def test_01_02_get_id_list(self):
file_name = os.path.join(self.root_dir, "ExampleSBSImages",
"Channel1-01-A-01.tif")
ip = I.load_imageplus(file_name)
W.set_current_image(ip)
id_list = W.get_id_list()
self.assertTrue(ip.getID() in id_list)
def test_01_08_get_current_image(self):
file_name = os.path.join(self.root_dir, "ExampleSBSImages",
"Channel1-01-A-01.tif")
ip = I.load_imageplus(file_name)
W.set_current_image(ip)
ip_out = W.get_current_image()
self.assertEqual(ip.getID(), ip_out.getID())
def test_01_02_get_id_list(self):
file_name = os.path.join(self.root_dir,
"ExampleSBSImages", "Channel1-01-A-01.tif")
ip = I.load_imageplus(file_name)
W.set_current_image(ip)
id_list = W.get_id_list()
self.assertTrue(ip.getID() in id_list)
def test_01_08_get_current_image(self):
file_name = os.path.join(self.root_dir,
"ExampleSBSImages", "Channel1-01-A-01.tif")
ip = I.load_imageplus(file_name)
W.set_current_image(ip)
ip_out = W.get_current_image()
self.assertEqual(ip.getID(), ip_out.getID())
def inject_image(self, pixels, name=''):
'''inject an image into ImageJ for processing'''
ij_processor = ijiproc.make_image_processor((pixels * 255.0).astype('float32'))
image_plus = ijip.make_imageplus_from_processor(name, ij_processor)
if sys.platform == "darwin":
ijwm.set_temp_current_image(image_plus)
else:
ijwm.set_current_image(image_plus)
def test_01_01_set_current_image(self):
file_name = os.path.join(self.root_dir, "ExampleSBSImages",
"Channel1-01-A-01.tif")
ip = I.load_imageplus(file_name)
W.set_current_image(ip)
def run(self, workspace):
"""Run the imageJ command"""
image_set = workspace.image_set
d = self.get_dictionary(workspace.image_set_list)
if self.wants_to_set_current_image:
input_image_name = self.current_input_image_name.value
img = image_set.get_image(input_image_name, must_be_grayscale=True)
if self.show_window:
workspace.display_data.image_sent_to_ij = img.pixel_data
else:
img = None
display_service = ij2.get_display_service(get_context())
#
# Run a command or macro on the first image of the set
#
if d.get(D_FIRST_IMAGE_SET) == image_set.image_number:
self.do_imagej(workspace, D_FIRST_IMAGE_SET)
ij1_mode = self.command_or_macro == CM_MACRO
#
# Install the input image as the current image
#
if img is not None:
ijpixels = img.pixel_data * IMAGEJ_SCALE
if ij1_mode:
ij_processor = ijiproc.make_image_processor(ijpixels.astype("float32"))
image_plus = ijip.make_imageplus_from_processor(input_image_name, ij_processor)
ijwm.set_current_image(image_plus)
else:
dataset = ij2.create_dataset(get_context(), ijpixels, input_image_name)
display = display_service.createDisplay(input_image_name, dataset)
display_service.setActiveDisplay(display)
self.do_imagej(workspace)
#
# Get the output image
#
if self.wants_to_get_current_image:
output_image_name = self.current_output_image_name.value
if ij1_mode:
image_plus = ijwm.get_current_image()
ij_processor = image_plus.getProcessor()
pixels = ijiproc.get_image(ij_processor).astype("float32") / IMAGEJ_SCALE
image = cpi.Image(pixels)
workspace.image_set.add(output_image_name, image)
else:
for attempt in range(4):
display = display_service.getActiveImageDisplay()
if display.o is not None:
break
#
# Possible synchronization problem with ImageJ 1.0
# Possible error involving user changing window focus
#
import time
time.sleep(0.25)
else:
raise ValueError("Failed to retrieve active display")
pixels = self.save_display_as_image(workspace, display, output_image_name)
if self.show_window:
workspace.display_data.image_acquired_from_ij = pixels
#
# Execute the post-group macro or command
#
if d.get(D_LAST_IMAGE_SET) == image_set.image_number:
self.do_imagej(workspace, D_LAST_IMAGE_SET)
#
# Save the current ImageJ image after executing the post-group
# command or macro
#
if self.post_group_choice != CM_NOTHING and self.wants_post_group_image:
output_image_name = self.post_group_output_image.value
if ij1_mode:
image_plus = ijwm.get_current_image()
ij_processor = image_plus.getProcessor()
pixels = ijiproc.get_image(ij_processor).astype("float32") / IMAGEJ_SCALE
image = cpi.Image(pixels, mask=mask)
workspace.image_set.add(output_image_name, image)
else:
display = display_service.getActiveImageDisplay()
self.save_display_as_image(workspace, display, output_image_name)
def test_01_01_set_current_image(self):
file_name = os.path.join(self.root_dir,
"ExampleSBSImages", "Channel1-01-A-01.tif")
ip = I.load_imageplus(file_name)
W.set_current_image(ip)
def test_01_08_get_current_image(self):
ip = I.load_imageplus(self.file_name)
W.set_current_image(ip)
ip_out = W.get_current_image()
self.assertEqual(ip.getID(), ip_out.getID())
def test_01_02_get_id_list(self):
ip = I.load_imageplus(self.file_name)
W.set_current_image(ip)
id_list = W.get_id_list()
self.assertTrue(ip.getID() in id_list)
def test_01_01_set_current_image(self):
ip = I.load_imageplus(self.file_name)
W.set_current_image(ip)
def run(self, workspace):
'''Run the imageJ command'''
image_set = workspace.image_set
d = self.get_dictionary(workspace.image_set_list)
if self.wants_to_set_current_image:
input_image_name = self.current_input_image_name.value
img = image_set.get_image(input_image_name, must_be_grayscale=True)
if self.show_window:
workspace.display_data.image_sent_to_ij = img.pixel_data
else:
img = None
display_service = ij2.get_display_service(get_context())
#
# Run a command or macro on the first image of the set
#
if d.get(D_FIRST_IMAGE_SET) == image_set.image_number:
self.do_imagej(workspace, D_FIRST_IMAGE_SET)
ij1_mode = self.command_or_macro == CM_MACRO
#
# Install the input image as the current image
#
if img is not None:
ijpixels = img.pixel_data * IMAGEJ_SCALE
if ij1_mode:
ij_processor = ijiproc.make_image_processor(
ijpixels.astype('float32'))
image_plus = ijip.make_imageplus_from_processor(
input_image_name, ij_processor)
ijwm.set_current_image(image_plus)
else:
dataset = ij2.create_dataset(get_context(), ijpixels,
input_image_name)
display = display_service.createDisplay(
input_image_name, dataset)
display_service.setActiveDisplay(display)
self.do_imagej(workspace)
#
# Get the output image
#
if self.wants_to_get_current_image:
output_image_name = self.current_output_image_name.value
if ij1_mode:
image_plus = ijwm.get_current_image()
ij_processor = image_plus.getProcessor()
pixels = ijiproc.get_image(ij_processor).\
astype('float32') / IMAGEJ_SCALE
image = cpi.Image(pixels)
workspace.image_set.add(output_image_name, image)
else:
for attempt in range(4):
display = display_service.getActiveImageDisplay()
if display.o is not None:
break
#
# Possible synchronization problem with ImageJ 1.0
# Possible error involving user changing window focus
#
import time
time.sleep(.25)
else:
raise ValueError("Failed to retrieve active display")
pixels = self.save_display_as_image(workspace, display,
output_image_name)
if self.show_window:
workspace.display_data.image_acquired_from_ij = pixels
#
# Execute the post-group macro or command
#
if d.get(D_LAST_IMAGE_SET) == image_set.image_number:
self.do_imagej(workspace, D_LAST_IMAGE_SET)
#
# Save the current ImageJ image after executing the post-group
# command or macro
#
if (self.post_group_choice != CM_NOTHING
and self.wants_post_group_image):
output_image_name = self.post_group_output_image.value
if ij1_mode:
image_plus = ijwm.get_current_image()
ij_processor = image_plus.getProcessor()
pixels = ijiproc.get_image(ij_processor).\
astype('float32') / IMAGEJ_SCALE
image = cpi.Image(pixels, mask=mask)
workspace.image_set.add(output_image_name, image)
else:
display = display_service.getActiveImageDisplay()
self.save_display_as_image(workspace, display,
output_image_name)
def test_01_08_get_current_image(self):
ip = I.load_imageplus(self.file_name)
W.set_current_image(ip)
ip_out = W.get_current_image()
self.assertEqual(ip.getID(), ip_out.getID())
def test_01_02_get_id_list(self):
ip = I.load_imageplus(self.file_name)
W.set_current_image(ip)
id_list = W.get_id_list()
self.assertTrue(ip.getID() in id_list)
def test_01_01_set_current_image(self):
ip = I.load_imageplus(self.file_name)
W.set_current_image(ip)