Functional z stack Thing

src/openflexure_microscope_server/things/smart_scan.py

@@ -32,6 +32,7 @@ from openflexure_microscope_server.utilities import ErrorCapturingThread
 from openflexure_microscope_server.things.autofocus import AutofocusThing
 from openflexure_microscope_server.things.camera_stage_mapping import CameraStageMapper
 from openflexure_microscope_server.things.background_detect import BackgroundDetectThing
+from openflexure_microscope_server.things.z_stack import ZStackThing
 from openflexure_microscope_server import scan_planners
 
 CSMDep = direct_thing_client_dependency(CameraStageMapper, "/camera_stage_mapping/")
@@ -139,6 +140,7 @@ class SmartScanThing(Thing):
         self._background_detect: Optional[BackgroundDep] = None
         self._ongoing_scan_name: Optional[str] = None
         self._starting_position: Optional[Mapping[str, int]] = None
+        self._z_stack: Optional[ZStackDep] = None
         self._capture_thread: Optional[ErrorCapturingThread] = None
         self._scan_images_taken: Optional[int] = None
         # TODO Scan data is a dict during refactoring, should become a dataclass
@@ -155,6 +157,7 @@ class SmartScanThing(Thing):
         metadata_getter: GetThingStates,
         csm: CSMDep,
         background_detect: BackgroundDep,
+        z_stack: ZStackDep,
         scan_name: str = "",
     ):
         """Move the stage to cover an area, taking images that can be tiled together.
@@ -178,6 +181,7 @@ class SmartScanThing(Thing):
         self._csm = csm
         self._background_detect = background_detect
         self._capture_thread = None
+        self._z_stack = z_stack
         self._scan_images_taken = 0
 
         # Don't set self._scan_data dictionary. This is done at the start of _run_scan
@@ -213,6 +217,7 @@ class SmartScanThing(Thing):
             self._ongoing_scan_name = None
             self._scan_images_taken = None
             self._scan_data = None
+            self._z_stack = None
             self._scan_lock.release()
 
     def promote_stitch_files(