fix calibrate manipulator

DeMarcoLab · Oct 18, 2023 · 6a59f43 · 6a59f43
1 parent 28deed1
commit 6a59f43
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Showing 2 changed files with 29 additions and 5 deletions.
diff --git a/fibsem/calibration.py b/fibsem/calibration.py
@@ -271,11 +271,27 @@ def _calibrate_manipulator_thermo(microscope:FibsemMicroscope, settings:Microsco
     from fibsem.segmentation.model import load_model
     import matplotlib.pyplot as plt
 
-    from autolamella.workflows.ui import _validate_det_ui_v2
+    from autolamella.workflows.ui import _validate_det_ui_v2, ask_user
 
-    model = load_model("autolamella-mega-01-nc5-34.pt", encoder="resnet34", nc=5)
+    if parent_ui:
+        ret = ask_user(parent_ui, 
+            msg="Please complete the EasyLift alignment procedure in the xT UI until Step 5. Press Continue to proceed.",
+            pos="Continue", neg="Cancel")
+        if ret is False:
+            return
+    else:
+        input("Please complete the EasyLift alignment procedure in the xT UI until Step 5. Press Enter to proceed.")
 
-    hfws = [900e-6, 400e-6, 150e-6]
+
+    model = load_model("autolamella-mega-latest.pt", encoder="resnet34", nc=5)
+    settings.protocol["ml"]["checkpoint"] = "autolamella-mega-latest.pt"
+    settings.image.autocontrast = True
+
+    hfws = [2000e-6, 900e-6, 400e-6, 150e-6]
+
+    # set working distance
+    wd = microscope.get("working_distance", BeamType.ELECTRON)
+    microscope.set("working_distance", settings.system.electron.eucentric_height, BeamType.ELECTRON)
 
     for hfw in hfws:
         for beam_type in [BeamType.ELECTRON, BeamType.ION]:
@@ -298,4 +314,11 @@ def _calibrate_manipulator_thermo(microscope:FibsemMicroscope, settings:Microsco
             move_x = bool(beam_type == BeamType.ELECTRON) # ION calibration only in z
             detection.move_based_on_detection(microscope, settings, det, beam_type, move_x=move_x, _move_system="manipulator")
 
+    # restore working distance
+    microscope.set("working_distance", wd, BeamType.ELECTRON)
+
+    if parent_ui:
+        ask_user(parent_ui, 
+            msg="Alignment of EasyLift complete. Please complete the procedure in xT UI. Press Continue to proceed.",
+            pos="Continue")
     print(f"The manipulator should now be centred in both beams.")
diff --git a/fibsem/detection/detection.py b/fibsem/detection/detection.py
@@ -667,7 +667,7 @@ def take_image_and_detect_features(
 
     # load model
     ml_protocol = settings.protocol.get("ml", {})
-    checkpoint = ml_protocol.get("checkpoint", "openfibsem-baseline-34.pt")
+    checkpoint = ml_protocol.get("checkpoint", "autolamella-mega-latest.pt")
     encoder = ml_protocol.get("encoder", "resnet34")
     num_classes = int(ml_protocol.get("num_classes", 3))
     model = load_model(checkpoint=checkpoint, encoder=encoder, nc=num_classes)
@@ -950,7 +950,8 @@ def detect_multi_features(image: np.ndarray, mask: np.ndarray, feature: Feature,
 
     if features == []:
         logging.info(f"No features detected for {feature.name}")
-        feature.px = Point(0, 0)
+        # set at centre of image
+        feature.px = Point(x=image.shape[1]//2, y=image.shape[0]//2)
         features = [deepcopy(feature)]
 
     return features