Moved default processing parameters for align-and-merge CLEM workflow to 'processing_params'

Author: tieneupin

src/murfey/workflows/clem/register_preprocessing_results.py

@@ -12,7 +12,6 @@
 import traceback
 from ast import literal_eval
 from pathlib import Path
-from typing import Literal, Optional
 
 from pydantic import BaseModel, validator
 from sqlmodel import Session, select
@@ -26,19 +25,15 @@
     CLEMTIFFFile,
 )
 from murfey.util.db import Session as MurfeySession
+from murfey.util.processing_params import (
+    default_clem_align_and_merge_parameters as processing_params,
+)
 from murfey.workflows.clem import get_db_entry
 from murfey.workflows.clem.align_and_merge import submit_cluster_request
 
 logger = logging.getLogger("murfey.workflows.clem.register_preprocessing_results")
 
 
-# Define align and merge parameters here
-crop_to_n_frames: Optional[int] = 50
-align_self: Literal["enabled", ""] = "enabled"
-flatten: Literal["mean", "min", "max", ""] = "mean"
-align_across: Literal["enabled", ""] = "enabled"
-
-
 class LIFPreprocessingResult(BaseModel):
     image_stack: Path
     metadata: Path
@@ -195,10 +190,10 @@ def register_lif_preprocessing_result(
             series_name=result.series_name,
             images=image_stacks,
             metadata=result.metadata,
-            crop_to_n_frames=crop_to_n_frames,
-            align_self=align_self,
-            flatten=flatten,
-            align_across=align_across,
+            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,
         )
         if cluster_response is False:
@@ -378,10 +373,10 @@ def register_tiff_preprocessing_result(
             series_name=result.series_name,
             images=image_stacks,
             metadata=result.metadata,
-            crop_to_n_frames=crop_to_n_frames,
-            align_self=align_self,
-            flatten=flatten,
-            align_across=align_across,
+            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,
         )
         if cluster_response is False: