Revise 04_LFP nb

CBroz1 · Jul 28, 2023 · 4d71854 · 4d71854
1 parent b134470
commit 4d71854
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Showing 5 changed files with 418 additions and 672 deletions.
diff --git a/franklab_scripts/nightly_cleanup.py b/franklab_scripts/nightly_cleanup.py
@@ -7,15 +7,12 @@
 
 import numpy as np
 
-from spyglass.decoding.clusterless import (
-    MarkParameters,
-    UnitMarkParameters,
-    UnitMarks,
-)
+from spyglass.decoding.clusterless import MarkParameters, UnitMarkParameters, UnitMarks
 
 warnings.simplefilter("ignore", category=DeprecationWarning)
 warnings.simplefilter("ignore", category=ResourceWarning)
-os.environ["SPIKE_SORTING_STORAGE_DIR"] = "/stelmo/nwb/spikesorting"
+# NOTE: "SPIKE_SORTING_STORAGE_DIR" -> "SPYGLASS_SORTING_DIR"
+os.environ["SPYGLASS_SORTING_DIR"] = "/stelmo/nwb/spikesorting"
 
 
 # import tables so that we can call them easily

diff --git a/franklab_scripts/sort.py b/franklab_scripts/sort.py
@@ -11,7 +11,7 @@ def main():
 
     os.environ["SPYGLASS_BASE_DIR"] = str(data_dir)
     os.environ["KACHERY_STORAGE_DIR"] = str(data_dir / "kachery-storage")
-    os.environ["SPIKE_SORTING_STORAGE_DIR"] = str(data_dir / "spikesorting")
+    os.environ["SPYGLASS_SORTING_DIR"] = str(data_dir / "spikesorting")
 
     # session_id = 'jaq_01'
     # nwb_file_name = (sg.common.Session() & {'session_id': session_id}).fetch1('nwb_file_name')

diff --git a/notebooks/03_lfp.ipynb b/notebooks/03_lfp.ipynb
diff --git a/src/spyglass/settings.py b/src/spyglass/settings.py
@@ -17,7 +17,7 @@
         raw="raw",
         analysis="analysis",
         recording="recording",
-        spike_sorting_storage="spikesorting",
+        sorting="spikesorting",  # "SPYGLASS_SORTING_DIR"
         waveforms="waveforms",
         temp="tmp",
     ),

diff --git a/src/spyglass/spikesorting/spikesorting_sorting.py b/src/spyglass/spikesorting/spikesorting_sorting.py
@@ -14,6 +14,7 @@
 
 from ..common.common_lab import LabMember, LabTeam
 from ..common.common_nwbfile import AnalysisNwbfile
+from ..settings import load_config
 from ..utils.dj_helper_fn import fetch_nwb
 from .spikesorting_artifact import ArtifactRemovedIntervalList
 from .spikesorting_recording import (
@@ -134,7 +135,7 @@ def make(self, key: dict):
            (this is redundant with 2; will change in the future)
 
         """
-
+        # CBroz: does this not work w/o arg? as .populate() ?
         recording_path = (SpikeSortingRecording & key).fetch1("recording_path")
         recording = si.load_extractor(recording_path)
 
@@ -227,7 +228,9 @@ def make(self, key: dict):
         key["time_of_sort"] = int(time.time())
 
         print("Saving sorting results...")
-        sorting_folder = Path(os.getenv("SPYGLASS_SORTING_DIR"))
+
+        sorting_folder = Path(load_config().get("SPYGLASS_SORTING_DIR"))
+
         sorting_name = self._get_sorting_name(key)
         key["sorting_path"] = str(sorting_folder / Path(sorting_name))
         if os.path.exists(key["sorting_path"]):