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'neurodata_type': 'VectorData', 'namespace': 'core'}),
DatasetBuilder('z', data=[3.0, 3.0, 3.0, 3.0],
attributes={'description': 'the z coordinate of the channel location',
'neurodata_type': 'VectorData', 'namespace': 'core'}),
DatasetBuilder('imp', data=[-1.0, -2.0, -3.0, -4.0],
attributes={'description': 'the impedance of the channel',
'neurodata_type': 'VectorData', 'namespace': 'core'}),
DatasetBuilder('location', data=['CA1', 'CA1', 'CA1', 'CA1'],
attributes={'description': 'the location of channel within the subject e.g. brain region',
'neurodata_type': 'VectorData', 'namespace': 'core'}),
DatasetBuilder('filtering', data=['none', 'none', 'none', 'none'],
attributes={'description': 'description of hardware filtering',
'neurodata_type': 'VectorData', 'namespace': 'core'}),
DatasetBuilder('group', data=[ReferenceBuilder(self.eg_builder),
ReferenceBuilder(self.eg_builder),
ReferenceBuilder(self.eg_builder),
ReferenceBuilder(self.eg_builder)],
attributes={'description': 'a reference to the ElectrodeGroup this electrode is a part of',
'neurodata_type': 'VectorData', 'namespace': 'core'}),
DatasetBuilder('group_name', data=['tetrode1', 'tetrode1', 'tetrode1', 'tetrode1'],
attributes={'description': 'the name of the ElectrodeGroup this electrode is a part of',
'neurodata_type': 'VectorData', 'namespace': 'core'}),
]
return GroupBuilder('electrodes', datasets={d.name: d for d in datasets},
attributes={'colnames': (b'x',
b'y',
b'z',
b'imp',
b'location',
b'filtering',
b'group',
b'group_name'),
'format': DatasetBuilder('format', 'tiff'),
'dimension': DatasetBuilder('dimension', [2]),
})
self.pixel_masks_builder = DatasetBuilder('pixel_mask', self.pix_mask,
attributes={
'namespace': 'core',
'neurodata_type': 'VectorData',
'description': 'Pixel masks for each ROI',
'help': 'Values for a list of elements'})
self.pxmsk_index_builder = DatasetBuilder('pixel_mask_index', self.pxmsk_index,
attributes={
'namespace': 'core',
'neurodata_type': 'VectorIndex',
'target': ReferenceBuilder(self.pixel_masks_builder),
'help': 'indexes into a list of values for a list of elements'})
self.image_masks_builder = DatasetBuilder('image_mask', self.img_mask,
attributes={
'namespace': 'core',
'neurodata_type': 'VectorData',
'description': 'Image masks for each ROI',
'help': 'Values for a list of elements'})
ps_builder = GroupBuilder(
'test_plane_seg_name',
attributes={
'neurodata_type': 'PlaneSegmentation',
'namespace': 'core',
'description': 'plane segmentation description',
'colnames': (b'image_mask', b'pixel_mask'),
'description': 'no description',
'neurodata_type': 'ElectricalSeries'},
datasets={'data': data_builder,
'timestamps': timestamps_builder,
'electrodes': elec_builder})
data = list(zip(reversed(range(10)), reversed(range(10, 20))))
data_builder = DatasetBuilder('data', data,
attributes={'unit': 'volts',
'conversion': 1.0,
'resolution': 0.0})
timestamps_builder = DatasetBuilder('timestamps', timestamps, attributes={'unit': 'seconds', 'interval': 1})
elec_builder = DatasetBuilder('electrodes', data=[1, 3],
attributes={'neurodata_type': 'DynamicTableRegion',
'namespace': 'core',
'table': ReferenceBuilder(table_builder),
'description': 'the second and fourth electrodes'})
es2 = GroupBuilder('test_eS2',
attributes={'namespace': base.CORE_NAMESPACE,
'comments': 'no comments',
'description': 'no description',
'neurodata_type': 'ElectricalSeries'},
datasets={'data': data_builder,
'timestamps': timestamps_builder,
'electrodes': elec_builder})
return es1, es2
'help': ('ROI responses over an imaging plane. Each element on the second dimension of data[] '
'should correspond to the signal from one ROI')},
datasets={
'data': DatasetBuilder(
'data', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
attributes={
'unit': 'lumens',
'conversion': 1.0,
'resolution': 0.0}
),
'timestamps': DatasetBuilder('timestamps', [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9],
attributes={'unit': 'Seconds', 'interval': 1}),
'rois': DatasetBuilder('rois', data=[0],
attributes={'help': 'a subset (i.e. slice or region) of a DynamicTable',
'description': 'the first of two ROIs',
'table': ReferenceBuilder(ps_builder),
'namespace': 'core',
'neurodata_type': 'DynamicTableRegion'}),
})
def setUpBuilder(self):
table_builder = self.get_table_builder(self)
data = list(zip(range(10), range(10, 20)))
timestamps = list(map(lambda x: x/10, range(10)))
data_builder = DatasetBuilder('data', data,
attributes={'unit': 'volts',
'conversion': 1.0,
'resolution': 0.0})
timestamps_builder = DatasetBuilder('timestamps', timestamps, attributes={'unit': 'seconds', 'interval': 1})
elec_builder = DatasetBuilder('electrodes', data=[0, 2],
attributes={'neurodata_type': 'DynamicTableRegion',
'namespace': 'core',
'table': ReferenceBuilder(table_builder),
'description': 'the first and third electrodes'})
return GroupBuilder('test_eS',
attributes={'namespace': base.CORE_NAMESPACE,
'comments': 'no comments',
'description': 'no description',
'neurodata_type': 'ElectricalSeries'},
datasets={'data': data_builder,
'timestamps': timestamps_builder,
'electrodes': elec_builder})