Update subpackage name references

control/adafruithat/planktoscope/imager/__init__.py

@@ -1 +1 @@
-"""imagernew provides high-level functionality for performing image acquisition."""
+"""imager provides high-level functionality for performing image acquisition."""

control/adafruithat/planktoscope/imager/mqtt.py

@@ -12,7 +12,7 @@
 
 from planktoscope import identity, integrity, mqtt
 from planktoscope.camera import mqtt as camera
-from planktoscope.imagernew import stopflow
+from planktoscope.imager import stopflow
 
 loguru.logger.info("planktoscope.imager is loaded")
 
@@ -62,7 +62,9 @@ def run(self) -> None:
         couldn't be started (e.g. because the camera is missing), it will clean up and then wait
         until the `stop_event` event is set before quitting.
         """
-        loguru.logger.info(f"The imager control thread has been started in process {os.getpid()}")
+        loguru.logger.info(
+            f"The imager control thread has been started in process {os.getpid()}"
+        )
         self._mqtt = mqtt.MQTT_Client(topic="imager/#", name="imager_client")
         self._mqtt.client.publish("status/imager", '{"status":"Starting up"}')
 
@@ -75,10 +77,16 @@ def run(self) -> None:
         self._camera = camera.Worker()
         self._camera.start()
         if self._camera.camera is None:
-            loguru.logger.error("Missing camera - maybe it's disconnected or it never started?")
+            loguru.logger.error(
+                "Missing camera - maybe it's disconnected or it never started?"
+            )
             # TODO(ethanjli): officially add this error status to the MQTT API!
-            self._mqtt.client.publish("status/imager", '{"status": "Error: missing camera"}')
-            loguru.logger.success("Preemptively preparing to shut down since there's no camera...")
+            self._mqtt.client.publish(
+                "status/imager", '{"status": "Error: missing camera"}'
+            )
+            loguru.logger.success(
+                "Preemptively preparing to shut down since there's no camera..."
+            )
             self._cleanup()
             # TODO(ethanjli): currently we just wait and do nothing until we receive the shutdown
             # signal, because if we return early then the hardware controller will either shut down
@@ -95,7 +103,10 @@ def run(self) -> None:
         self._mqtt.client.publish("status/imager", '{"status":"Ready"}')
         try:
             while not self._stop_event_loop.is_set():
-                if self._active_routine is not None and not self._active_routine.is_alive():
+                if (
+                    self._active_routine is not None
+                    and not self._active_routine.is_alive()
+                ):
                     # Garbage-collect any finished image-acquisition routine threads so that we're
                     # ready for the next configuration update command which arrives:
                     self._active_routine.stop()
@@ -163,8 +174,12 @@ def _update_metadata(self, latest_message: dict[str, typing.Any]) -> None:
             return
 
         if "config" not in latest_message:
-            loguru.logger.error(f"Received message is missing field 'config': {latest_message}")
-            self._mqtt.client.publish("status/imager", '{"status":"Configuration message error"}')
+            loguru.logger.error(
+                f"Received message is missing field 'config': {latest_message}"
+            )
+            self._mqtt.client.publish(
+                "status/imager", '{"status":"Configuration message error"}'
+            )
             return
 
         loguru.logger.info("Updating configuration...")
@@ -178,16 +193,22 @@ def _start_acquisition(self, latest_message: dict[str, typing.Any]) -> None:
         assert self._pump is not None
         assert self._camera is not None
 
-        if (acquisition_settings := _parse_acquisition_settings(latest_message)) is None:
+        if (
+            acquisition_settings := _parse_acquisition_settings(latest_message)
+        ) is None:
             self._mqtt.client.publish("status/imager", '{"status":"Error"}')
             return
         if self._camera.camera is None:
             loguru.logger.error("Missing camera - maybe it was closed?")
             # TODO(ethanjli): officially add this error status to the MQTT API!
-            self._mqtt.client.publish("status/imager", '{"status": "Error: missing camera"}')
+            self._mqtt.client.publish(
+                "status/imager", '{"status": "Error: missing camera"}'
+            )
             raise RuntimeError("Camera is not available")
 
-        assert (capture_size := self._camera.camera.stream_config.capture_size) is not None
+        assert (
+            capture_size := self._camera.camera.stream_config.capture_size
+        ) is not None
         camera_settings = self._camera.camera.settings
         assert (image_gain := camera_settings.image_gain) is not None
         machine_name = identity.load_machine_name()
@@ -216,7 +237,9 @@ def _start_acquisition(self, latest_message: dict[str, typing.Any]) -> None:
             return
 
         self._active_routine = ImageAcquisitionRoutine(
-            stopflow.Routine(output_path, acquisition_settings, self._pump, self._camera.camera),
+            stopflow.Routine(
+                output_path, acquisition_settings, self._pump, self._camera.camera
+            ),
             self._mqtt,
         )
         self._active_routine.start()
@@ -250,7 +273,9 @@ def _parse_acquisition_settings(
             total_images=int(latest_message["nb_frame"]),
             stabilization_duration=float(latest_message["sleep"]),
             pump=stopflow.DiscretePumpSettings(
-                direction=stopflow.PumpDirection(latest_message.get("pump_direction", "FORWARD")),
+                direction=stopflow.PumpDirection(
+                    latest_message.get("pump_direction", "FORWARD")
+                ),
                 flowrate=float(latest_message.get("pump_flowrate", 2)),
                 volume=float(latest_message["volume"]),
             ),
@@ -317,7 +342,9 @@ class ImageAcquisitionRoutine(threading.Thread):
     # TODO(ethanjli): instead of taking an arg of type mqtt.MQTT_CLIENT, just take an arg of
     # whatever `mqtt_client.client`'s type is supposed to be. Or maybe we should just initialize
     # our own MQTT client in here?
-    def __init__(self, routine: stopflow.Routine, mqtt_client: mqtt.MQTT_Client) -> None:
+    def __init__(
+        self, routine: stopflow.Routine, mqtt_client: mqtt.MQTT_Client
+    ) -> None:
         """Initialize the thread.
 
         Args:
@@ -335,7 +362,9 @@ def run(self) -> None:
             if (result := self._routine.run_step()) is None:
                 if self._routine.interrupted:
                     loguru.logger.debug("Image-acquisition routine was interrupted!")
-                    self._mqtt_client.publish("status/imager", '{"status":"Interrupted"}')
+                    self._mqtt_client.publish(
+                        "status/imager", '{"status":"Interrupted"}'
+                    )
                     break
                 loguru.logger.debug("Image-acquisition routine ran to completion!")
                 self._mqtt_client.publish("status/imager", '{"status":"Done"}')
@@ -415,7 +444,9 @@ def _receive_messages(self) -> None:
                 continue
 
             if self._mqtt.msg["payload"]["status"] not in {"Done", "Interrupted"}:
-                loguru.logger.debug(f"Ignoring pump status update: {self._mqtt.msg['payload']}")
+                loguru.logger.debug(
+                    f"Ignoring pump status update: {self._mqtt.msg['payload']}"
+                )
                 self._mqtt.read_message()
                 continue
 

control/planktoscopehat/planktoscope/imager/__init__.py

@@ -1 +1 @@
-"""imagernew provides high-level functionality for performing image acquisition."""
+"""imager provides high-level functionality for performing image acquisition."""

control/planktoscopehat/planktoscope/imager/mqtt.py

@@ -12,7 +12,7 @@
 
 from planktoscope import identity, integrity, mqtt
 from planktoscope.camera import mqtt as camera
-from planktoscope.imagernew import stopflow
+from planktoscope.imager import stopflow
 
 loguru.logger.info("planktoscope.imager is loaded")
 
@@ -62,7 +62,9 @@ def run(self) -> None:
         couldn't be started (e.g. because the camera is missing), it will clean up and then wait
         until the `stop_event` event is set before quitting.
         """
-        loguru.logger.info(f"The imager control thread has been started in process {os.getpid()}")
+        loguru.logger.info(
+            f"The imager control thread has been started in process {os.getpid()}"
+        )
         self._mqtt = mqtt.MQTT_Client(topic="imager/#", name="imager_client")
         self._mqtt.client.publish("status/imager", '{"status":"Starting up"}')
 
@@ -75,10 +77,16 @@ def run(self) -> None:
         self._camera = camera.Worker()
         self._camera.start()
         if self._camera.camera is None:
-            loguru.logger.error("Missing camera - maybe it's disconnected or it never started?")
+            loguru.logger.error(
+                "Missing camera - maybe it's disconnected or it never started?"
+            )
             # TODO(ethanjli): officially add this error status to the MQTT API!
-            self._mqtt.client.publish("status/imager", '{"status": "Error: missing camera"}')
-            loguru.logger.success("Preemptively preparing to shut down since there's no camera...")
+            self._mqtt.client.publish(
+                "status/imager", '{"status": "Error: missing camera"}'
+            )
+            loguru.logger.success(
+                "Preemptively preparing to shut down since there's no camera..."
+            )
             self._cleanup()
             # TODO(ethanjli): currently we just wait and do nothing until we receive the shutdown
             # signal, because if we return early then the hardware controller will either shut down
@@ -95,7 +103,10 @@ def run(self) -> None:
         self._mqtt.client.publish("status/imager", '{"status":"Ready"}')
         try:
             while not self._stop_event_loop.is_set():
-                if self._active_routine is not None and not self._active_routine.is_alive():
+                if (
+                    self._active_routine is not None
+                    and not self._active_routine.is_alive()
+                ):
                     # Garbage-collect any finished image-acquisition routine threads so that we're
                     # ready for the next configuration update command which arrives:
                     self._active_routine.stop()
@@ -163,8 +174,12 @@ def _update_metadata(self, latest_message: dict[str, typing.Any]) -> None:
             return
 
         if "config" not in latest_message:
-            loguru.logger.error(f"Received message is missing field 'config': {latest_message}")
-            self._mqtt.client.publish("status/imager", '{"status":"Configuration message error"}')
+            loguru.logger.error(
+                f"Received message is missing field 'config': {latest_message}"
+            )
+            self._mqtt.client.publish(
+                "status/imager", '{"status":"Configuration message error"}'
+            )
             return
 
         loguru.logger.info("Updating configuration...")
@@ -178,16 +193,22 @@ def _start_acquisition(self, latest_message: dict[str, typing.Any]) -> None:
         assert self._pump is not None
         assert self._camera is not None
 
-        if (acquisition_settings := _parse_acquisition_settings(latest_message)) is None:
+        if (
+            acquisition_settings := _parse_acquisition_settings(latest_message)
+        ) is None:
             self._mqtt.client.publish("status/imager", '{"status":"Error"}')
             return
         if self._camera.camera is None:
             loguru.logger.error("Missing camera - maybe it was closed?")
             # TODO(ethanjli): officially add this error status to the MQTT API!
-            self._mqtt.client.publish("status/imager", '{"status": "Error: missing camera"}')
+            self._mqtt.client.publish(
+                "status/imager", '{"status": "Error: missing camera"}'
+            )
             raise RuntimeError("Camera is not available")
 
-        assert (capture_size := self._camera.camera.stream_config.capture_size) is not None
+        assert (
+            capture_size := self._camera.camera.stream_config.capture_size
+        ) is not None
         camera_settings = self._camera.camera.settings
         assert (image_gain := camera_settings.image_gain) is not None
         machine_name = identity.load_machine_name()
@@ -216,7 +237,9 @@ def _start_acquisition(self, latest_message: dict[str, typing.Any]) -> None:
             return
 
         self._active_routine = ImageAcquisitionRoutine(
-            stopflow.Routine(output_path, acquisition_settings, self._pump, self._camera.camera),
+            stopflow.Routine(
+                output_path, acquisition_settings, self._pump, self._camera.camera
+            ),
             self._mqtt,
         )
         self._active_routine.start()
@@ -250,7 +273,9 @@ def _parse_acquisition_settings(
             total_images=int(latest_message["nb_frame"]),
             stabilization_duration=float(latest_message["sleep"]),
             pump=stopflow.DiscretePumpSettings(
-                direction=stopflow.PumpDirection(latest_message.get("pump_direction", "FORWARD")),
+                direction=stopflow.PumpDirection(
+                    latest_message.get("pump_direction", "FORWARD")
+                ),
                 flowrate=float(latest_message.get("pump_flowrate", 2)),
                 volume=float(latest_message["volume"]),
             ),
@@ -317,7 +342,9 @@ class ImageAcquisitionRoutine(threading.Thread):
     # TODO(ethanjli): instead of taking an arg of type mqtt.MQTT_CLIENT, just take an arg of
     # whatever `mqtt_client.client`'s type is supposed to be. Or maybe we should just initialize
     # our own MQTT client in here?
-    def __init__(self, routine: stopflow.Routine, mqtt_client: mqtt.MQTT_Client) -> None:
+    def __init__(
+        self, routine: stopflow.Routine, mqtt_client: mqtt.MQTT_Client
+    ) -> None:
         """Initialize the thread.
 
         Args:
@@ -335,7 +362,9 @@ def run(self) -> None:
             if (result := self._routine.run_step()) is None:
                 if self._routine.interrupted:
                     loguru.logger.debug("Image-acquisition routine was interrupted!")
-                    self._mqtt_client.publish("status/imager", '{"status":"Interrupted"}')
+                    self._mqtt_client.publish(
+                        "status/imager", '{"status":"Interrupted"}'
+                    )
                     break
                 loguru.logger.debug("Image-acquisition routine ran to completion!")
                 self._mqtt_client.publish("status/imager", '{"status":"Done"}')
@@ -415,7 +444,9 @@ def _receive_messages(self) -> None:
                 continue
 
             if self._mqtt.msg["payload"]["status"] not in {"Done", "Interrupted"}:
-                loguru.logger.debug(f"Ignoring pump status update: {self._mqtt.msg['payload']}")
+                loguru.logger.debug(
+                    f"Ignoring pump status update: {self._mqtt.msg['payload']}"
+                )
                 self._mqtt.read_message()
                 continue