Do not pass align-and-merge processing parameters via Murfey; set them directly in the recipe

Author: tieneupin

src/murfey/util/processing_params.py

@@ -1,7 +1,6 @@
 from datetime import datetime
 from functools import lru_cache
 from pathlib import Path
-from typing import Literal, Optional
 
 from pydantic import BaseModel
 from werkzeug.utils import secure_filename
@@ -60,12 +59,6 @@ class CLEMProcessingParameters(BaseModel):
     # Atlas vs GridSquare registration threshold
     atlas_threshold: float = 0.0015  # in m
 
-    # Image alignment and merging-specific parameters
-    crop_to_n_frames: Optional[int] = 50
-    align_self: Literal["enabled", ""] = "enabled"
-    flatten: Literal["mean", "min", "max", ""] = "mean"
-    align_across: Literal["enabled", ""] = "enabled"
-
 
 default_clem_processing_parameters = CLEMProcessingParameters()
 

src/murfey/workflows/clem/align_and_merge.py

@@ -6,7 +6,7 @@
 from __future__ import annotations
 
 from pathlib import Path
-from typing import Literal, Optional
+from typing import Optional
 
 from murfey.util.config import get_machine_config
 
@@ -24,11 +24,6 @@ def run(
     series_name: str,
     images: list[Path],
     metadata: Path,
-    # Optional processing parameters
-    crop_to_n_frames: Optional[int] = None,
-    align_self: Literal["enabled", ""] = "",
-    flatten: Literal["mean", "min", "max", ""] = "mean",
-    align_across: Literal["enabled", ""] = "",
     # Optional session parameters
     messenger: Optional[TransportManager] = None,
 ):
@@ -65,10 +60,6 @@ def run(
                 "series_name": series_name,
                 "images": [str(file) for file in images],
                 "metadata": str(metadata),
-                "crop_to_n_frames": crop_to_n_frames,
-                "align_self": align_self,
-                "flatten": flatten,
-                "align_across": align_across,
                 # Other recipe parameters
                 "session_dir": str(session_dir),
                 "session_id": session_id,

src/murfey/workflows/clem/register_preprocessing_results.py

@@ -658,10 +658,6 @@ def run(message: dict, murfey_db: Session) -> dict[str, bool]:
                     series_name=result.series_name,
                     images=image_combo,
                     metadata=result.metadata,
-                    crop_to_n_frames=processing_params.crop_to_n_frames,
-                    align_self=processing_params.align_self,
-                    flatten=processing_params.flatten,
-                    align_across=processing_params.align_across,
                     messenger=_transport_object,
                 )
             except Exception: