def run(self, workspace):
#
# Get the measurements object - we put the measurements we
# make in here
#
meas = workspace.measurements
assert isinstance(meas, cpmeas.Measurements)
#
# We record some statistics which we will display later.
# We format them so that Matplotlib can display them in a table.
# The first row is a header that tells what the fields are.
#
statistics = [ [ "Feature", "Mean", "Median", "SD"] ]
#
# Put the statistics in the workspace display data so we
# can get at them when we display
#
workspace.display_data.statistics = statistics
#
# Get the input image and object. You need to get the .value
# because otherwise you'll get the setting object instead of
# the string name.
#
input_image_name = self.input_image_name.value
input_object_name = self.input_object_name.value
################################################################
#
# GETTING AN IMAGE FROM THE IMAGE SET
#
# Get the image set. The image set has all of the images in it.
#
image_set = workspace.image_set
#
# Get the input image object. We want a grayscale image here.
# The image set will convert a color image to a grayscale one
# and warn the user.
#
input_image = image_set.get_image(input_image_name,
must_be_grayscale = True)
#
# Get the pixels - these are a 2-d Numpy array.
#
pixels = input_image.pixel_data
#
###############################################################
#
# GETTING THE LABELS MATRIX FROM THE OBJECT SET
#
# The object set has all of the objects in it.
#
object_set = workspace.object_set
assert isinstance(object_set, cpo.ObjectSet)
#
# Get objects from the object set. The most useful array in
# the objects is "objects.segmented" which is a labels matrix
# in which each pixel has an integer value.
#
# The value, "0", is reserved for "background" - a pixel with
# a zero value is not in an object. Each object has an object
# number, starting at "1" and each pixel in the object is
# labeled with that number.
#
# The other useful array is "objects.small_removed_segmented" which
# is another labels matrix. There are objects that touch the edge of
# the image and get filtered out and there are large objects that
# get filtered out. Modules like "IdentifySecondaryObjects" may
# want to associate pixels near the objects in the labels matrix to
# those objects - the large and touching objects should compete with
# the real ones, so you should use "objects.small_removed_segmented"
# for those cases.
#
objects = object_set.get_objects(input_object_name)
labels = objects.segmented
#
###########################################
#
# The minimum enclosing circle (MEC) is the smallest circle that
# will fit around the object. We get the centers and radii of
# all of the objects at once. You'll see how that lets us
# compute the X and Y position of each pixel in a label all at
# one go.
#
# First, get an array that lists the whole range of indexes in
# the labels matrix.
#
indexes = objects.get_indices()
#
# Then ask for the minimum_enclosing_circle for each object named
# in those indexes. MEC returns the i and j coordinate of the center
# and the radius of the circle and that defines the circle entirely.
#
centers, radius = minimum_enclosing_circle(labels, indexes)
###############################################################
#
# The module computes a measurement based on the image intensity
# inside an object times a Zernike polynomial inscribed in the
# minimum enclosing circle around the object. The details are
# in the "measure_zernike" function. We call into the function with
# an N and M which describe the polynomial.
#
for n, m in self.get_zernike_indexes():
# Compute the zernikes for each object, returned in an array
zr, zi = self.measure_zernike(
pixels, labels, indexes, centers, radius, n, m)
# Get the name of the measurement feature for this zernike
feature = self.get_measurement_name(n, m)
# Add a measurement for this kind of object
if m != 0:
meas.add_measurement(input_object_name, feature, zr)
#
# Do the same with -m
#
feature = self.get_measurement_name(n, -m)
meas.add_measurement(input_object_name, feature, zi)
else:
# For zero, the total is the sum of real and imaginary parts
meas.add_measurement(input_object_name, feature, zr + zi)
#
# Record the statistics.
#
zmean = np.mean(zr)
zmedian = np.median(zr)
zsd = np.std(zr)
statistics.append( [ feature, zmean, zmedian, zsd ] )
def measure_zernike(self, pixels, labels, n, m):
# I'll put some documentation in here to explain what it does.
# If someone ever wants to call it, their editor might display
# the documentation.
'''Measure the intensity of the image with Zernike (N, M)
pixels - the intensity image to be measured
labels - the labels matrix that labels each object with an integer
n, m - the Zernike coefficients.
See http://en.wikipedia.org/wiki/Zernike_polynomials for an
explanation of the Zernike polynomials
'''
#
# The strategy here is to operate on the whole array instead
# of operating on one object at a time. The most important thing
# is to avoid having to run the Python interpreter once per pixel
# in the image and the second most important is to avoid running
# it per object in case there are hundreds of objects.
#
# We play lots of indexing tricks here to operate on the whole image.
# I'll try to explain some - hopefully, you can reuse.
#
# You could move the calculation of the minimum enclosing circle
# outside of this function. The function gets called more than
# 10 times, so the same calculation is performed 10 times.
# It would make the code a little more confusing, so I'm leaving
# it as-is.
###########################################
#
# The minimum enclosing circle (MEC) is the smallest circle that
# will fit around the object. We get the centers and radii of
# all of the objects at once. You'll see how that lets us
# compute the X and Y position of each pixel in a label all at
# one go.
#
# First, get an array that lists the whole range of indexes in
# the labels matrix.
#
indexes = np.arange(1, np.max(labels) + 1, dtype=np.int32)
#
# Then ask for the minimum_enclosing_circle for each object named
# in those indexes. MEC returns the i and j coordinate of the center
# and the radius of the circle and that defines the circle entirely.
#
centers, radius = minimum_enclosing_circle(labels, indexes)
center_x = centers[:, 1]
center_y = centers[:, 0]
#
# Make up fake values for 0 (the background). This lets us do our
# indexing tricks. Really, we're going to ignore the background,
# but we want to do the indexing without ignoring the background
# because that's easier.
#
center_x = np.hstack([[0], center_x])
center_y = np.hstack([[0], center_y])
radius = np.hstack([[1], radius])
#
# Now get one array that's the y coordinate of each pixel and one
# that's the x coordinate. This might look stupid and wasteful,
# but these "arrays" are never actually realized and made into
# real memory.
#
y, x = np.mgrid[0:labels.shape[0], 0:labels.shape[1]]
#
# Get the x and y coordinates relative to the object centers.
# This uses Numpy broadcasting. For each pixel, we use the
# value in the labels matrix as an index into the appropriate
# one-dimensional array. So we get the value for that object.
#
y -= center_y[labels]
x -= center_x[labels]
#
# Zernikes take x and y values from zero to one. We scale the
# integer coordinate values by dividing them by the radius of
# the circle. Again, we use the indexing trick to look up the
# values for each object.
#
y = y.astype(float) / radius[labels]
x = x.astype(float) / radius[labels]
#
#################################
#
# ZERNIKE POLYNOMIALS
#
# Now we can get Zernike polynomials per-pixel where each pixel
# value is calculated according to its object's MEC.
#
# We use a mask of all of the non-zero labels so the calculation
# runs a little faster.
#
zernike_polynomial = construct_zernike_polynomials(
x, y, np.array([[n, m]]))
#
# Multiply the Zernike polynomial by the image to dissect
# the image by the Zernike basis set.
#
output_pixels = pixels * zernike_polynomial[:, :, 0]
#
# The zernike polynomial is a complex number. We get a power
# spectrum here to combine the real and imaginary parts
#
output_pixels = np.sqrt(output_pixels * output_pixels.conjugate())
#
# Finally, we use Scipy to sum the intensities. Scipy has different
# versions with different quirks. The "fix" function takes all
# of that into account.
#
# The sum function calculates the sum of the pixel values for
# each pixel in an object, using the labels matrix to name
# the pixels in an object
#
result = fix(scind.sum(output_pixels.real, labels, indexes))
#
# And we're done! Did you like it? Did you get it?
#
return result
def measure_zernike(self, pixels, labels, n, m):
# I'll put some documentation in here to explain what it does.
# If someone ever wants to call it, their editor might display
# the documentation.
'''Measure the intensity of the image with Zernike (N, M)
pixels - the intensity image to be measured
labels - the labels matrix that labels each object with an integer
n, m - the Zernike coefficients.
See http://en.wikipedia.org/wiki/Zernike_polynomials for an
explanation of the Zernike polynomials
'''
#
# The strategy here is to operate on the whole array instead
# of operating on one object at a time. The most important thing
# is to avoid having to run the Python interpreter once per pixel
# in the image and the second most important is to avoid running
# it per object in case there are hundreds of objects.
#
# We play lots of indexing tricks here to operate on the whole image.
# I'll try to explain some - hopefully, you can reuse.
#
# You could move the calculation of the minimum enclosing circle
# outside of this function. The function gets called more than
# 10 times, so the same calculation is performed 10 times.
# It would make the code a little more confusing, so I'm leaving
# it as-is.
###########################################
#
# The minimum enclosing circle (MEC) is the smallest circle that
# will fit around the object. We get the centers and radii of
# all of the objects at once. You'll see how that lets us
# compute the X and Y position of each pixel in a label all at
# one go.
#
# First, get an array that lists the whole range of indexes in
# the labels matrix.
#
indexes = np.arange(1, np.max(labels)+1,dtype=np.int32)
#
# Then ask for the minimum_enclosing_circle for each object named
# in those indexes. MEC returns the i and j coordinate of the center
# and the radius of the circle and that defines the circle entirely.
#
centers, radius = minimum_enclosing_circle(labels, indexes)
center_x = centers[:, 1]
center_y = centers[:, 0]
#
# Make up fake values for 0 (the background). This lets us do our
# indexing tricks. Really, we're going to ignore the background,
# but we want to do the indexing without ignoring the background
# because that's easier.
#
center_x = np.hstack([[0], center_x])
center_y = np.hstack([[0], center_y])
radius = np.hstack([[1], radius])
#
# Now get one array that's the y coordinate of each pixel and one
# that's the x coordinate. This might look stupid and wasteful,
# but these "arrays" are never actually realized and made into
# real memory.
#
y, x = np.mgrid[0:labels.shape[0], 0:labels.shape[1]]
#
# Get the x and y coordinates relative to the object centers.
# This uses Numpy broadcasting. For each pixel, we use the
# value in the labels matrix as an index into the appropriate
# one-dimensional array. So we get the value for that object.
#
y -= center_y[labels]
x -= center_x[labels]
#
# Zernikes take x and y values from zero to one. We scale the
# integer coordinate values by dividing them by the radius of
# the circle. Again, we use the indexing trick to look up the
# values for each object.
#
y = y.astype(float) / radius[labels]
x = x.astype(float) / radius[labels]
#
#################################
#
# ZERNIKE POLYNOMIALS
#
# Now we can get Zernike polynomials per-pixel where each pixel
# value is calculated according to its object's MEC.
#
# We use a mask of all of the non-zero labels so the calculation
# runs a little faster.
#
zernike_polynomial = construct_zernike_polynomials(
x, y, np.array([ [ n, m ]]))
#
# Multiply the Zernike polynomial by the image to dissect
# the image by the Zernike basis set.
#
output_pixels = pixels * zernike_polynomial[:,:,0]
#
# The zernike polynomial is a complex number. We get a power
# spectrum here to combine the real and imaginary parts
#
output_pixels = np.sqrt(output_pixels * output_pixels.conjugate())
#
# Finally, we use Scipy to sum the intensities. Scipy has different
# versions with different quirks. The "fix" function takes all
# of that into account.
#
# The sum function calculates the sum of the pixel values for
# each pixel in an object, using the labels matrix to name
# the pixels in an object
#
result = fix(scind.sum(output_pixels.real, labels, indexes))
#
# And we're done! Did you like it? Did you get it?
#
return result
def run(self, workspace):
#
# Get the measurements object - we put the measurements we
# make in here
#
meas = workspace.measurements
assert isinstance(meas, cpmeas.Measurements)
#
# We record some statistics which we will display later.
# We format them so that Matplotlib can display them in a table.
# The first row is a header that tells what the fields are.
#
statistics = [ [ "Feature", "Mean", "Median", "SD"] ]
#
# Put the statistics in the workspace display data so we
# can get at them when we display
#
workspace.display_data.statistics = statistics
#
# Get the input image and object. You need to get the .value
# because otherwise you'll get the setting object instead of
# the string name.
#
input_image_name = self.input_image_name.value
input_object_name = self.input_object_name.value
################################################################
#
# GETTING AN IMAGE FROM THE IMAGE SET
#
# Get the image set. The image set has all of the images in it.
#
image_set = workspace.image_set
#
# Get the input image object. We want a grayscale image here.
# The image set will convert a color image to a grayscale one
# and warn the user.
#
input_image = image_set.get_image(input_image_name,
must_be_grayscale = True)
#
# Get the pixels - these are a 2-d Numpy array.
#
pixels = input_image.pixel_data
#
###############################################################
#
# GETTING THE LABELS MATRIX FROM THE OBJECT SET
#
# The object set has all of the objects in it.
#
object_set = workspace.object_set
assert isinstance(object_set, cpo.ObjectSet)
#
# Get objects from the object set. The most useful array in
# the objects is "objects.segmented" which is a labels matrix
# in which each pixel has an integer value.
#
# The value, "0", is reserved for "background" - a pixel with
# a zero value is not in an object. Each object has an object
# number, starting at "1" and each pixel in the object is
# labeled with that number.
#
# The other useful array is "objects.small_removed_segmented" which
# is another labels matrix. There are objects that touch the edge of
# the image and get filtered out and there are large objects that
# get filtered out. Modules like "IdentifySecondaryObjects" may
# want to associate pixels near the objects in the labels matrix to
# those objects - the large and touching objects should compete with
# the real ones, so you should use "objects.small_removed_segmented"
# for those cases.
#
objects = object_set.get_objects(input_object_name)
labels = objects.segmented
#
###########################################
#
# The minimum enclosing circle (MEC) is the smallest circle that
# will fit around the object. We get the centers and radii of
# all of the objects at once. You'll see how that lets us
# compute the X and Y position of each pixel in a label all at
# one go.
#
# First, get an array that lists the whole range of indexes in
# the labels matrix.
#
indexes = objects.get_indices()
#
# Then ask for the minimum_enclosing_circle for each object named
# in those indexes. MEC returns the i and j coordinate of the center
# and the radius of the circle and that defines the circle entirely.
#
centers, radius = minimum_enclosing_circle(labels, indexes)
###############################################################
#
# The module computes a measurement based on the image intensity
# inside an object times a Zernike polynomial inscribed in the
# minimum enclosing circle around the object. The details are
# in the "measure_zernike" function. We call into the function with
# an N and M which describe the polynomial.
#
for n, m in self.get_zernike_indexes():
# Compute the zernikes for each object, returned in an array
zr, zi = self.measure_zernike(
pixels, labels, indexes, centers, radius, n, m)
# Get the name of the measurement feature for this zernike
feature = self.get_measurement_name(n, m)
# Add a measurement for this kind of object
if m != 0:
meas.add_measurement(input_object_name, feature, zr)
#
# Do the same with -m
#
feature = self.get_measurement_name(n, -m)
meas.add_measurement(input_object_name, feature, zi)
else:
# For zero, the total is the sum of real and imaginary parts
meas.add_measurement(input_object_name, feature, zr + zi)
#
# Record the statistics.
#
zmean = np.mean(zr)
zmedian = np.median(zr)
zsd = np.std(zr)
statistics.append( [ feature, zmean, zmedian, zsd ] )
