Renamed spa_params to processing_params, to store default processing parameters in

Author: tieneupin

src/murfey/cli/inject_spa_processing.py

@@ -21,7 +21,7 @@
     SPAFeedbackParameters,
     SPARelionParameters,
 )
-from murfey.util.spa_params import default_spa_parameters
+from murfey.util.processing_params import default_spa_parameters
 
 
 def run():

src/murfey/server/__init__.py

@@ -56,7 +56,7 @@
     get_microscope,
     get_security_config,
 )
-from murfey.util.spa_params import default_spa_parameters
+from murfey.util.processing_params import default_spa_parameters
 from murfey.util.state import global_state
 
 try:

src/murfey/server/api/__init__.py

@@ -105,7 +105,7 @@
     TiltSeriesInfo,
     Visit,
 )
-from murfey.util.spa_params import default_spa_parameters
+from murfey.util.processing_params import default_spa_parameters
 from murfey.util.state import global_state
 
 log = logging.getLogger("murfey.server.api")

src/murfey/server/demo_api.py

@@ -90,7 +90,7 @@
     TiltSeriesInfo,
     Visit,
 )
-from murfey.util.spa_params import default_spa_parameters
+from murfey.util.processing_params import default_spa_parameters
 from murfey.util.state import global_state
 
 log = logging.getLogger("murfey.server.demo_api")

src/murfey/util/spa_params.py src/murfey/util/processing_params.pysrc/murfey/util/spa_params.py renamed to src/murfey/util/processing_params.py

@@ -1,6 +1,18 @@
+from typing import Literal, Optional
+
 from pydantic import BaseModel
 
 
+class CLEMAlignAndMergeParameters(BaseModel):
+    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()
+
+
 class SPAParameters(BaseModel):
     nr_iter_2d: int = 25
     nr_iter_3d: int = 25