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@patrickcleeve2
patrickcleeve2 committed Jan 18, 2024
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146 changes: 86 additions & 60 deletions docs/autolamella/case_study_serial_liftout.md
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Original file line number Diff line number Diff line change
Expand Up @@ -241,18 +241,16 @@ We move to the milling orientation, and mill the grid bar to be ~20um thick.

```yaml

copper-bar-clean:
cleaning_cross_section: false
depth: 2.0e-05
height: 5.0e-6
width: 80.0e-06
hfw: 150.e-6
milling_voltage: 30.0e+3
milling_current: 65.0e-9
rotation: 0.0
scan_direction: TopToBottom
application_file: "autolamella"
type: "Rectangle"
prepare-copper-grid:
stages:
- application_file: autolamella
hfw: 0.00015
milling_current: 28.0e-9
milling_voltage: 30000
type: Rectangle
width: 100.0e-6
height: 5.0e-6
depth: 30.0e-6

```

Expand All @@ -268,7 +266,7 @@ milling_position = FibsemStagePosition(t=np.deg2rad(18))
microscope._safe_absolute_stage_movement(milling_position)

# get milling stages
stages = _get_milling_stages("copper-bar-clean", settings.protocol)
stages = _get_milling_stages("prepare-copper-grid", settings.protocol)

# run milling
milling.mill_stages(microscope, settings, stages)
Expand All @@ -291,65 +289,51 @@ C. Mill Chain of Blocks
We mill a chain of blocks into the copper bar, leaving them attached to each other on the side.

```yaml

copper-block-removal:
cleaning_cross_section: false
depth: 2.0e-05
height: 20.0e-6
width: 10.0e-06
hfw: 150.e-6
milling_voltage: 30.0e+3
milling_current: 65.0e-9
rotation: 0.0
scan_direction: TopToBottom
application_file: "autolamella"
type: "Rectangle"
copper-block-removal-top:
cleaning_cross_section: false
depth: 2.0e-05
height: 10.0e-6
width: 110.0e-06
hfw: 150.e-6
milling_voltage: 30.0e+3
milling_current: 65.0e-9
rotation: 0.0
scan_direction: TopToBottom
application_file: "autolamella"
type: "Rectangle"
prepare-copper-blocks:
stages:
- application_file: autolamella
hfw: 150.0e-6
milling_current: 28.0e-9
milling_voltage: 30000
depth: 10.0e-6
distance: 30.0e-6
height: 20.0e-6
width: 10.0e-6
type: SpotWeldVertical
passes: null
number: 4.0
scan_direction: TopToBottom
- application_file: autolamella
hfw: 0.00015
milling_current: 28.0e-9
milling_voltage: 30000
type: Rectangle
width: 100.0e-6
height: 7.50e-6
depth: 10.0e-6

```

```python

from fibsem import utils
from fibsem import utils, acquire
from fibsem.patterning import _get_milling_stages
from fibsem.ui.utils import _draw_milling_stages_on_image
from fibsem.structures import Point
from copy import deepcopy
import numpy as np

# get evenly spaced points
width = 100e-6
n_patterns = 4
pos_x = np.linspace(-width/2, width/2, n_patterns)
points = [Point(x, 0) for x in pos_x]

# acquire image for visualiation
settings.image.hfw = 150e-6
image = microscope.acquire_image(settings.image)

block_stages = []
for i, pt in enumerate(points):

# get milling stages, at each position
stage = _get_milling_stages("copper-block-removal", deepcopy(settings.protocol), deepcopy(pt))[0]
stage.name = f"Copper-Block-Removal-{i:02d}"
block_stages.append(deepcopy(stage))
# offset for top pattern
h1 = settings.protocol["prepare-copper-blocks"]["stages"][0]["height"]
h2 = settings.protocol["prepare-copper-blocks"]["stages"][1]["height"]
dy = h1/2 - h2/2
pts = [Point(0, 0), Point(0, dy)]

# get top removal stage
top_stages= _get_milling_stages("copper-block-removal-top", settings.protocol, Point(0, 10e-6))

stages = top_stages + block_stages
# get milling stages form protocol
stages = _get_milling_stages("prepare-copper-blocks", settings.protocol, pts)

# draw stages on image
fig = _draw_milling_stages_on_image(image, stages)
Expand Down Expand Up @@ -387,8 +371,50 @@ We make contact with the block face. We can run another milling stage to polish

G. Attach the Block


```yaml

prepare-copper-block-weld:
stages:
- height: 2.5e-6
width: 0.5e-6
depth: 4.0e-6
distance: 0.25e-6
number: 10
rotation: 0.0
passes: 1.0
milling_voltage: 30.0e+3
milling_current: 300.0e-12
hfw: 150.0e-6
application_file: "autolamella"
scan_direction: "TopToBottom"
type: "SpotWeldVertical"
preset: "30 keV; 2.5 nA"


```

H. Release the Block

```yaml

prepare-copper-release:
stages:
- application_file: autolamella
hfw: 150.0e-6
milling_current: 28.0e-9
milling_voltage: 30000
depth: 10.0e-6
distance: 30.0e-6
height: 20.0e-6
width: 5.0e-6
type: SpotWeldVertical
passes: null
number: 2.0
scan_direction: TopToBottom

```

I. Remove Manipulator

```python
Expand Down Expand Up @@ -1032,7 +1058,7 @@ We break this down into the following steps:
First we need to define our weld milling protocol. We already support these kind of milling patterns, under the type "Spot Weld". A spot weld consists of a set of equally horizontal patterns, and is used as the name suggests for redeposition welds. Similar to attaching the volume block to the adapter, setting passes = 1 is important so we don't mill over our redeposited material.

```yaml title="protocol-serial-liftout.yaml"
weld:
landing-weld:
stages:
# left weld
- height: 0.5e-6
Expand Down Expand Up @@ -1126,7 +1152,7 @@ Milling protocol

```yaml title="protocol-serial-liftout.yaml"

landing_sever:
landing-sever:
cleaning_cross_section: 0.0
depth: 20.0e-06
height: 0.25e-06
Expand Down Expand Up @@ -1157,7 +1183,7 @@ point = det.features[0].feature_m
point.y += v_offset

# get weld milling stages
stages = milling._get_milling_stages("landing_sever", settings.protocol, point)
stages = milling._get_milling_stages("landing-sever", settings.protocol, point)

# mill stages
milling.mill_stages(microscope=microscope, settings=settings, stages=stages)
Expand Down
8 changes: 4 additions & 4 deletions docs/autolamella/getting_started.md
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Expand Up @@ -200,7 +200,7 @@ flatten: # flatte
application_file: "autolamella"
type: "Rectangle"
preset: "30 keV; 20 nA"
liftout_sever: # liftout_sever: (autolamella-serial-liftout)
liftout-sever: # liftout-sever: (autolamella-serial-liftout)
cleaning_cross_section: 0.0
depth: 25.0e-06
height: 5.0e-06
Expand All @@ -212,7 +212,7 @@ liftout_sever: # liftou
application_file: "autolamella"
type: "Rectangle"
preset: "30 keV; 20 nA"
liftout_weld: # liftout_weld: (autolamella-serial-liftout)
liftout-weld: # liftout-weld: (autolamella-serial-liftout)
height: 5.0e-6
width: 0.5e-6
depth: 5.0e-6
Expand All @@ -226,7 +226,7 @@ liftout_weld: # liftou
scan_direction: "TopToBottom"
type: "SpotWeldVertical"
preset: "30 keV; 2.5 nA"
adapter_weld: # adapter_weld: (autolamella-serial-liftout)
prepare-copper-block-weld: # prepare-copper-block-weld: (autolamella-serial-liftout)
height: 5.0e-6
width: 0.5e-6
depth: 5.0e-6
Expand Down Expand Up @@ -268,7 +268,7 @@ weld: # weld:
scan_direction: "LeftToRight"
type: "SpotWeld"
preset: "30 keV; 2.5 nA"
landing_sever: # landing_sever: (autolamella-serial-liftout)
landing-sever: # landing-sever: (autolamella-serial-liftout)
cleaning_cross_section: 0.0
depth: 25.0e-06
height: 1.0e-06
Expand Down
1 change: 0 additions & 1 deletion docs/autolamella/protocol.md
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Expand Up @@ -123,7 +123,6 @@ microexpansion:
distance: 1.0e-05
height: 1.8e-05
hfw: 200e-6
lamella_width: 1.0e-05
milling_current: 2.0e-09
preset: 30 keV; 2.5 nA
width: 5.0e-07
Expand Down

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