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SpikeInterface · Mar 18, 2024 · 2f3ad49 · 2f3ad49
1 parent 354b063
commit 2f3ad49
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Showing 2 changed files with 16 additions and 16 deletions.
diff --git a/src/spikeinterface_pipelines/pipeline.py b/src/spikeinterface_pipelines/pipeline.py
@@ -54,8 +54,7 @@ def run_pipeline(
         preprocessing_params = PreprocessingParams(**preprocessing_params)
     if isinstance(spikesorting_params, dict):
         spikesorting_params = SpikeSortingParams(
-            sorter_name=spikesorting_params['sorter_name'],
-            sorter_kwargs=spikesorting_params['sorter_kwargs']
+            sorter_name=spikesorting_params["sorter_name"], sorter_kwargs=spikesorting_params["sorter_kwargs"]
         )
     if isinstance(postprocessing_params, dict):
         postprocessing_params = PostprocessingParams(**postprocessing_params)

diff --git a/src/spikeinterface_pipelines/spikesorting/params.py b/src/spikeinterface_pipelines/spikesorting/params.py
@@ -11,7 +11,7 @@ class SorterName(str, Enum):
 
 
 class Kilosort25Model(BaseModel):
-    model_config = ConfigDict(extra='forbid')
+    model_config = ConfigDict(extra="forbid")
     detect_threshold: float = Field(default=6, description="Threshold for spike detection")
     projection_threshold: List[float] = Field(default=[10, 4], description="Threshold on projections")
     preclust_threshold: float = Field(
@@ -53,22 +53,18 @@ class Kilosort25Model(BaseModel):
 
 
 class Kilosort3Model(BaseModel):
-    model_config = ConfigDict(extra='forbid')
+    model_config = ConfigDict(extra="forbid")
     pass
 
 
 class IronClustModel(BaseModel):
-    model_config = ConfigDict(extra='forbid')
+    model_config = ConfigDict(extra="forbid")
     pass
 
 
 class MountainSort5Model(BaseModel):
-    model_config = ConfigDict(extra='forbid')
-    scheme: str = Field(
-        default='2',
-        description="Sorting scheme",
-        json_schema_extra={'options': ["1", "2", "3"]}
-    )
+    model_config = ConfigDict(extra="forbid")
+    scheme: str = Field(default="2", description="Sorting scheme", json_schema_extra={"options": ["1", "2", "3"]})
     detect_threshold: float = Field(default=5.5, description="Threshold for spike detection")
     detect_sign: int = Field(default=-1, description="Sign of the peak")
     detect_time_radius_msec: float = Field(default=0.5, description="Time radius in milliseconds")
@@ -80,9 +76,13 @@ class MountainSort5Model(BaseModel):
     scheme1_detect_channel_radius: int = Field(default=150, description="Scheme 1 detect channel radius")
     scheme2_phase1_detect_channel_radius: int = Field(default=200, description="Scheme 2 phase 1 detect channel radius")
     scheme2_detect_channel_radius: int = Field(default=50, description="Scheme 2 detect channel radius")
-    scheme2_max_num_snippets_per_training_batch: int = Field(default=200, description="Scheme 2 max number of snippets per training batch")
+    scheme2_max_num_snippets_per_training_batch: int = Field(
+        default=200, description="Scheme 2 max number of snippets per training batch"
+    )
     scheme2_training_duration_sec: int = Field(default=300, description="Scheme 2 training duration in seconds")
-    scheme2_training_recording_sampling_mode: str = Field(default='uniform', description="Scheme 2 training recording sampling mode")
+    scheme2_training_recording_sampling_mode: str = Field(
+        default="uniform", description="Scheme 2 training recording sampling mode"
+    )
     scheme3_block_duration_sec: int = Field(default=1800, description="Scheme 3 block duration in seconds")
     freq_min: int = Field(default=300, description="High-pass filter cutoff frequency")
     freq_max: int = Field(default=6000, description="Low-pass filter cutoff frequency")
@@ -93,7 +93,8 @@ class MountainSort5Model(BaseModel):
 class SpikeSortingParams(BaseModel):
     sorter_name: SorterName = Field(description="Name of the sorter to use.")
     sorter_kwargs: Union[Kilosort25Model, Kilosort3Model, IronClustModel, MountainSort5Model] = Field(
-        description="Sorter specific kwargs.",
-        union_mode='left_to_right'
+        description="Sorter specific kwargs.", union_mode="left_to_right"
+    )
+    spikesort_by_group: bool = Field(
+        default=False, description="If True, spike sorting is run for each group separately."
     )
-    spikesort_by_group: bool = Field(default=False, description="If True, spike sorting is run for each group separately.")