def display(self, workspace, figure):
images = workspace.display_data.images
names = workspace.display_data.names
stats = workspace.display_data.stats
figure.set_subplots((1, len(images)))
figure.figure.clf()
nimages = len(images)
shrink = .05
for i in range(len(images)):
rect = [shrink + float(i)/float(nimages),
.5+shrink,
(1.0-2*shrink)/float(nimages),
.45*(1.0-2*shrink)]
axes = figure.figure.add_axes(rect)
axes.imshow(images[i], matplotlib.cm.Greys_r)
axes.set_title(names[i],
fontname=cpprefs.get_title_font_name(),
fontsize=cpprefs.get_title_font_size())
rect = [0.1,.1,.8,.35]
axes = figure.figure.add_axes(rect, frameon = False)
table = axes.table(cellText=stats,
colWidths=[1.0/7.0]*7,
loc='center',
cellLoc='left')
axes.set_axis_off()
table.auto_set_font_size(False)
table.set_fontsize(cpprefs.get_table_font_size())
def display():
if len(orig_axes.images) > 0:
# Save zoom and scale if coming through here a second time
x0, x1 = orig_axes.get_xlim()
y0, y1 = orig_axes.get_ylim()
set_lim = True
else:
set_lim = False
for axes, labels, title in ((orig_axes, orig_labels,
"Original: %s" % orig_objects_name),
(keep_axes, orig_labels * mask,
"Objects to keep"),
(remove_axes, orig_labels * (~mask),
"Objects to remove")):
assert isinstance(axes, matplotlib.axes.Axes)
labels = renumber_labels_for_display(labels)
axes.clear()
if np.all(labels == 0):
use_cm = matplotlib.cm.gray
is_blank = True
else:
use_cm = cm
is_blank = False
if wants_image_display[0]:
outlines = outline(labels)
image = workspace.image_set.get_image(
self.image_name.value)
image = image.pixel_data.astype(np.float)
image, _ = cpo.size_similarly(labels, image)
if image.ndim == 2:
image = np.dstack((image, image, image))
if not is_blank:
mappable = matplotlib.cm.ScalarMappable(cmap=use_cm)
mappable.set_clim(1, labels.max())
limage = mappable.to_rgba(labels)[:, :, :3]
image[outlines != 0, :] = limage[outlines != 0, :]
axes.imshow(image)
else:
axes.imshow(labels, cmap=use_cm)
axes.set_title(title,
fontname=cpprefs.get_title_font_name(),
fontsize=cpprefs.get_title_font_size())
if set_lim:
orig_axes.set_xlim((x0, x1))
orig_axes.set_ylim((y0, y1))
figure.canvas.draw()
panel.Refresh()
def run(self, workspace):
stats = [("Image", "Objects", "Bin # (innermost=1)", "Bin count",
"Fraction", "Intensity", "COV")]
d = {}
for image in self.images:
for o in self.objects:
for bin_count_settings in self.bin_counts:
stats += \
self.do_measurements(workspace,
image.image_name.value,
o.object_name.value,
o.center_object_name.value
if o.center_choice == C_OTHER
else None,
bin_count_settings,
d)
if workspace.frame is not None:
images = [d[key][0] for key in d.keys()]
names = d.keys()
figure = workspace.create_or_find_figure(
title="MeasureObjectRadialDistribution, image cycle #%d" %
(workspace.measurements.image_set_number),
subplots=(1, len(images)))
figure.figure.clf()
nimages = len(images)
shrink = .05
for i in range(len(images)):
rect = [
shrink + float(i) / float(nimages), .5 + shrink,
(1.0 - 2 * shrink) / float(nimages),
.45 * (1.0 - 2 * shrink)
]
axes = figure.figure.add_axes(rect)
axes.imshow(images[i], matplotlib.cm.Greys_r)
axes.set_title(names[i],
fontname=cpprefs.get_title_font_name(),
fontsize=cpprefs.get_title_font_size())
rect = [0.1, .1, .8, .35]
axes = figure.figure.add_axes(rect, frameon=False)
table = axes.table(cellText=stats,
colWidths=[1.0 / 7.0] * 7,
loc='center',
cellLoc='left')
axes.set_axis_off()
table.auto_set_font_size(False)
table.set_fontsize(cpprefs.get_table_font_size())
def display():
if len(orig_axes.images) > 0:
# Save zoom and scale if coming through here a second time
x0, x1 = orig_axes.get_xlim()
y0, y1 = orig_axes.get_ylim()
set_lim = True
else:
set_lim = False
for axes, labels, title in (
(orig_axes, orig_labels, "Original: %s"%orig_objects_name),
(keep_axes, orig_labels * mask,"Objects to keep"),
(remove_axes, orig_labels * (~ mask), "Objects to remove")):
assert isinstance(axes, matplotlib.axes.Axes)
labels = renumber_labels_for_display(labels)
axes.clear()
if np.all(labels == 0):
use_cm = matplotlib.cm.gray
is_blank = True
else:
use_cm = cm
is_blank = False
if wants_image_display[0]:
outlines = outline(labels)
image = workspace.image_set.get_image(self.image_name.value)
image = image.pixel_data.astype(np.float)
image, _ = cpo.size_similarly(labels, image)
if image.ndim == 2:
image = np.dstack((image, image, image))
if not is_blank:
mappable = matplotlib.cm.ScalarMappable(cmap=use_cm)
mappable.set_clim(1,labels.max())
limage = mappable.to_rgba(labels)[:,:,:3]
image[outlines != 0,:] = limage[outlines != 0, :]
axes.imshow(image)
else:
axes.imshow(labels, cmap = use_cm)
axes.set_title(title,
fontname=cpprefs.get_title_font_name(),
fontsize=cpprefs.get_title_font_size())
if set_lim:
orig_axes.set_xlim((x0, x1))
orig_axes.set_ylim((y0, y1))
figure.canvas.draw()
panel.Refresh()
def run(self, workspace):
stats = [("Image","Objects","Bin # (innermost=1)","Bin count","Fraction","Intensity","COV")]
d = {}
for image in self.images:
for o in self.objects:
for bin_count_settings in self.bin_counts:
stats += \
self.do_measurements(workspace,
image.image_name.value,
o.object_name.value,
o.center_object_name.value
if o.center_choice != C_SELF
else None,
o.center_choice.value,
bin_count_settings,
d)
if workspace.frame is not None:
images = [d[key][0] for key in d.keys()]
names = d.keys()
figure = workspace.create_or_find_figure(title="MeasureObjectRadialDistribution, image cycle #%d"%(
workspace.measurements.image_set_number),subplots=(1,len(images)))
figure.figure.clf()
nimages = len(images)
shrink = .05
for i in range(len(images)):
rect = [shrink + float(i)/float(nimages),
.5+shrink,
(1.0-2*shrink)/float(nimages),
.45*(1.0-2*shrink)]
axes = figure.figure.add_axes(rect)
axes.imshow(images[i], matplotlib.cm.Greys_r)
axes.set_title(names[i],
fontname=cpprefs.get_title_font_name(),
fontsize=cpprefs.get_title_font_size())
rect = [0.1,.1,.8,.35]
axes = figure.figure.add_axes(rect, frameon = False)
table = axes.table(cellText=stats,
colWidths=[1.0/7.0]*7,
loc='center',
cellLoc='left')
axes.set_axis_off()
table.auto_set_font_size(False)
table.set_fontsize(cpprefs.get_table_font_size())
def get_title_font(self):
return "%s,%f" % (cpprefs.get_title_font_name(),
cpprefs.get_title_font_size())
def get_title_font(self):
return "%s,%f"%(cpprefs.get_title_font_name(),
cpprefs.get_title_font_size())