v0.2.2 Release (04/08/2023) (#115)

v0.2.2 Release

Highlights:
- Waffle Method Integration
- New User Interface
- Minimap Integration

.gitignore

@@ -19,4 +19,8 @@ autolamella/*protocol*.y*ml
 autolamella/_version.py
 *.code-workspace
 .vscode/*
-protocol*
+autolamella/waffle/*
+waffle/*
+old_protocol/*.y*ml
+old_protocol/*
+dist/*

autolamella/__init__.py

@@ -0,0 +1,5 @@
+try:
+    import importlib.metadata
+    __version__ = importlib.metadata.version('autolamella')
+except ModuleNotFoundError:
+    __version__ = "unknown"

autolamella/config.py

@@ -1,8 +1,15 @@
 import os
+from pathlib import Path
 
-BASE_PATH = os.path.dirname(__file__)
-LOG_PATH = os.path.join(BASE_PATH, 'log')
 
+BASE_PATH: Path = os.path.dirname(__file__)
+LOG_PATH: Path = os.path.join(BASE_PATH, 'log')
+CONFIG_PATH: Path = os.path.join(BASE_PATH)
+PROTOCOL_PATH: Path = os.path.join(BASE_PATH, "protocol", "protocol.yaml")
+SYSTEM_PATH: Path = os.path.join(CONFIG_PATH, "system.yaml")
+
+
+EXPERIMENT_NAME = "AutoLamella"
 HFW_THRESHOLD = 0.005 # 0.5% of the image height
 
 DEFAULT_PROTOCOL = {

autolamella/default_protocol.yaml

@@ -11,25 +11,43 @@ fiducial:
   milling_current: 28.e-9
   preset: "30 keV; 20 nA" # TESCAN only
 
+trench:
+  lamella_width: 22.e-6
+  lamella_height: 30.0e-6
+  milling_current: 16.0e-9
+  trench_height: 32.e-6
+  depth: 1.5e-6
+  offset: 0.0e-6
+  size_ratio: 0.5
+  preset: "30 keV; 2.5 nA" # TESCAN only
+  hfw: 180.0e-6
+
+
 lamella:
   beam_shift_attempts: 3.0
   alignment_current: "Imaging"
   lamella_width: 10.e-6
   lamella_height: 800.e-9
-  protocol_stages:
+  stages:
   - trench_height: 10.e-6
+    lamella_width: 10.e-6
+    lamella_height: 800.e-9
     depth: 1.e-6
     offset: 2.e-6
     size_ratio: 1.0
     milling_current: 2.e-9
     preset: "30 keV; 2.5 nA" # TESCAN only
   - trench_height: 2.e-6
+    lamella_width: 10.e-6
+    lamella_height: 800.e-9
     depth: 1.e-6
     offset: 0.5e-6
     size_ratio: 1.0
     milling_current: 0.74e-9
     preset: "30 keV; 1 nA" # TESCAN only
   - trench_height: 0.5e-6
+    lamella_width: 10.e-6
+    lamella_height: 800.e-9
     depth: 0.4e-6
     offset: 0.0e-6
     size_ratio: 1.0
@@ -39,4 +57,16 @@ lamella:
 microexpansion:
   width: 0.5e-6
   height: 18.e-6
-  distance: 10.e-6 # Does not include Lamella width. So centre of microexpansion is lamella_width/2 + distance.
+  distance: 10.e-6 # Does not include Lamella width. So centre of microexpansion is lamella_width/2 + distance.
+
+notch: 
+  vheight: 5.0e-6
+  vwidth: 1.0e-6
+  hwidth: 5.0e-6
+  hheight: 1.0e-6
+  depth: 5.0e-6
+  distance: 5.0e-6
+  flip: 0
+  milling_current: 2.e-9
+  preset: "30 keV; 2.5 nA" # TESCAN only
+  hfw: 80e-6

autolamella/model.yaml

@@ -1,25 +1,36 @@
-# this file is used to define the microscope model, and enabled components
-
-system:
-  name: "FIBSEM"
-  manufacturer: "Demo"
-  description: "FIBSEM"
-  version: "0.1"
-  id: 00000
-
-# define the microscope model
 electron:
-  enabled: True
+    enabled: true
+gis:
+    enabled: true
+    multichem: true
 ion:
-  enabled: True
-stage:
-  enabled: True
-  rotation: True
-  tilt: True
+    enabled: true
 manipulator:
-  enabled: True
-  rotation: True
-  tilt: True
-gis:
-  enabled: True
-  multichem: True
+    enabled: true
+    positions:
+        calibrated: true
+        parking:
+            x: -0.008918395
+            y: 0.0006548000000000001
+            z: -0.004848865
+        standby:
+            x: 0.0
+            y: 0.0
+            z: 0.00545
+        working:
+            x: 0.0
+            y: 0.0
+            z: 0.00585
+    rotation: false
+    tilt: false
+
+stage:
+    enabled: true
+    rotation: true
+    tilt: true
+system:
+    description: FIBSEM
+    id: 0
+    manufacturer: Demo
+    name: FIBSEM
+    version: '0.1'

autolamella/napari.yaml

@@ -0,0 +1,13 @@
+name: autolamella
+display_name: AutoLamella
+contributions:
+  commands:
+
+      # Widgets
+    - id: autolamella.viewer
+      python_name: autolamella.autolamella_ui:UiInterface
+      title: AutoLamella UI
+
+  widgets:
+    - command: autolamella.viewer
+      display_name: AutoLamella UI