def save_final_images(microscope, settings, lamella_number):
"""Aquire and save ion beam & SEM images after complete milling stage."""
from autoscript_sdb_microscope_client.structures import (GrabFrameSettings,
Rectangle)
output_dir = settings["save_directory"]
fullfield_cam_settings = GrabFrameSettings(
reduced_area=Rectangle(0, 0, 1, 1),
resolution=settings["fiducial"]["reduced_area_resolution"],
dwell_time=settings["imaging"]["dwell_time"],
)
if settings["imaging"]["autocontrast"]:
microscope.imaging.set_active_view(2) # the ion beam view
microscope.auto_functions.run_auto_cb()
if settings["imaging"]["full_field_ib_images"]:
original_ion_current = microscope.beams.ion_beam.beam_current.value
microscope.beams.ion_beam.beam_current.value = 20e-12 # ion imaging
image = grab_ion_image(microscope, fullfield_cam_settings)
filename = os.path.join(
output_dir,
"IB_lamella{}-milling-complete.tif".format(lamella_number + 1))
image.save(filename)
microscope.beams.ion_beam.beam_current.value = original_ion_current
sem_adorned_image = grab_sem_image(microscope, fullfield_cam_settings)
sem_fname = "SEM_lamella{}-milling-complete.tif".format(lamella_number + 1)
sem_filename = os.path.join(output_dir, sem_fname)
sem_adorned_image.save(sem_filename)
def create_camera_settings(imaging_settings, reduced_area=None):
"""Camera settings for acquiring images on the microscope.
Parameters
----------
imaging_settings : dictionary
User input as dictionary containing keys "resolution" and "dwell_time".
reduced_area : Rectangle, optional
Reduced area view for image acquisition.
By default None, which will create a Rectangle(0, 0, 1, 1),
which means the whole field of view will be imaged.
Returns
-------
GrabFrameSettings
Camera acquisition settings
"""
from autoscript_sdb_microscope_client.structures import (GrabFrameSettings,
Rectangle)
if reduced_area is None:
reduced_area = Rectangle(0, 0, 1, 1)
camera_settings = GrabFrameSettings(
resolution=imaging_settings["resolution"],
dwell_time=imaging_settings["dwell_time"],
reduced_area=reduced_area,
)
return camera_settings
def fiducial_reduced_area_rect(fiducial_relative_center,
fiducial_relative_size):
"""Return autoscript Rectangle object describing the fiducial reduced area
Returns
-------
Autoscript Rectangle
Fiducial reduced area rectangle, in relative units.
"""
from autoscript_sdb_microscope_client.structures import Rectangle
width, height = fiducial_relative_size
top_left_x = fiducial_relative_center[0] - (width / 2)
top_left_y = fiducial_relative_center[1] - (height / 2)
if top_left_x < 0:
top_left_x = 0
if top_left_x > 1:
raise ValueError(
"top_left_x relative coordinate cannot be larger than 1")
if top_left_y < 0:
top_left_y = 0
if top_left_y > 1:
raise ValueError(
"top_left_y relative coordinate cannot be larger than 1")
# create the relative rectangle
fiducial_reduced_area = Rectangle(top_left_x, top_left_y, width, height)
print("fiducial_reduced_area", fiducial_reduced_area)
return fiducial_reduced_area
def run_drift_corrected_milling(microscope,
correction_interval,
reduced_area=None):
"""
Parameters
----------
microscope : Autoscript microscope object
correction_interval : Time in seconds between drift correction realignment
reduced_area : Autoscript Rectangle() object
Describes the reduced area view in relative coordinates, with the
origin in the top left corner.
Default value is None, which will create a Rectangle(0, 0, 1, 1),
which means the imaging will use the whole field of view.
"""
from autoscript_core.common import ApplicationServerException
from autoscript_sdb_microscope_client.structures import (GrabFrameSettings,
Rectangle)
if reduced_area is None:
reduced_area = Rectangle(0, 0, 1, 1)
s = GrabFrameSettings(reduced_area=reduced_area)
reference_image = microscope.imaging.grab_frame(s)
# start drift corrected patterning (is a blocking function, not asynchronous)
microscope.patterning.start()
while microscope.patterning.state == "Running":
time.sleep(correction_interval)
try:
microscope.patterning.pause()
except ApplicationServerException:
continue
else:
new_image = microscope.imaging.grab_frame(s)
realign(microscope, new_image, reference_image)
microscope.patterning.resume()
def test_create_camera_settings(microscope):
from autoscript_sdb_microscope_client.structures import GrabFrameSettings
imaging_settings = {"resolution": "1536x1024", "dwell_time": 1e-6}
result = autolamella.acquire.create_camera_settings(imaging_settings,
reduced_area=Rectangle(
0, 0, 1, 1))
assert isinstance(result, GrabFrameSettings)
def set_sem_image(self, microscope, settings):
from autoscript_sdb_microscope_client.structures import (
GrabFrameSettings,
Rectangle,
)
microscope.imaging.set_active_view(1) # SEM beam view
camera_settings = GrabFrameSettings(
reduced_area=Rectangle(0, 0, 1, 1),
resolution=settings["imaging"]["resolution"],
)
self.sem_image = microscope.imaging.grab_frame(camera_settings)
microscope.imaging.set_active_view(2) # Restore ion beam view
return self.sem_image
def grab_images(microscope, settings, my_lamella, prefix="", suffix=""):
"""Aquire and save images, with optional autocontrast.
Parameters
----------
microscope : Autoscript microscope object.
settings : dictionary
Dictionary continaing user input parameters.
my_lamella : Lamella object
prefix : str, optional
Prefix to use when saving image files, by default ""
suffix : str, optional
Suffix to use when saving image files, by default ""
Returns
-------
AdornedImage
The reduced area ion beam image (shows just the fiducial marker).
"""
from autoscript_sdb_microscope_client.structures import (GrabFrameSettings,
Rectangle)
output_dir = settings["save_directory"]
# Reduced area images (must reset camera settings each time, because different samples have different reduced areas)
camera_settings = GrabFrameSettings(
reduced_area=my_lamella.fiducial_reduced_area,
resolution=settings["fiducial"]["reduced_area_resolution"],
dwell_time=settings["imaging"]["dwell_time"],
)
fullfield_cam_settings = GrabFrameSettings(
reduced_area=Rectangle(0, 0, 1, 1),
resolution=settings["fiducial"]["reduced_area_resolution"],
dwell_time=settings["imaging"]["dwell_time"],
)
# Optional autocontrast (you cannot do autocontrast on a reduced area)
if settings["imaging"]["autocontrast"]:
microscope.imaging.set_active_view(2) # the ion beam view
autocontrast(microscope)
image = grab_ion_image(microscope, camera_settings)
filename = os.path.join(output_dir, prefix + "_" + suffix + ".tif")
image.save(filename)
# Optional full field images
acquire_many_images = settings["imaging"]["full_field_ib_images"]
if acquire_many_images:
fullfield_image = grab_ion_image(microscope, fullfield_cam_settings)
fname_fullfield = prefix + "_FullField_" + suffix + ".tif"
filename_fullfield = os.path.join(output_dir, fname_fullfield)
fullfield_image.save(filename_fullfield)
return image
def camera_settings():
imaging_settings = {"resolution": "3072x2048", "dwell_time": 1e-6}
camera_settings = autolamella.acquire.create_camera_settings(
imaging_settings, reduced_area=Rectangle(0, 0, 1, 1))
return camera_settings
def add_single_sample(microscope, settings):
"""Create a single lamella object.
Parameters
----------
microscope : Autoscript microscope object.
settings : Dictionary of user input argument settings.
Returns
-------
my_lamella
A single Lamella() object.
"""
from autoscript_core.common import ApplicationServerException
from autoscript_sdb_microscope_client.structures import (GrabFrameSettings,
Rectangle)
autolamella.autoscript.reset_state(microscope, settings)
demo_mode = settings["demo_mode"]
acquire_many_images = settings["imaging"]["full_field_ib_images"]
# Reset microscope state
autolamella.autoscript.reset_state(microscope, settings)
microscope.beams.ion_beam.beam_current.value = settings["lamella"][
"milling_current"]
# Optional autocontrast
if settings["imaging"]["autocontrast"]:
microscope.imaging.set_active_view(2) # the ion beam view
autolamella.acquire.autocontrast(microscope)
# Take full field image
full_field_camera_settings = autolamella.acquire.create_camera_settings(
settings["imaging"], reduced_area=Rectangle(0, 0, 1, 1))
original_image = grab_ion_image(microscope, full_field_camera_settings)
# Select fiducial posiion
print("Please select where to put a fiducial marker.")
my_fiducial = autolamella.fiducial.fiducial(
microscope,
original_image,
settings["fiducial"]["fiducial_length"],
settings["fiducial"]["fiducial_width"],
settings["fiducial"]["fiducial_image_size_x"],
settings["fiducial"]["fiducial_image_size_y"],
settings["fiducial"]["fiducial_milling_depth"],
)
if my_fiducial is None:
print("No fiducial location selected, cancelling.")
microscope.patterning.clear_patterns()
return
#
fiducial_coord_realspace, fiducial_coord_relative, fiducial_coord_pixels = (
my_fiducial)
pixelsize_x = original_image.metadata.binary_result.pixel_size.x
fiducial_image_relative_size = [
settings["fiducial"]["fiducial_image_size_x"] /
(original_image.width * pixelsize_x),
settings["fiducial"]["fiducial_image_size_y"] /
(original_image.height * pixelsize_x),
]
reduced_area_fiducial = autolamella.fiducial.fiducial_reduced_area_rect(
fiducial_coord_relative, fiducial_image_relative_size)
camera_settings = autolamella.acquire.create_camera_settings(
settings["imaging"], reduced_area=reduced_area_fiducial)
cropped_original_image = grab_ion_image(microscope, camera_settings)
my_lamella = Lamella(microscope)
my_lamella.fiducial_image_relative_size = fiducial_image_relative_size
my_fiducial = my_lamella.set_fiducial(
cropped_original_image,
fiducial_coord_realspace,
fiducial_coord_relative,
fiducial_coord_pixels,
reduced_area_fiducial,
)
# Select the lamella position
print("Please select the center point of your lamella.")
my_lamella.original_image = original_image
lamella_center = my_lamella.set_center(original_image, settings)
if lamella_center == []:
print("No lamella position selected, cancelling.")
microscope.patterning.clear_patterns()
return
# Ask user for decision
message = "Are you happy with this position? [y]/n\n"
if ask_user(message, default="yes"):
message = "Do you want to mill a fiducial marker here? [y]/n\n"
if ask_user(message, default="yes"):
print("Milling fiducial marker...")
if not demo_mode:
microscope.beams.ion_beam.beam_current.value = settings[
"fiducial"]["fiducial_milling_current"]
microscope.imaging.set_active_view(2) # the ion beam view
try:
microscope.patterning.run()
except ApplicationServerException:
logging.error(
"ApplicationServerException: could not mill!")
microscope.patterning.clear_patterns()
return # returns None which gets stripped from sample list
if acquire_many_images:
full_field_camera_settings = GrabFrameSettings(
reduced_area=Rectangle(0, 0, 1, 1),
resolution=settings["imaging"]["resolution"],
dwell_time=settings["imaging"]["dwell_time"],
)
microscope.auto_functions.run_auto_cb()
reference_image = grab_ion_image(microscope,
full_field_camera_settings)
my_lamella.reference_image = reference_image
camera_settings = GrabFrameSettings(
reduced_area=reduced_area_fiducial,
resolution=settings["fiducial"]["reduced_area_resolution"],
dwell_time=settings["imaging"]["dwell_time"],
)
cropped_reference_image = grab_ion_image(microscope,
camera_settings)
message = "Do you want to re-mill the fiducial marker? y/[n]\n"
if ask_user(message, default="no"):
print("Milling fiducial marker again...")
if not demo_mode:
microscope.imaging.set_active_view(2) # the ion beam view
try:
microscope.patterning.run()
except ApplicationServerException:
logging.error(
"ApplicationServerException: could not mill")
microscope.patterning.clear_patterns()
return # returns None which gets stripped from sample list
if acquire_many_images:
full_field_camera_settings = GrabFrameSettings(
reduced_area=Rectangle(0, 0, 1, 1),
resolution=settings["imaging"]["resolution"],
dwell_time=settings["imaging"]["dwell_time"],
)
microscope.auto_functions.run_auto_cb()
reference_image = grab_ion_image(
microscope, full_field_camera_settings)
my_lamella.reference_image = reference_image
microscope.patterning.clear_patterns()
else:
print("Ok, deleting those milling patterns.")
microscope.patterning.clear_patterns()
return # returns None, which gets stripped from sample list later
# Continue on
camera_settings = GrabFrameSettings(
reduced_area=reduced_area_fiducial,
resolution=settings["fiducial"]["reduced_area_resolution"],
dwell_time=settings["imaging"]["dwell_time"],
)
cropped_reference_image = grab_ion_image(microscope, camera_settings)
my_lamella.set_fiducial(
cropped_reference_image,
fiducial_coord_realspace,
fiducial_coord_relative,
fiducial_coord_pixels,
reduced_area_fiducial,
)
if not acquire_many_images:
my_lamella.reference_image = cropped_reference_image
my_lamella.set_sem_image(microscope, settings)
my_lamella.set_custom_milling_depth()
return my_lamella
