENGTH,
major_axis_length)
self.record_measurement(workspace, object_name, F_MINOR_AXIS_LENGTH,
minor_axis_length)
self.record_measurement(workspace, object_name, F_ORIENTATION,
theta * 180 / np.pi)
self.record_measurement(workspace, object_name, F_COMPACTNESS,
compactness)
is_first = False
if len(objects.indices) == 0:
nobjects = 0
else:
nobjects = np.max(objects.indices)
mcenter_x = np.zeros(nobjects)
mcenter_y = np.zeros(nobjects)
mextent = np.zeros(nobjects)
mperimeters = np.zeros(nobjects)
msolidity = np.zeros(nobjects)
euler = np.zeros(nobjects)
max_radius = np.zeros(nobjects)
median_radius = np.zeros(nobjects)
mean_radius = np.zeros(nobjects)
min_feret_diameter = np.zeros(nobjects)
max_feret_diameter = np.zeros(nobjects)
zernike_numbers = self.get_zernike_numbers()
zf = {}
for n, m in zernike_numbers:
zf[(n, m)] = np.zeros(nobjects)
if nobjects > 0:
chulls, chull_counts = convex_hull_ijv(objects.ijv,
objects.indices)
for labels, indices in objects.get_labels():
to_indices = indices - 1
distances = distance_to_edge(labels)
mcenter_y[to_indices], mcenter_x[to_indices] =\
maximum_position_of_labels(distances, labels, indices)
max_radius[to_indices] = fix(
scind.maximum(distances, labels, indices))
mean_radius[to_indices] = fix(
scind.mean(distances, labels, indices))
median_radius[to_indices] = median_of_labels(
distances, labels, indices)
#
# The extent (area / bounding box area)
#
mextent[to_indices] = calculate_extents(labels, indices)
#
# The perimeter distance
#
mperimeters[to_indices] = calculate_perimeters(labels, indices)
#
# Solidity
#
msolidity[to_indices] = calculate_solidity(labels, indices)
#
# Euler number
#
euler[to_indices] = euler_number(labels, indices)
#
# Zernike features
#
zf_l = cpmz.zernike(zernike_numbers, labels, indices)
for (n, m), z in zip(zernike_numbers, zf_l.transpose()):
zf[(n, m)][to_indices] = z
#
# Form factor
#
ff = 4.0 * np.pi * objects.areas / mperimeters**2
#
# Feret diameter
#
min_feret_diameter, max_feret_diameter = \
feret_diameter(chulls, chull_counts, objects.indices)
else:
ff = np.zeros(0)
for f, m in ([(F_AREA, objects.areas), (F_CENTER_X, mcenter_x),
(F_CENTER_Y, mcenter_y), (F_EXTENT, mextent),
(F_PERIMETER, mperimeters), (F_SOLIDITY, msolidity),
(F_FORM_FACTOR, ff), (F_EULER_NUMBER, euler),
(F_MAXIMUM_RADIUS, max_radius),
(F_MEAN_RADIUS, mean_radius),
(F_MEDIAN_RADIUS, median_radius),
(F_MIN_FERET_DIAMETER, min_feret_diameter),
(F_MAX_FERET_DIAMETER, max_feret_diameter)] +
[(self.get_zernike_name((n, m)), zf[(n, m)])
for n, m in zernike_numbers]):
self.record_measurement(workspace, object_name, f, m)
def run_on_objects(self, object_name, workspace):
"""Run, computing the area measurements for a single map of objects"""
objects = workspace.get_objects(object_name)
assert isinstance(objects, cpo.Objects)
#
# Do the ellipse-related measurements
#
i, j, l = objects.ijv.transpose()
centers, eccentricity, major_axis_length, minor_axis_length, \
theta, compactness =\
ellipse_from_second_moments_ijv(i, j, 1, l, objects.indices, True)
del i
del j
del l
self.record_measurement(workspace, object_name,
F_ECCENTRICITY, eccentricity)
self.record_measurement(workspace, object_name,
F_MAJOR_AXIS_LENGTH, major_axis_length)
self.record_measurement(workspace, object_name,
F_MINOR_AXIS_LENGTH, minor_axis_length)
self.record_measurement(workspace, object_name, F_ORIENTATION,
theta * 180 / np.pi)
self.record_measurement(workspace, object_name, F_COMPACTNESS,
compactness)
is_first = False
if len(objects.indices) == 0:
nobjects = 0
else:
nobjects = np.max(objects.indices)
mcenter_x = np.zeros(nobjects)
mcenter_y = np.zeros(nobjects)
mextent = np.zeros(nobjects)
mperimeters = np.zeros(nobjects)
msolidity = np.zeros(nobjects)
euler = np.zeros(nobjects)
max_radius = np.zeros(nobjects)
median_radius = np.zeros(nobjects)
mean_radius = np.zeros(nobjects)
min_feret_diameter = np.zeros(nobjects)
max_feret_diameter = np.zeros(nobjects)
zernike_numbers = self.get_zernike_numbers()
zf = {}
for n,m in zernike_numbers:
zf[(n,m)] = np.zeros(nobjects)
if nobjects > 0:
chulls, chull_counts = convex_hull_ijv(objects.ijv, objects.indices)
for labels, indices in objects.get_labels():
to_indices = indices-1
distances = distance_to_edge(labels)
mcenter_y[to_indices], mcenter_x[to_indices] =\
maximum_position_of_labels(distances, labels, indices)
max_radius[to_indices] = fix(scind.maximum(
distances, labels, indices))
mean_radius[to_indices] = fix(scind.mean(
distances, labels, indices))
median_radius[to_indices] = median_of_labels(
distances, labels, indices)
#
# The extent (area / bounding box area)
#
mextent[to_indices] = calculate_extents(labels, indices)
#
# The perimeter distance
#
mperimeters[to_indices] = calculate_perimeters(labels, indices)
#
# Solidity
#
msolidity[to_indices] = calculate_solidity(labels, indices)
#
# Euler number
#
euler[to_indices] = euler_number(labels, indices)
#
# Zernike features
#
zf_l = cpmz.zernike(zernike_numbers, labels, indices)
for (n,m), z in zip(zernike_numbers, zf_l.transpose()):
zf[(n,m)][to_indices] = z
#
# Form factor
#
ff = 4.0 * np.pi * objects.areas / mperimeters**2
#
# Feret diameter
#
min_feret_diameter, max_feret_diameter = \
feret_diameter(chulls, chull_counts, objects.indices)
else:
ff = np.zeros(0)
for f, m in ([(F_AREA, objects.areas),
(F_CENTER_X, mcenter_x),
(F_CENTER_Y, mcenter_y),
(F_EXTENT, mextent),
(F_PERIMETER, mperimeters),
(F_SOLIDITY, msolidity),
(F_FORM_FACTOR, ff),
(F_EULER_NUMBER, euler),
(F_MAXIMUM_RADIUS, max_radius),
(F_MEAN_RADIUS, mean_radius),
(F_MEDIAN_RADIUS, median_radius),
(F_MIN_FERET_DIAMETER, min_feret_diameter),
(F_MAX_FERET_DIAMETER, max_feret_diameter)] +
[(self.get_zernike_name((n,m)), zf[(n,m)])
for n,m in zernike_numbers]):
self.record_measurement(workspace, object_name, f, m)
def run_on_objects(self, object_name, workspace):
"""Run, computing the area measurements for a single map of objects"""
objects = workspace.get_objects(object_name)
if len(objects.shape) == 2:
#
# Do the ellipse-related measurements
#
i, j, l = objects.ijv.transpose()
centers, eccentricity, major_axis_length, minor_axis_length, \
theta, compactness = \
ellipse_from_second_moments_ijv(i, j, 1, l, objects.indices, True)
del i
del j
del l
self.record_measurement(workspace, object_name,
F_ECCENTRICITY, eccentricity)
self.record_measurement(workspace, object_name,
F_MAJOR_AXIS_LENGTH, major_axis_length)
self.record_measurement(workspace, object_name,
F_MINOR_AXIS_LENGTH, minor_axis_length)
self.record_measurement(workspace, object_name, F_ORIENTATION,
theta * 180 / np.pi)
self.record_measurement(workspace, object_name, F_COMPACTNESS,
compactness)
is_first = False
if len(objects.indices) == 0:
nobjects = 0
else:
nobjects = np.max(objects.indices)
mcenter_x = np.zeros(nobjects)
mcenter_y = np.zeros(nobjects)
mextent = np.zeros(nobjects)
mperimeters = np.zeros(nobjects)
msolidity = np.zeros(nobjects)
euler = np.zeros(nobjects)
max_radius = np.zeros(nobjects)
median_radius = np.zeros(nobjects)
mean_radius = np.zeros(nobjects)
min_feret_diameter = np.zeros(nobjects)
max_feret_diameter = np.zeros(nobjects)
zernike_numbers = self.get_zernike_numbers()
zf = {}
for n, m in zernike_numbers:
zf[(n, m)] = np.zeros(nobjects)
if nobjects > 0:
chulls, chull_counts = convex_hull_ijv(objects.ijv, objects.indices)
for labels, indices in objects.get_labels():
to_indices = indices - 1
distances = distance_to_edge(labels)
mcenter_y[to_indices], mcenter_x[to_indices] = \
maximum_position_of_labels(distances, labels, indices)
max_radius[to_indices] = fix(scind.maximum(
distances, labels, indices))
mean_radius[to_indices] = fix(scind.mean(
distances, labels, indices))
median_radius[to_indices] = median_of_labels(
distances, labels, indices)
#
# The extent (area / bounding box area)
#
mextent[to_indices] = calculate_extents(labels, indices)
#
# The perimeter distance
#
mperimeters[to_indices] = calculate_perimeters(labels, indices)
#
# Solidity
#
msolidity[to_indices] = calculate_solidity(labels, indices)
#
# Euler number
#
euler[to_indices] = euler_number(labels, indices)
#
# Zernike features
#
if self.calculate_zernikes.value:
zf_l = cpmz.zernike(zernike_numbers, labels, indices)
for (n, m), z in zip(zernike_numbers, zf_l.transpose()):
zf[(n, m)][to_indices] = z
#
# Form factor
#
ff = 4.0 * np.pi * objects.areas / mperimeters ** 2
#
# Feret diameter
#
min_feret_diameter, max_feret_diameter = \
feret_diameter(chulls, chull_counts, objects.indices)
else:
ff = np.zeros(0)
for f, m in ([(F_AREA, objects.areas),
(F_CENTER_X, mcenter_x),
(F_CENTER_Y, mcenter_y),
(F_CENTER_Z, np.ones_like(mcenter_x)),
(F_EXTENT, mextent),
(F_PERIMETER, mperimeters),
(F_SOLIDITY, msolidity),
(F_FORM_FACTOR, ff),
(F_EULER_NUMBER, euler),
(F_MAXIMUM_RADIUS, max_radius),
(F_MEAN_RADIUS, mean_radius),
(F_MEDIAN_RADIUS, median_radius),
(F_MIN_FERET_DIAMETER, min_feret_diameter),
(F_MAX_FERET_DIAMETER, max_feret_diameter)] +
[(self.get_zernike_name((n, m)), zf[(n, m)])
for n, m in zernike_numbers]):
self.record_measurement(workspace, object_name, f, m)
else:
labels = objects.segmented
props = skimage.measure.regionprops(labels)
# Area
areas = [prop.area for prop in props]
self.record_measurement(workspace, object_name, F_AREA, areas)
# Extent
extents = [prop.extent for prop in props]
self.record_measurement(workspace, object_name, F_EXTENT, extents)
# Centers of mass
centers = objects.center_of_mass()
center_z, center_y, center_x = centers.transpose()
self.record_measurement(workspace, object_name, F_CENTER_X, center_x)
self.record_measurement(workspace, object_name, F_CENTER_Y, center_y)
self.record_measurement(workspace, object_name, F_CENTER_Z, center_z)
# Perimeters
perimeters = []
for label in np.unique(labels):
if label == 0:
continue
volume = np.zeros_like(labels, dtype='bool')
volume[labels == label] = True
verts, faces, _, _ = skimage.measure.marching_cubes(
volume,
spacing=objects.parent_image.spacing if objects.has_parent_image else (1.0,) * labels.ndim,
level=0
)
perimeters += [skimage.measure.mesh_surface_area(verts, faces)]
if len(perimeters) == 0:
self.record_measurement(workspace, object_name, F_PERIMETER, [0])
else:
self.record_measurement(workspace, object_name, F_PERIMETER, perimeters)
for feature in self.get_feature_names():
if feature in [F_AREA, F_EXTENT, F_CENTER_X, F_CENTER_Y, F_CENTER_Z, F_PERIMETER]:
continue
self.record_measurement(workspace, object_name, feature, [np.nan])