Update FIBContext and backend logic for detecting, handling and making GIFs of drift correction images

src/murfey/server/api/workflow.py

@@ -5,7 +5,6 @@
 from pathlib import Path
 from typing import Any, Dict, List, Optional
 
-import numpy as np
 import sqlalchemy
 from fastapi import APIRouter, Depends
 from ispyb.sqlalchemy import (
@@ -21,11 +20,6 @@
 from sqlmodel import col, select
 from werkzeug.utils import secure_filename
 
-try:
-    from PIL import Image
-except ImportError:
-    Image = None
-
 try:
     from smartem_backend.api_client import SmartEMAPIClient
     from smartem_common.schemas import (
@@ -1194,71 +1188,3 @@ def register_sample_image(
     if _transport_object:
         return _transport_object.do_insert_sample_image(record)
     return {"success": False}
-
-
-class MillingParameters(BaseModel):
-    lamella_number: int
-    images: List[str]
-    raw_directory: str
-
-
-@correlative_router.post(
-    "/year/{year}/visits/{visit_name}/sessions/{session_id}/make_milling_gif"
-)
-async def make_gif(
-    year: int,
-    visit_name: str,
-    session_id: int,
-    gif_params: MillingParameters,
-    db=murfey_db,
-):
-    instrument_name = (
-        db.exec(select(Session).where(Session.id == session_id)).one().instrument_name
-    )
-    machine_config = get_machine_config(instrument_name=instrument_name)[
-        instrument_name
-    ]
-    output_dir = (
-        (machine_config.rsync_basepath or Path("")).resolve()
-        / secure_filename(str(year))
-        / secure_filename(visit_name)
-        / "processed"
-    )
-    output_dir.mkdir(exist_ok=True)
-    os.chmod(output_dir, mode=machine_config.mkdir_chmod)
-    output_dir = output_dir / secure_filename(gif_params.raw_directory)
-    output_dir.mkdir(exist_ok=True)
-    os.chmod(output_dir, mode=machine_config.mkdir_chmod)
-    output_path = output_dir / f"lamella_{gif_params.lamella_number}_milling.gif"
-
-    if Image is not None:
-        images = [Image.open(f) for f in gif_params.images]
-    else:
-        images = []
-    for im in images:
-        im.thumbnail((512, 512))
-
-    # Normalize and convert individual frames to 8-bit
-    arr: list[np.ndarray] = []
-    for im in images:
-        frame = np.array(im).astype(np.float32)
-        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)
-        arr.append(frame.astype(np.uint8))
-    arr = np.array(arr).astype(np.uint8)
-
-    # Convert back to Image objects and save as GIF
-    converted = [Image.fromarray(arr[f], mode="L") for f in range(len(images))]
-    converted[0].save(
-        output_path,
-        format="GIF",
-        append_images=converted[1:],
-        save_all=True,
-        duration=30,
-        loop=0,
-    )
-
-    return {"output_gif": str(output_path)}

src/murfey/server/api/workflow_fib.py

@@ -1,14 +1,20 @@
 import json
 import logging
+import os
 from importlib.metadata import entry_points
 from pathlib import Path
 
+import numpy as np
+import PIL.Image
 from fastapi import APIRouter, Depends
 from pydantic import BaseModel
-from sqlmodel import Session
+from sqlmodel import Session, select
 
+import murfey.util.db as MurfeyDB
 from murfey.server.api.auth import validate_instrument_token
 from murfey.server.murfey_db import murfey_db
+from murfey.util import sanitise_path
+from murfey.util.config import get_machine_config
 from murfey.util.models import LamellaSiteInfo
 
 logger = logging.getLogger("murfey.server.api.workflow_fib")
@@ -57,3 +63,77 @@ def register_fib_milling_progress(
         "Received the following FIB metadata for registration:\n"
         f"{json.dumps(site_info.model_dump(exclude_none=True), indent=2, default=str)}"
     )
+
+
+class FIBGIFParameters(BaseModel):
+    lamella_number: int
+    images: list[Path]
+    output_file: Path
+
+
+@router.post("/sessions/{session_id}/make_gif")
+async def make_gif(
+    session_id: int,
+    gif_params: FIBGIFParameters,
+    db=murfey_db,
+):
+    # Load machine config and session info
+    session_entry = 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):
+        logger.error("Output file path is not permitted")
+        raise ValueError
+
+    # 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}")
+            try:
+                os.chmod(current_path, mode=machine_config.mkdir_chmod)
+            except PermissionError:
+                logger.warning(
+                    f"Insufficient permissions to modify directory {current_path}"
+                )
+                continue
+
+    # Load the images as PIL Image objects
+    images = [PIL.Image.open(f) for f in gif_params.images]
+    for im in images:
+        im.thumbnail((512, 512))
+
+    # Normalize and convert individual frames to 8-bit
+    arr: list[np.ndarray] = []
+    for im in images:
+        frame = np.array(im).astype(np.float32)
+        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)
+        arr.append(frame.astype(np.uint8))
+    arr = np.array(arr).astype(np.uint8)
+
+    # Convert back to PIL.Image objects and save as GIF
+    converted = [PIL.Image.fromarray(arr[f], mode="L") for f in range(len(images))]
+    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 {"output_gif": str(output_file)}

src/murfey/util/models.py

@@ -128,20 +128,22 @@ class StagePositionInfo(BaseModel):
     "ChunkCoincidenceStagePosition" currently correspond to.
     """
 
+    # Top-level values
     preparation: StagePositionValues | None = (
         None  # PreparationSiteLocation/StagePosition/StagePosition
     )
-    chunk_coincidence: StagePositionValues | None = (
-        None  # Parameters/ChunkCoincidenceStagePosition/StagePosition
-    )
     chunk: StagePositionValues | None = (
         None  # ChunkSiteLocation/StagePosition/StagePosition
     )
     thinning_1: StagePositionValues | None = (
-        None  # Parameters/ThinningStagePosition/StagePosition
+        None  # ThinningSiteLocation/StagePosition/StagePosition
+    )
+    # Stored under Parameters
+    chunk_coincidence: StagePositionValues | None = (
+        None  # Parameters/ChunkCoincidenceStagePosition/StagePosition
     )
     thinning_2: StagePositionValues | None = (
-        None  # ThinningSiteLocation/StagePosition/StagePosition
+        None  # Parameters/ThinningStagePosition/StagePosition
     )
 
 

src/murfey/util/route_manifest.yaml

@@ -1270,17 +1270,6 @@ murfey.server.api.workflow.correlative_router:
         type: str
     methods:
       - POST
-  - path: /workflow/correlative/year/{year}/visits/{visit_name}/sessions/{session_id}/make_milling_gif
-    function: make_gif
-    path_params:
-      - name: year
-        type: int
-      - name: visit_name
-        type: str
-      - name: session_id
-        type: int
-    methods:
-      - POST
 murfey.server.api.workflow.router:
   - path: /workflow/visits/{visit_name}/sessions/{session_id}/register_data_collection_group
     function: register_dc_group
@@ -1447,3 +1436,10 @@ murfey.server.api.workflow_fib.router:
         type: int
     methods:
       - POST
+  - path: /workflow/fib/sessions/{session_id}/make_gif
+    function: make_gif
+    path_params:
+      - name: session_id
+        type: int
+    methods:
+      - POST