eegdash 0.0.1__py3-none-any.whl → 0.0.2__py3-none-any.whl

eegdash/SignalStore/signalstore/operations/helpers/spikeinterface_helper.py

@@ -1,100 +0,0 @@
-from neo.rawio.mearecrawio import MEArecRawIO
-from signalstorestore.data_access_objects import DataArrayDAO, RecordDAO
-
-import numpy as np
-import xarray as xr
-import neo
-import pickle
-from datetime import datetime, timezone
-
-
-class SpikeinterfaceMEArecHelper:
-
-    def __init__(self):
-        self._mearec_rawio = None
-        self._recordings_dataarray = None
-        self._sampling_rate_dataarray = None
-        self._recording_info_record = None
-        self._spiketrain_records = []
-
-    @property
-    def recordings_dataarray(self):
-        return self._recordings_dataarray
-
-    @property
-    def sampling_rate_dataarray(self):
-        return self._sampling_rate_dataarray
-
-    @property
-    def recording_info_record(self):
-        return self._recording_info_record
-
-    @property
-    def spiketrain_records(self):
-        return self._spiketrain_records
-
-    def load(self, mearec_rawio: MEArecRawIO, hrid: str):
-        self._mearec_rawio = mearec_rawio
-        self._mearec_rawio._parse_header()
-
-        self._recordings_dataarray = xr.DataArray(
-                name = "mearec_recordings",
-                data = np.array(self._mearec_rawio._recordings),
-                dims = ["x", "y"],
-                coords = {
-                    "x": np.array(range(self._mearec_rawio._recordings.shape[0])),
-                    "y": np.array(range(self._mearec_rawio._recordings.shape[1])),
-                    },
-                attrs = {
-                    "hrid": hrid,
-                    "schema_name": "spikeinterface_recordings",
-                    }
-                )
-
-        self._sampling_rate_dataarray = xr.DataArray(
-                name = "mearec_sampling_rate",
-                data = self._mearec_rawio._recgen.info['recordings']['fs'],
-                dims = ["x"],
-                coords = {
-                    "x": np.array(range(1)),
-                    },
-                attrs = {
-                    "hrid": hrid,
-                    "schema_name": "spikeinterface_sampling_rate",
-                    }
-                )
-
-        self._recording_info_record = {
-                "hrid": hrid,
-                "schema_name": "spikeinterface_recording_info",
-                "has_data": False,
-                "info_pickle": pickle.dumps(self._mearec_rawio._recgen.info),
-                }
-
-        self._spiketrain_records = list(map(self._build_spiketrain_record(hrid), enumerate(self._mearec_rawio._spiketrains)))
-
-    def _build_spiketrain_record(self, hrid):
-        def build_fn(idx_and_spiketrain):
-            idx, spiketrain = idx_and_spiketrain
-            return {
-                    "hrid": f"{hrid}-{idx}",
-                    "schema_name": "spikeinterface_spiketrain",
-                    "has_data": False,
-                    "times": pickle.dumps(spiketrain.as_quantity()),
-                    "t_stop": pickle.dumps(spiketrain.t_stop),
-                    "units": pickle.dumps(spiketrain.units),
-                    "dtype": pickle.dumps(spiketrain.dtype),
-                    "copy": True,
-                    "sampling_rate": pickle.dumps(spiketrain.sampling_rate),
-                    "t_start": pickle.dumps(spiketrain.t_start),
-                    "waveforms": pickle.dumps(spiketrain.waveforms),
-                    "left_sweep": spiketrain.left_sweep,
-                    "name": spiketrain.name,
-                    "file_origin": spiketrain.file_origin,
-                    "description": spiketrain.description,
-                    "array_annotations": spiketrain.array_annotations,
-                    "annotations_pickle": pickle.dumps(spiketrain.annotations),
-                    }
-        return build_fn
-
-

eegdash/SignalStore/signalstore/operations/helpers/wrappers/neo_wrappers.py

@@ -1,21 +0,0 @@
-import neo.core as neoc
-
-def to_analog_signal(signal):
-    st = to_seconds(signal.attrs['start_time'])
-    et = to_seconds(signal.attrs['end_time'])
-    sampling_period = (et - st)
-    annotations = {key: value for key, value in signal.attrs.copy() if key not in ['start_time', 'end_time', 'sampling_rate']}
-    return neoc.AnalogSignal(signal.data,
-                           units=None,
-                           dtype=type(signal.data),
-                           copy=True,
-                           t_start=signal.attrs['start_time'],
-                           sampling_rate=signal.attrs['sampling_rate'],
-                           sampling_period=sampling_period,
-                           name=signal.attrs['name'],
-                           file_origin=None,
-                           description=None,
-                           array_annotations=None
-                           **annotations)
-
-

eegdash/SignalStore/signalstore/operations/helpers/wrappers/nwb_wrappers.py

@@ -1,27 +0,0 @@
-import pynwb.ecephys as nwbp
-
-def to_electrical_series(signal):
-    """
-    Convert a Signal object to a pynwb ElectricalSeries object.
-    """
-
-    channel_group = nwbp.channelGroup(...
-    )
-
-    return nwbp.ElectricalSeries(
-        name=signal.name,
-        data=signal.data,
-        channels=channel_group,
-        channel_conversion=None,
-        filtering=None,
-        resolution=-1.0,
-        conversion=1.0,
-        timestamps=None,
-        starting_time=None,
-        rate=None,
-        comments='no comments',
-        description='no description',
-        control=None,
-        control_description=None,
-        offset=0.0
-    )

eegdash/SignalStore/signalstore/store/__init__.py

@@ -1,8 +0,0 @@
-from eegdash.SignalStore.signalstore.store.unit_of_work_provider import UnitOfWorkProvider
-
-from eegdash.SignalStore.signalstore.store.datafile_adapters import (
-    XarrayDataArrayNetCDFAdapter,
-    XarrayDataArrayZarrAdapter
-)
-
-__all__ = ['UnitOfWorkProvider', 'XarrayDataArrayNetCDFAdapter', 'XarrayDataArrayZarrAdapter']