def get_skeleton_points(self, obj):
'''Get points by skeletonizing the objects and decimating'''
ii = []
jj = []
total_skel = np.zeros(obj.shape, bool)
for labels, indexes in obj.get_labels():
colors = morph.color_labels(labels)
for color in range(1, np.max(colors) + 1):
labels_mask = colors == color
skel = morph.skeletonize(
labels_mask,
ordering=distance_transform_edt(labels_mask) *
poisson_equation(labels_mask))
total_skel = total_skel | skel
n_pts = np.sum(total_skel)
if n_pts == 0:
return np.zeros(0, np.int32), np.zeros(0, np.int32)
i, j = np.where(total_skel)
if n_pts > self.max_points.value:
#
# Decimate the skeleton by finding the branchpoints in the
# skeleton and propagating from those.
#
markers = np.zeros(total_skel.shape, np.int32)
branchpoints = \
morph.branchpoints(total_skel) | morph.endpoints(total_skel)
markers[branchpoints] = np.arange(np.sum(branchpoints)) + 1
#
# We compute the propagation distance to that point, then impose
# a slightly arbitarary order to get an unambiguous ordering
# which should number the pixels in a skeleton branch monotonically
#
ts_labels, distances = propagate(np.zeros(markers.shape), markers,
total_skel, 1)
order = np.lexsort((j, i, distances[i, j], ts_labels[i, j]))
#
# Get a linear space of self.max_points elements with bounds at
# 0 and len(order)-1 and use that to select the points.
#
order = order[np.linspace(0,
len(order) - 1,
self.max_points.value).astype(int)]
return i[order], j[order]
return i, j
def get_skeleton_points(self, obj):
'''Get points by skeletonizing the objects and decimating'''
ii = []
jj = []
total_skel = np.zeros(obj.shape, bool)
for labels, indexes in obj.get_labels():
colors = morph.color_labels(labels)
for color in range(1, np.max(colors) + 1):
labels_mask = colors == color
skel = morph.skeletonize(
labels_mask,
ordering = distance_transform_edt(labels_mask) *
poisson_equation(labels_mask))
total_skel = total_skel | skel
n_pts = np.sum(total_skel)
if n_pts == 0:
return np.zeros(0, np.int32), np.zeros(0, np.int32)
i, j = np.where(total_skel)
if n_pts > self.max_points.value:
#
# Decimate the skeleton by finding the branchpoints in the
# skeleton and propagating from those.
#
markers = np.zeros(total_skel.shape, np.int32)
branchpoints = \
morph.branchpoints(total_skel) | morph.endpoints(total_skel)
markers[branchpoints] = np.arange(np.sum(branchpoints))+1
#
# We compute the propagation distance to that point, then impose
# a slightly arbitarary order to get an unambiguous ordering
# which should number the pixels in a skeleton branch monotonically
#
ts_labels, distances = propagate(np.zeros(markers.shape),
markers, total_skel, 1)
order = np.lexsort((j, i, distances[i, j], ts_labels[i, j]))
#
# Get a linear space of self.max_points elements with bounds at
# 0 and len(order)-1 and use that to select the points.
#
order = order[
np.linspace(0, len(order)-1, self.max_points.value).astype(int)]
return i[order], j[order]
return i, j
def do_measurements(self, workspace, image_name, object_name,
center_object_name, center_choice,
bin_count_settings, dd):
'''Perform the radial measurements on the image set
workspace - workspace that holds images / objects
image_name - make measurements on this image
object_name - make measurements on these objects
center_object_name - use the centers of these related objects as
the centers for radial measurements. None to use the
objects themselves.
center_choice - the user's center choice for this object:
C_SELF, C_CENTERS_OF_OBJECTS or C_EDGES_OF_OBJECTS.
bin_count_settings - the bin count settings group
d - a dictionary for saving reusable partial results
returns one statistics tuple per ring.
'''
assert isinstance(workspace, cpw.Workspace)
assert isinstance(workspace.object_set, cpo.ObjectSet)
bin_count = bin_count_settings.bin_count.value
wants_scaled = bin_count_settings.wants_scaled.value
maximum_radius = bin_count_settings.maximum_radius.value
image = workspace.image_set.get_image(image_name,
must_be_grayscale=True)
objects = workspace.object_set.get_objects(object_name)
labels, pixel_data = cpo.crop_labels_and_image(objects.segmented,
image.pixel_data)
nobjects = np.max(objects.segmented)
measurements = workspace.measurements
assert isinstance(measurements, cpmeas.Measurements)
heatmaps = {}
for heatmap in self.heatmaps:
if heatmap.object_name.get_objects_name() == object_name and \
image_name == heatmap.image_name.get_image_name() and \
heatmap.get_number_of_bins() == bin_count:
dd[id(heatmap)] = \
heatmaps[MEASUREMENT_ALIASES[heatmap.measurement.value]] = \
np.zeros(labels.shape)
if nobjects == 0:
for bin in range(1, bin_count + 1):
for feature in (F_FRAC_AT_D, F_MEAN_FRAC, F_RADIAL_CV):
feature_name = (
(feature + FF_GENERIC) % (image_name, bin, bin_count))
measurements.add_measurement(
object_name, "_".join([M_CATEGORY, feature_name]),
np.zeros(0))
if not wants_scaled:
measurement_name = "_".join([M_CATEGORY, feature,
image_name, FF_OVERFLOW])
measurements.add_measurement(
object_name, measurement_name, np.zeros(0))
return [(image_name, object_name, "no objects", "-", "-", "-", "-")]
name = (object_name if center_object_name is None
else "%s_%s" % (object_name, center_object_name))
if dd.has_key(name):
normalized_distance, i_center, j_center, good_mask = dd[name]
else:
d_to_edge = distance_to_edge(labels)
if center_object_name is not None:
#
# Use the center of the centering objects to assign a center
# to each labeled pixel using propagation
#
center_objects = workspace.object_set.get_objects(center_object_name)
center_labels, cmask = cpo.size_similarly(
labels, center_objects.segmented)
pixel_counts = fix(scind.sum(
np.ones(center_labels.shape),
center_labels,
np.arange(1, np.max(center_labels) + 1, dtype=np.int32)))
good = pixel_counts > 0
i, j = (centers_of_labels(center_labels) + .5).astype(int)
ig = i[good]
jg = j[good]
lg = np.arange(1, len(i) + 1)[good]
if center_choice == C_CENTERS_OF_OTHER:
#
# Reduce the propagation labels to the centers of
# the centering objects
#
center_labels = np.zeros(center_labels.shape, int)
center_labels[ig, jg] = lg
cl, d_from_center = propagate(np.zeros(center_labels.shape),
center_labels,
labels != 0, 1)
#
# Erase the centers that fall outside of labels
#
cl[labels == 0] = 0
#
# If objects are hollow or crescent-shaped, there may be
# objects without center labels. As a backup, find the
# center that is the closest to the center of mass.
#
missing_mask = (labels != 0) & (cl == 0)
missing_labels = np.unique(labels[missing_mask])
if len(missing_labels):
all_centers = centers_of_labels(labels)
missing_i_centers, missing_j_centers = \
all_centers[:, missing_labels - 1]
di = missing_i_centers[:, np.newaxis] - ig[np.newaxis, :]
dj = missing_j_centers[:, np.newaxis] - jg[np.newaxis, :]
missing_best = lg[np.argsort((di * di + dj * dj,))[:, 0]]
best = np.zeros(np.max(labels) + 1, int)
best[missing_labels] = missing_best
cl[missing_mask] = best[labels[missing_mask]]
#
# Now compute the crow-flies distance to the centers
# of these pixels from whatever center was assigned to
# the object.
#
iii, jjj = np.mgrid[0:labels.shape[0], 0:labels.shape[1]]
di = iii[missing_mask] - i[cl[missing_mask] - 1]
dj = jjj[missing_mask] - j[cl[missing_mask] - 1]
d_from_center[missing_mask] = np.sqrt(di * di + dj * dj)
else:
# Find the point in each object farthest away from the edge.
# This does better than the centroid:
# * The center is within the object
# * The center tends to be an interesting point, like the
# center of the nucleus or the center of one or the other
# of two touching cells.
#
i, j = maximum_position_of_labels(d_to_edge, labels, objects.indices)
center_labels = np.zeros(labels.shape, int)
center_labels[i, j] = labels[i, j]
#
# Use the coloring trick here to process touching objects
# in separate operations
#
colors = color_labels(labels)
ncolors = np.max(colors)
d_from_center = np.zeros(labels.shape)
cl = np.zeros(labels.shape, int)
for color in range(1, ncolors + 1):
mask = colors == color
l, d = propagate(np.zeros(center_labels.shape),
center_labels,
mask, 1)
d_from_center[mask] = d[mask]
cl[mask] = l[mask]
good_mask = cl > 0
if center_choice == C_EDGES_OF_OTHER:
# Exclude pixels within the centering objects
# when performing calculations from the centers
good_mask = good_mask & (center_labels == 0)
i_center = np.zeros(cl.shape)
i_center[good_mask] = i[cl[good_mask] - 1]
j_center = np.zeros(cl.shape)
j_center[good_mask] = j[cl[good_mask] - 1]
normalized_distance = np.zeros(labels.shape)
if wants_scaled:
total_distance = d_from_center + d_to_edge
normalized_distance[good_mask] = (d_from_center[good_mask] /
(total_distance[good_mask] + .001))
else:
normalized_distance[good_mask] = \
d_from_center[good_mask] / maximum_radius
dd[name] = [normalized_distance, i_center, j_center, good_mask]
ngood_pixels = np.sum(good_mask)
good_labels = labels[good_mask]
bin_indexes = (normalized_distance * bin_count).astype(int)
bin_indexes[bin_indexes > bin_count] = bin_count
labels_and_bins = (good_labels - 1, bin_indexes[good_mask])
histogram = coo_matrix((pixel_data[good_mask], labels_and_bins),
(nobjects, bin_count + 1)).toarray()
sum_by_object = np.sum(histogram, 1)
sum_by_object_per_bin = np.dstack([sum_by_object] * (bin_count + 1))[0]
fraction_at_distance = histogram / sum_by_object_per_bin
number_at_distance = coo_matrix((np.ones(ngood_pixels), labels_and_bins),
(nobjects, bin_count + 1)).toarray()
object_mask = number_at_distance > 0
sum_by_object = np.sum(number_at_distance, 1)
sum_by_object_per_bin = np.dstack([sum_by_object] * (bin_count + 1))[0]
fraction_at_bin = number_at_distance / sum_by_object_per_bin
mean_pixel_fraction = fraction_at_distance / (fraction_at_bin +
np.finfo(float).eps)
masked_fraction_at_distance = masked_array(fraction_at_distance,
~object_mask)
masked_mean_pixel_fraction = masked_array(mean_pixel_fraction,
~object_mask)
# Anisotropy calculation. Split each cell into eight wedges, then
# compute coefficient of variation of the wedges' mean intensities
# in each ring.
#
# Compute each pixel's delta from the center object's centroid
i, j = np.mgrid[0:labels.shape[0], 0:labels.shape[1]]
imask = i[good_mask] > i_center[good_mask]
jmask = j[good_mask] > j_center[good_mask]
absmask = (abs(i[good_mask] - i_center[good_mask]) >
abs(j[good_mask] - j_center[good_mask]))
radial_index = (imask.astype(int) + jmask.astype(int) * 2 +
absmask.astype(int) * 4)
statistics = []
for bin in range(bin_count + (0 if wants_scaled else 1)):
bin_mask = (good_mask & (bin_indexes == bin))
bin_pixels = np.sum(bin_mask)
bin_labels = labels[bin_mask]
bin_radial_index = radial_index[bin_indexes[good_mask] == bin]
labels_and_radii = (bin_labels - 1, bin_radial_index)
radial_values = coo_matrix((pixel_data[bin_mask],
labels_and_radii),
(nobjects, 8)).toarray()
pixel_count = coo_matrix((np.ones(bin_pixels), labels_and_radii),
(nobjects, 8)).toarray()
mask = pixel_count == 0
radial_means = masked_array(radial_values / pixel_count, mask)
radial_cv = np.std(radial_means, 1) / np.mean(radial_means, 1)
radial_cv[np.sum(~mask, 1) == 0] = 0
for measurement, feature, overflow_feature in (
(fraction_at_distance[:, bin], MF_FRAC_AT_D, OF_FRAC_AT_D),
(mean_pixel_fraction[:, bin], MF_MEAN_FRAC, OF_MEAN_FRAC),
(np.array(radial_cv), MF_RADIAL_CV, OF_RADIAL_CV)):
if bin == bin_count:
measurement_name = overflow_feature % image_name
else:
measurement_name = feature % (image_name, bin + 1, bin_count)
measurements.add_measurement(object_name,
measurement_name,
measurement)
if feature in heatmaps:
heatmaps[feature][bin_mask] = measurement[bin_labels - 1]
radial_cv.mask = np.sum(~mask, 1) == 0
bin_name = str(bin + 1) if bin < bin_count else "Overflow"
statistics += [(image_name, object_name, bin_name, str(bin_count),
round(np.mean(masked_fraction_at_distance[:, bin]), 4),
round(np.mean(masked_mean_pixel_fraction[:, bin]), 4),
round(np.mean(radial_cv), 4))]
return statistics
def do_measurements(self, workspace, image_name, object_name,
center_object_name, center_choice,
bin_count_settings, dd):
'''Perform the radial measurements on the image set
workspace - workspace that holds images / objects
image_name - make measurements on this image
object_name - make measurements on these objects
center_object_name - use the centers of these related objects as
the centers for radial measurements. None to use the
objects themselves.
center_choice - the user's center choice for this object:
C_SELF, C_CENTERS_OF_OBJECTS or C_EDGES_OF_OBJECTS.
bin_count_settings - the bin count settings group
d - a dictionary for saving reusable partial results
returns one statistics tuple per ring.
'''
assert isinstance(workspace, cpw.Workspace)
assert isinstance(workspace.object_set, cpo.ObjectSet)
bin_count = bin_count_settings.bin_count.value
wants_scaled = bin_count_settings.wants_scaled.value
maximum_radius = bin_count_settings.maximum_radius.value
image = workspace.image_set.get_image(image_name,
must_be_grayscale=True)
objects = workspace.object_set.get_objects(object_name)
labels, pixel_data = cpo.crop_labels_and_image(objects.segmented,
image.pixel_data)
nobjects = np.max(objects.segmented)
measurements = workspace.measurements
assert isinstance(measurements, cpmeas.Measurements)
heatmaps = {}
for heatmap in self.heatmaps:
if heatmap.object_name.get_objects_name() == object_name and \
image_name == heatmap.image_name.get_image_name() and \
heatmap.get_number_of_bins() == bin_count:
dd[id(heatmap)] = \
heatmaps[MEASUREMENT_ALIASES[heatmap.measurement.value]] = \
np.zeros(labels.shape)
if nobjects == 0:
for bin in range(1, bin_count + 1):
for feature in (F_FRAC_AT_D, F_MEAN_FRAC, F_RADIAL_CV):
feature_name = (
(feature + FF_GENERIC) % (image_name, bin, bin_count))
measurements.add_measurement(
object_name, "_".join([M_CATEGORY, feature_name]),
np.zeros(0))
if not wants_scaled:
measurement_name = "_".join([M_CATEGORY, feature,
image_name, FF_OVERFLOW])
measurements.add_measurement(
object_name, measurement_name, np.zeros(0))
return [(image_name, object_name, "no objects", "-", "-", "-", "-")]
name = (object_name if center_object_name is None
else "%s_%s" % (object_name, center_object_name))
if dd.has_key(name):
normalized_distance, i_center, j_center, good_mask = dd[name]
else:
d_to_edge = distance_to_edge(labels)
if center_object_name is not None:
#
# Use the center of the centering objects to assign a center
# to each labeled pixel using propagation
#
center_objects = workspace.object_set.get_objects(center_object_name)
center_labels, cmask = cpo.size_similarly(
labels, center_objects.segmented)
pixel_counts = fix(scind.sum(
np.ones(center_labels.shape),
center_labels,
np.arange(1, np.max(center_labels) + 1, dtype=np.int32)))
good = pixel_counts > 0
i, j = (centers_of_labels(center_labels) + .5).astype(int)
ig = i[good]
jg = j[good]
lg = np.arange(1, len(i) + 1)[good]
if center_choice == C_CENTERS_OF_OTHER:
#
# Reduce the propagation labels to the centers of
# the centering objects
#
center_labels = np.zeros(center_labels.shape, int)
center_labels[ig, jg] = lg
cl, d_from_center = propagate(np.zeros(center_labels.shape),
center_labels,
labels != 0, 1)
#
# Erase the centers that fall outside of labels
#
cl[labels == 0] = 0
#
# If objects are hollow or crescent-shaped, there may be
# objects without center labels. As a backup, find the
# center that is the closest to the center of mass.
#
missing_mask = (labels != 0) & (cl == 0)
missing_labels = np.unique(labels[missing_mask])
if len(missing_labels):
all_centers = centers_of_labels(labels)
missing_i_centers, missing_j_centers = \
all_centers[:, missing_labels - 1]
di = missing_i_centers[:, np.newaxis] - ig[np.newaxis, :]
dj = missing_j_centers[:, np.newaxis] - jg[np.newaxis, :]
missing_best = lg[np.argsort((di * di + dj * dj,))[:, 0]]
best = np.zeros(np.max(labels) + 1, int)
best[missing_labels] = missing_best
cl[missing_mask] = best[labels[missing_mask]]
#
# Now compute the crow-flies distance to the centers
# of these pixels from whatever center was assigned to
# the object.
#
iii, jjj = np.mgrid[0:labels.shape[0], 0:labels.shape[1]]
di = iii[missing_mask] - i[cl[missing_mask] - 1]
dj = jjj[missing_mask] - j[cl[missing_mask] - 1]
d_from_center[missing_mask] = np.sqrt(di * di + dj * dj)
else:
# Find the point in each object farthest away from the edge.
# This does better than the centroid:
# * The center is within the object
# * The center tends to be an interesting point, like the
# center of the nucleus or the center of one or the other
# of two touching cells.
#
i, j = maximum_position_of_labels(d_to_edge, labels, objects.indices)
center_labels = np.zeros(labels.shape, int)
center_labels[i, j] = labels[i, j]
#
# Use the coloring trick here to process touching objects
# in separate operations
#
colors = color_labels(labels)
ncolors = np.max(colors)
d_from_center = np.zeros(labels.shape)
cl = np.zeros(labels.shape, int)
for color in range(1, ncolors + 1):
mask = colors == color
l, d = propagate(np.zeros(center_labels.shape),
center_labels,
mask, 1)
d_from_center[mask] = d[mask]
cl[mask] = l[mask]
good_mask = cl > 0
if center_choice == C_EDGES_OF_OTHER:
# Exclude pixels within the centering objects
# when performing calculations from the centers
good_mask = good_mask & (center_labels == 0)
i_center = np.zeros(cl.shape)
i_center[good_mask] = i[cl[good_mask] - 1]
j_center = np.zeros(cl.shape)
j_center[good_mask] = j[cl[good_mask] - 1]
normalized_distance = np.zeros(labels.shape)
if wants_scaled:
total_distance = d_from_center + d_to_edge
normalized_distance[good_mask] = (d_from_center[good_mask] /
(total_distance[good_mask] + .001))
else:
normalized_distance[good_mask] = \
d_from_center[good_mask] / maximum_radius
dd[name] = [normalized_distance, i_center, j_center, good_mask]
ngood_pixels = np.sum(good_mask)
good_labels = labels[good_mask]
bin_indexes = (normalized_distance * bin_count).astype(int)
bin_indexes[bin_indexes > bin_count] = bin_count
labels_and_bins = (good_labels - 1, bin_indexes[good_mask])
histogram = coo_matrix((pixel_data[good_mask], labels_and_bins),
(nobjects, bin_count + 1)).toarray()
sum_by_object = np.sum(histogram, 1)
sum_by_object_per_bin = np.dstack([sum_by_object] * (bin_count + 1))[0]
fraction_at_distance = histogram / sum_by_object_per_bin
number_at_distance = coo_matrix((np.ones(ngood_pixels), labels_and_bins),
(nobjects, bin_count + 1)).toarray()
object_mask = number_at_distance > 0
sum_by_object = np.sum(number_at_distance, 1)
sum_by_object_per_bin = np.dstack([sum_by_object] * (bin_count + 1))[0]
fraction_at_bin = number_at_distance / sum_by_object_per_bin
mean_pixel_fraction = fraction_at_distance / (fraction_at_bin +
np.finfo(float).eps)
masked_fraction_at_distance = masked_array(fraction_at_distance,
~object_mask)
masked_mean_pixel_fraction = masked_array(mean_pixel_fraction,
~object_mask)
# Anisotropy calculation. Split each cell into eight wedges, then
# compute coefficient of variation of the wedges' mean intensities
# in each ring.
#
# Compute each pixel's delta from the center object's centroid
i, j = np.mgrid[0:labels.shape[0], 0:labels.shape[1]]
imask = i[good_mask] > i_center[good_mask]
jmask = j[good_mask] > j_center[good_mask]
absmask = (abs(i[good_mask] - i_center[good_mask]) >
abs(j[good_mask] - j_center[good_mask]))
radial_index = (imask.astype(int) + jmask.astype(int) * 2 +
absmask.astype(int) * 4)
statistics = []
for bin in range(bin_count + (0 if wants_scaled else 1)):
bin_mask = (good_mask & (bin_indexes == bin))
bin_pixels = np.sum(bin_mask)
bin_labels = labels[bin_mask]
bin_radial_index = radial_index[bin_indexes[good_mask] == bin]
labels_and_radii = (bin_labels - 1, bin_radial_index)
radial_values = coo_matrix((pixel_data[bin_mask],
labels_and_radii),
(nobjects, 8)).toarray()
pixel_count = coo_matrix((np.ones(bin_pixels), labels_and_radii),
(nobjects, 8)).toarray()
mask = pixel_count == 0
radial_means = masked_array(radial_values / pixel_count, mask)
radial_cv = np.std(radial_means, 1) / np.mean(radial_means, 1)
radial_cv[np.sum(~mask, 1) == 0] = 0
for measurement, feature, overflow_feature in (
(fraction_at_distance[:, bin], MF_FRAC_AT_D, OF_FRAC_AT_D),
(mean_pixel_fraction[:, bin], MF_MEAN_FRAC, OF_MEAN_FRAC),
(np.array(radial_cv), MF_RADIAL_CV, OF_RADIAL_CV)):
if bin == bin_count:
measurement_name = overflow_feature % image_name
else:
measurement_name = feature % (image_name, bin + 1, bin_count)
measurements.add_measurement(object_name,
measurement_name,
measurement)
if feature in heatmaps:
heatmaps[feature][bin_mask] = measurement[bin_labels - 1]
radial_cv.mask = np.sum(~mask, 1) == 0
bin_name = str(bin + 1) if bin < bin_count else "Overflow"
statistics += [(image_name, object_name, bin_name, str(bin_count),
round(np.mean(masked_fraction_at_distance[:, bin]), 4),
round(np.mean(masked_mean_pixel_fraction[:, bin]), 4),
round(np.mean(radial_cv), 4))]
return statistics
def run(self, workspace):
#
# Get some things we need from the workspace
#
measurements = workspace.measurements
object_set = workspace.object_set
#
# Get the objects
#
objects_name = self.objects_name.value
objects = object_set.get_objects(objects_name)
#
# First, I do it the (1) way to show how that code should look.
# Later, I do it the (3) way and that will work even if objects.has_ijv
# is False.
if self.method == SUPPORT_BASIC:
labels = objects.segmented
#
# The indices are the integer values representing each of the objects
# in the labels matrix. scipy.ndimage functions often take an optional
# argument that tells them which objects should be analyzed.
# For instance, scipy.ndimage.mean takes an input image, a labels matrix
# and the indices. If you don't supply the indices, it will just take
# the mean of all labeled pixels, returning a single number.
#
indices = objects.indices
#
# Find the labeled pixels using labels != 0
#
foreground = labels != 0
#
# use scipy.ndimage.distance_transform_edt to find the distance of
# every foreground pixel from the object edge
#
distance = scipy.ndimage.distance_transform_edt(foreground)
#
# call scipy.ndimage.mean(distance, labels, indices) to find the
# mean distance in each object from its edge
#
values = scipy.ndimage.mean(distance, labels, indices)
#
# record the measurement using measurements.add_measurement
# with an object name of "objects_name" and a measurement name
# of M_MEAN_DISTANCE
#
measurements.add_measurement(objects_name, M_MEAN_DISTANCE, values)
elif self.method == SUPPORT_OVERLAPPING:
#
# I'll use objects.get_labels to get labels matrices. This involves
# a little extra work coallating the values, but not so bad.
#
# First of all, labels indices start at 1, but arrays start at
# zero, so for "values", I'm going to cheat and waste values[0].
# Later, I'll only use values[1:]
#
values = np.zeros(objects.count + 1)
#
# Now for the loop
#
for labels, indices in objects.get_labels():
foreground = labels != 0
distance = scipy.ndimage.distance_transform_edt(foreground)
v1 = scipy.ndimage.mean(distance, labels, indices)
#
# We copy the values above into the appropriate slots
#
values[indices] = v1
measurements.add_measurement(objects_name, M_MEAN_DISTANCE,
values[1:])
else:
#
# It's just a little expensive finding out which labels are
# touching others. The trick here is to use a function from
# cpmorphology called "color_labels". This is akin to the
# four color theorem - you want to color objects so that no
# two adjacent ones have the same color.
#
# After we've done that, we process each of the colors in turn,
# knowing that each object is colored only once and none of its
# neighbors have the same color.
#
# This is a good demo of why Python and Numpy are good choices
# for image processing. We're handling some pretty abstract
# concepts in just a few lines of code and the result, I hope,
# is clear and readable.
#
from centrosome.cpmorphology import color_labels
values = np.zeros(objects.count + 1)
for labels, indices in objects.get_labels():
clabels = color_labels(labels)
#
# np.unique returns the unique #s in an array.
#
colors = np.unique(clabels)
for color in colors:
# 0 = background, so ignore it.
if color == 0:
continue
#
# Ok, here's a trick. clabels == color gets converted
# to either 1 (is the current color) or 0 (is not) and
# we can use that to mask only the labels for the current
# color by multiplying (0 * anything = 0)
#
foreground = clabels == color
mini_labels = labels * foreground
distance = scipy.ndimage.distance_transform_edt(foreground)
#
# And here's another trick - scipy.ndimage.mean returns
# NaN for any index that doesn't appear because the
# mean isn't computable. How lucky!
#
v1 = scipy.ndimage.mean(distance, mini_labels, indices)
good_v1 = ~np.isnan(v1)
values[indices[good_v1]] = v1[good_v1]
measurements.add_measurement(objects_name, M_MEAN_DISTANCE,
values[1:])
def run(self, workspace):
#
# Get some things we need from the workspace
#
measurements = workspace.measurements
object_set = workspace.object_set
#
# Get the objects
#
objects_name = self.objects_name.value
objects = object_set.get_objects(objects_name)
#
# First, I do it the (1) way to show how that code should look.
# Later, I do it the (3) way and that will work even if objects.has_ijv
# is False.
if self.method == SUPPORT_BASIC:
labels = objects.segmented
#
# The indices are the integer values representing each of the objects
# in the labels matrix. scipy.ndimage functions often take an optional
# argument that tells them which objects should be analyzed.
# For instance, scipy.ndimage.mean takes an input image, a labels matrix
# and the indices. If you don't supply the indices, it will just take
# the mean of all labeled pixels, returning a single number.
#
indices = objects.indices
#
# Find the labeled pixels using labels != 0
#
foreground = labels != 0
#
# use scipy.ndimage.distance_transform_edt to find the distance of
# every foreground pixel from the object edge
#
distance = scipy.ndimage.distance_transform_edt(foreground)
#
# call scipy.ndimage.mean(distance, labels, indices) to find the
# mean distance in each object from its edge
#
values = scipy.ndimage.mean(distance, labels, indices)
#
# record the measurement using measurements.add_measurement
# with an object name of "objects_name" and a measurement name
# of M_MEAN_DISTANCE
#
measurements.add_measurement(objects_name, M_MEAN_DISTANCE, values)
elif self.method == SUPPORT_OVERLAPPING:
#
# I'll use objects.get_labels to get labels matrices. This involves
# a little extra work coallating the values, but not so bad.
#
# First of all, labels indices start at 1, but arrays start at
# zero, so for "values", I'm going to cheat and waste values[0].
# Later, I'll only use values[1:]
#
values = np.zeros(objects.count + 1)
#
# Now for the loop
#
for labels, indices in objects.get_labels():
foreground = labels != 0
distance = scipy.ndimage.distance_transform_edt(foreground)
v1 = scipy.ndimage.mean(distance, labels, indices)
#
# We copy the values above into the appropriate slots
#
values[indices] = v1
measurements.add_measurement(objects_name, M_MEAN_DISTANCE, values[1:])
else:
#
# It's just a little expensive finding out which labels are
# touching others. The trick here is to use a function from
# cpmorphology called "color_labels". This is akin to the
# four color theorem - you want to color objects so that no
# two adjacent ones have the same color.
#
# After we've done that, we process each of the colors in turn,
# knowing that each object is colored only once and none of its
# neighbors have the same color.
#
# This is a good demo of why Python and Numpy are good choices
# for image processing. We're handling some pretty abstract
# concepts in just a few lines of code and the result, I hope,
# is clear and readable.
#
from centrosome.cpmorphology import color_labels
values = np.zeros(objects.count + 1)
for labels, indices in objects.get_labels():
clabels = color_labels(labels)
#
# np.unique returns the unique #s in an array.
#
colors = np.unique(clabels)
for color in colors:
# 0 = background, so ignore it.
if color == 0:
continue
#
# Ok, here's a trick. clabels == color gets converted
# to either 1 (is the current color) or 0 (is not) and
# we can use that to mask only the labels for the current
# color by multiplying (0 * anything = 0)
#
foreground = clabels == color
mini_labels = labels * foreground
distance = scipy.ndimage.distance_transform_edt(foreground)
#
# And here's another trick - scipy.ndimage.mean returns
# NaN for any index that doesn't appear because the
# mean isn't computable. How lucky!
#
v1 = scipy.ndimage.mean(distance, mini_labels, indices)
good_v1 = ~np.isnan(v1)
values[indices[good_v1]] = v1[good_v1]
measurements.add_measurement(objects_name, M_MEAN_DISTANCE, values[1:])