Fix changes

notebooks/10_Spike_SortingV1.ipynb

@@ -718,6 +718,14 @@
     "sgs.CurationV1()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "9ff6aff5-7020-40d6-832f-006d66d54a7e",
+   "metadata": {},
+   "source": [
+    "We now insert the curated spike sorting to a `Merge` table for feeding into downstream processing pipelines."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -731,33 +739,63 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a59b78e2-b76a-4958-b012-708ed5600be6",
+   "id": "5047f866-7435-4dea-9ed8-a9b2d8365682",
    "metadata": {},
    "outputs": [],
    "source": [
-    "SpikeSortingOutput.insert_from_source(key, source=\"CurationV1\")"
+    "SpikeSortingOutput()"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "582a40d9-ffb0-401c-ae9d-287336e47911",
+   "id": "d2702410-01e1-4af0-a987-891c42c6c099",
    "metadata": {},
    "outputs": [],
    "source": [
-    "SpikeSortingOutput()"
+    "key"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b20c2c9e-0c97-4669-b45d-4b1c50fd2fcc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "SpikeSortingOutput.insert([key], part_name='CurationV1')"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "55b2b015-e9a3-4ab1-b2bc-4925bd8e9438",
+   "id": "184c3401-8df3-46f0-9dd0-c9fa98395c34",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "SpikeSortingOutput.merge_view()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e2b083a5-b700-438a-8a06-2e2eb041072d",
    "metadata": {},
    "outputs": [],
    "source": [
     "SpikeSortingOutput.CurationV1()"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "10b8afa1-d4a6-4ac1-959b-f4e84e582f2e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "SpikeSortingOutput.CuratedSpikeSorting()"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

src/spyglass/spikesorting/merge.py

@@ -15,7 +15,7 @@
 @schema
 class SpikeSortingOutput(_Merge):
     definition = """
-    # Output of spike sorting pipelines. Use `insert_from_source` method to insert rows.
+    # Output of spike sorting pipelines.
     merge_id: uuid
     ---
     source: varchar(32)

src/spyglass/spikesorting/v1/__init__.py

@@ -1,22 +1,22 @@
-from .recording import (
-    SortGroup,
-    SpikeSortingPreprocessingParameters,
-    SpikeSortingRecordingSelection,
-    SpikeSortingRecording,
-)
 from .artifact import (
+    ArtifactDetection,
     ArtifactDetectionParameters,
     ArtifactDetectionSelection,
-    ArtifactDetection,
 )
-from .sorting import SpikeSorterParameters, SpikeSortingSelection, SpikeSorting
 from .curation import CurationV1
+from .figurl_curation import FigURLCuration, FigURLCurationSelection
 from .metric_curation import (
-    WaveformParameters,
-    MetricParameters,
+    MetricCuration,
     MetricCurationParameters,
     MetricCurationSelection,
-    MetricCuration,
+    MetricParameters,
+    WaveformParameters,
+)
+from .recording import (
+    SortGroup,
+    SpikeSortingPreprocessingParameters,
+    SpikeSortingRecording,
+    SpikeSortingRecordingSelection,
 )
-from .figurl_curation import FigURLCurationSelection, FigURLCuration
-from .utils import get_spiking_v1_merge_ids
+from .sorting import SpikeSorterParameters, SpikeSorting, SpikeSortingSelection
+from .utils import get_spiking_sorting_v1_merge_ids

src/spyglass/spikesorting/v1/artifact.py

@@ -261,7 +261,7 @@ def _get_artifact_times(
     # turn ms to remove total into s to remove from either side of each detected artifact
     half_removal_window_s = removal_window_ms / 2 / 1000
 
-    if not artifact_frames:
+    if len(artifact_frames) == 0:
         recording_interval = np.asarray(
             [[valid_timestamps[0], valid_timestamps[-1]]]
         )
@@ -312,16 +312,16 @@ def _init_artifact_worker(
     amplitude_thresh_uV=None,
     proportion_above_thresh=1.0,
 ):
-    """Create a local dict per worker"""
+    # create a local dict per worker
+    worker_ctx = {}
     if isinstance(recording, dict):
-        return dict(recording=si.load_extractor(recording))
+        worker_ctx["recording"] = si.load_extractor(recording)
     else:
-        return dict(
-            recording=recording,
-            zscore_thresh=zscore_thresh,
-            amplitude_thresh_uV=amplitude_thresh_uV,
-            proportion_above_thresh=proportion_above_thresh,
-        )
+        worker_ctx["recording"] = recording
+    worker_ctx["zscore_thresh"] = zscore_thresh
+    worker_ctx["amplitude_thresh_uV"] = amplitude_thresh_uV
+    worker_ctx["proportion_above_thresh"] = proportion_above_thresh
+    return worker_ctx
 
 
 def _compute_artifact_chunk(segment_index, start_frame, end_frame, worker_ctx):
@@ -341,7 +341,7 @@ def _compute_artifact_chunk(segment_index, start_frame, end_frame, worker_ctx):
     )
 
     # find the artifact occurrences using one or both thresholds, across channels
-    if amplitude_thresh_uV and not zscore_thresh:
+    if (amplitude_thresh_uV is not None) and (zscore_thresh is None):
         above_a = np.abs(traces) > amplitude_thresh_uV
         above_thresh = (
             np.ravel(np.argwhere(np.sum(above_a, axis=1) >= nelect_above))
@@ -393,13 +393,14 @@ def _check_artifact_thresholds(
     ValueError: if signal thresholds are negative
     """
     # amplitude or zscore thresholds should be negative, as they are applied to an absolute signal
-    def is_negative(value):
-        return value < 0 if value is not None else False
-
-    if is_negative(amplitude_thresh_uV) or is_negative(zscore_thresh):
-        raise ValueError(
-            "Amplitude and Z-Score thresholds must be >= 0, or None"
-        )
+    signal_thresholds = [
+        t for t in [amplitude_thresh_uV, zscore_thresh] if t is not None
+    ]
+    for t in signal_thresholds:
+        if t < 0:
+            raise ValueError(
+                "Amplitude and Z-Score thresholds must be >= 0, or None"
+            )
 
     # proportion_above_threshold should be in [0:1] inclusive
     if proportion_above_thresh < 0:

src/spyglass/spikesorting/v1/curation.py

@@ -112,7 +112,7 @@ def insert_curation(
             "parent_curation_id": parent_curation_id,
             "analysis_file_name": analysis_file_name,
             "object_id": object_id,
-            "merges_applied": str(apply_merge),
+            "merges_applied": apply_merge,
             "description": description,
         }
         cls.insert1(
@@ -168,7 +168,7 @@ def get_recording(cls, key: dict) -> si.BaseRecording:
             primary key of CurationV1 table
         """
 
-        analysis_file_abs_path = (
+        analysis_file_name = (
             SpikeSortingRecording * SpikeSortingSelection & key
         ).fetch1("analysis_file_name")
         analysis_file_abs_path = AnalysisNwbfile.get_abs_path(
@@ -343,11 +343,12 @@ def _write_sorting_to_nwb_with_curation(
             )
         # add labels, merge groups, metrics
         if labels is not None:
-            label_values = [
-                labels.get(unit_id, [])
-                for unit_id in unit_ids
-                if unit_id in labels
-            ]
+            label_values = []
+            for unit_id in unit_ids:
+                if unit_id not in labels:
+                    label_values.append([])
+                else:
+                    label_values.append(labels[unit_id])
             nwbf.add_unit_column(
                 name="curation_label",
                 description="curation label",

src/spyglass/spikesorting/v1/recording.py

@@ -575,7 +575,6 @@ def _consolidate_intervals(intervals, timestamps):
 
     # Loop through the rest of the intervals to join them if needed
     for next_start, next_stop in zip(start_indices, stop_indices):
-
         # If the stop time of the current interval is equal to or greater than the next start time minus 1
         if stop >= next_start - 1:
             stop = max(