Simplify FIB milling GIF creation workflow (#904)

* Let 'feedback_callback' handle database closure and any raised exceptions

Author: tieneupin

src/murfey/workflows/fib/make_milling_gif.py

@@ -15,72 +15,60 @@
 
 
 def run(message: dict[str, Any], murfey_db: SQLModelSession):
-    # Outer try-finally block to close Murfey DB with
-    try:
-        try:
-            # Parse and unpack incoming message
-            session_id = int(message["session_id"])
-            gif_params = FIBGIFParameters(**message["gif_params"])
-        except Exception:
-            logger.error("Error parsing contents of message", exc_info=True)
-            return {"success": False, "requeue": False}
+    # Parse and unpack incoming message
+    session_id = int(message["session_id"])
+    gif_params = FIBGIFParameters(**message["gif_params"])
 
-        # Load machine config and session info
-        session_entry = murfey_db.exec(
-            select(MurfeyDB.Session).where(MurfeyDB.Session.id == session_id)
-        ).one()
-        instrument_name = session_entry.instrument_name
-        visit_name = session_entry.visit
-        machine_config = get_machine_config(instrument_name=instrument_name)[
-            instrument_name
-        ]
-        rsync_basepath = machine_config.rsync_basepath or Path(".").resolve()
+    # Load machine config and session info
+    session_entry = murfey_db.exec(
+        select(MurfeyDB.Session).where(MurfeyDB.Session.id == session_id)
+    ).one()
+    instrument_name = session_entry.instrument_name
+    visit_name = session_entry.visit
+    machine_config = get_machine_config(instrument_name=instrument_name)[
+        instrument_name
+    ]
+    rsync_basepath = machine_config.rsync_basepath or Path(".").resolve()
 
-        # Sanitise and verify that the output directory is relative to rsync basepath
-        output_file = sanitise_path(gif_params.output_file)
-        if not output_file.is_relative_to(rsync_basepath):
-            raise ValueError("Output file path is not permitted")
+    # Sanitise and verify that the output directory is relative to rsync basepath
+    output_file = sanitise_path(gif_params.output_file)
+    if not output_file.is_relative_to(rsync_basepath):
+        raise ValueError("Output file path is not permitted")
 
-        # Create folders in the visit directory and onwards and change permissions
-        visit_index = output_file.parts.index(visit_name)
-        for current_path in list(reversed(output_file.parents))[visit_index + 1 :]:
-            if not current_path.exists():
-                current_path.mkdir(parents=True)
-                logger.debug(f"Created output directory {current_path}")
-                safe_chmod(current_path, mode=machine_config.mkdir_chmod)
+    # Create folders in the visit directory and onwards and change permissions
+    visit_index = output_file.parts.index(visit_name)
+    for current_path in list(reversed(output_file.parents))[visit_index + 1 :]:
+        if not current_path.exists():
+            current_path.mkdir(parents=True)
+            logger.debug(f"Created output directory {current_path}")
+            safe_chmod(current_path, mode=machine_config.mkdir_chmod)
 
-        # Load the images as PIL Image objects
-        converted: list[PIL.Image.Image] = []
-        for f in gif_params.images:
-            with PIL.Image.open(f) as im:
-                im.thumbnail((512, 512))
-                frame = np.array(im, dtype=np.float32)
-            # Normalise to 8-bit
-            vmin, vmax = np.percentile(frame, (0.5, 99.5))
-            scale = 255 / ((vmax - vmin) or 1)
-            np.clip(frame, a_min=vmin, a_max=vmax, out=frame)
-            np.subtract(frame, vmin, out=frame)
-            np.multiply(frame, scale, out=frame)
-            # Convert back to PIL Image
-            converted.append(
-                PIL.Image.fromarray(frame.astype(np.uint8), mode="L").copy()
-            )
-            del frame  # Explicitly remove frame from memory
-        # Save stack as a GIF
-        if not converted:
-            raise ValueError("No images were provided or loaded")
-        converted[0].save(
-            output_file,
-            format="GIF",
-            append_images=converted[1:],
-            save_all=True,
-            duration=30,
-            loop=0,
-        )
-        logger.info(f"Created GIF file {output_file}")
-        return {"success": True}
-    except Exception:
-        logger.error("Error creating FIB milling GIF", exc_info=True)
-        return {"success": False, "requeue": False}
-    finally:
-        murfey_db.close()
+    # Load the images as PIL Image objects
+    converted: list[PIL.Image.Image] = []
+    for f in gif_params.images:
+        with PIL.Image.open(f) as im:
+            im.thumbnail((512, 512))
+            frame = np.array(im, dtype=np.float32)
+        # Normalise to 8-bit
+        vmin, vmax = np.percentile(frame, (0.5, 99.5))
+        scale = 255 / ((vmax - vmin) or 1)
+        np.clip(frame, a_min=vmin, a_max=vmax, out=frame)
+        np.subtract(frame, vmin, out=frame)
+        np.multiply(frame, scale, out=frame)
+        # Convert back to PIL Image
+        converted.append(PIL.Image.fromarray(frame.astype(np.uint8), mode="L").copy())
+        del frame  # Explicitly remove frame from memory
+
+    # Save stack as a GIF
+    if not converted:
+        raise ValueError("No images were provided or loaded")
+    converted[0].save(
+        output_file,
+        format="GIF",
+        append_images=converted[1:],
+        save_all=True,
+        duration=30,
+        loop=0,
+    )
+    logger.info(f"Created GIF file {output_file}")
+    return {"success": True}