Minor Issues (#1270)

* error if fetch1_dataframe on multiple

* 1262 fix

* tools to check table disc usage

* set orientation to nan for single led data

* remove humanize dependency

* fix function call

* 1240 fix

* update test expected value for null orientation in single led

* 1211 fix

* 1042_fix

* log python env in analysis files

* update changelog

* fix spelling

* Fix f-string

Co-authored-by: Copilot <[email protected]>

* apply suggestions from review

* Revert accidental inclusion of interval list change

* remove on as confirmation option

* cleanup size check function

* update fetch1_dataframe error

* linting

* Apply suggestions from code review

Co-authored-by: Copilot <[email protected]>

* more fetch1_dataframe error message updates

* move human readable to util

* fix docstring

---------

Co-authored-by: Copilot <[email protected]>

Author: samuelbray32

CHANGELOG.md

@@ -79,6 +79,8 @@ ImportedLFP().drop()
 - Only add merge parts to `source_class_dict` if present in codebase #1237
 - Remove cli module #1250
 - Fix column error in `check_threads` method #1256
+- Export python env and store in newly created analysis files #1270
+- Enforce single table entry in `fetch1_dataframe` calls #1270
 - Add recompute ability for `SpikeSortingRecording` for both v0 and v1 #1093,
     #1311
 - Track Spyglass version in dedicated table for enforcing updates #1281
@@ -96,6 +98,7 @@ ImportedLFP().drop()
 - Common
     - Default `AnalysisNwbfile.create` permissions are now 777 #1226
     - Make `Nwbfile.fetch_nwb` functional # 1256
+    - Calculate mode of timestep size in log scale when estimating sampling rate #1270
     - Ingest all `ImageSeries` objects in nwb file to `VideoFile` #1278
     - Allow ingestion of multi-row task epoch tables #1278
     - Add `SensorData` to `populate_all_common` #1281
@@ -111,6 +114,8 @@ ImportedLFP().drop()
         of `DLCPoseEstimation` #1208
     - Enable import of existing pose data to `ImportedPose` in position pipeline
         #1247
+    - Change key value `position_source` to "imported" during ingestion #1270
+    - Define orientation as `nan` for single-led data #1270
     - Sanitize new project names for unix file system #1247
     - Add arg to return percent below threshold in `get_subthresh_inds` #1304,
         #1305
@@ -123,6 +128,8 @@ ImportedLFP().drop()
     - Revise cleanup for `v0.SpikeSorting` #1271
     - Fix type compatibility of `time_slice` in
         `SortedSpikesGroup.fetch_spike_data` #1261
+    - Update transaction and parallel make settings for `v0` and `v1`
+      `SpikeSorting` tables #1270
     - Disable make transactionsfor `CuratedSpikeSorting` #1288
     - Refactor `SpikeSortingOutput.get_restricted_merge_ids` #1304
     - Add burst merge curation #1209

src/spyglass/behavior/v1/moseq.py

@@ -403,6 +403,7 @@ def make(self, key):
         self.insert1(key)
 
     def fetch1_dataframe(self):
+        self.ensure_single_entry()
         dataframe = self.fetch_nwb()[0]["moseq"]
         dataframe.set_index("time", inplace=True)
         return dataframe

src/spyglass/common/common_behav.py

@@ -79,7 +79,7 @@ def insert_from_nwbfile(cls, nwb_file_name, skip_duplicates=False) -> None:
         nwbf = get_nwb_file(nwb_file_name)
         all_pos = get_all_spatial_series(nwbf, verbose=True)
         sess_key = Nwbfile.get_file_key(nwb_file_name)
-        src_key = dict(**sess_key, source="trodes", import_file_name="")
+        src_key = dict(**sess_key, source="imported", import_file_name="")
 
         if all_pos is None:
             return

src/spyglass/common/common_ephys.py

@@ -575,6 +575,7 @@ def nwb_object(self, key):
 
     def fetch1_dataframe(self, *attrs, **kwargs) -> pd.DataFrame:
         """Fetch the LFP data as a pandas DataFrame."""
+        self.ensure_single_entry()
         nwb_lfp = self.fetch_nwb()[0]
         return pd.DataFrame(
             nwb_lfp["lfp"].data,
@@ -951,6 +952,7 @@ def make(self, key):
 
     def fetch1_dataframe(self, *attrs, **kwargs) -> pd.DataFrame:
         """Fetch the LFP band data as a pandas DataFrame."""
+        self.ensure_single_entry()
         filtered_nwb = self.fetch_nwb()[0]
         return pd.DataFrame(
             filtered_nwb["filtered_data"].data,

src/spyglass/common/common_nwbfile.py

@@ -1,6 +1,7 @@
 import os
 import random
 import string
+import subprocess
 from pathlib import Path
 from typing import Dict, Optional, Union
 from uuid import uuid4
@@ -223,7 +224,7 @@ def create(
                             nwb_object.pop(module)
             # add the version of spyglass that created this file
             if nwbf.source_script is None:
-                nwbf.source_script = f"spyglass={sg_version}"
+                nwbf.source_script = self._logged_env_info()
             else:
                 alter_source_script = True
 
@@ -267,11 +268,22 @@ def create(
 
         return analysis_file_name
 
-    @staticmethod
-    def _alter_spyglass_version(nwb_file_path: str) -> None:
+    @classmethod
+    def _alter_spyglass_version(cls, nwb_file_path: str) -> None:
         """Change the source script to the current version of spyglass"""
         with h5py.File(nwb_file_path, "a") as f:
-            f["/general/source_script"][()] = f"spyglass={sg_version}"
+            f["/general/source_script"][()] = cls._logged_env_info()
+
+    @staticmethod
+    def _logged_env_info():
+        """Get the environment information for logging."""
+        env_info = f"spyglass={sg_version} \n\n"
+        env_info += "Python Environment:\n"
+        python_env = subprocess.check_output(
+            ["conda", "env", "export"], text=True
+        )
+        env_info += python_env
+        return env_info
 
     @classmethod
     def __get_new_file_name(cls, nwb_file_name: str) -> str:

src/spyglass/common/common_position.py

@@ -464,6 +464,13 @@ def calculate_position_info(
         # convert back to between -pi and pi
         orientation[~is_nan] = np.angle(np.exp(1j * orientation[~is_nan]))
 
+        # set orientation to NaN in single LED data
+        if np.all(front_LED == 0) or np.all(back_LED == 0):
+            logger.warning(
+                "Single LED data detected. Setting orientation to NaN."
+            )
+            orientation = np.full_like(orientation, np.nan)
+
         velocity = get_velocity(
             position,
             time=time,
@@ -482,6 +489,7 @@ def calculate_position_info(
 
     def fetch1_dataframe(self) -> pd.DataFrame:
         """Fetches the position data as a pandas dataframe."""
+        self.ensure_single_entry()
         return self._data_to_df(self.fetch_nwb()[0])
 
     @staticmethod

src/spyglass/common/common_sensors.py

@@ -105,8 +105,7 @@ def fetch1_dataframe(
         """
         if len(self) == 0:
             return None
-        if len(self) > 1:
-            raise ValueError("More than one sensor data object found.")
+        self.ensure_single_entry()
 
         nwb = self.fetch_nwb()[0]
         columns = nwb["sensor_data"].description.split()

src/spyglass/decoding/v0/clusterless.py

@@ -266,6 +266,7 @@ def make(self, key):
 
     def fetch1_dataframe(self) -> pd.DataFrame:
         """Convenience function for returning the marks in a readable format"""
+        self.ensure_single_entry()
         return self.fetch_dataframe()[0]
 
     def fetch_dataframe(self) -> list[pd.DataFrame]:
@@ -450,6 +451,7 @@ def plot_all_marks(
 
     def fetch1_dataframe(self) -> pd.DataFrame:
         """Convenience function for returning the first dataframe"""
+        self.ensure_single_entry()
         return self.fetch_dataframe()[0]
 
     def fetch_dataframe(self) -> list[pd.DataFrame]:

src/spyglass/decoding/v0/sorted_spikes.py

@@ -164,6 +164,7 @@ def make(self, key):
 
     def fetch1_dataframe(self) -> pd.DataFrame:
         """Return the first spike indicator as a dataframe."""
+        self.ensure_single_entry()
         return self.fetch_dataframe()[0]
 
     def fetch_dataframe(self) -> list[pd.DataFrame]:

src/spyglass/lfp/analysis/v1/lfp_band.py

@@ -478,15 +478,8 @@ def make(self, key: dict) -> None:
 
     def fetch1_dataframe(self, *attrs, **kwargs) -> pd.DataFrame:
         """Fetches the filtered data as a dataframe"""
-        filtered_nwb = self.fetch_nwb()
-
-        if len(filtered_nwb) != 1:
-            raise ValueError(
-                "Expected 1 filtered data, but got "
-                + f"{len(filtered_nwb)} for this LFPBandSelection"
-            )
-
-        filtered_nwb = filtered_nwb[0]
+        self.ensure_single_entry()
+        filtered_nwb = self.fetch_nwb()[0]
         return pd.DataFrame(
             filtered_nwb["lfp_band"].data,
             index=pd.Index(filtered_nwb["lfp_band"].timestamps, name="time"),