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more flexibilty
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Patrick Cleeve committed Sep 29, 2022
1 parent f8d1b85 commit 1f50be6
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Showing 8 changed files with 122 additions and 67 deletions.
141 changes: 91 additions & 50 deletions liftout/autoliftout.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@
from liftout.gui.milling_window import GUIMillingWindow
from liftout.patterning import MillingPattern
from liftout.structures import (AutoLiftoutStage, Lamella, ReferenceImages, Sample)
from liftout.structures import ReferenceHFW
from liftout.structures import ReferenceHFW, AutoLiftoutMode

# autoliftout workflow functions

Expand All @@ -35,6 +35,7 @@ def mill_lamella_trench(
):

# bookkeeping
mode = AutoLiftoutMode.Auto if bool(settings.protocol["options"]["auto"]["trench"]) else AutoLiftoutMode.Manual
settings.image.save_path = lamella.path

# move to lamella position
Expand All @@ -52,6 +53,7 @@ def mill_lamella_trench(
settings=settings,
milling_pattern=MillingPattern.Trench,
point=Point(0, 0),
auto_continue=bool(mode is AutoLiftoutMode.Auto)
)

# discharge check
Expand All @@ -73,6 +75,7 @@ def mill_lamella_jcut(
) -> Lamella:

# bookkeeping
mode = AutoLiftoutMode.Auto if bool(settings.protocol["options"]["auto"]["jcut"]) else AutoLiftoutMode.Manual
settings.image.save_path = lamella.path
settings.image.save = False

Expand Down Expand Up @@ -108,12 +111,13 @@ def mill_lamella_jcut(
)

# confirm
fibsem_ui_windows.ask_user_movement(
microscope,
settings,
msg_type="eucentric",
msg="Confirm lamella is centred in Ion Beam",
)
if mode is AutoLiftoutMode.Manual:
fibsem_ui_windows.ask_user_movement(
microscope,
settings,
msg_type="eucentric",
msg="Confirm lamella is centred in Ion Beam",
)

# take reference, pre-tilting
settings.image.beam_type = BeamType.ION
Expand Down Expand Up @@ -147,6 +151,7 @@ def mill_lamella_jcut(
settings=settings,
milling_pattern=MillingPattern.JCut,
point=Point(0, 0),
auto_continue=bool(mode is AutoLiftoutMode.Auto)
)

# take reference images of the jcut (tilted)
Expand Down Expand Up @@ -189,6 +194,7 @@ def liftout_lamella(
) -> Lamella:

# bookkeeping
mode = AutoLiftoutMode.Auto if bool(settings.protocol["options"]["auto"]["liftout"]) else AutoLiftoutMode.Manual
settings.image.save_path = lamella.path

# convenience
Expand All @@ -208,12 +214,13 @@ def liftout_lamella(
)

# confirm
fibsem_ui_windows.ask_user_movement(
microscope,
settings,
msg_type="eucentric",
msg="Confirm lamella is centred in Ion Beam",
)
if mode is AutoLiftoutMode.Manual:
fibsem_ui_windows.ask_user_movement(
microscope,
settings,
msg_type="eucentric",
msg="Confirm lamella is centred in Ion Beam",
)

# reference images for needle location
settings.image.save = True
Expand All @@ -222,25 +229,29 @@ def liftout_lamella(
acquire.take_reference_images(microscope, settings.image)

# land needle on lamella
lamella = land_needle_on_milled_lamella(microscope, settings, lamella)
lamella = land_needle_on_milled_lamella(microscope, settings, lamella, mode=mode)

# mill weld
open_milling_window(
microscope=microscope,
settings=settings,
milling_pattern=MillingPattern.Weld,
point=Point(),
)
# TODO: joining options: none, weld, platinum
if settings.protocol["options"]["joining_method"] == "weld":
# mill weld
open_milling_window(
microscope=microscope,
settings=settings,
milling_pattern=MillingPattern.Weld,
point=Point(),
auto_continue=bool(mode is AutoLiftoutMode.Auto)
)
if settings.protocol["options"]["joining_method"] == "platinum":
# sputter platinum
fibsem_utils.sputter_platinum(
microscope,
settings.protocol["platinum"],
whole_grid=False,
default_application_file=settings.system.application_file,
)

# sputter platinum
# fibsem_utils.sputter_platinum(
# microscope,
# settings.protocol["platinum"],
# whole_grid=False,
# default_application_file=settings.system.application_file,
# )
logging.info(
f"{lamella.current_state.stage.name}: lamella to needle welding complete."
f"{lamella.current_state.stage.name}: lamella to needle joining complete."
)

settings.image.save = True
Expand All @@ -256,6 +267,7 @@ def liftout_lamella(
point=Point(
x=settings.protocol["lamella"]["lamella_width"] / 2, y=0
), # half the lamella width
auto_continue=bool(mode is AutoLiftoutMode.Auto)
)

# take reference images
Expand Down Expand Up @@ -291,7 +303,8 @@ def liftout_lamella(


def land_needle_on_milled_lamella(
microscope: SdbMicroscopeClient, settings: MicroscopeSettings, lamella: Lamella,
microscope: SdbMicroscopeClient, settings: MicroscopeSettings, lamella: Lamella,
mode: AutoLiftoutMode = AutoLiftoutMode.Manual
) -> Lamella:

# bookkeeping
Expand All @@ -314,6 +327,15 @@ def land_needle_on_milled_lamella(
settings.image.label = f"needle_liftout_start_position"
acquire.take_reference_images(microscope, settings.image)

if mode is AutoLiftoutMode.Manual:
# check with user? # TODO: confusing wording
response = fibsem_ui_windows.ask_user_interaction(
microscope,
msg="""Confirm the needle is in the trench, to the left of the lamella edge.
\nIf not, please move manually then press yes to continue.""",
beam_type=BeamType.ION,
)

# take image

# measure brightness
Expand Down Expand Up @@ -357,11 +379,14 @@ def land_needle_on_milled_lamella(
f"iter: {iteration_count}: brightness: {brightness}, prevs: {previous_brightness}, MEAN BRIGHTNESS: {MEAN_BRIGHTNESS}"
)

if brightness > MEAN_BRIGHTNESS * BRIGHTNESS_FACTOR:
above_brightness_threshold = (brightness > MEAN_BRIGHTNESS * BRIGHTNESS_FACTOR)

if above_brightness_threshold or mode is AutoLiftoutMode.Manual:

# needle has landed...
logging.info("THRESHOLD REACHED STOPPPING")

# check with user?
# check with user? # TODO: confusing wording
response = fibsem_ui_windows.ask_user_interaction(
microscope,
msg="Has the needle landed on the lamella? \nPress Yes to continue, or No to redo the final movement",
Expand Down Expand Up @@ -396,6 +421,7 @@ def land_lamella(
) -> Lamella:

# bookkeeping
mode = AutoLiftoutMode.Auto if bool(settings.protocol["options"]["auto"]["landing"]) else AutoLiftoutMode.Manual
settings.image.save_path = lamella.path
settings.image.save = False

Expand All @@ -409,9 +435,10 @@ def land_lamella(
calibration.auto_link_stage(microscope)

# confirm eucentricity
fibsem_ui_windows.ask_user_movement(
microscope, settings, msg_type="eucentric"
)
if mode is AutoLiftoutMode.Manual:
fibsem_ui_windows.ask_user_movement(
microscope, settings, msg_type="eucentric"
)

logging.info(
f"{lamella.current_state.stage.name}: initial landing calibration complete."
Expand All @@ -436,6 +463,7 @@ def land_lamella(
acquire.take_reference_images(microscope, settings.image)

# repeat final movement until user confirms landing
VALIDATE = (mode is AutoLiftoutMode.Manual)
response = False
while response is False:
#### X-MOVE
Expand All @@ -453,7 +481,7 @@ def land_lamella(
DetectionFeature(DetectionType.LamellaEdge, None),
DetectionFeature(DetectionType.LandingPost, None),
],
validate=True,
validate=VALIDATE,
)

movement.move_needle_relative_with_corrected_movement(
Expand All @@ -472,11 +500,14 @@ def land_lamella(
microscope=microscope, image_settings=settings.image
)

response = fibsem_ui_windows.ask_user_interaction(
microscope,
msg="Has the lamella landed on the post? \nPress Yes to continue, or No to redo the final movement",
beam_type=BeamType.ION,
)
if mode is AutoLiftoutMode.Manual:
response = fibsem_ui_windows.ask_user_interaction(
microscope,
msg="Has the lamella landed on the post? \nPress Yes to continue, or No to redo the final movement",
beam_type=BeamType.ION,
)
else:
response = True

#################################################################################################

Expand All @@ -487,6 +518,7 @@ def land_lamella(
settings=settings,
milling_pattern=MillingPattern.Weld,
point=Point(),
auto_continue=bool(mode is AutoLiftoutMode.Auto)
)

# final reference images
Expand Down Expand Up @@ -515,7 +547,7 @@ def land_lamella(

# back out needle from lamella , no cut required?

for i in range(5):
for i in range(10):

# move needle back
movement.move_needle_relative_with_corrected_movement(
Expand Down Expand Up @@ -576,6 +608,7 @@ def reset_needle(
) -> Lamella:

# bookkeeping
mode = AutoLiftoutMode.Auto if bool(settings.protocol["options"]["auto"]["reset"]) else AutoLiftoutMode.Manual
settings.image.save_path = lamella.path

# convienence
Expand Down Expand Up @@ -620,6 +653,7 @@ def reset_needle(
settings=settings,
milling_pattern=MillingPattern.Sharpen,
point=Point(),
auto_continue=bool(mode is AutoLiftoutMode.Auto)
)

#################################################################################################
Expand Down Expand Up @@ -654,6 +688,7 @@ def thin_lamella(
) -> Lamella:

# bookkeeping
mode = AutoLiftoutMode.Auto if bool(settings.protocol["options"]["auto"]["thin"]) else AutoLiftoutMode.Manual
settings.image.save_path = lamella.path

# move to the initial landing coordinates
Expand Down Expand Up @@ -716,6 +751,7 @@ def thin_lamella(
settings=settings,
milling_pattern=MillingPattern.Thin,
point=Point(),
auto_continue=bool(mode is AutoLiftoutMode.Auto)
)

# # take reference images
Expand All @@ -739,6 +775,7 @@ def polish_lamella(
) -> Lamella:

# bookkeeping
mode = AutoLiftoutMode.Auto if bool(settings.protocol["options"]["auto"]["polish"]) else AutoLiftoutMode.Manual
settings.image.save_path = lamella.path

# # restore state from thinning stage
Expand Down Expand Up @@ -803,6 +840,7 @@ def polish_lamella(
settings=settings,
milling_pattern=MillingPattern.Polish,
point=Point(),
auto_continue=bool(mode is AutoLiftoutMode.Auto)
)

# take reference images (ultra, super, high)
Expand All @@ -827,8 +865,8 @@ def run_autoliftout_workflow(
parent_ui=None,
) -> Sample:

HIGH_THROUGHPUT = True
CONFIRM_WORKFLOW_ADVANCE = True
BATCH_MODE = bool(settings.protocol["options"]["batch_mode"])
CONFIRM_WORKFLOW_ADVANCE = bool(settings.protocol["options"]["confirm_advance"])

# autoliftout_workflow
autoliftout_stages = {
Expand All @@ -845,10 +883,9 @@ def run_autoliftout_workflow(
logging.info(f"AutoLiftout Workflow started for {len(sample.positions)} lamellae.")
settings.image.save = False
settings.image.label = f"{fibsem_utils.current_timestamp()}"


# high throughput workflow
if HIGH_THROUGHPUT:
# batch mode workflow
if BATCH_MODE:
for terminal_stage in [
AutoLiftoutStage.MillTrench,
AutoLiftoutStage.MillJCut,
Expand Down Expand Up @@ -1343,6 +1380,7 @@ def open_milling_window(
milling_pattern: patterning.MillingPattern,
point: Point = Point(),
parent=None,
auto_continue: bool = False
):
"""Open the Milling Window ready for milling
Expand All @@ -1357,7 +1395,10 @@ def open_milling_window(
milling_pattern_type=milling_pattern,
point = point,
parent=parent,
auto_continue = auto_continue
)

milling_window.show()
milling_window.exec_()

# show and pause, if not auto continuing
if not auto_continue:
milling_window.show()
milling_window.exec_()
1 change: 1 addition & 0 deletions liftout/gui/main.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ def __init__(self):
config_path = config.config_path,
protocol_path = config.protocol_path
)
# NB cant use setup session, because log dir cant be loaded until later...very silly

# setup ui
self.setupUi(self)
Expand Down
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