Skip to content

curation_figurl.py

CurationFigurl

Bases: SpyglassMixin, Computed

Source code in src/spyglass/spikesorting/v0/curation_figurl.py 
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
@schema
class CurationFigurl(SpyglassMixin, dj.Computed):
    definition = """
    -> CurationFigurlSelection
    ---
    url: varchar(2000)
    initial_curation_uri: varchar(2000)
    new_curation_uri: varchar(2000)
    """

    def make(self, key: dict):
        """Create a Curation Figurl
        Parameters
        ----------
        key : dict
            primary key of an entry from CurationFigurlSelection table
        """

        # get new_curation_uri from selection table
        new_curation_uri = (CurationFigurlSelection & key).fetch1(
            "new_curation_uri"
        )

        # fetch
        recording_path = (SpikeSortingRecording & key).fetch1("recording_path")
        sorting_path = (SpikeSorting & key).fetch1("sorting_path")
        recording_label = SpikeSortingRecording._get_recording_name(key)
        sorting_label = SpikeSorting._get_sorting_name(key)
        unit_metrics = _reformat_metrics(
            (Curation & key).fetch1("quality_metrics")
        )
        initial_labels = (Curation & key).fetch1("curation_labels")
        initial_merge_groups = (Curation & key).fetch1("merge_groups")

        # new_curation_uri = key["new_curation_uri"]

        # Create the initial curation and store it in kachery
        for k, v in initial_labels.items():
            new_list = []
            for item in v:
                if item not in new_list:
                    new_list.append(item)
            initial_labels[k] = new_list
        initial_curation = {
            "labelsByUnit": initial_labels,
            "mergeGroups": initial_merge_groups,
        }
        initial_curation_uri = kcl.store_json(initial_curation)

        # Get the recording/sorting extractors
        R = si.load_extractor(recording_path)
        if R.get_num_segments() > 1:
            R = si.concatenate_recordings([R])
        S = si.load_extractor(sorting_path)

        # Generate the figURL
        url = _generate_the_figurl(
            R=R,
            S=S,
            initial_curation_uri=initial_curation_uri,
            new_curation_uri=new_curation_uri,
            recording_label=recording_label,
            sorting_label=sorting_label,
            unit_metrics=unit_metrics,
        )

        # insert
        key["url"] = url
        key["initial_curation_uri"] = initial_curation_uri
        key["new_curation_uri"] = new_curation_uri
        self.insert1(key)

make(key)

Create a Curation Figurl

Parameters:

Name Type Description Default
key dict

primary key of an entry from CurationFigurlSelection table

 required
Source code in src/spyglass/spikesorting/v0/curation_figurl.py 
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
def make(self, key: dict):
    """Create a Curation Figurl
    Parameters
    ----------
    key : dict
        primary key of an entry from CurationFigurlSelection table
    """

    # get new_curation_uri from selection table
    new_curation_uri = (CurationFigurlSelection & key).fetch1(
        "new_curation_uri"
    )

    # fetch
    recording_path = (SpikeSortingRecording & key).fetch1("recording_path")
    sorting_path = (SpikeSorting & key).fetch1("sorting_path")
    recording_label = SpikeSortingRecording._get_recording_name(key)
    sorting_label = SpikeSorting._get_sorting_name(key)
    unit_metrics = _reformat_metrics(
        (Curation & key).fetch1("quality_metrics")
    )
    initial_labels = (Curation & key).fetch1("curation_labels")
    initial_merge_groups = (Curation & key).fetch1("merge_groups")

    # new_curation_uri = key["new_curation_uri"]

    # Create the initial curation and store it in kachery
    for k, v in initial_labels.items():
        new_list = []
        for item in v:
            if item not in new_list:
                new_list.append(item)
        initial_labels[k] = new_list
    initial_curation = {
        "labelsByUnit": initial_labels,
        "mergeGroups": initial_merge_groups,
    }
    initial_curation_uri = kcl.store_json(initial_curation)

    # Get the recording/sorting extractors
    R = si.load_extractor(recording_path)
    if R.get_num_segments() > 1:
        R = si.concatenate_recordings([R])
    S = si.load_extractor(sorting_path)

    # Generate the figURL
    url = _generate_the_figurl(
        R=R,
        S=S,
        initial_curation_uri=initial_curation_uri,
        new_curation_uri=new_curation_uri,
        recording_label=recording_label,
        sorting_label=sorting_label,
        unit_metrics=unit_metrics,
    )

    # insert
    key["url"] = url
    key["initial_curation_uri"] = initial_curation_uri
    key["new_curation_uri"] = new_curation_uri
    self.insert1(key)