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SpikeSortingView.py

SpikeSortingView

Bases: SpyglassMixin, Computed

Source code in src/spyglass/spikesorting/v0/figurl_views/SpikeSortingView.py 
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@schema
class SpikeSortingView(SpyglassMixin, dj.Computed):
    definition = """
    # Schema for storing figurl views of spike sorting
    -> SpikeSorting
    ---
    figurl: varchar(10000)
    """

    def make(self, key):
        """Populates SpikeSortingView.

        1. Fetches...
            - the recording from SpikeSortingRecording
            - the sorting from SpikeSorting
        2. Loads each with spikeinterface and passes to SpikeSortingView from
            sortingview package.
        3. Creates...
            - Summary
            - Autocorrelograms
            - Average waveforms
            - Spike amplitudes
            - Electrode geometry
        4. Creates a mountain layout with the above figures and generates a URL.
        """
        recording_record = (
            SpikeSortingRecording & {"recording_id": key["recording_id"]}
        ).fetch1()
        sorting_record = (
            SpikeSorting & {"sorting_id": key["sorting_id"]}
        ).fetch1()

        recording_path = recording_record["recording_path"]
        sorting_path = sorting_record["sorting_path"]

        # Load the SI extractors
        recording: si.BaseRecording = si.load_extractor(recording_path)
        sorting: si.BaseSorting = si.load_extractor(sorting_path)

        with kcl.TemporaryDirectory() as tmpdir:
            fname = f"{tmpdir}/spikesortingview.h5"
            logger.info("Preparing spikesortingview data")
            prepare_spikesortingview_data(
                recording=recording,
                sorting=sorting,
                segment_duration_sec=60 * 20,
                snippet_len=(20, 20),
                max_num_snippets_per_segment=100,
                channel_neighborhood_size=7,
                output_file_name=fname,
            )

            logger.info("Creating view object")
            X = SortingViewSpikeSortingView(fname)

            logger.info("Creating summary")
            f1 = X.create_summary()
            # f2 = X.create_units_table(unit_ids=X.unit_ids, unit_metrics=unit_metrics)
            logger.info("Creating autocorrelograms")
            f3 = X.create_autocorrelograms(unit_ids=X.unit_ids)
            logger.info("Creating raster plot")
            f4 = X.create_raster_plot(unit_ids=X.unit_ids)
            logger.info("Creating average waveforms")
            f5 = X.create_average_waveforms(unit_ids=X.unit_ids)
            logger.info("Creating spike amplitudes")
            f6 = X.create_spike_amplitudes(unit_ids=X.unit_ids)
            logger.info("Creating electrode geometry")
            f7 = X.create_electrode_geometry()
            # f8 = X.create_live_cross_correlograms()

            sorting_curation_uri = None

            nwb_file_name = recording_record["nwb_file_name"]
            sort_group_id = sorting_record["sort_group_id"]
            sort_interval_name = sorting_record["sort_interval_name"]
            sorter = sorting_record["sorter"]
            sorter_params_name = sorting_record["sorter_params_name"]
            label = f"{nwb_file_name}:{sort_group_id}:{sort_interval_name}:{sorter}:{sorter_params_name}"
            logger.info(label)

            logger.info("Creating mountain layout")
            mountain_layout = X.create_mountain_layout(
                figures=[f1, f3, f4, f5, f6, f7],
                label=label,
                sorting_curation_uri=sorting_curation_uri,
            )

            logger.info("Making URL")
            url = mountain_layout.url()

            # Insert row into table
            key2 = dict(key, **{"figurl": url})
            self.insert1(key2)

make(key)

Populates SpikeSortingView.

  1. Fetches...
    • the recording from SpikeSortingRecording
    • the sorting from SpikeSorting
  2. Loads each with spikeinterface and passes to SpikeSortingView from sortingview package.
  3. Creates...
    • Summary
    • Autocorrelograms
    • Average waveforms
    • Spike amplitudes
    • Electrode geometry
  4. Creates a mountain layout with the above figures and generates a URL.
Source code in src/spyglass/spikesorting/v0/figurl_views/SpikeSortingView.py 
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def make(self, key):
    """Populates SpikeSortingView.

    1. Fetches...
        - the recording from SpikeSortingRecording
        - the sorting from SpikeSorting
    2. Loads each with spikeinterface and passes to SpikeSortingView from
        sortingview package.
    3. Creates...
        - Summary
        - Autocorrelograms
        - Average waveforms
        - Spike amplitudes
        - Electrode geometry
    4. Creates a mountain layout with the above figures and generates a URL.
    """
    recording_record = (
        SpikeSortingRecording & {"recording_id": key["recording_id"]}
    ).fetch1()
    sorting_record = (
        SpikeSorting & {"sorting_id": key["sorting_id"]}
    ).fetch1()

    recording_path = recording_record["recording_path"]
    sorting_path = sorting_record["sorting_path"]

    # Load the SI extractors
    recording: si.BaseRecording = si.load_extractor(recording_path)
    sorting: si.BaseSorting = si.load_extractor(sorting_path)

    with kcl.TemporaryDirectory() as tmpdir:
        fname = f"{tmpdir}/spikesortingview.h5"
        logger.info("Preparing spikesortingview data")
        prepare_spikesortingview_data(
            recording=recording,
            sorting=sorting,
            segment_duration_sec=60 * 20,
            snippet_len=(20, 20),
            max_num_snippets_per_segment=100,
            channel_neighborhood_size=7,
            output_file_name=fname,
        )

        logger.info("Creating view object")
        X = SortingViewSpikeSortingView(fname)

        logger.info("Creating summary")
        f1 = X.create_summary()
        # f2 = X.create_units_table(unit_ids=X.unit_ids, unit_metrics=unit_metrics)
        logger.info("Creating autocorrelograms")
        f3 = X.create_autocorrelograms(unit_ids=X.unit_ids)
        logger.info("Creating raster plot")
        f4 = X.create_raster_plot(unit_ids=X.unit_ids)
        logger.info("Creating average waveforms")
        f5 = X.create_average_waveforms(unit_ids=X.unit_ids)
        logger.info("Creating spike amplitudes")
        f6 = X.create_spike_amplitudes(unit_ids=X.unit_ids)
        logger.info("Creating electrode geometry")
        f7 = X.create_electrode_geometry()
        # f8 = X.create_live_cross_correlograms()

        sorting_curation_uri = None

        nwb_file_name = recording_record["nwb_file_name"]
        sort_group_id = sorting_record["sort_group_id"]
        sort_interval_name = sorting_record["sort_interval_name"]
        sorter = sorting_record["sorter"]
        sorter_params_name = sorting_record["sorter_params_name"]
        label = f"{nwb_file_name}:{sort_group_id}:{sort_interval_name}:{sorter}:{sorter_params_name}"
        logger.info(label)

        logger.info("Creating mountain layout")
        mountain_layout = X.create_mountain_layout(
            figures=[f1, f3, f4, f5, f6, f7],
            label=label,
            sorting_curation_uri=sorting_curation_uri,
        )

        logger.info("Making URL")
        url = mountain_layout.url()

        # Insert row into table
        key2 = dict(key, **{"figurl": url})
        self.insert1(key2)