コード例 #1
0
def build_toy_example():
    load_namespaces(ns_path)
    CompartmentSeries = get_class('CompartmentSeries', project_name)
    membrane_potential = CompartmentSeries(source='source',
                                           name='membrane_potential',
                                           gid=[1, 2, 3],
                                           index_pointer=[1, 2, 3],
                                           cell_var='Membrane potential (mV)',
                                           data=[[1., 2., 4.], [1., 2., 4.]],
                                           timestamps=np.arange(2),
                                           element_id=[0, 0, 0],
                                           element_pos=[1., 1., 1.],
                                           unit='µV')

    nwbfile = NWBFile(source='source',
                      session_description='session_description',
                      identifier='identifier',
                      session_start_time=datetime.now(),
                      file_create_date=datetime.now(),
                      institution='institution',
                      lab='lab')

    module = nwbfile.create_processing_module(name='membrane_potential',
                                              source='source',
                                              description='description')
    module.add_container(membrane_potential)

    with NWBHDF5IO('mem_potential_toy.nwb', mode='w') as io:
        io.write(nwbfile)
コード例 #2
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ファイル: test_extension.py プロジェクト: pattanaikay/pynwb
    def test_lab_meta_auto(self):
        ns_builder = NWBNamespaceBuilder('Extension for use in my Lab',
                                         self.prefix,
                                         version='0.1.0')
        test_meta_ext = NWBGroupSpec(neurodata_type_def='MyTestMetaData',
                                     neurodata_type_inc='LabMetaData',
                                     doc='my test meta data',
                                     attributes=[
                                         NWBAttributeSpec(name='test_attr',
                                                          dtype='float',
                                                          doc='test_dtype')
                                     ])
        ns_builder.add_spec(self.ext_source, test_meta_ext)
        ns_builder.export(self.ns_path, outdir=self.tempdir)
        ns_abs_path = os.path.join(self.tempdir, self.ns_path)

        load_namespaces(ns_abs_path)

        MyTestMetaData = get_class('MyTestMetaData', self.prefix)

        nwbfile = NWBFile("a file with header data", "NB123A",
                          datetime(2017, 5, 1, 12, 0, 0, tzinfo=tzlocal()))

        nwbfile.add_lab_meta_data(
            MyTestMetaData(name='test_name', test_attr=5.))
コード例 #3
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def build_real_example():
    load_namespaces(ns_path)
    VarTable = get_class('VarTable', project_name)
    input_data = h5py.File('sim_data/cell_vars.h5', 'r')
    vmtable = VarTable(source='source',
                       name='vm_table',
                       data=np.array(input_data['/v/data']),
                       gid=np.array(input_data['mapping/gids']),
                       index_pointer=np.array(
                           input_data['mapping/index_pointer']),
                       cell_var='Membrane potential (mV)',
                       element_id=np.array(input_data['mapping/element_id']),
                       element_pos=np.array(input_data['mapping/element_pos']))

    nwbfile = NWBFile(source='source',
                      session_description='session_description',
                      identifier='identifier',
                      session_start_time=datetime.now(),
                      file_create_date=datetime.now(),
                      institution='institution',
                      lab='lab')

    module = nwbfile.create_processing_module(name='name',
                                              source='source',
                                              description='description')
    module.add_container(vmtable)

    io = NWBHDF5IO('mem_potential_toy.nwb', mode='w')
    io.write(nwbfile)
    io.close()
コード例 #4
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ファイル: metadata.py プロジェクト: vrhaynes/AllenSDK
def load_pynwb_extension(schema, prefix: str):
    neurodata_type = schema.neurodata_type
    outdir = os.path.abspath(os.path.dirname(__file__))
    ns_path = f'{prefix}.namespace.yaml'

    # Read spec and load namespace:
    ns_abs_path = os.path.join(outdir, ns_path)
    pynwb.load_namespaces(ns_abs_path)

    return pynwb.get_class(neurodata_type, prefix)
コード例 #5
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def load_pynwb_extension(schema, prefix: str):

    docval_list, attributes, nwbfields_list = extract_from_schema(schema)
    neurodata_type = schema.neurodata_type
    outdir = os.path.abspath(os.path.dirname(__file__))
    ns_path = f'{prefix}.namespace.yaml'

    # Read spec and load namespace:
    ns_abs_path = os.path.join(outdir, ns_path)
    pynwb.load_namespaces(ns_abs_path)

    return pynwb.get_class(neurodata_type, prefix)
コード例 #6
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ファイル: test_extension.py プロジェクト: ecmyhre/pynwb
 def test_load_namespace_with_reftype_attribute_check_autoclass_const(self):
     ns_builder = NWBNamespaceBuilder('Extension for use in my Lab',
                                      self.prefix)
     test_ds_ext = NWBDatasetSpec(
         doc='test dataset to add an attr',
         name='test_data',
         shape=(None, ),
         attributes=[
             NWBAttributeSpec(name='target_ds',
                              doc='the target the dataset applies to',
                              dtype=RefSpec('TimeSeries', 'object'))
         ],
         neurodata_type_def='my_new_type')
     ns_builder.add_spec(self.ext_source, test_ds_ext)
     ns_builder.export(self.ns_path, outdir=self.tempdir)
     load_namespaces(os.path.join(self.tempdir, self.ns_path))
     my_new_type = get_class('my_new_type', self.prefix)
     docval = None
     for tmp in get_docval(my_new_type.__init__):
         if tmp['name'] == 'target_ds':
             docval = tmp
             break
     self.assertIsNotNone(docval)
     self.assertEqual(docval['type'], TimeSeries)
コード例 #7
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import os
from pynwb import load_namespaces, get_class
import ndx_events

# Set path of the namespace.yaml file to the expected install location
ndx_ellipse_eye_tracking_specpath = os.path.join(
    os.path.dirname(__file__),
    'spec',
    'ndx-ellipse-eye-tracking.namespace.yaml'
)

# If the extension has not been installed yet but we are running directly from
# the git repo
if not os.path.exists(ndx_ellipse_eye_tracking_specpath):
    ndx_ellipse_eye_tracking_specpath = os.path.abspath(os.path.join(
        os.path.dirname(__file__),
        '..', '..', '..',
        'spec',
        'ndx-ellipse-eye-tracking.namespace.yaml'
    ))

# Load the namespace
load_namespaces(ndx_events.ndx_events_specpath)
load_namespaces(ndx_ellipse_eye_tracking_specpath)

# TODO: import your classes here or define your class using get_class to make
# them accessible at the package level

EllipseSeries = get_class('EllipseSeries', 'ndx-ellipse-eye-tracking')
EllipseEyeTracking = get_class('EllipseEyeTracking', 'ndx-ellipse-eye-tracking')
コード例 #8
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import numpy as np
from pynwb import get_class, load_namespaces
from datetime import datetime
from pynwb import NWBFile
from form.backends.hdf5 import HDF5IO
from pynwb import get_build_manager


ns_path = "alleninstitute.namespace.yaml"
load_namespaces(ns_path)

PopulationSpikeTrain = get_class('PopulationSpikeTrain', 'alleninstitute')
fs = PopulationSpikeTrain(data=(10*np.random.random(5)).astype(np.int),
                          name='my_population',
                          source='acquisition',
                          unit='second',
                          timestamps=np.random.rand(5))

f = NWBFile(source='noone',
            session_description='my first synthetic recording',
            file_name='tmp.nwb',
            identifier='hi',
            experimenter='Dr. Bilbo Baggins',
            lab='Bag End Labatory',
            institution='University of Middle Earth at the Shire',
            experiment_description='empty',
            session_id='LONELYMTN',
            session_start_time=datetime.now())

f.add_raw_timeseries(fs)
コード例 #9
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 def test_get_class(self):
     self.test_load_namespace()
     TetrodeSeries = get_class('TetrodeSeries',
                               'pynwb_test_extension')  # noqa: F841
コード例 #10
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from pynwb import get_class
from .maze_extension import MazeExtension

LabMetaDataExtension = get_class('LabMetaDataExtension', 'ndx-tank-metadata')
RigExtension = get_class('RigExtension', 'ndx-tank-metadata')
コード例 #11
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ファイル: __init__.py プロジェクト: rly/ndx-bipolar-scheme
import os
from pynwb import load_namespaces, get_class

# Set path of the namespace.yaml file to the expected install location
ndx_bipolar_scheme_specpath = os.path.join(
    os.path.dirname(__file__), 'spec', 'ndx-bipolar-scheme.namespace.yaml')

# If the extension has not been installed yet but we are running directly from
# the git repo
if not os.path.exists(ndx_bipolar_scheme_specpath):
    ndx_bipolar_scheme_specpath = os.path.abspath(
        os.path.join(os.path.dirname(__file__), '..', '..', '..', 'spec',
                     'ndx-bipolar-scheme.namespace.yaml'))

# Load the namespace
load_namespaces(ndx_bipolar_scheme_specpath)

EcephysExt = get_class('EcephysExt', 'ndx-bipolar-scheme')
コード例 #12
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#     and :py:func:`~pynwb.form.utils.get_docval`
#
# When extending :py:class:`~pynwb.core.NWBContainer` or :py:class:`~pynwb.core.NWBContainer`
# subclasses, you should defining the class field ``__nwbfields__``. This will
# tell PyNWB the properties of the :py:class:`~pynwb.core.NWBContainer` extension.
#
# If you do not want to write additional code to read your extensions, PyNWB is able to dynamically
# create an :py:class:`~pynwb.core.NWBContainer` subclass for use within the PyNWB API.
# Dynamically created classes can be inspected using the built-in :py:func:`.help` or the :py:mod:`inspect` module.

from pynwb import get_class, load_namespaces

ns_path = "mylab.namespace.yaml"
load_namespaces(ns_path)

AutoTetrodeSeries = get_class('TetrodeSeries', 'mylab')

####################
# .. note::
#
#     When defining your own :py:class:`~pynwb.core.NWBContainer`, the subclass name does not need to be the same
#     as the extension type name. However, it is encouraged to keep class and extension names the same for the
#     purposes of readibility.

####################
# .. _caching_extension:
#
# Caching extensions to file
# -----------------------------------------------------
#
# Extensions can be cached to file so that your NWB file will carry the extensions needed to read the file with it.
コード例 #13
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ファイル: test_extension.py プロジェクト: ecmyhre/pynwb
 def test_get_class(self):
     self.test_load_namespace()
     TetrodeSeries = get_class('TetrodeSeries', self.prefix)  # noqa: F841
コード例 #14
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        where these are (this is) the compartment(s)
    compartment_labels: str | Iterable(str) (optional)
        or where these are (this is) the label(s)

    Returns
    -------

    np.array(dtype=int)

    """
    if compartment_numbers is not None and compartment_labels is not None:
        raise ValueError('you cannot specify both compartments and compartment_labels')
    if cell == 0:
        start_ind = 0
    else:
        start_ind = self.compartments['number_index'].data[cell-1]
    cell_compartments = self.compartments['number'][cell]
    if compartment_numbers is not None:
        return self._compartment_finder(cell_compartments, compartment_numbers, int, start_ind)
    elif compartment_labels is not None:
        return self._compartment_finder(cell_compartments, compartment_labels, str, start_ind)
    else:
        return np.arange(start_ind, start_ind + len(cell_compartments), dtype=int)


CompartmentSeries = get_class('CompartmentSeries', name)
CompartmentSeries._compartment_finder = _compartment_finder
CompartmentSeries.find_compartments = find_compartments

SimulationMetaData = get_class('SimulationMetaData', name)
コード例 #15
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#ns_builder.add_spec(ext_source, blender_surface)

blender_plane_segmentation = NWBGroupSpec(
    'A plane to store data from blender',
    neurodata_type_inc='PlaneSegmentation',
    neurodata_type_def='BlenderPlaneSegmentation',
    groups=[blender_surface])

ns_builder.add_spec(ext_source, blender_plane_segmentation)

#Writes YAML files
ns_builder.export(ns_path)

load_namespaces('blenderbits.namespace.yaml')
BlenderSurface = get_class('BlenderSurface', 'TanLab')
BlenderPlaneSegmentation = get_class('BlenderPlaneSegmentation', 'TanLab')

#Read in OBJ
os.chdir(
    'C:/Users/Mrika/OneDrive/TanLab/NWBHackathonFiles/HackthonFiles/ObjectModels'
)
soma_triangles = o3d.io.read_triangle_mesh("soma.obj")
soma_triangles = np.asarray(soma_triangles.triangles)

#Testing stuff
soma_surface = BlenderSurface(vertices=[[0.0, 1.0, 1.0], [1.0, 1.0, 2.0],
                                        [2.0, 2.0, 1.0], [2.0, 1.0, 1.0],
                                        [1.0, 2.0, 1.0]],
                              faces=soma_triangles,
                              name='soma')
コード例 #16
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import os
from pynwb import load_namespaces, get_class

ibl_metadata_specpath = os.path.join(
    os.path.dirname(__file__),
    'spec',
    'ndx-ibl-metadata.namespace.yaml'
)

if not os.path.exists(ibl_metadata_specpath):
    ibl_metadata_specpath = os.path.abspath(os.path.join(
        os.path.dirname(__file__),
        '..', '..', '..',
        'spec',
        'ndx-ibl-metadata.namespace.yaml'
    ))

# Load the namespace
load_namespaces(ibl_metadata_specpath)

IblSessionData = get_class('IblSessionData', 'ndx-ibl-metadata')
IblSubject = get_class('IblSubject', 'ndx-ibl-metadata')
IblProbes = get_class('IblProbes', 'ndx-ibl-metadata')
コード例 #17
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import os
from pynwb import load_namespaces, get_class
from os import path

from pynwb.file import MultiContainerInterface
from pynwb import register_class
from pynwb.file import LabMetaData

name = 'ndx-task'

here = path.abspath(path.dirname(__file__))
ns_path = os.path.join(here, 'spec', name + '.namespace.yaml')

load_namespaces(ns_path)

Task = get_class('Task', name)


@register_class('Tasks', name)
class Tasks(MultiContainerInterface, LabMetaData):
    """
    Purpose:
        Topological graph representing connected components of a behavioral Environment.

    Arguments:
        name (str): name of this Environment
        tasks (list): list of Environment objects

    """

    __nwbfields__ = ('name', 'tasks')
コード例 #18
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from pynwb import load_namespaces, get_class
from os import path

from pynwb.file import MultiContainerInterface
from pynwb import register_class
from pynwb.file import LabMetaData

name = 'ndx-maze'

here = path.abspath(path.dirname(__file__))
ns_path = os.path.join(here, 'spec', name + '.namespace.yaml')

load_namespaces(ns_path)


Node = get_class('Node', name)
Edge = get_class('Edge', name)
PointNode = get_class('PointNode', name)
SegmentNode = get_class('SegmentNode', name)
PolygonNode = get_class('PolygonNode', name)


@register_class('Environment', name)
class Environment(MultiContainerInterface):
    """
    Purpose:
        Topological graph representing connected components of a beahvioral Environment.

    Arguments:
        name (str): name of this Environment
        nodes (list): list of Node objects contained in this Environment
コード例 #19
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import os
from pynwb import load_namespaces, get_class
from os import path

name = 'ndx-nonrigid-motion-correction'

here = path.abspath(path.dirname(__file__))
ns_path = os.path.join(here, 'spec', name + '.namespace.yaml')

load_namespaces(ns_path)

NonrigidMotionCorrection = get_class('NonrigidMotionCorrection', name)


def local_interpolation(transform, image, npixels=1):
    """

    Parameters
    ----------
    transform
    image
    npixels: int

    Returns
    -------

    """
    pass


def nonrigid_motion_correction_apply(self, ts):
コード例 #20
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import os
from pynwb import load_namespaces, get_class
from os import path

name = 'ndx-fret'

here = path.abspath(path.dirname(__file__))
ns_path = os.path.join(here, 'spec', name + '.namespace.yaml')

load_namespaces(ns_path)

FRETSeries = get_class('FRETSeries', name)

FRET = get_class('FRET', name)
コード例 #21
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# If the extension has not been installed yet but we are running directly from
# the git repo
if not os.path.exists(ndx_photometry_specpath):
    ndx_photometry_specpath = os.path.abspath(
        os.path.join(
            os.path.dirname(__file__),
            "..",
            "..",
            "..",
            "spec",
            "ndx-photometry.namespace.yaml",
        ))

# Load the namespace
load_namespaces(ndx_photometry_specpath)

# TODO: import your classes here or define your class using get_class to make

from .fibers_table import FibersTable

# them accessible at the package level
(CommandedVoltageSeries, ExcitationSourcesTable, PhotodetectorsTable,
 DeconvolvedRoiResponseSeries, MultiCommandedVoltage, FiberPhotometry,
 FluorophoresTable) = [
     get_class(x, "ndx-photometry")
     for x in ("CommandedVoltageSeries", "ExcitationSourcesTable",
               "PhotodetectorsTable", "DeconvolvedRoiResponseSeries",
               "MultiCommandedVoltage", 'FiberPhotometry', "FluorophoresTable")
 ]
コード例 #22
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import numpy as np
import pandas as pd
from bs4 import BeautifulSoup

from pynwb import load_namespaces, get_class
from pynwb.misc import UnitTimes
from general import gzip

import pdb

name = 'general'
ns_path = name + '.namespace.yaml'

load_namespaces(ns_path)
PopulationSpikeTimes = get_class('PopulationSpikeTimes', name)


def load_xml(filepath):
    with open(filepath, 'r') as xml_file:
        contents = xml_file.read()
        soup = BeautifulSoup(contents, 'xml')
    return soup


def get_channel_groups(xml_filepath):
    """Get the groups of channels that are recorded on each shank from the xml
    file

    Parameters
    ----------
コード例 #23
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#     and :py:func:`~hdmf.utils.get_docval`
#
# When extending :py:class:`~pynwb.core.NWBContainer` or :py:class:`~pynwb.core.NWBContainer`
# subclasses, you should define the class field ``__nwbfields__``. This will
# tell PyNWB the properties of the :py:class:`~pynwb.core.NWBContainer` extension.
#
# If you do not want to write additional code to read your extensions, PyNWB is able to dynamically
# create an :py:class:`~pynwb.core.NWBContainer` subclass for use within the PyNWB API.
# Dynamically created classes can be inspected using the built-in :py:mod:`inspect` module.

from pynwb import get_class, load_namespaces

ns_path = "mylab.namespace.yaml"
load_namespaces(ns_path)

AutoTetrodeSeries = get_class('TetrodeSeries', 'mylab')

####################
# .. note::
#
#     When defining your own :py:class:`~pynwb.core.NWBContainer`, the subclass name does not need to be the same
#     as the extension type name. However, it is encouraged to keep class and extension names the same for the
#     purposes of readability.

####################
# .. _caching_extension:
#
# Caching extensions to file
# -----------------------------------------------------
#
# By default, extensions are cached to file so that your NWB file will carry the extensions needed to read the file
コード例 #24
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ファイル: __init__.py プロジェクト: luiztauffer/ndx-spectrum
import os
from pynwb import load_namespaces, get_class
from os import path

name = 'ndx-spectrum'

here = path.abspath(path.dirname(__file__))
ns_path = os.path.join(here, 'spec', name + '.namespace.yaml')

load_namespaces(ns_path)

Spectrum = get_class('Spectrum', name)
コード例 #25
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import os

import pandas as pd
from pynwb import load_namespaces, get_class
from pynwb.misc import AnnotationSeries

name = 'ndx-miniscope'

here = os.path.abspath(os.path.dirname(__file__))
ns_path = os.path.join(here, 'spec', name + '.namespace.yaml')

load_namespaces(ns_path)

Miniscope = get_class('Miniscope', name)


def load_miniscope_timestamps(fpath, cam_num=1):
    """Reads timestamp.dat and outputs a list of times in seconds

    Parameters
    ----------
    fpath: str
        data directory or path to timestamp.dat
    cam_num: int
        number of feed

    Returns
    -------
    numpy.ndarray list if times in seconds

    """
コード例 #26
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import os
from pynwb import load_namespaces, get_class

# Set path of the namespace.yaml file to the expected install location
ndx_stimulus_template_specpath = os.path.join(
    os.path.dirname(__file__),
    'ndx-aibs-stimulus-template.namespace.yaml'
)

# Load the namespace
load_namespaces(ndx_stimulus_template_specpath)


StimulusTemplateExtension = get_class('StimulusTemplate',
                                      'ndx-aibs-stimulus-template')
コード例 #27
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import os
from pynwb import load_namespaces, get_class
from pynwb import register_class, docval
from hdmf.utils import call_docval_func
from pynwb.file import MultiContainerInterface
from hdmf.common.table import DynamicTable, ElementIdentifiers

name = 'ndx-tempo'
here = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..', '..'))
ns_path = os.path.join(here, 'spec', name + '.namespace.yaml')

load_namespaces(ns_path)

Measurement = get_class('Measurement', name)
LaserLine = get_class('LaserLine', name)
PhotoDetector = get_class('PhotoDetector', name)


@register_class('LockInAmplifier', name)
class LockInAmplifier(DynamicTable):
    __columns__ = (
        {'name': 'channel_name',
         'description': 'name of the channel of lock_in_amp'},
        {'name': 'offset',
         'description': 'offset for channel of lock_in_amp'},
        {'name': 'gain',
         'description': 'gain for channel of lock_in_amp'}
    )

    @docval({'name': 'name', 'type': str, 'doc': 'Name of this Compartments object',
             'default': 'compartments'},
コード例 #28
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import os
from pynwb import load_namespaces, get_class

# Set path of the namespace.yaml file to the expected install location
ndx_ophys_events_specpath = os.path.join(
    os.path.dirname(__file__),
    'ndx-aibs-ophys-event-detection.namespace.yaml'
)

# Load the namespace
load_namespaces(ndx_ophys_events_specpath)


OphysEventDetection = get_class('OphysEventDetection',
                                'ndx-aibs-ophys-event-detection')
コード例 #29
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ファイル: __init__.py プロジェクト: wesley-jones/AllenSDK
from pathlib import Path

import pynwb

file_dir = Path(__file__).parent
namespace_path = (file_dir / "ndx-aibs-ecephys.namespace.yaml").resolve()
pynwb.load_namespaces(str(namespace_path))

EcephysProbe = pynwb.get_class('EcephysProbe', 'ndx-aibs-ecephys')

EcephysElectrodeGroup = pynwb.get_class('EcephysElectrodeGroup',
                                        'ndx-aibs-ecephys')

EcephysSpecimen = pynwb.get_class('EcephysSpecimen', 'ndx-aibs-ecephys')

EcephysEyeTrackingRigMetadata = pynwb.get_class(
    'EcephysEyeTrackingRigMetadata', 'ndx-aibs-ecephys')

EcephysCSD = pynwb.get_class('EcephysCSD', 'ndx-aibs-ecephys')
コード例 #30
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import os

from pynwb import load_namespaces, get_class

name = 'ndx-bipolar-scheme'

# Set path of the namespace.yaml file to the expected install location
ndx_bipolar_scheme_specpath = os.path.join(os.path.dirname(__file__), 'spec',
                                           name + '.namespace.yaml')

# If the extension has not been installed yet but we are running directly from
# the git repo
if not os.path.exists(ndx_bipolar_scheme_specpath):
    ndx_bipolar_scheme_specpath = os.path.abspath(
        os.path.join(os.path.dirname(__file__), '..', '..', '..', 'spec',
                     name + '.namespace.yaml'))

# Load the namespace
load_namespaces(ndx_bipolar_scheme_specpath)

BipolarSchemeTable = get_class('BipolarSchemeTable', 'ndx-bipolar-scheme')
NdxBipolarScheme = get_class('NdxBipolarScheme', 'ndx-bipolar-scheme')