Merge branch 'main' of https://github.com/DeMarcoLab/fibsem

.gitignore

@@ -26,4 +26,5 @@ fibsem/segmentation/training/*
 site/*
 scratch/training/*
 fibsem/_version.py
-scratch/figure/wd_*/*
+scratch/figure/wd_*/*
+demo_*/*

fibsem/config.py

@@ -33,6 +33,7 @@
     MillingPattern.Polish: "polish_lamella",
     MillingPattern.Flatten: "flatten_landing",
     MillingPattern.Fiducial: "fiducial",
+    MillingPattern.SpotWeld: "spot_weld",
 }
 
 # MILLING UI
@@ -56,5 +57,6 @@
     "needle_angle",
     "percentage_roi_height",
     "percentage_from_lamella_surface",
-    "cleaning_cross_section"
+    "cleaning_cross_section",
+    "number"
 ]

fibsem/config/system.yaml

@@ -20,7 +20,7 @@ system:
   stage:
     rotation_flat_to_electron: 49 # degrees
     rotation_flat_to_ion: 229 # degrees
-    tilt_flat_to_electron: 35 # degrees (pre-tilt)
+    tilt_flat_to_electron: 35 # degrees (pre-tilt)s
     tilt_flat_to_ion: 52 # degrees
     pre_tilt: 35
     needle_stage_height_limit: 3.7e-3

fibsem/patterning.py

@@ -24,6 +24,7 @@ class MillingPattern(Enum):
     Polish = 8
     Flatten = 9
     Fiducial = 10
+    SpotWeld = 11
 
 
 ############################## PATTERNS ##############################
@@ -74,16 +75,18 @@ def spot_weld_pattern(
 ) -> list[RectanglePattern]:
     # ref: spotweld terminology https://www.researchgate.net/publication/351737991_A_Modular_Platform_for_Streamlining_Automated_Cryo-FIB_Workflows#pf14
 
-    n_patterns = protocol["number"]
+    n_patterns = int(protocol["number"])
     mill_settings = MillingSettings.__from_dict__(protocol)
     mill_settings.centre_x = point.x
     mill_settings.centre_y = (
         point.y - (n_patterns - 1) * (protocol["offset"] + protocol["height"]) / 2
     )
+    mill_settings.cleaning_cross_section = bool(protocol["cleaning_cross_section"])
 
     patterns = []
     for i in range(n_patterns):
         pattern = milling._draw_rectangle_pattern_v2(microscope, mill_settings)
+        pattern.scan_direction = protocol["scan_direction"]
         patterns.append(pattern)
         mill_settings.centre_y += protocol["offset"] + protocol["height"]
 
@@ -333,6 +336,9 @@ def create_milling_patterns(
         mill_settings.centre_y = point.y
         patterns = milling._draw_fiducial_patterns(microscope, mill_settings)
 
+    if milling_pattern_type == MillingPattern.SpotWeld:
+        patterns = spot_weld_pattern(microscope, milling_protocol, point)
+
     # convert patterns is list
     if not isinstance(patterns, list):
         patterns = [patterns]

fibsem/ui/FibsemDetectionUI.py

@@ -43,7 +43,8 @@ def __init__(
 
         # images
         from fibsem.segmentation.utils import image_blend
-        self.image = image_blend(self.detected_features.image, self.detected_features.mask)
+        # self.image = image_blend(self.detected_features.image, self.detected_features.mask)
+        self.image = self.detected_features.image
         self._USER_CORRECTED = False
 
         # pattern drawing

fibsem/ui/FibsemMillingUI.py

@@ -417,7 +417,7 @@ def main():
         protocol_path=liftout_config.protocol_path
     )
     settings.image.hfw = 150e-6
-    milling_pattern = MillingPattern.JCut
+    milling_pattern = MillingPattern.SpotWeld
     point = None
     change_pattern = True
     validate = True

fibsem/utils.py

@@ -113,6 +113,8 @@ def sputter_platinum(
     microscope.imaging.set_active_view(original_active_view)
     microscope.patterning.set_default_beam_type(BeamType.ION.value)  # set ion beam
     multichem.retract()
+
+    microscope.beams.electron_beam.turn_on()
     logging.info("sputtering platinum finished.")