[MSD-265][fix] METEOR GUI FIBSEM tab: untangle milling pattern handling

src/odemis/acq/milling/millmng.py

@@ -283,6 +283,8 @@ def get_associated_tasks(wt: MillingWorkflowTask,
     :return: List of associated tasks."""
     associated_tasks = []
     for task in milling_tasks.values():
+        if not task.selected:
+            continue
 
         if wt.value in task.name:
             associated_tasks.append(task)

src/odemis/acq/milling/tasks.py

@@ -71,8 +71,10 @@ class MillingTaskSettings:
 
     def __init__(self, milling: MillingSettings,
                  patterns: List[MillingPatternParameters],
-                 name: str):
+                 name: str,
+                 selected: bool = True):
         self.name: str = name
+        self.selected: bool = selected  # Whether this task should be executed or not
         self.milling: MillingSettings = milling
         self.patterns: List[MillingPatternParameters] = patterns
 
@@ -81,6 +83,7 @@ def to_dict(self) -> dict:
         :return: dictionary containing the milling task settings
         """
         return {"name": self.name,
+                "selected": self.selected,
                 "milling": self.milling.to_dict(),
                 "patterns": [pattern.to_dict() for pattern in self.patterns]}
 
@@ -91,6 +94,7 @@ def from_dict(data: dict) -> "MillingTaskSettings":
         :return: MillingTaskSettings"""
         return MillingTaskSettings(
             name=data.get("name", "Milling Task"),
+            selected=data.get("selected", True),
             milling=MillingSettings.from_dict(data["milling"]),
             patterns=[PATTERN_NAME_TO_CLASS[p["pattern"]].from_dict(p) for p in data["patterns"]])
 
@@ -102,6 +106,9 @@ def generate(self) -> List[MillingPatternParameters]:
         :return: list of individual shapes to be drawn on the microscope
         """
         patterns = []
+        if not self.selected:
+            return patterns
+
         for pattern in self.patterns:
             patterns.extend(pattern.generate())
         return patterns

src/odemis/acq/milling/test/tasks_test.py

@@ -89,6 +89,7 @@ def test_milling_task_settings(self):
 
         dict_data = milling_task_settings.to_dict()
         self.assertEqual(dict_data["name"], "Milling Task")
+        self.assertEqual(dict_data["selected"], True)
         self.assertEqual(dict_data["milling"], milling_settings.to_dict())
         self.assertEqual(dict_data["patterns"][0], trench_pattern.to_dict())
 

src/odemis/gui/cont/acquisition/cryo_acq.py

@@ -60,6 +60,7 @@
 from odemis.gui.cont.acquisition.overview_stream_acq import (
     OverviewStreamAcquiController, CorrelationDialogController,
 )
+from odemis.gui.cont.milling import pos_to_relative
 from odemis.gui.util import call_in_wx_main, wxlimit_invocation
 from odemis.gui.util.widgets import (
     ProgressiveFutureConnector,
@@ -805,13 +806,13 @@ def _on_close_dialog(self, z_stack):
 
             # redraw milling position
             fibsem_tab = self._tab_data.main.getTabByName("meteor-fibsem")
-            if self._tab_data.main.currentFeature.value:
-                correlation_dict = self._tab_data.main.currentFeature.value.correlation_data
+            feature = self._tab_data.main.currentFeature.value
+            if feature:
+                correlation_dict = feature.correlation_data
                 if correlation_dict and correlation_dict.fib_projected_pois:
                     if correlation_dict.fm_pois:
                         # Update feature position according to POI in FM
                         pm = self._tab_data.main.posture_manager
-                        feature = self._tab_data.main.currentFeature.value
                         feature_stage_bare = feature.get_posture_position(FM_IMAGING)
                         poi = correlation_dict.fm_pois[0]
                         poi_coords = poi.coordinates.value
@@ -823,8 +824,8 @@ def _on_close_dialog(self, z_stack):
                         feature.fm_focus_position.value = {"z": poi_coords[2]}
                     # Draw milling position in FIBSEM tab around the projected POI
                     target = correlation_dict.fib_projected_pois[0]
-                    fibsem_tab.milling_task_controller.draw_milling_tasks(pos=(target.coordinates.value[0],
-                                                                               target.coordinates.value[1]))
+                    rel_pos = pos_to_relative(target.coordinates.value[:2], feature.reference_image)
+                    fibsem_tab.milling_task_controller.move_milling_tasks(rel_pos)
 
     @call_in_wx_main
     def _on_filename(self, name):

src/odemis/gui/cont/features.py

@@ -214,22 +214,6 @@ def save_milling_position(self, evt: wx.Event):
         self._tab_data_model.main.currentFeature.value = None
         self._tab_data_model.main.currentFeature.value = feature
 
-    def save_milling_tasks(self,
-                    milling_tasks: Dict[str, MillingTaskSettings],
-                    selected_milling_tasks: List[str]) -> None:
-        feature: CryoFeature = self._tab_data_model.main.currentFeature.value
-        if feature is None:
-            logging.warning("No feature selected")
-            return
-
-        # filter out the selected tasks
-        milling_tasks = {k: v for k, v in milling_tasks.items() if k in selected_milling_tasks}
-
-        feature.milling_tasks = copy.deepcopy(milling_tasks)
-        save_features(self._tab.conf.pj_last_path, self._tab_data_model.main.features.value)
-
-    # TODO: pattern size not updating
-
     def _display_go_to_feature_warning(self) -> bool:
         box = wx.MessageDialog(self._tab.main_frame,
                                message="The stage is currently in the SEM imaging position. "
@@ -393,10 +377,6 @@ def _on_current_feature_changes(self, feature):
                                                                     ctrl_2_va=self._on_ctrl_feature_z_change,
                                                                     va_2_ctrl=self._on_feature_focus_pos)
 
-        # if FIBSEM mode, and milling tasks are available, re-draw
-        if self.acqui_mode is guimod.AcquiMode.FIBSEM:
-            self._tab.milling_task_controller.set_milling_tasks(feature.milling_tasks)
-
     def _on_feature_focus_pos(self, fm_focus_position: dict):
         # Set the feature Z ctrl with the focus position
         self._panel.ctrl_feature_z.SetValue(fm_focus_position["z"])