def run(self, workspace):
"""Run the module
workspace - The workspace contains
pipeline - instance of cpp for this run
image_set - the images in the image set being processed
object_set - the objects (labeled masks) in this image set
measurements - the measurements for this run
frame - the parent frame to whatever frame is created. None means don't draw.
"""
background_image = self.get_background_image(workspace, None)
if (self.each_or_once == EO_ONCE
and self.get_good_gridding(workspace) is not None):
gridding = self.get_good_gridding(workspace)
if self.auto_or_manual == AM_AUTOMATIC:
gridding = self.run_automatic(workspace)
elif self.manual_choice == MAN_COORDINATES:
gridding = self.run_coordinates(workspace)
elif self.manual_choice == MAN_MOUSE:
gridding = workspace.interaction_request(
self, background_image,
workspace.measurements.image_set_number)
self.set_good_gridding(workspace, gridding)
workspace.set_grid(self.grid_image.value, gridding)
#
# Save measurements
#
self.add_measurement(workspace, F_X_LOCATION_OF_LOWEST_X_SPOT,
gridding.x_location_of_lowest_x_spot)
self.add_measurement(workspace, F_Y_LOCATION_OF_LOWEST_Y_SPOT,
gridding.y_location_of_lowest_y_spot)
self.add_measurement(workspace, F_ROWS, gridding.rows)
self.add_measurement(workspace, F_COLUMNS, gridding.columns)
self.add_measurement(workspace, F_X_SPACING, gridding.x_spacing)
self.add_measurement(workspace, F_Y_SPACING, gridding.y_spacing)
# update background image
background_image = self.get_background_image(workspace, gridding)
workspace.display_data.gridding = gridding.serialize()
workspace.display_data.background_image = background_image
workspace.display_data.image_set_number = workspace.measurements.image_set_number
if self.wants_image:
import matplotlib.transforms
from cellprofiler.gui.cpfigure_tools import figure_to_image
figure = matplotlib.figure.Figure()
canvas = matplotlib.backends.backend_agg.FigureCanvasAgg(figure)
ax = figure.add_subplot(1, 1, 1)
self.display_grid(background_image, gridding,
workspace.measurements.image_set_number, ax)
#
# This is the recipe for just showing the axis
#
figure.set_frameon(False)
ax.set_axis_off()
figure.subplots_adjust(0, 0, 1, 1, 0, 0)
ai = ax.images[0]
shape = ai.get_size()
dpi = figure.dpi
width = float(shape[1]) / dpi
height = float(shape[0]) / dpi
figure.set_figheight(height)
figure.set_figwidth(width)
bbox = matplotlib.transforms.Bbox(
np.array([[0.0, 0.0], [width, height]]))
transform = matplotlib.transforms.Affine2D(
np.array([[dpi, 0, 0], [0, dpi, 0], [0, 0, 1]]))
figure.bbox = matplotlib.transforms.TransformedBbox(
bbox, transform)
image_pixels = figure_to_image(figure, dpi=dpi)
image = cpi.Image(image_pixels)
workspace.image_set.add(self.save_image_name.value, image)
def run(self, workspace):
import matplotlib
import matplotlib.cm
import matplotlib.backends.backend_agg
import matplotlib.transforms
from cellprofiler.gui.cpfigure_tools import figure_to_image, only_display_image
#
# Get the image
#
image = workspace.image_set.get_image(self.image_name.value)
if self.wants_image:
pixel_data = image.pixel_data
else:
pixel_data = np.zeros(image.pixel_data.shape[:2])
object_set = workspace.object_set
if self.objects_or_image == OI_OBJECTS:
if self.objects_name.value in object_set.get_object_names():
objects = object_set.get_objects(self.objects_name.value)
else:
objects = None
workspace.display_data.pixel_data = pixel_data
if self.use_color_map():
workspace.display_data.labels = objects.segmented
#
# Get the measurements and positions
#
measurements = workspace.measurements
if self.objects_or_image == OI_IMAGE:
value = measurements.get_current_image_measurement(
self.measurement.value)
values = [value]
x = [pixel_data.shape[1] / 2]
x_offset = np.random.uniform(high=1.0,low=-1.0)
x[0] += x_offset
y = [pixel_data.shape[0] / 2]
y_offset = np.sqrt(1 - x_offset**2)
y[0] += y_offset
else:
values = measurements.get_current_measurement(
self.objects_name.value,
self.measurement.value)
if objects is not None and len(values) < objects.count:
temp = np.zeros(objects.count, values.dtype)
temp[:len(values)] = values
temp[len(values):] = np.nan
values = temp
x = measurements.get_current_measurement(
self.objects_name.value, M_LOCATION_CENTER_X)
x_offset = np.random.uniform(high=1.0,low=-1.0,size=x.shape)
y_offset = np.sqrt(1 - x_offset**2)
x += self.offset.value*x_offset
y = measurements.get_current_measurement(
self.objects_name.value, M_LOCATION_CENTER_Y)
y += self.offset.value*y_offset
mask = ~(np.isnan(values) | np.isnan(x) | np.isnan(y))
values = values[mask]
x = x[mask]
y = y[mask]
workspace.display_data.mask = mask
workspace.display_data.values = values
workspace.display_data.x = x
workspace.display_data.y = y
fig = matplotlib.figure.Figure()
axes = fig.add_subplot(1,1,1)
def imshow_fn(pixel_data):
# Note: requires typecast to avoid failure during
# figure_to_image (IMG-764)
img = pixel_data * 255
img[img < 0] = 0
img[img > 255] = 255
img = img.astype(np.uint8)
axes.imshow(img, cmap = matplotlib.cm.Greys_r)
self.display_on_figure(workspace, axes, imshow_fn)
canvas = matplotlib.backends.backend_agg.FigureCanvasAgg(fig)
if self.saved_image_contents == E_AXES:
fig.set_frameon(False)
if not self.use_color_map():
fig.subplots_adjust(0.1,.1,.9,.9,0,0)
shape = pixel_data.shape
width = float(shape[1]) / fig.dpi
height = float(shape[0]) / fig.dpi
fig.set_figheight(height)
fig.set_figwidth(width)
elif self.saved_image_contents == E_IMAGE:
if self.use_color_map():
fig.axes[1].set_visible(False)
only_display_image(fig, pixel_data.shape)
else:
if not self.use_color_map():
fig.subplots_adjust(.1,.1,.9,.9,0,0)
pixel_data = figure_to_image(fig, dpi=fig.dpi)
image = cpi.Image(pixel_data)
workspace.image_set.add(self.display_image.value, image)
def run(self, workspace):
import matplotlib
import matplotlib.cm
import matplotlib.backends.backend_agg
import matplotlib.transforms
from cellprofiler.gui.cpfigure_tools import figure_to_image, only_display_image
#
# Get the image
#
image = workspace.image_set.get_image(self.image_name.value)
workspace.display_data.pixel_data = image.pixel_data
if self.use_color_map():
workspace.display_data.labels = \
workspace.object_set.get_objects(self.objects_name.value).segmented
#
# Get the measurements and positions
#
measurements = workspace.measurements
if self.objects_or_image == OI_IMAGE:
value = measurements.get_current_image_measurement(
self.measurement.value)
values = [value]
x = [image.pixel_data.shape[1] / 2]
x_offset = np.random.uniform(high=1.0, low=-1.0)
x[0] += x_offset
y = [image.pixel_data.shape[0] / 2]
y_offset = np.sqrt(1 - x_offset**2)
y[0] += y_offset
else:
values = measurements.get_current_measurement(
self.objects_name.value, self.measurement.value)
x = measurements.get_current_measurement(self.objects_name.value,
M_LOCATION_CENTER_X)
x_offset = np.random.uniform(high=1.0, low=-1.0, size=x.shape)
y_offset = np.sqrt(1 - x_offset**2)
x += self.offset.value * x_offset
y = measurements.get_current_measurement(self.objects_name.value,
M_LOCATION_CENTER_Y)
y += self.offset.value * y_offset
mask = ~(np.isnan(values) | np.isnan(x) | np.isnan(y))
values = values[mask]
x = x[mask]
y = y[mask]
workspace.display_data.values = values
workspace.display_data.x = x
workspace.display_data.y = y
fig = matplotlib.figure.Figure()
axes = fig.add_subplot(1, 1, 1)
def imshow_fn(pixel_data):
# Note: requires typecast to avoid failure during
# figure_to_image (IMG-764)
img = pixel_data * 255
img[img < 0] = 0
img[img > 255] = 255
img = img.astype(np.uint8)
axes.imshow(img, cmap=matplotlib.cm.Greys_r)
self.display_on_figure(workspace, axes, imshow_fn)
canvas = matplotlib.backends.backend_agg.FigureCanvasAgg(fig)
if self.saved_image_contents == E_AXES:
fig.set_frameon(False)
if not self.use_color_map():
fig.subplots_adjust(0.1, .1, .9, .9, 0, 0)
shape = workspace.display_data.pixel_data.shape
width = float(shape[1]) / fig.dpi
height = float(shape[0]) / fig.dpi
fig.set_figheight(height)
fig.set_figwidth(width)
elif self.saved_image_contents == E_IMAGE:
if self.use_color_map():
fig.axes[1].set_visible(False)
only_display_image(fig, workspace.display_data.pixel_data.shape)
else:
if not self.use_color_map():
fig.subplots_adjust(.1, .1, .9, .9, 0, 0)
pixel_data = figure_to_image(fig, dpi=fig.dpi)
image = cpi.Image(pixel_data)
workspace.image_set.add(self.display_image.value, image)
def run(self, workspace):
"""Run the module
workspace - The workspace contains
pipeline - instance of cpp for this run
image_set - the images in the image set being processed
object_set - the objects (labeled masks) in this image set
measurements - the measurements for this run
frame - the parent frame to whatever frame is created. None means don't draw.
"""
background_image = self.get_background_image(workspace, None)
if (self.each_or_once == EO_ONCE and
self.get_good_gridding(workspace) is not None):
gridding = self.get_good_gridding(workspace)
if self.auto_or_manual == AM_AUTOMATIC:
gridding = self.run_automatic(workspace)
elif self.manual_choice == MAN_COORDINATES:
gridding = self.run_coordinates(workspace)
elif self.manual_choice == MAN_MOUSE:
gridding = workspace.interaction_request(self, background_image,
workspace.measurements.image_set_number)
self.set_good_gridding(workspace, gridding)
workspace.set_grid(self.grid_image.value, gridding)
#
# Save measurements
#
self.add_measurement(workspace, F_X_LOCATION_OF_LOWEST_X_SPOT,
gridding.x_location_of_lowest_x_spot)
self.add_measurement(workspace, F_Y_LOCATION_OF_LOWEST_Y_SPOT,
gridding.y_location_of_lowest_y_spot)
self.add_measurement(workspace, F_ROWS, gridding.rows)
self.add_measurement(workspace, F_COLUMNS, gridding.columns)
self.add_measurement(workspace, F_X_SPACING, gridding.x_spacing)
self.add_measurement(workspace, F_Y_SPACING, gridding.y_spacing)
# update background image
background_image = self.get_background_image(workspace, gridding)
workspace.display_data.gridding = gridding
workspace.display_data.background_image = background_image
workspace.display_data.image_set_number = workspace.measurements.image_set_number
if self.wants_image:
import matplotlib.transforms
from cellprofiler.gui.cpfigure_tools import figure_to_image
figure = matplotlib.figure.Figure()
canvas = matplotlib.backends.backend_agg.FigureCanvasAgg(figure)
ax = figure.add_subplot(1, 1, 1)
self.display_grid(background_image, gridding,
workspace.measurements.image_set_number, ax)
#
# This is the recipe for just showing the axis
#
figure.set_frameon(False)
ax.set_axis_off()
figure.subplots_adjust(0, 0, 1, 1, 0, 0)
ai = ax.images[0]
shape = ai.get_size()
dpi = figure.dpi
width = float(shape[1]) / dpi
height = float(shape[0]) / dpi
figure.set_figheight(height)
figure.set_figwidth(width)
bbox = matplotlib.transforms.Bbox(
np.array([[0.0, 0.0], [width, height]]))
transform = matplotlib.transforms.Affine2D(
np.array([[dpi, 0, 0],
[0, dpi, 0],
[0, 0, 1]]))
figure.bbox = matplotlib.transforms.TransformedBbox(bbox, transform)
image_pixels = figure_to_image(figure, dpi=dpi)
image = cpi.Image(image_pixels)
workspace.image_set.add(self.save_image_name.value, image)