Updated default extensions to subclass structure

openflexure_microscope/api/default_extensions/__init__.py

@@ -2,6 +2,8 @@ import logging
 import traceback
 from contextlib import contextmanager
 
+LABTHINGS_EXTENSIONS = []
+
 
 @contextmanager
 def handle_extension_error(extension_name):
@@ -17,14 +19,28 @@ def handle_extension_error(extension_name):
 
 
 with handle_extension_error("autofocus"):
-    from .autofocus import autofocus_extension_v2
+    from .autofocus import AutofocusExtension
+
+    LABTHINGS_EXTENSIONS.append(AutofocusExtension)
 with handle_extension_error("scan"):
-    from .scan import scan_extension_v2
+    from .scan import ScanExtension
+
+    LABTHINGS_EXTENSIONS.append(ScanExtension)
 with handle_extension_error("zip builder"):
-    from .zip_builder import zip_extension_v2
+    from .zip_builder import ZipBuilderExtension
+
+    LABTHINGS_EXTENSIONS.append(ZipBuilderExtension)
 with handle_extension_error("autostorage"):
-    from .autostorage import autostorage_extension_v2
+    from .autostorage import AutostorageExtension
+
+    LABTHINGS_EXTENSIONS.append(AutostorageExtension)
+
+with handle_extension_error("lens shading calibration"):
+    from .picamera_autocalibrate import LSTExtension
+
+    LABTHINGS_EXTENSIONS.append(LSTExtension)
+
 with handle_extension_error("camera stage mapping"):
     from camera_stage_mapping.ofm_extension import csm_extension
-with handle_extension_error("lens shading calibration"):
+
-    from .picamera_autocalibrate import lst_extension_v2
+    LABTHINGS_EXTENSIONS.append(csm_extension)

openflexure_microscope/api/default_extensions/autofocus.py

@@ -109,6 +109,16 @@ class JPEGSharpnessMonitor:
         return data
 
 
+@contextmanager
+def monitor_sharpness(microscope: Microscope):
+    m = JPEGSharpnessMonitor(microscope)
+    m.start()
+    try:
+        yield m
+    finally:
+        m.stop()
+
+
 def sharpness_sum_lap2(rgb_image: np.ndarray):
     """Return an image sharpness metric: sum(laplacian(image)**")"""
     image_bw = np.mean(rgb_image, 2)
@@ -129,7 +139,29 @@ def sharpness_edge(image: np.ndarray):
 ### Autofocus extension
 
 
-def measure_sharpness(microscope: Microscope, metric_fn: Callable = sharpness_sum_lap2):
+class AutofocusExtension(BaseExtension):
+    def __init__(self):
+        super().__init__(
+            "org.openflexure.autofocus",
+            version="2.0.0",
+            description="Actions to move the microscope in Z and pick the point with the sharpest image.",
+        )
+        self.add_view(
+            MeasureSharpnessAPI, "/measure_sharpness", endpoint="measure_sharpness"
+        )
+        self.add_view(AutofocusAPI, "/autofocus", endpoint="autofocus")
+        self.add_view(FastAutofocusAPI, "/fast_autofocus", endpoint="fast_autofocus")
+        self.add_view(
+            UpDownUpAutofocusAPI, "/updownup_autofocus", endpoint="updownup_autofocus"
+        )
+
+        self.add_view(
+            MoveAndMeasureAPI, "/move_and_measure", endpoint="move_and_measure"
+        )
+
+    def measure_sharpness(
+        self, microscope: Microscope, metric_fn: Callable = sharpness_sum_lap2
+    ):
         """Measure the sharpness of the camera's current view."""
 
         if hasattr(microscope.camera, "array") and callable(
@@ -139,13 +171,13 @@ def measure_sharpness(microscope: Microscope, metric_fn: Callable = sharpness_su
         else:
             raise RuntimeError(f"Object {microscope.camera} has no method `array`")
 
-
+    def autofocus(
-def autofocus(
+        self,
         microscope: Microscope,
         dz: List[int],
         settle: float = 0.5,
         metric_fn: Callable = sharpness_sum_lap2,
-):
+    ):
         """Perform a simple autofocus routine.
         The stage is moved to z positions (relative to current position) in dz,
         and at each position an image is captured and the sharpness function 
@@ -169,39 +201,26 @@ def autofocus(
                     return
                 positions.append(stage.position[2])
                 time.sleep(settle)
-            sharpnesses.append(measure_sharpness(microscope, metric_fn))
+                sharpnesses.append(self.measure_sharpness(microscope, metric_fn))
 
             newposition = positions[np.argmax(sharpnesses)]
             stage.move_rel((0, 0, newposition - stage.position[2]))
 
         return positions, sharpnesses
 
-
+    def move_and_find_focus(self, microscope: Microscope, dz: int):
-@contextmanager
-def monitor_sharpness(microscope: Microscope):
-    m = JPEGSharpnessMonitor(microscope)
-    m.start()
-    try:
-        yield m
-    finally:
-        m.stop()
-
-
-def move_and_find_focus(microscope: Microscope, dz: int):
         """Make a relative Z move and return the peak sharpness position"""
         with monitor_sharpness(microscope) as m:
             m.focus_rel(dz)
             return m.sharpest_z_on_move(0)
 
-
+    def move_and_measure(self, microscope: Microscope, dz: int):
-def move_and_measure(microscope: Microscope, dz: int):
         """Make a relative Z move and return the sharpness data"""
         with monitor_sharpness(microscope) as m:
             m.focus_rel(dz)
             return m.data_dict()
 
-
+    def fast_autofocus(self, microscope: Microscope, dz: int = 2000):
-def fast_autofocus(microscope: Microscope, dz: int = 2000):
         """Perform a down-up-down-up autofocus"""
         with microscope.camera.lock, microscope.stage.lock:
             with monitor_sharpness(microscope) as m:
@@ -222,14 +241,14 @@ def fast_autofocus(microscope: Microscope, dz: int = 2000):
                 # Return all focus data
                 return m.data_dict()
 
-
+    def fast_up_down_up_autofocus(
-def fast_up_down_up_autofocus(
+        self,
         microscope: Microscope,
         dz: int = 2000,
         target_z: int = 0,
         initial_move_up: bool = True,
         mini_backlash: int = 25,
-):
+    ):
         """Autofocus by measuring on the way down, and moving back up with feedback.
 
         This autofocus method is very efficient, as it only passes the peak once.
@@ -316,7 +335,7 @@ class MeasureSharpnessAPI(View):
         if not microscope:
             abort(503, "No microscope connected. Unable to measure sharpness.")
 
-        return {"sharpness": measure_sharpness(microscope)}
+        return {"sharpness": self.extension.measure_sharpness(microscope)}
 
 
 class MoveAndMeasureAPI(ActionView):
@@ -335,7 +354,7 @@ class MoveAndMeasureAPI(ActionView):
         if microscope.has_real_stage():
             # Acquire microscope lock with 1s timeout
             with microscope.camera.lock, microscope.stage.lock:
-                return move_and_measure(microscope, dz=args.get("dz"))
+                return self.extension.move_and_measure(microscope, dz=args.get("dz"))
 
         else:
             abort(503, "No stage connected. Unable to autofocus.")
@@ -361,7 +380,7 @@ class AutofocusAPI(ActionView):
             logging.debug("Running autofocus...")
 
             # return a handle on the autofocus task
-            return autofocus(microscope, dz)
+            return self.extension.autofocus(microscope, dz)
 
         else:
             abort(503, "No stage connected. Unable to autofocus.")
@@ -385,7 +404,7 @@ class FastAutofocusAPI(ActionView):
             # Acquire microscope lock with 1s timeout
             with microscope.lock(timeout=1):
                 # Run fast_autofocus
-                return fast_autofocus(microscope, dz=args.get("dz"))
+                return self.extension.fast_autofocus(microscope, dz=args.get("dz"))
 
         else:
             abort(503, "No stage connected. Unable to autofocus.")
@@ -417,38 +436,9 @@ class UpDownUpAutofocusAPI(ActionView):
             # Acquire microscope lock with 1s timeout
             with microscope.lock(timeout=1):
                 # Run fast_up_down_up_autofocus
-                return fast_up_down_up_autofocus(
+                return self.extension.fast_up_down_up_autofocus(
                     microscope, dz=dz, mini_backlash=backlash
                 )
 
         else:
             abort(503, "No stage connected. Unable to autofocus.")
-
-
-autofocus_extension_v2 = BaseExtension(
-    "org.openflexure.autofocus",
-    version="2.0.0",
-    description="Actions to move the microscope in Z and pick the point with the sharpest image.",
-)
-
-autofocus_extension_v2.add_method(fast_autofocus, "fast_autofocus")
-autofocus_extension_v2.add_method(
-    fast_up_down_up_autofocus, "fast_up_down_up_autofocus"
-)
-autofocus_extension_v2.add_method(autofocus, "autofocus")
-autofocus_extension_v2.add_method(move_and_measure, "move_and_measure")
-
-autofocus_extension_v2.add_view(
-    MeasureSharpnessAPI, "/measure_sharpness", endpoint="measure_sharpness"
-)
-autofocus_extension_v2.add_view(AutofocusAPI, "/autofocus", endpoint="autofocus")
-autofocus_extension_v2.add_view(
-    FastAutofocusAPI, "/fast_autofocus", endpoint="fast_autofocus"
-)
-autofocus_extension_v2.add_view(
-    UpDownUpAutofocusAPI, "/updownup_autofocus", endpoint="updownup_autofocus"
-)
-
-autofocus_extension_v2.add_view(
-    MoveAndMeasureAPI, "/move_and_measure", endpoint="move_and_measure"
-)

openflexure_microscope/api/default_extensions/autostorage.py

@@ -93,12 +93,43 @@ class AutostorageExtension(BaseExtension):
 
         # We'll store a reference to a CaptureManager object, who's capture paths will be modified
         self.capture_manager: Optional[CaptureManager] = None
-
         self.initial_location: str = get_default_location()
 
         # Register the on_microscope function to run when the microscope is attached
         self.on_component("org.openflexure.microscope", self.on_microscope)
 
+        self.add_view(GetLocationsView, "/list-locations")
+        self.add_view(PreferredLocationView, "/location")
+        self.add_view(PreferredLocationGUIView, "/location-from-title")
+        self.add_meta("gui", build_gui(self.dynamic_form, self))
+
+    def dynamic_form(self):
+        self.check_location()
+        return {
+            "icon": "sd_storage",
+            "title": "Storage",
+            "viewPanel": "gallery",
+            "forms": [
+                {
+                    "name": "Autostorage",
+                    "isCollapsible": False,
+                    "isTask": False,
+                    "route": "/location-from-title",
+                    "emitOnResponse": "globalUpdateCaptures",
+                    "submitLabel": "Set path",
+                    "schema": [
+                        {
+                            "fieldType": "selectList",
+                            "name": "new_path_title",
+                            "label": "Capture storage path",
+                            "options": self.get_titles(),
+                            "value": self.get_preferred_title(),
+                        }
+                    ],
+                }
+            ],
+        }
+
     def on_microscope(self, microscope_obj: Microscope):
         """Function to automatically call when the parent LabThing has a microscope attached."""
         logging.debug("Autostorage extension found microscope %s", microscope_obj)
@@ -204,12 +235,9 @@ class AutostorageExtension(BaseExtension):
         return self.key_to_title(self.get_preferred_key())
 
 
-autostorage_extension_v2 = AutostorageExtension()
-
-
 class GetLocationsView(PropertyView):
     def get(self):
-        autostorage_extension_v2.check_location()
+        self.extension.check_location()
         return autostorage_extension_v2.get_locations()
 
 
@@ -217,8 +245,8 @@ class PreferredLocationView(PropertyView):
     schema = fields.String(required=True, example="Default")
 
     def get(self):
-        autostorage_extension_v2.check_location()
+        self.extension.check_location()
-        return autostorage_extension_v2.get_preferred_key()
+        return self.extension.get_preferred_key()
 
     def post(self, new_path_key):
         microscope = find_component("org.openflexure.microscope")
@@ -226,8 +254,8 @@ class PreferredLocationView(PropertyView):
         if not microscope:
             abort(503, "No microscope connected. Unable to autofocus.")
 
-        autostorage_extension_v2.check_location()
+        self.extension.check_location()
-        autostorage_extension_v2.set_preferred_key(new_path_key)
+        self.extension.set_preferred_key(new_path_key)
         microscope.save_settings()
 
 
@@ -237,46 +265,11 @@ class PreferredLocationGUIView(View):
         new_path_title = args.get("new_path_title")
         logging.debug(new_path_title)
 
-        new_path_key = autostorage_extension_v2.title_to_key(new_path_title)
+        new_path_key = self.extension.title_to_key(new_path_title)
         logging.debug(new_path_key)
 
-        autostorage_extension_v2.check_location()
+        self.extension.check_location()
-        autostorage_extension_v2.set_preferred_key(new_path_key)
+        self.extension.set_preferred_key(new_path_key)
 
         return new_path_title
 
-
-def dynamic_form():
-    autostorage_extension_v2.check_location()
-    return {
-        "icon": "sd_storage",
-        "title": "Storage",
-        "viewPanel": "gallery",
-        "forms": [
-            {
-                "name": "Autostorage",
-                "isCollapsible": False,
-                "isTask": False,
-                "route": "/location-from-title",
-                "emitOnResponse": "globalUpdateCaptures",
-                "submitLabel": "Set path",
-                "schema": [
-                    {
-                        "fieldType": "selectList",
-                        "name": "new_path_title",
-                        "label": "Capture storage path",
-                        "options": autostorage_extension_v2.get_titles(),
-                        "value": autostorage_extension_v2.get_preferred_title(),
-                    }
-                ],
-            }
-        ],
-    }
-
-
-autostorage_extension_v2.add_view(GetLocationsView, "/list-locations")
-autostorage_extension_v2.add_view(PreferredLocationView, "/location")
-autostorage_extension_v2.add_view(PreferredLocationGUIView, "/location-from-title")
-autostorage_extension_v2.add_meta(
-    "gui", build_gui(dynamic_form, autostorage_extension_v2)
-)

openflexure_microscope/api/default_extensions/picamera_autocalibrate/__init__.py

@@ -1 +1 @@
-from .extension import lst_extension_v2
+from .extension import LSTExtension

openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py

@@ -42,7 +42,27 @@ def pause_stream(scamera: BaseCamera):
                 scamera.start_stream()
 
 
-def recalibrate(microscope: Microscope):
+class LSTExtension(BaseExtension):
+    def __init__(self) -> None:
+        super().__init__(
+            "org.openflexure.calibration.picamera",
+            version="2.0.0-beta.1",
+            description="Routines to perform flat-field correction on the camera.",
+        )
+
+        self.add_view(RecalibrateView, "/recalibrate", endpoint="recalibrate")
+        self.add_view(
+            FlattenLSTView,
+            "/flatten_lens_shading_table",
+            endpoint="flatten_lens_shading_table",
+        )
+        self.add_view(
+            DeleteLSTView,
+            "/delete_lens_shading_table",
+            endpoint="delete_lens_shading_table",
+        )
+
+    def recalibrate(self, microscope: Microscope):
         """Reset the camera's settings.
 
         This generates new gains, exposure time, and lens shading
@@ -70,7 +90,7 @@ class RecalibrateView(ActionView):
 
         logging.info("Starting microscope recalibration...")
 
-        return recalibrate(microscope)
+        return self.extension.recalibrate(microscope)
 
 
 class FlattenLSTView(ActionView):
@@ -102,22 +122,3 @@ class DeleteLSTView(ActionView):
         with pause_stream(microscope.camera) as scamera:
             scamera.camera.lens_shading_table = None
         microscope.save_settings()
-
-
-lst_extension_v2 = BaseExtension(
-    "org.openflexure.calibration.picamera",
-    version="2.0.0-beta.1",
-    description="Routines to perform flat-field correction on the camera.",
-)
-
-lst_extension_v2.add_method(
-    recalibrate, "org.openflexure.calibration.picamera.recalibrate"
-)
-
-lst_extension_v2.add_view(RecalibrateView, "/recalibrate", endpoint="recalibrate")
-lst_extension_v2.add_view(
-    FlattenLSTView, "/flatten_lens_shading_table", endpoint="flatten_lens_shading_table"
-)
-lst_extension_v2.add_view(
-    DeleteLSTView, "/delete_lens_shading_table", endpoint="delete_lens_shading_table"
-)

openflexure_microscope/api/default_extensions/scan.py

@@ -99,9 +99,12 @@ def construct_grid(
 
 class ScanExtension(BaseExtension):
     def __init__(self):
+        BaseExtension.__init__(self, "org.openflexure.scan", version="2.0.0")
+
         self._images_to_be_captured: int = 1
         self._images_captured_so_far: int = 0
-        BaseExtension.__init__(self, "org.openflexure.scan", version="2.0.0")
+
+        self.add_view(TileScanAPI, "/tile", endpoint="tile")
 
     def capture(
         self,
@@ -356,9 +359,6 @@ class ScanExtension(BaseExtension):
                 microscope.stage.move_abs(initial_position)
 
 
-scan_extension_v2 = ScanExtension()
-
-
 class TileScanArgs(FullCaptureArgs):
     namemode = fields.String(missing="coordinates", example="coordinates")
     grid = fields.List(fields.Integer, missing=[3, 3, 3], example=[3, 3, 3])
@@ -398,7 +398,7 @@ class TileScanAPI(ActionView):
         # Acquire microscope lock with 1s timeout
         with microscope.lock(timeout=1):
             # Run scan_extension_v2
-            return scan_extension_v2.tile(
+            return self.extension.scan_extension_v2.tile(
                 microscope,
                 basename=args.get("filename"),
                 namemode=args.get("namemode"),
@@ -414,6 +414,3 @@ class TileScanAPI(ActionView):
                 annotations=args.get("annotations"),
                 tags=args.get("tags"),
             )
-
-
-scan_extension_v2.add_view(TileScanAPI, "/tile", endpoint="tile")

openflexure_microscope/api/default_extensions/zip_builder.py

@@ -131,8 +131,18 @@ class ZipManager:
             zd.close()
 
 
-# Create a global ZIP manager
+class ZipBuilderExtension(BaseExtension):
-default_zip_manager = ZipManager()
+    def __init__(self):
+        super().__init__(
+            "org.openflexure.zipbuilder",
+            version="2.0.0",
+            description="Build and download capture collections as ZIP files",
+        )
+        self.manager = ZipManager()
+
+        self.add_view(ZipGetterAPIView, "/get/<string:session_id>", endpoint="get_id")
+        self.add_view(ZipListAPIView, "/get", endpoint="get")
+        self.add_view(ZipBuilderAPIView, "/build", endpoint="build")
 
 
 class ZipBuilderAPIView(ActionView):
@@ -142,7 +152,7 @@ class ZipBuilderAPIView(ActionView):
         microscope = find_component("org.openflexure.microscope")
 
         # Return a handle on the autofocus task
-        return default_zip_manager.marshaled_build_zip_from_capture_ids(
+        return self.extension.manager.marshaled_build_zip_from_capture_ids(
             microscope, args
         )
 
@@ -151,7 +161,7 @@ class ZipListAPIView(PropertyView):
     schema = ZipObjectSchema(many=True)
 
     def get(self):
-        return default_zip_manager.session_zips.values()
+        return self.extension.manager.session_zips.values()
 
 
 class ZipGetterAPIView(View):
@@ -163,13 +173,13 @@ class ZipGetterAPIView(View):
         """
         Download a particular capture collection ZIP file
         """
-        if not session_id in default_zip_manager.session_zips:
+        if not session_id in self.extension.manager.session_zips:
             return abort(404)  # 404 Not Found
 
         logging.info("Session ID: %s", session_id)
 
         return send_file(
-            default_zip_manager.zip_fp_from_id(session_id).name,
+            self.extension.manager.zip_fp_from_id(session_id).name,
             mimetype="application/zip",
             as_attachment=True,
             attachment_filename=f"{session_id}.zip",
@@ -179,26 +189,12 @@ class ZipGetterAPIView(View):
         """
         Close and delete a particular capture collection ZIP file
         """
-        if not session_id in default_zip_manager.session_zips:
+        if not session_id in self.extension.manager.session_zips:
             return abort(404)  # 404 Not Found
 
         # Close the file
-        default_zip_manager.session_zips[session_id].close()
+        self.extension.manager.session_zips[session_id].close()
         # Delete the file reference
-        del default_zip_manager.session_zips[session_id]
+        del self.extension.manager.session_zips[session_id]
 
         return {"return": session_id}
-
-
-zip_extension_v2 = BaseExtension(
-    "org.openflexure.zipbuilder",
-    version="2.0.0",
-    description="Build and download capture collections as ZIP files",
-)
-
-zip_extension_v2.add_view(
-    ZipGetterAPIView, "/get/<string:session_id>", endpoint="get_id"
-)
-zip_extension_v2.add_view(ZipListAPIView, "/get", endpoint="get")
-
-zip_extension_v2.add_view(ZipBuilderAPIView, "/build", endpoint="build")

openflexure_microscope/api/dev_extensions/__init__.py

@@ -1 +1,3 @@
 from .tools import devtools_extension_v2
+
+LABTHINGS_EXTENSIONS = [devtools_extension_v2]