Renamed 'CLEMAlignaAndMergeParameters' to 'CLEMProcessingParameters', and added the threshold at which a dataset is considered an Atlas database entry to it

Author: tieneupin

src/murfey/util/processing_params.py

@@ -54,14 +54,18 @@ def cryolo_model_path(visit: str, instrument_name: str) -> Path:
     return machine_config.default_model
 
 
-class CLEMAlignAndMergeParameters(BaseModel):
+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_align_and_merge_parameters = CLEMAlignAndMergeParameters()
+default_clem_processing_parameters = CLEMProcessingParameters()
 
 
 class SPAParameters(BaseModel):

src/murfey/workflows/clem/register_preprocessing_results.py

@@ -22,7 +22,7 @@
 from murfey.server import _transport_object
 from murfey.util.models import GridSquareParameters
 from murfey.util.processing_params import (
-    default_clem_align_and_merge_parameters as processing_params,
+    default_clem_processing_parameters as processing_params,
 )
 from murfey.workflows.clem import get_db_entry
 from murfey.workflows.clem.align_and_merge import submit_cluster_request
@@ -55,7 +55,7 @@ def _is_clem_atlas(result: CLEMPreprocessingResult):
     # If an image has a width/height of at least 1.5 mm, it should qualify as an atlas
     return (
         max(result.pixels_x * result.pixel_size, result.pixels_y * result.pixel_size)
-        >= 0.0015  # In metres
+        >= processing_params.atlas_threshold
     )