segmenter: Fix nb_frame count for interrupted acquisition

controller/imager/main.py

@@ -228,6 +228,7 @@ def _start_acquisition(self, latest_message: dict[str, typing.Any]) -> None:
         self._active_routine = ImageAcquisitionRoutine(
             stopflow.Routine(output_path, acquisition_settings, self._pump, self._camera.camera),
             self._mqtt,
+            metadata,
         )
         self._active_routine.start()
 
@@ -276,8 +277,9 @@ def _initialize_acquisition_directory(
 ) -> typing.Optional[str]:
     """Make the directory where images will be saved for the current image-acquisition routine.
 
-    This also saves the metadata to a `metadata.json` file and initializes a file integrity log in
-    the directory.
+    This also initializes a file integrity log in the directory. The metadata is not written
+    here — it is finalized at the end of acquisition so that `nb_frame` reflects the actual
+    number of frames captured (which may be less than planned if the run is interrupted).
 
     Args:
         base_path: directory under which a subdirectory tree will be created for the image
@@ -311,13 +313,7 @@ def _initialize_acquisition_directory(
         raise ValueError("Chosen id are already in use!")
 
     os.makedirs(acq_dir_path)
-    loguru.logger.info("Saving metadata...")
-    metadata_filepath = os.path.join(acq_dir_path, "metadata.json")
-    with open(metadata_filepath, "w", encoding="utf-8") as metadata_file:
-        json.dump(metadata, metadata_file, indent=4)
-        loguru.logger.debug(f"Saved metadata to {metadata_file}: {metadata}")
     integrity.create_integrity_file(acq_dir_path)
-    integrity.append_to_integrity_file(metadata_filepath)
     return acq_dir_path
 
 
@@ -327,35 +323,41 @@ 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,
+        metadata: dict[str, typing.Any],
+    ) -> None:
         """Initialize the thread.
 
         Args:
             routine: the image-acquisition routine to run.
             mqtt_client: an MQTT client which will be used to broadcast updates.
+            metadata: the acquisition metadata to write to `metadata.json` once the routine
+              finishes. `nb_frame` is overwritten with the actual number of frames captured.
         """
         super().__init__()
         self._routine = routine
         self._mqtt_client = mqtt_client.client
+        self._metadata = metadata
 
     def run(self) -> None:
         """Run a stop-flow image-acquisition routine until completion or interruption."""
         self._mqtt_client.publish("status/imager", '{"status":"Started"}')
+        final_status: str = ""
         while True:
             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"}')
+                    final_status = '{"status":"Interrupted"}'
                     break
                 loguru.logger.debug("Image-acquisition routine ran to completion!")
-                self._mqtt_client.publish(
-                    "status/imager",
-                    json.dumps(
-                        {
-                            "status": "Done",
-                            "path": self._routine.output_path,
-                        }
-                    ),
+                final_status = json.dumps(
+                    {
+                        "status": "Done",
+                        "path": self._routine.output_path,
+                    }
                 )
                 break
 
@@ -364,10 +366,9 @@ def run(self) -> None:
             try:
                 integrity.append_to_integrity_file(path)
             except FileNotFoundError:
-                self._mqtt_client.publish(
-                    "status/imager",
+                final_status = (
                     f'{{"status":"Image {index + 1}/{self._routine.settings.total_images} '
-                    + 'WAS NOT CAPTURED! STOPPING THE PROCESS!"}}',
+                    + 'WAS NOT CAPTURED! STOPPING THE PROCESS!"}}'
                 )
                 break
 
@@ -389,6 +390,21 @@ def run(self) -> None:
                 ),
             )
 
+        # Finalize metadata.json with the actual frame count before announcing the final
+        # status, so that downstream consumers (e.g. the segmenter) cannot observe the
+        # acquisition as finished without a metadata file on disk.
+        self._metadata["nb_frame"] = self._routine.progress
+        metadata_filepath = os.path.join(self._routine.output_path, "metadata.json")
+        with open(metadata_filepath, "w", encoding="utf-8") as metadata_file:
+            json.dump(self._metadata, metadata_file, indent=4)
+        integrity.append_to_integrity_file(metadata_filepath)
+        loguru.logger.debug(
+            f"Saved metadata to {metadata_filepath} with nb_frame={self._routine.progress}"
+        )
+
+        if final_status:
+            self._mqtt_client.publish("status/imager", final_status)
+
     def pause(self) -> None:
         """Pause the acquisition between steps."""
         self._routine.pause()

controller/imager/stopflow.py

@@ -177,3 +177,9 @@ def paused(self) -> bool:
     def interrupted(self) -> bool:
         """Check whether the routine was manually interrupted."""
         return self._interrupted.is_set()
+
+    @property
+    def progress(self) -> int:
+        """The number of images actually captured so far."""
+        with self._progress_lock:
+            return self._progress