Merge pull request #311 from DeMarcoLab/v0.2-dev

v0.2.5 Release

fibsem/alignment.py

@@ -52,6 +52,7 @@ def beam_shift_alignment(
     image_settings: ImageSettings,
     ref_image: FibsemImage,
     reduced_area: Optional[FibsemRectangle] = None,
+    alignment_current: Optional[float] = None,
 ):
     """Aligns the images by adjusting the beam shift instead of moving the stage.
 
@@ -71,6 +72,10 @@ def beam_shift_alignment(
         ValueError: If `image_settings.beam_type` is not set to `BeamType.ION`.
 
     """
+    if alignment_current is not None:
+        initial_current = microscope.get("current", image_settings.beam_type)
+        microscope.set("current", alignment_current, image_settings.beam_type)
+
     import time
     time.sleep(3) # threading is too fast?
     image_settings = ImageSettings.fromFibsemImage(ref_image)
@@ -86,6 +91,10 @@ def beam_shift_alignment(
     # adjust beamshift 
     microscope.beam_shift(dx, dy, image_settings.beam_type)
 
+    # reset beam current
+    if alignment_current is not None:
+        microscope.set("current", initial_current, image_settings.beam_type)
+
 
 def correct_stage_drift(
     microscope: FibsemMicroscope,
@@ -233,7 +242,7 @@ def align_using_reference_images(
 
         # vertical constraint = eucentric movement
         if constrain_vertical:
-            microscope.eucentric_move(
+            microscope.vertical_move(
                 settings=settings, dx=0, dy=-dy
             )  # FLAG_TEST
         else:
@@ -457,4 +466,24 @@ def _save_alignment_data(
         df_tmp = pd.read_csv(DATAFRAME_PATH)
         df = pd.concat([df_tmp, df], axis=0, ignore_index=True)
 
-    df.to_csv(DATAFRAME_PATH, index=False)
+    df.to_csv(DATAFRAME_PATH, index=False)
+
+from fibsem.structures import ImageSettings
+def _multi_step_alignment(microscope: FibsemMicroscope, image_settings: ImageSettings, 
+    ref_image: FibsemImage, reduced_area: FibsemRectangle, alignment_current: float, steps:int = 3) -> None:
+
+    # set alignment current
+    if alignment_current is not None:
+        initial_current = microscope.get("current", image_settings.beam_type)
+        microscope.set("current", alignment_current, image_settings.beam_type)
+
+    base_label = image_settings.label
+    for i in range(steps):
+        image_settings.label = f"{base_label}_{i:02d}"
+        image_settings.beam_type = BeamType.ION
+        beam_shift_alignment(microscope, image_settings, 
+                                        ref_image=ref_image,
+                                            reduced_area=reduced_area)
+    # reset beam current
+    if alignment_current is not None:
+        microscope.set("current", initial_current, image_settings.beam_type)

fibsem/alignment2.py

@@ -213,7 +213,7 @@ def eucentric_correct_stage_drift(
 
     # target images
     targets = (BeamType.ELECTRON, BeamType.ELECTRON, BeamType.ION)#, BeamType.ELECTRON, BeamType.ION)
-    eucentric_move = (False, False, True) 
+    vertical_move = (False, False, True) 
 
     # lp, hp, sigma
     params = [
@@ -237,7 +237,7 @@ def eucentric_correct_stage_drift(
         # TODO: this is wrong now
 
     # align lowres, then highres
-    for i, (ref_image, target, euc_move) in enumerate(zip(ref_order, targets, eucentric_move)):
+    for i, (ref_image, target, euc_move) in enumerate(zip(ref_order, targets, vertical_move)):
 
         ref_mask = masks.create_circle_mask(ref_image.data.shape, radius=512)
 

fibsem/calibration.py

@@ -265,3 +265,60 @@ def auto_home_and_link_v2(
     # move to saved linked state
     microscope.set_microscope_state(state)
 
+
+def _calibrate_manipulator_thermo(microscope:FibsemMicroscope, settings:MicroscopeSettings, parent_ui = None):
+    from fibsem.detection import detection
+    from fibsem.segmentation.model import load_model
+    import matplotlib.pyplot as plt
+
+    from autolamella.workflows.ui import _validate_det_ui_v2, ask_user
+
+    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.")
+
+
+    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]:
+            settings.image.hfw = hfw
+            settings.image.beam_type = beam_type
+
+            features = [detection.NeedleTip(), detection.ImageCentre()] if np.isclose(microscope.get("scan_rotation", beam_type), 0) else [detection.NeedleTipBottom(), detection.ImageCentre()]
+
+            if parent_ui:
+                det = _validate_det_ui_v2(microscope, settings, features, parent_ui, validate = True, msg = f"Confirm Feature Detection. Press Continue to proceed.")
+            else:
+                image = acquire.new_image(microscope, settings.image)
+                det = detection.detect_features(image, model, features=features, pixelsize=image.metadata.pixel_size.x)
+                detection.plot_detection(det)
+                ret  = input("continue? (y/n)")
+
+                if ret != "y":
+                    return
+
+            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.")

fibsem/config.py

@@ -65,9 +65,10 @@
 os.makedirs(DATA_CC_PATH, exist_ok=True)
 os.makedirs(DATA_TILE_PATH, exist_ok=True)
 
+DATABASE_PATH = os.path.join(BASE_PATH, "fibsem", "db", "fibsem.db")
+os.makedirs(os.path.dirname(DATABASE_PATH), exist_ok=True)
 import yaml
 
-
 def load_yaml(fname):
     """
     Load a YAML file and return its contents as a dictionary.
@@ -89,4 +90,9 @@ def load_yaml(fname):
 
 __SUPPORTED_MANUFACTURERS__ = ["Thermo", "Tescan", "Demo"]
 __DEFAULT_MANUFACTURER__ = "Thermo"
-__DEFAULT_IP_ADDRESS__ = "10.0.0.1"
+__DEFAULT_IP_ADDRESS__ = "10.0.0.1"
+
+
+_LIVE_IMAGING_ENABLED = False
+_MINIMAP_VISUALISATION = False
+_MINIMAP_MOVE_WITH_TRANSLATION = True