Merge pull request #121 from ttngu207/main

parameterize run_CatGT step from parameters retrieved from `ClusteringParamSet` table

Author: CBroz1

CHANGELOG.md

@@ -5,6 +5,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 
 ## [0.2.1] - Unreleased
 
++ Update - parameterize run_CatGT step from parameters retrieved from `ClusteringParamSet` table
 + Update - clustering step, update duration for "median_subtraction" step
 + Bugfix - handles single probe recording in "Neuropix-PXI" format
 + Update - safeguard in creating/inserting probe types upon probe activation

element_array_ephys/ephys_acute.py

@@ -841,6 +841,10 @@ def make(self, key):
                         spikeglx_meta_filepath.parent
                     )
                     spikeglx_recording.validate_file("ap")
+                    run_CatGT = (
+                        params.pop("run_CatGT", True)
+                        and "_tcat." not in spikeglx_meta_filepath.stem
+                    )
 
                     if clustering_method.startswith("pykilosort"):
                         kilosort_triggering.run_pykilosort(
@@ -861,7 +865,7 @@ def make(self, key):
                             ks_output_dir=kilosort_dir,
                             params=params,
                             KS2ver=f'{Decimal(clustering_method.replace("kilosort", "")):.1f}',
-                            run_CatGT=True,
+                            run_CatGT=run_CatGT,
                         )
                         run_kilosort.run_modules()
                 elif acq_software == "Open Ephys":

element_array_ephys/ephys_chronic.py

@@ -773,6 +773,10 @@ def make(self, key):
                         spikeglx_meta_filepath.parent
                     )
                     spikeglx_recording.validate_file("ap")
+                    run_CatGT = (
+                        params.pop("run_CatGT", True)
+                        and "_tcat." not in spikeglx_meta_filepath.stem
+                    )
 
                     if clustering_method.startswith("pykilosort"):
                         kilosort_triggering.run_pykilosort(
@@ -793,7 +797,7 @@ def make(self, key):
                             ks_output_dir=kilosort_dir,
                             params=params,
                             KS2ver=f'{Decimal(clustering_method.replace("kilosort", "")):.1f}',
-                            run_CatGT=True,
+                            run_CatGT=run_CatGT,
                         )
                         run_kilosort.run_modules()
                 elif acq_software == "Open Ephys":

element_array_ephys/ephys_no_curation.py

@@ -847,6 +847,10 @@ def make(self, key):
                         spikeglx_meta_filepath.parent
                     )
                     spikeglx_recording.validate_file("ap")
+                    run_CatGT = (
+                        params.pop("run_CatGT", True)
+                        and "_tcat." not in spikeglx_meta_filepath.stem
+                    )
 
                     if clustering_method.startswith("pykilosort"):
                         kilosort_triggering.run_pykilosort(
@@ -867,7 +871,7 @@ def make(self, key):
                             ks_output_dir=kilosort_dir,
                             params=params,
                             KS2ver=f'{Decimal(clustering_method.replace("kilosort", "")):.1f}',
-                            run_CatGT=True,
+                            run_CatGT=run_CatGT,
                         )
                         run_kilosort.run_modules()
                 elif acq_software == "Open Ephys":

element_array_ephys/readers/spikeglx.py

@@ -165,8 +165,12 @@ def validate_file(self, file_type="ap"):
         file_path = self.root_dir / (self.root_name + f".{file_type}.bin")
         file_size = file_path.stat().st_size
 
-        meta_mapping = {"ap": self.apmeta, "lf": self.lfmeta}
-        meta = meta_mapping[file_type]
+        if file_type == "ap":
+            meta = self.apmeta
+        elif file_type == "lf":
+            meta = self.lfmeta
+        else:
+            raise KeyError(f"Unknown file_type {file_type} - must be 'ap' or 'lf'")
 
         if file_size != meta.meta["fileSizeBytes"]:
             raise IOError(