def save_display_as_image(self, workspace, display, image_name):
'''Convert an ImageJ display to an image and save in the image set
workspace - current workspace
display - an ImageJ Display
image_name - save the image in the image set using this name.
'''
display_view = display.getActiveView()
dataset = ij2.wrap_dataset(display_view.getData())
pixel_data = dataset.get_pixel_data() / IMAGEJ_SCALE
mask = ij2.create_mask(display)
image = cpi.Image(pixel_data, mask=mask)
workspace.image_set.add(image_name, image)
return pixel_data
def save_display_as_image(self, workspace, display, image_name):
'''Convert an ImageJ display to an image and save in the image set
workspace - current workspace
display - an ImageJ Display
image_name - save the image in the image set using this name.
'''
display_view = display.getActiveView()
dataset = ij2.wrap_dataset(display_view.getData())
pixel_data = dataset.get_pixel_data() / IMAGEJ_SCALE
mask = ij2.create_mask(display)
image = cpi.Image(pixel_data, mask=mask)
workspace.image_set.add(image_name, image)
return pixel_data
def test_09_08_check_stride(self):
# Rotate the image by 90 degrees to make sure the pixel copy
# was properly strided
#
svc = ij2.get_display_service(self.context)
i, j = np.mgrid[0:5, 0:70:10]
image = i + j
ds = ij2.create_dataset(self.context, image, "Foo")
display = svc.createDisplay("Foo", ds)
outputs = dict(display=None)
self.run_command("imagej.core.commands.rotate.Rotate90DegreesLeft",
dict(display=display), outputs)
display_out = ij2.wrap_display(outputs["display"])
dataset = ij2.wrap_dataset(display_out.getActiveView().getData())
image_out = dataset.get_pixel_data()
self.assertSequenceEqual(image_out.shape, list(reversed(image.shape)))
np.testing.assert_array_equal(np.rot90(image), image_out)
def test_09_08_check_stride(self):
# Rotate the image by 90 degrees to make sure the pixel copy
# was properly strided
#
svc = ij2.get_display_service(self.context)
i, j = np.mgrid[0:5, 0:70:10]
image = i+j
ds = ij2.create_dataset(self.context, image, "Foo")
display = svc.createDisplay("Foo", ds)
outputs = dict(display=None)
self.run_command("imagej.core.commands.rotate.Rotate90DegreesLeft",
dict(display=display),
outputs)
display_out = ij2.wrap_display(outputs["display"])
dataset = ij2.wrap_dataset(display_out.getActiveView().getData())
image_out = dataset.get_pixel_data()
self.assertSequenceEqual(image_out.shape, list(reversed(image.shape)))
np.testing.assert_array_equal(np.rot90(image), image_out)
def test_09_09_check_overlay(self):
svc = ij2.get_display_service(self.context)
r = np.random.RandomState()
i, j = np.mgrid[0:11, 0:1300:100]
image = i+j
ds = ij2.create_dataset(self.context, image, "Foo")
display = svc.createDisplay("Foo", ds)
mask = np.zeros(image.shape, bool)
mask[2:-1, 3:-4] = 1
overlay = ij2.create_overlay(self.context, mask)
ij2.get_overlay_service(self.context).addOverlays(
display.o, J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
self.run_command("imagej.core.commands.imglib.CropImage",
dict(display=display), {})
dataset = ij2.wrap_dataset(display.getActiveView().getData())
image_out = dataset.get_pixel_data()
self.assertSequenceEqual(image_out.shape, [7, 5])
np.testing.assert_array_equal(image[2:-2, 3:-5], image_out)