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regenerate models

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sneakers-the-rat 2024-07-08 19:10:19 -07:00
parent b9ed7c0026
commit 78de59a0f1
Signed by untrusted user who does not match committer: jonny
GPG key ID: 6DCB96EF1E4D232D
111 changed files with 560 additions and 558 deletions
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2
nwb_linkml/src/nwb_linkml/adapters/dataset.py
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@ -447,7 +447,7 @@ class DatasetAdapter(ClassAdapter):
""" """
Orchestrator class for datasets - calls the set of applicable mapping classes Orchestrator class for datasets - calls the set of applicable mapping classes
""" """
TYPE = Dataset TYPE: Type = Dataset
cls: Dataset cls: Dataset

4
nwb_linkml/src/nwb_linkml/adapters/group.py
View file

@ -2,6 +2,8 @@
Adapter for NWB groups to linkml Classes Adapter for NWB groups to linkml Classes
""" """
from typing import Type
from linkml_runtime.linkml_model import SlotDefinition from linkml_runtime.linkml_model import SlotDefinition
from nwb_linkml.adapters.adapter import BuildResult from nwb_linkml.adapters.adapter import BuildResult
@ -16,7 +18,7 @@ class GroupAdapter(ClassAdapter):
""" """
Adapt NWB Groups to LinkML Classes Adapt NWB Groups to LinkML Classes
""" """
TYPE = Group TYPE: Type = Group
cls: Group cls: Group

12
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_base.py
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@ -53,7 +53,7 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_1_0.hdmf_common_table import Container, Data, DynamicTable from ...hdmf_common.v1_1_0.hdmf_common_table import Data, Container, DynamicTable
metamodel_version = "None" metamodel_version = "None"
@ -118,8 +118,8 @@ class Image(NWBData):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -204,9 +204,9 @@ class TimeSeriesData(ConfiguredBaseModel):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* num_times"], Any], NDArray[Shape["* num_times"], Any],
NDArray[Shape["* num_times, * num_DIM2"], Any], NDArray[Shape["* num_times, * num_dim2"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3, * num_DIM4"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3, * num_dim4"], Any],
] ]
] = Field(None) ] = Field(None)

6
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_ecephys.py
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@ -53,16 +53,16 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_1_0.hdmf_common_table import DynamicTable, DynamicTableRegion
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime,
NWBDataInterface, NWBDataInterface,
TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
TimeSeries, TimeSeries,
NWBContainer, NWBContainer,
) )
from ...hdmf_common.v1_1_0.hdmf_common_table import DynamicTable, DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.2.0" version = "2.2.0"

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_epoch.py
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@ -54,9 +54,9 @@ if TYPE_CHECKING:
from ...hdmf_common.v1_1_0.hdmf_common_table import ( from ...hdmf_common.v1_1_0.hdmf_common_table import (
VectorIndex,
VectorData, VectorData,
DynamicTable, DynamicTable,
VectorIndex,
) )
from .core_nwb_base import TimeSeries from .core_nwb_base import TimeSeries

16
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_file.py
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@ -53,26 +53,26 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_misc import Units
from .core_nwb_device import Device from .core_nwb_device import Device
from .core_nwb_ecephys import ElectrodeGroup from .core_nwb_ecephys import ElectrodeGroup
from .core_nwb_epoch import TimeIntervals
from .core_nwb_base import NWBContainer, TimeSeries, ProcessingModule, NWBDataInterface
from .core_nwb_ophys import ImagingPlane from .core_nwb_ophys import ImagingPlane
from .core_nwb_icephys import SweepTable, IntracellularElectrode from .core_nwb_icephys import IntracellularElectrode, SweepTable
from .core_nwb_base import NWBContainer, TimeSeries, NWBDataInterface, ProcessingModule
from .core_nwb_epoch import TimeIntervals
from ...hdmf_common.v1_1_0.hdmf_common_table import ( from ...hdmf_common.v1_1_0.hdmf_common_table import (
DynamicTable,
VectorIndex, VectorIndex,
VectorData, VectorData,
DynamicTable,
) )
from .core_nwb_misc import Units
from .core_nwb_ogen import OptogeneticStimulusSite from .core_nwb_ogen import OptogeneticStimulusSite

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_icephys.py
View file

@ -61,9 +61,9 @@ from .core_nwb_base import (
) )
from ...hdmf_common.v1_1_0.hdmf_common_table import ( from ...hdmf_common.v1_1_0.hdmf_common_table import (
DynamicTable,
VectorIndex, VectorIndex,
VectorData, VectorData,
DynamicTable,
) )

18
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_image.py
View file

@ -53,7 +53,7 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, Image, TimeSeries from .core_nwb_base import Image, TimeSeriesStartingTime, TimeSeriesSync, TimeSeries
metamodel_version = "None" metamodel_version = "None"
@ -109,8 +109,8 @@ class GrayscaleImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -131,8 +131,8 @@ class RGBImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -153,8 +153,8 @@ class RGBAImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -291,8 +291,8 @@ class OpticalSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width, height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width, height, depth"], float], NDArray[Shape["3 width_height_depth"], float],
] ]
] = Field( ] = Field(
None, None,

6
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_misc.py
View file

@ -54,10 +54,10 @@ if TYPE_CHECKING:
from ...hdmf_common.v1_1_0.hdmf_common_table import ( from ...hdmf_common.v1_1_0.hdmf_common_table import (
VectorIndex,
VectorData, VectorData,
DynamicTable, DynamicTable,
DynamicTableRegion, DynamicTableRegion,
VectorIndex,
) )
from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, TimeSeries from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, TimeSeries
@ -313,7 +313,7 @@ class DecompositionSeriesBands(DynamicTable):
band_name: Optional[List[str] | str] = Field( band_name: Optional[List[str] | str] = Field(
default_factory=list, description="""Name of the band, e.g. theta.""" default_factory=list, description="""Name of the band, e.g. theta."""
) )
band_limits: NDArray[Shape["* num_bands, 2 low, high"], float] = Field( band_limits: NDArray[Shape["* num_bands, 2 low_high"], float] = Field(
..., ...,
description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""", description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""",
) )
@ -359,7 +359,7 @@ class Units(DynamicTable):
obs_intervals_index: Optional[str] = Field( obs_intervals_index: Optional[str] = Field(
None, description="""Index into the obs_intervals dataset.""" None, description="""Index into the obs_intervals dataset."""
) )
obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start|end"], float]] = ( obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start_end"], float]] = (
Field(None, description="""Observation intervals for each unit.""") Field(None, description="""Observation intervals for each unit.""")
) )
electrodes_index: Optional[str] = Field( electrodes_index: Optional[str] = Field(

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_ogen.py
View file

@ -54,10 +54,10 @@ if TYPE_CHECKING:
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesSync,
NWBContainer, NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync,
) )

20
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_ophys.py
View file

@ -53,16 +53,16 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_image import ImageSeriesExternalFile, ImageSeries
from .core_nwb_base import ( from .core_nwb_base import (
NWBDataInterface,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBDataInterface,
TimeSeries, TimeSeries,
NWBContainer, NWBContainer,
) )
from .core_nwb_image import ImageSeriesExternalFile, ImageSeries
from ...hdmf_common.v1_1_0.hdmf_common_table import DynamicTable, DynamicTableRegion from ...hdmf_common.v1_1_0.hdmf_common_table import DynamicTable, DynamicTableRegion
@ -117,8 +117,8 @@ class TwoPhotonSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width|height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width|height"], float], NDArray[Shape["3 width_height"], float],
] ]
] = Field( ] = Field(
None, None,
@ -179,7 +179,7 @@ class RoiResponseSeries(TimeSeries):
name: str = Field(...) name: str = Field(...)
data: Union[ data: Union[
NDArray[Shape["* num_times"], float], NDArray[Shape["* num_times"], float],
NDArray[Shape["* num_times, * num_ROIs"], float], NDArray[Shape["* num_times, * num_rois"], float],
] = Field(..., description="""Signals from ROIs.""") ] = Field(..., description="""Signals from ROIs.""")
rois: str = Field( rois: str = Field(
..., ...,
@ -325,8 +325,8 @@ class ImagingPlaneManifold(ConfiguredBaseModel):
) )
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* height, * width, * depth, 3 x, y, z"], float], NDArray[Shape["* height, * width, * depth, 3 x_y_z"], float],
NDArray[Shape["* height, * width, 3 x, y, z"], float], NDArray[Shape["* height, * width, 3 x_y_z"], float],
] ]
] = Field(None) ] = Field(None)
@ -342,7 +342,7 @@ class ImagingPlaneOriginCoords(ConfiguredBaseModel):
None, None,
description="""Measurement units for origin_coords. The default value is 'meters'.""", description="""Measurement units for origin_coords. The default value is 'meters'.""",
) )
array: Optional[NDArray[Shape["2 x, y, 3 x, y, z"], float]] = Field(None) array: Optional[NDArray[Shape["2 x_y, 3 x_y_z"], float]] = Field(None)
class ImagingPlaneGridSpacing(ConfiguredBaseModel): class ImagingPlaneGridSpacing(ConfiguredBaseModel):
@ -356,7 +356,7 @@ class ImagingPlaneGridSpacing(ConfiguredBaseModel):
None, None,
description="""Measurement units for grid_spacing. The default value is 'meters'.""", description="""Measurement units for grid_spacing. The default value is 'meters'.""",
) )
array: Optional[NDArray[Shape["2 x, y, 3 x, y, z"], float]] = Field(None) array: Optional[NDArray[Shape["2 x_y, 3 x_y_z"], float]] = Field(None)
class OpticalChannel(NWBContainer): class OpticalChannel(NWBContainer):

14
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_retinotopy.py
View file

@ -53,7 +53,7 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_base import NWBData, NWBDataInterface from .core_nwb_base import NWBDataInterface, NWBData
from .core_nwb_image import GrayscaleImage from .core_nwb_image import GrayscaleImage
@ -162,8 +162,8 @@ class RetinotopyImage(GrayscaleImage):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -336,8 +336,8 @@ class ImagingRetinotopyFocalDepthImage(RetinotopyImage):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -372,8 +372,8 @@ class ImagingRetinotopyVasculatureImage(RetinotopyImage):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)

12
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_base.py
View file

@ -53,7 +53,7 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_1_2.hdmf_common_table import Container, Data, DynamicTable from ...hdmf_common.v1_1_2.hdmf_common_table import Data, Container, DynamicTable
metamodel_version = "None" metamodel_version = "None"
@ -118,8 +118,8 @@ class Image(NWBData):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -204,9 +204,9 @@ class TimeSeriesData(ConfiguredBaseModel):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* num_times"], Any], NDArray[Shape["* num_times"], Any],
NDArray[Shape["* num_times, * num_DIM2"], Any], NDArray[Shape["* num_times, * num_dim2"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3, * num_DIM4"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3, * num_dim4"], Any],
] ]
] = Field(None) ] = Field(None)

6
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_ecephys.py
View file

@ -53,16 +53,16 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_1_2.hdmf_common_table import DynamicTable, DynamicTableRegion
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime,
NWBDataInterface, NWBDataInterface,
TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
TimeSeries, TimeSeries,
NWBContainer, NWBContainer,
) )
from ...hdmf_common.v1_1_2.hdmf_common_table import DynamicTable, DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.2.1" version = "2.2.1"

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_epoch.py
View file

@ -54,9 +54,9 @@ if TYPE_CHECKING:
from ...hdmf_common.v1_1_2.hdmf_common_table import ( from ...hdmf_common.v1_1_2.hdmf_common_table import (
VectorIndex,
VectorData, VectorData,
DynamicTable, DynamicTable,
VectorIndex,
) )
from .core_nwb_base import TimeSeries from .core_nwb_base import TimeSeries

16
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_file.py
View file

@ -53,26 +53,26 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_misc import Units
from .core_nwb_device import Device from .core_nwb_device import Device
from .core_nwb_ecephys import ElectrodeGroup from .core_nwb_ecephys import ElectrodeGroup
from .core_nwb_epoch import TimeIntervals
from .core_nwb_base import NWBContainer, TimeSeries, ProcessingModule, NWBDataInterface
from .core_nwb_ophys import ImagingPlane from .core_nwb_ophys import ImagingPlane
from .core_nwb_icephys import SweepTable, IntracellularElectrode from .core_nwb_icephys import IntracellularElectrode, SweepTable
from .core_nwb_base import NWBContainer, TimeSeries, NWBDataInterface, ProcessingModule
from .core_nwb_epoch import TimeIntervals
from ...hdmf_common.v1_1_2.hdmf_common_table import ( from ...hdmf_common.v1_1_2.hdmf_common_table import (
DynamicTable,
VectorIndex, VectorIndex,
VectorData, VectorData,
DynamicTable,
) )
from .core_nwb_misc import Units
from .core_nwb_ogen import OptogeneticStimulusSite from .core_nwb_ogen import OptogeneticStimulusSite

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_icephys.py
View file

@ -61,9 +61,9 @@ from .core_nwb_base import (
) )
from ...hdmf_common.v1_1_2.hdmf_common_table import ( from ...hdmf_common.v1_1_2.hdmf_common_table import (
DynamicTable,
VectorIndex, VectorIndex,
VectorData, VectorData,
DynamicTable,
) )

18
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_image.py
View file

@ -53,7 +53,7 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, Image, TimeSeries from .core_nwb_base import Image, TimeSeriesStartingTime, TimeSeriesSync, TimeSeries
metamodel_version = "None" metamodel_version = "None"
@ -109,8 +109,8 @@ class GrayscaleImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -131,8 +131,8 @@ class RGBImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -153,8 +153,8 @@ class RGBAImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -291,8 +291,8 @@ class OpticalSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width, height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width, height, depth"], float], NDArray[Shape["3 width_height_depth"], float],
] ]
] = Field( ] = Field(
None, None,

6
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_misc.py
View file

@ -54,10 +54,10 @@ if TYPE_CHECKING:
from ...hdmf_common.v1_1_2.hdmf_common_table import ( from ...hdmf_common.v1_1_2.hdmf_common_table import (
VectorIndex,
VectorData, VectorData,
DynamicTable, DynamicTable,
DynamicTableRegion, DynamicTableRegion,
VectorIndex,
) )
from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, TimeSeries from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, TimeSeries
@ -313,7 +313,7 @@ class DecompositionSeriesBands(DynamicTable):
band_name: Optional[List[str] | str] = Field( band_name: Optional[List[str] | str] = Field(
default_factory=list, description="""Name of the band, e.g. theta.""" default_factory=list, description="""Name of the band, e.g. theta."""
) )
band_limits: NDArray[Shape["* num_bands, 2 low, high"], float] = Field( band_limits: NDArray[Shape["* num_bands, 2 low_high"], float] = Field(
..., ...,
description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""", description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""",
) )
@ -359,7 +359,7 @@ class Units(DynamicTable):
obs_intervals_index: Optional[str] = Field( obs_intervals_index: Optional[str] = Field(
None, description="""Index into the obs_intervals dataset.""" None, description="""Index into the obs_intervals dataset."""
) )
obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start|end"], float]] = ( obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start_end"], float]] = (
Field(None, description="""Observation intervals for each unit.""") Field(None, description="""Observation intervals for each unit.""")
) )
electrodes_index: Optional[str] = Field( electrodes_index: Optional[str] = Field(

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_ogen.py
View file

@ -54,10 +54,10 @@ if TYPE_CHECKING:
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesSync,
NWBContainer, NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync,
) )

20
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_ophys.py
View file

@ -53,16 +53,16 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_image import ImageSeriesExternalFile, ImageSeries
from .core_nwb_base import ( from .core_nwb_base import (
NWBDataInterface,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBDataInterface,
TimeSeries, TimeSeries,
NWBContainer, NWBContainer,
) )
from .core_nwb_image import ImageSeriesExternalFile, ImageSeries
from ...hdmf_common.v1_1_2.hdmf_common_table import DynamicTable, DynamicTableRegion from ...hdmf_common.v1_1_2.hdmf_common_table import DynamicTable, DynamicTableRegion
@ -117,8 +117,8 @@ class TwoPhotonSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width|height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width|height"], float], NDArray[Shape["3 width_height"], float],
] ]
] = Field( ] = Field(
None, None,
@ -179,7 +179,7 @@ class RoiResponseSeries(TimeSeries):
name: str = Field(...) name: str = Field(...)
data: Union[ data: Union[
NDArray[Shape["* num_times"], float], NDArray[Shape["* num_times"], float],
NDArray[Shape["* num_times, * num_ROIs"], float], NDArray[Shape["* num_times, * num_rois"], float],
] = Field(..., description="""Signals from ROIs.""") ] = Field(..., description="""Signals from ROIs.""")
rois: str = Field( rois: str = Field(
..., ...,
@ -325,8 +325,8 @@ class ImagingPlaneManifold(ConfiguredBaseModel):
) )
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* height, * width, * depth, 3 x, y, z"], float], NDArray[Shape["* height, * width, * depth, 3 x_y_z"], float],
NDArray[Shape["* height, * width, 3 x, y, z"], float], NDArray[Shape["* height, * width, 3 x_y_z"], float],
] ]
] = Field(None) ] = Field(None)
@ -342,7 +342,7 @@ class ImagingPlaneOriginCoords(ConfiguredBaseModel):
None, None,
description="""Measurement units for origin_coords. The default value is 'meters'.""", description="""Measurement units for origin_coords. The default value is 'meters'.""",
) )
array: Optional[NDArray[Shape["2 x, y, 3 x, y, z"], float]] = Field(None) array: Optional[NDArray[Shape["2 x_y, 3 x_y_z"], float]] = Field(None)
class ImagingPlaneGridSpacing(ConfiguredBaseModel): class ImagingPlaneGridSpacing(ConfiguredBaseModel):
@ -356,7 +356,7 @@ class ImagingPlaneGridSpacing(ConfiguredBaseModel):
None, None,
description="""Measurement units for grid_spacing. The default value is 'meters'.""", description="""Measurement units for grid_spacing. The default value is 'meters'.""",
) )
array: Optional[NDArray[Shape["2 x, y, 3 x, y, z"], float]] = Field(None) array: Optional[NDArray[Shape["2 x_y, 3 x_y_z"], float]] = Field(None)
class OpticalChannel(NWBContainer): class OpticalChannel(NWBContainer):

14
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_retinotopy.py
View file

@ -53,7 +53,7 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_base import NWBData, NWBDataInterface from .core_nwb_base import NWBDataInterface, NWBData
from .core_nwb_image import GrayscaleImage from .core_nwb_image import GrayscaleImage
@ -162,8 +162,8 @@ class RetinotopyImage(GrayscaleImage):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -336,8 +336,8 @@ class ImagingRetinotopyFocalDepthImage(RetinotopyImage):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -372,8 +372,8 @@ class ImagingRetinotopyVasculatureImage(RetinotopyImage):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)

12
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_base.py
View file

@ -53,7 +53,7 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_1_3.hdmf_common_table import Container, Data, DynamicTable from ...hdmf_common.v1_1_3.hdmf_common_table import Data, Container, DynamicTable
metamodel_version = "None" metamodel_version = "None"
@ -118,8 +118,8 @@ class Image(NWBData):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -204,9 +204,9 @@ class TimeSeriesData(ConfiguredBaseModel):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* num_times"], Any], NDArray[Shape["* num_times"], Any],
NDArray[Shape["* num_times, * num_DIM2"], Any], NDArray[Shape["* num_times, * num_dim2"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3, * num_DIM4"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3, * num_dim4"], Any],
] ]
] = Field(None) ] = Field(None)

6
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_ecephys.py
View file

@ -53,16 +53,16 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, DynamicTableRegion
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime,
NWBDataInterface, NWBDataInterface,
TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
TimeSeries, TimeSeries,
NWBContainer, NWBContainer,
) )
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.2.2" version = "2.2.2"

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_epoch.py
View file

@ -54,9 +54,9 @@ if TYPE_CHECKING:
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
VectorIndex,
VectorData, VectorData,
DynamicTable, DynamicTable,
VectorIndex,
) )
from .core_nwb_base import TimeSeries from .core_nwb_base import TimeSeries

16
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_file.py
View file

@ -53,26 +53,26 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_misc import Units
from .core_nwb_device import Device from .core_nwb_device import Device
from .core_nwb_ecephys import ElectrodeGroup from .core_nwb_ecephys import ElectrodeGroup
from .core_nwb_epoch import TimeIntervals
from .core_nwb_base import NWBContainer, TimeSeries, ProcessingModule, NWBDataInterface
from .core_nwb_ophys import ImagingPlane from .core_nwb_ophys import ImagingPlane
from .core_nwb_icephys import SweepTable, IntracellularElectrode from .core_nwb_icephys import IntracellularElectrode, SweepTable
from .core_nwb_base import NWBContainer, TimeSeries, NWBDataInterface, ProcessingModule
from .core_nwb_epoch import TimeIntervals
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
DynamicTable,
VectorIndex, VectorIndex,
VectorData, VectorData,
DynamicTable,
) )
from .core_nwb_misc import Units
from .core_nwb_ogen import OptogeneticStimulusSite from .core_nwb_ogen import OptogeneticStimulusSite

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_icephys.py
View file

@ -61,9 +61,9 @@ from .core_nwb_base import (
) )
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
DynamicTable,
VectorIndex, VectorIndex,
VectorData, VectorData,
DynamicTable,
) )

20
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_image.py
View file

@ -53,7 +53,7 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, Image, TimeSeries from .core_nwb_base import Image, TimeSeriesStartingTime, TimeSeriesSync, TimeSeries
metamodel_version = "None" metamodel_version = "None"
@ -109,8 +109,8 @@ class GrayscaleImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -131,8 +131,8 @@ class RGBImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -153,8 +153,8 @@ class RGBAImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -291,8 +291,8 @@ class OpticalSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width, height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width, height, depth"], float], NDArray[Shape["3 width_height_depth"], float],
] ]
] = Field( ] = Field(
None, None,
@ -300,7 +300,7 @@ class OpticalSeries(ImageSeries):
) )
data: Union[ data: Union[
NDArray[Shape["* frame, * x, * y"], float], NDArray[Shape["* frame, * x, * y"], float],
NDArray[Shape["* frame, * x, * y, 3 r, g, b"], float], NDArray[Shape["* frame, * x, * y, 3 r_g_b"], float],
] = Field( ] = Field(
..., description="""Images presented to subject, either grayscale or RGB""" ..., description="""Images presented to subject, either grayscale or RGB"""
) )

6
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_misc.py
View file

@ -54,10 +54,10 @@ if TYPE_CHECKING:
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
VectorIndex,
VectorData, VectorData,
DynamicTable, DynamicTable,
DynamicTableRegion, DynamicTableRegion,
VectorIndex,
) )
from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, TimeSeries from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, TimeSeries
@ -313,7 +313,7 @@ class DecompositionSeriesBands(DynamicTable):
band_name: Optional[List[str] | str] = Field( band_name: Optional[List[str] | str] = Field(
default_factory=list, description="""Name of the band, e.g. theta.""" default_factory=list, description="""Name of the band, e.g. theta."""
) )
band_limits: NDArray[Shape["* num_bands, 2 low, high"], float] = Field( band_limits: NDArray[Shape["* num_bands, 2 low_high"], float] = Field(
..., ...,
description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""", description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""",
) )
@ -359,7 +359,7 @@ class Units(DynamicTable):
obs_intervals_index: Optional[str] = Field( obs_intervals_index: Optional[str] = Field(
None, description="""Index into the obs_intervals dataset.""" None, description="""Index into the obs_intervals dataset."""
) )
obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start|end"], float]] = ( obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start_end"], float]] = (
Field(None, description="""Observation intervals for each unit.""") Field(None, description="""Observation intervals for each unit.""")
) )
electrodes_index: Optional[str] = Field( electrodes_index: Optional[str] = Field(

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_ogen.py
View file

@ -54,10 +54,10 @@ if TYPE_CHECKING:
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesSync,
NWBContainer, NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync,
) )

12
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_ophys.py
View file

@ -53,16 +53,16 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_image import ImageSeriesExternalFile, ImageSeries
from .core_nwb_base import ( from .core_nwb_base import (
NWBDataInterface,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBDataInterface,
TimeSeries, TimeSeries,
NWBContainer, NWBContainer,
) )
from .core_nwb_image import ImageSeriesExternalFile, ImageSeries
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, DynamicTableRegion from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, DynamicTableRegion
@ -117,8 +117,8 @@ class TwoPhotonSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width|height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width|height"], float], NDArray[Shape["3 width_height"], float],
] ]
] = Field( ] = Field(
None, None,
@ -179,7 +179,7 @@ class RoiResponseSeries(TimeSeries):
name: str = Field(...) name: str = Field(...)
data: Union[ data: Union[
NDArray[Shape["* num_times"], float], NDArray[Shape["* num_times"], float],
NDArray[Shape["* num_times, * num_ROIs"], float], NDArray[Shape["* num_times, * num_rois"], float],
] = Field(..., description="""Signals from ROIs.""") ] = Field(..., description="""Signals from ROIs.""")
rois: str = Field( rois: str = Field(
..., ...,

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_retinotopy.py
View file

@ -114,7 +114,7 @@ class ImagingRetinotopy(NWBDataInterface):
None, None,
description="""Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""", description="""Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""",
) )
axis_descriptions: NDArray[Shape["2 axis_1, axis_2"], str] = Field( axis_descriptions: NDArray[Shape["2 axis_1_axis_2"], str] = Field(
..., ...,
description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""", description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""",
) )

12
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_base.py
View file

@ -53,7 +53,7 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_1_3.hdmf_common_table import Container, Data, DynamicTable from ...hdmf_common.v1_1_3.hdmf_common_table import Data, Container, DynamicTable
metamodel_version = "None" metamodel_version = "None"
@ -118,8 +118,8 @@ class Image(NWBData):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -204,9 +204,9 @@ class TimeSeriesData(ConfiguredBaseModel):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* num_times"], Any], NDArray[Shape["* num_times"], Any],
NDArray[Shape["* num_times, * num_DIM2"], Any], NDArray[Shape["* num_times, * num_dim2"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3, * num_DIM4"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3, * num_dim4"], Any],
] ]
] = Field(None) ] = Field(None)

6
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_ecephys.py
View file

@ -53,16 +53,16 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, DynamicTableRegion
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime,
NWBDataInterface, NWBDataInterface,
TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
TimeSeries, TimeSeries,
NWBContainer, NWBContainer,
) )
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.2.4" version = "2.2.4"

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_epoch.py
View file

@ -54,9 +54,9 @@ if TYPE_CHECKING:
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
VectorIndex,
VectorData, VectorData,
DynamicTable, DynamicTable,
VectorIndex,
) )
from .core_nwb_base import TimeSeries from .core_nwb_base import TimeSeries

16
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_file.py
View file

@ -53,32 +53,32 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_misc import Units
from .core_nwb_device import Device from .core_nwb_device import Device
from .core_nwb_ecephys import ElectrodeGroup from .core_nwb_ecephys import ElectrodeGroup
from .core_nwb_epoch import TimeIntervals from .core_nwb_ophys import ImagingPlane
from .core_nwb_icephys import IntracellularElectrode, SweepTable
from .core_nwb_base import ( from .core_nwb_base import (
NWBContainer, NWBContainer,
NWBData, NWBData,
TimeSeries, TimeSeries,
ProcessingModule,
NWBDataInterface, NWBDataInterface,
ProcessingModule,
) )
from .core_nwb_ophys import ImagingPlane from .core_nwb_epoch import TimeIntervals
from .core_nwb_icephys import SweepTable, IntracellularElectrode
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
DynamicTable,
VectorIndex, VectorIndex,
VectorData, VectorData,
DynamicTable,
) )
from .core_nwb_misc import Units
from .core_nwb_ogen import OptogeneticStimulusSite from .core_nwb_ogen import OptogeneticStimulusSite

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_icephys.py
View file

@ -61,9 +61,9 @@ from .core_nwb_base import (
) )
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
DynamicTable,
VectorIndex, VectorIndex,
VectorData, VectorData,
DynamicTable,
) )

20
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_image.py
View file

@ -53,7 +53,7 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, Image, TimeSeries from .core_nwb_base import Image, TimeSeriesStartingTime, TimeSeriesSync, TimeSeries
metamodel_version = "None" metamodel_version = "None"
@ -109,8 +109,8 @@ class GrayscaleImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -131,8 +131,8 @@ class RGBImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -153,8 +153,8 @@ class RGBAImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -291,8 +291,8 @@ class OpticalSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width, height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width, height, depth"], float], NDArray[Shape["3 width_height_depth"], float],
] ]
] = Field( ] = Field(
None, None,
@ -300,7 +300,7 @@ class OpticalSeries(ImageSeries):
) )
data: Union[ data: Union[
NDArray[Shape["* frame, * x, * y"], float], NDArray[Shape["* frame, * x, * y"], float],
NDArray[Shape["* frame, * x, * y, 3 r, g, b"], float], NDArray[Shape["* frame, * x, * y, 3 r_g_b"], float],
] = Field( ] = Field(
..., description="""Images presented to subject, either grayscale or RGB""" ..., description="""Images presented to subject, either grayscale or RGB"""
) )

6
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_misc.py
View file

@ -54,10 +54,10 @@ if TYPE_CHECKING:
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
VectorIndex,
VectorData, VectorData,
DynamicTable, DynamicTable,
DynamicTableRegion, DynamicTableRegion,
VectorIndex,
) )
from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, TimeSeries from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, TimeSeries
@ -313,7 +313,7 @@ class DecompositionSeriesBands(DynamicTable):
band_name: Optional[List[str] | str] = Field( band_name: Optional[List[str] | str] = Field(
default_factory=list, description="""Name of the band, e.g. theta.""" default_factory=list, description="""Name of the band, e.g. theta."""
) )
band_limits: NDArray[Shape["* num_bands, 2 low, high"], float] = Field( band_limits: NDArray[Shape["* num_bands, 2 low_high"], float] = Field(
..., ...,
description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""", description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""",
) )
@ -359,7 +359,7 @@ class Units(DynamicTable):
obs_intervals_index: Optional[str] = Field( obs_intervals_index: Optional[str] = Field(
None, description="""Index into the obs_intervals dataset.""" None, description="""Index into the obs_intervals dataset."""
) )
obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start|end"], float]] = ( obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start_end"], float]] = (
Field(None, description="""Observation intervals for each unit.""") Field(None, description="""Observation intervals for each unit.""")
) )
electrodes_index: Optional[str] = Field( electrodes_index: Optional[str] = Field(

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_ogen.py
View file

@ -54,10 +54,10 @@ if TYPE_CHECKING:
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesSync,
NWBContainer, NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync,
) )

24
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_ophys.py
View file

@ -53,15 +53,6 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_image import ImageSeriesExternalFile, ImageSeries
from ...hdmf_common.v1_1_3.hdmf_common_table import (
DynamicTableRegion,
VectorData,
VectorIndex,
DynamicTable,
)
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime, TimeSeriesStartingTime,
NWBContainer, NWBContainer,
@ -70,6 +61,15 @@ from .core_nwb_base import (
TimeSeriesSync, TimeSeriesSync,
) )
from .core_nwb_image import ImageSeries, ImageSeriesExternalFile
from ...hdmf_common.v1_1_3.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorIndex,
VectorData,
)
metamodel_version = "None" metamodel_version = "None"
version = "2.2.4" version = "2.2.4"
@ -122,8 +122,8 @@ class TwoPhotonSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width|height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width|height"], float], NDArray[Shape["3 width_height"], float],
] ]
] = Field( ] = Field(
None, None,
@ -184,7 +184,7 @@ class RoiResponseSeries(TimeSeries):
name: str = Field(...) name: str = Field(...)
data: Union[ data: Union[
NDArray[Shape["* num_times"], float], NDArray[Shape["* num_times"], float],
NDArray[Shape["* num_times, * num_ROIs"], float], NDArray[Shape["* num_times, * num_rois"], float],
] = Field(..., description="""Signals from ROIs.""") ] = Field(..., description="""Signals from ROIs.""")
rois: str = Field( rois: str = Field(
..., ...,

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_retinotopy.py
View file

@ -114,7 +114,7 @@ class ImagingRetinotopy(NWBDataInterface):
None, None,
description="""Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""", description="""Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""",
) )
axis_descriptions: NDArray[Shape["2 axis_1, axis_2"], str] = Field( axis_descriptions: NDArray[Shape["2 axis_1_axis_2"], str] = Field(
..., ...,
description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""", description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""",
) )

12
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_base.py
View file

@ -53,7 +53,7 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_1_3.hdmf_common_table import Container, Data, DynamicTable from ...hdmf_common.v1_1_3.hdmf_common_table import Data, Container, DynamicTable
metamodel_version = "None" metamodel_version = "None"
@ -118,8 +118,8 @@ class Image(NWBData):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -204,9 +204,9 @@ class TimeSeriesData(ConfiguredBaseModel):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* num_times"], Any], NDArray[Shape["* num_times"], Any],
NDArray[Shape["* num_times, * num_DIM2"], Any], NDArray[Shape["* num_times, * num_dim2"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3, * num_DIM4"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3, * num_dim4"], Any],
] ]
] = Field(None) ] = Field(None)

6
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_ecephys.py
View file

@ -53,16 +53,16 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, DynamicTableRegion
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime,
NWBDataInterface, NWBDataInterface,
TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
TimeSeries, TimeSeries,
NWBContainer, NWBContainer,
) )
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.2.5" version = "2.2.5"

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_epoch.py
View file

@ -54,9 +54,9 @@ if TYPE_CHECKING:
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
VectorIndex,
VectorData, VectorData,
DynamicTable, DynamicTable,
VectorIndex,
) )
from .core_nwb_base import TimeSeries from .core_nwb_base import TimeSeries

16
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_file.py
View file

@ -53,32 +53,32 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_misc import Units
from .core_nwb_device import Device from .core_nwb_device import Device
from .core_nwb_ecephys import ElectrodeGroup from .core_nwb_ecephys import ElectrodeGroup
from .core_nwb_epoch import TimeIntervals from .core_nwb_ophys import ImagingPlane
from .core_nwb_icephys import IntracellularElectrode, SweepTable
from .core_nwb_base import ( from .core_nwb_base import (
NWBContainer, NWBContainer,
NWBData, NWBData,
TimeSeries, TimeSeries,
ProcessingModule,
NWBDataInterface, NWBDataInterface,
ProcessingModule,
) )
from .core_nwb_ophys import ImagingPlane from .core_nwb_epoch import TimeIntervals
from .core_nwb_icephys import SweepTable, IntracellularElectrode
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
DynamicTable,
VectorIndex, VectorIndex,
VectorData, VectorData,
DynamicTable,
) )
from .core_nwb_misc import Units
from .core_nwb_ogen import OptogeneticStimulusSite from .core_nwb_ogen import OptogeneticStimulusSite

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_icephys.py
View file

@ -61,9 +61,9 @@ from .core_nwb_base import (
) )
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
DynamicTable,
VectorIndex, VectorIndex,
VectorData, VectorData,
DynamicTable,
) )

20
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_image.py
View file

@ -53,7 +53,7 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, Image, TimeSeries from .core_nwb_base import Image, TimeSeriesStartingTime, TimeSeriesSync, TimeSeries
metamodel_version = "None" metamodel_version = "None"
@ -109,8 +109,8 @@ class GrayscaleImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -131,8 +131,8 @@ class RGBImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -153,8 +153,8 @@ class RGBAImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -291,8 +291,8 @@ class OpticalSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width, height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width, height, depth"], float], NDArray[Shape["3 width_height_depth"], float],
] ]
] = Field( ] = Field(
None, None,
@ -300,7 +300,7 @@ class OpticalSeries(ImageSeries):
) )
data: Union[ data: Union[
NDArray[Shape["* frame, * x, * y"], float], NDArray[Shape["* frame, * x, * y"], float],
NDArray[Shape["* frame, * x, * y, 3 r, g, b"], float], NDArray[Shape["* frame, * x, * y, 3 r_g_b"], float],
] = Field( ] = Field(
..., description="""Images presented to subject, either grayscale or RGB""" ..., description="""Images presented to subject, either grayscale or RGB"""
) )

6
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_misc.py
View file

@ -54,10 +54,10 @@ if TYPE_CHECKING:
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
VectorIndex,
VectorData, VectorData,
DynamicTable, DynamicTable,
DynamicTableRegion, DynamicTableRegion,
VectorIndex,
) )
from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, TimeSeries from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, TimeSeries
@ -313,7 +313,7 @@ class DecompositionSeriesBands(DynamicTable):
band_name: Optional[List[str] | str] = Field( band_name: Optional[List[str] | str] = Field(
default_factory=list, description="""Name of the band, e.g. theta.""" default_factory=list, description="""Name of the band, e.g. theta."""
) )
band_limits: NDArray[Shape["* num_bands, 2 low, high"], float] = Field( band_limits: NDArray[Shape["* num_bands, 2 low_high"], float] = Field(
..., ...,
description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""", description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""",
) )
@ -359,7 +359,7 @@ class Units(DynamicTable):
obs_intervals_index: Optional[str] = Field( obs_intervals_index: Optional[str] = Field(
None, description="""Index into the obs_intervals dataset.""" None, description="""Index into the obs_intervals dataset."""
) )
obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start|end"], float]] = ( obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start_end"], float]] = (
Field(None, description="""Observation intervals for each unit.""") Field(None, description="""Observation intervals for each unit.""")
) )
electrodes_index: Optional[str] = Field( electrodes_index: Optional[str] = Field(

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_ogen.py
View file

@ -54,10 +54,10 @@ if TYPE_CHECKING:
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesSync,
NWBContainer, NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync,
) )

24
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_ophys.py
View file

@ -53,15 +53,6 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_image import ImageSeriesExternalFile, ImageSeries
from ...hdmf_common.v1_1_3.hdmf_common_table import (
DynamicTableRegion,
VectorData,
VectorIndex,
DynamicTable,
)
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime, TimeSeriesStartingTime,
NWBContainer, NWBContainer,
@ -70,6 +61,15 @@ from .core_nwb_base import (
TimeSeriesSync, TimeSeriesSync,
) )
from .core_nwb_image import ImageSeries, ImageSeriesExternalFile
from ...hdmf_common.v1_1_3.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorIndex,
VectorData,
)
metamodel_version = "None" metamodel_version = "None"
version = "2.2.5" version = "2.2.5"
@ -122,8 +122,8 @@ class TwoPhotonSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width|height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width|height|depth"], float], NDArray[Shape["3 width_height_depth"], float],
] ]
] = Field( ] = Field(
None, None,
@ -184,7 +184,7 @@ class RoiResponseSeries(TimeSeries):
name: str = Field(...) name: str = Field(...)
data: Union[ data: Union[
NDArray[Shape["* num_times"], float], NDArray[Shape["* num_times"], float],
NDArray[Shape["* num_times, * num_ROIs"], float], NDArray[Shape["* num_times, * num_rois"], float],
] = Field(..., description="""Signals from ROIs.""") ] = Field(..., description="""Signals from ROIs.""")
rois: str = Field( rois: str = Field(
..., ...,

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_retinotopy.py
View file

@ -114,7 +114,7 @@ class ImagingRetinotopy(NWBDataInterface):
None, None,
description="""Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""", description="""Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""",
) )
axis_descriptions: NDArray[Shape["2 axis_1, axis_2"], str] = Field( axis_descriptions: NDArray[Shape["2 axis_1_axis_2"], str] = Field(
..., ...,
description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""", description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""",
) )

12
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_base.py
View file

@ -53,7 +53,7 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_base import Container, Data from ...hdmf_common.v1_5_0.hdmf_common_base import Data, Container
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable
@ -120,8 +120,8 @@ class Image(NWBData):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -210,9 +210,9 @@ class TimeSeriesData(ConfiguredBaseModel):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* num_times"], Any], NDArray[Shape["* num_times"], Any],
NDArray[Shape["* num_times, * num_DIM2"], Any], NDArray[Shape["* num_times, * num_dim2"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3, * num_DIM4"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3, * num_dim4"], Any],
] ]
] = Field(None) ] = Field(None)

6
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_ecephys.py
View file

@ -53,16 +53,16 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, DynamicTableRegion
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime,
NWBDataInterface, NWBDataInterface,
TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
TimeSeries, TimeSeries,
NWBContainer, NWBContainer,
) )
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.3.0" version = "2.3.0"

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_epoch.py
View file

@ -54,9 +54,9 @@ if TYPE_CHECKING:
from ...hdmf_common.v1_5_0.hdmf_common_table import ( from ...hdmf_common.v1_5_0.hdmf_common_table import (
VectorIndex,
VectorData, VectorData,
DynamicTable, DynamicTable,
VectorIndex,
) )
from .core_nwb_base import TimeSeries from .core_nwb_base import TimeSeries

14
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_file.py
View file

@ -53,27 +53,27 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_misc import Units
from .core_nwb_device import Device from .core_nwb_device import Device
from .core_nwb_ecephys import ElectrodeGroup from .core_nwb_ecephys import ElectrodeGroup
from .core_nwb_epoch import TimeIntervals from .core_nwb_ophys import ImagingPlane
from .core_nwb_icephys import IntracellularElectrode, SweepTable
from .core_nwb_base import ( from .core_nwb_base import (
NWBContainer, NWBContainer,
NWBData, NWBData,
TimeSeries, TimeSeries,
ProcessingModule,
NWBDataInterface, NWBDataInterface,
ProcessingModule,
) )
from .core_nwb_ophys import ImagingPlane from .core_nwb_epoch import TimeIntervals
from .core_nwb_icephys import SweepTable, IntracellularElectrode from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, VectorData
from ...hdmf_common.v1_5_0.hdmf_common_table import VectorData, DynamicTable from .core_nwb_misc import Units
from .core_nwb_ogen import OptogeneticStimulusSite from .core_nwb_ogen import OptogeneticStimulusSite

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_icephys.py
View file

@ -61,9 +61,9 @@ from .core_nwb_base import (
) )
from ...hdmf_common.v1_5_0.hdmf_common_table import ( from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTable,
VectorIndex, VectorIndex,
VectorData, VectorData,
DynamicTable,
) )

20
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_image.py
View file

@ -53,7 +53,7 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, Image, TimeSeries from .core_nwb_base import Image, TimeSeriesStartingTime, TimeSeriesSync, TimeSeries
metamodel_version = "None" metamodel_version = "None"
@ -109,8 +109,8 @@ class GrayscaleImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -131,8 +131,8 @@ class RGBImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -153,8 +153,8 @@ class RGBAImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -291,8 +291,8 @@ class OpticalSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width, height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width, height, depth"], float], NDArray[Shape["3 width_height_depth"], float],
] ]
] = Field( ] = Field(
None, None,
@ -300,7 +300,7 @@ class OpticalSeries(ImageSeries):
) )
data: Union[ data: Union[
NDArray[Shape["* frame, * x, * y"], float], NDArray[Shape["* frame, * x, * y"], float],
NDArray[Shape["* frame, * x, * y, 3 r, g, b"], float], NDArray[Shape["* frame, * x, * y, 3 r_g_b"], float],
] = Field( ] = Field(
..., description="""Images presented to subject, either grayscale or RGB""" ..., description="""Images presented to subject, either grayscale or RGB"""
) )

18
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_misc.py
View file

@ -53,16 +53,16 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_table import ( from .core_nwb_base import TimeSeriesStartingTime, TimeSeries, TimeSeriesSync
DynamicTableRegion,
VectorIndex,
VectorData,
DynamicTable,
)
from .core_nwb_ecephys import ElectrodeGroup from .core_nwb_ecephys import ElectrodeGroup
from .core_nwb_base import TimeSeriesStartingTime, TimeSeries, TimeSeriesSync from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorIndex,
VectorData,
)
metamodel_version = "None" metamodel_version = "None"
@ -341,7 +341,7 @@ class DecompositionSeriesBands(DynamicTable):
band_name: Optional[List[str] | str] = Field( band_name: Optional[List[str] | str] = Field(
default_factory=list, description="""Name of the band, e.g. theta.""" default_factory=list, description="""Name of the band, e.g. theta."""
) )
band_limits: NDArray[Shape["* num_bands, 2 low, high"], float] = Field( band_limits: NDArray[Shape["* num_bands, 2 low_high"], float] = Field(
..., ...,
description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""", description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""",
) )
@ -384,7 +384,7 @@ class Units(DynamicTable):
obs_intervals_index: Optional[str] = Field( obs_intervals_index: Optional[str] = Field(
None, description="""Index into the obs_intervals dataset.""" None, description="""Index into the obs_intervals dataset."""
) )
obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start|end"], float]] = ( obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start_end"], float]] = (
Field(None, description="""Observation intervals for each unit.""") Field(None, description="""Observation intervals for each unit.""")
) )
electrodes_index: Optional[str] = Field( electrodes_index: Optional[str] = Field(

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_ogen.py
View file

@ -54,10 +54,10 @@ if TYPE_CHECKING:
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesSync,
NWBContainer, NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync,
) )

24
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_ophys.py
View file

@ -53,15 +53,6 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_image import ImageSeriesExternalFile, ImageSeries
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTableRegion,
VectorData,
VectorIndex,
DynamicTable,
)
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime, TimeSeriesStartingTime,
NWBContainer, NWBContainer,
@ -70,6 +61,15 @@ from .core_nwb_base import (
TimeSeriesSync, TimeSeriesSync,
) )
from .core_nwb_image import ImageSeries, ImageSeriesExternalFile
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorIndex,
VectorData,
)
metamodel_version = "None" metamodel_version = "None"
version = "2.3.0" version = "2.3.0"
@ -122,8 +122,8 @@ class TwoPhotonSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width|height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width|height|depth"], float], NDArray[Shape["3 width_height_depth"], float],
] ]
] = Field( ] = Field(
None, None,
@ -184,7 +184,7 @@ class RoiResponseSeries(TimeSeries):
name: str = Field(...) name: str = Field(...)
data: Union[ data: Union[
NDArray[Shape["* num_times"], float], NDArray[Shape["* num_times"], float],
NDArray[Shape["* num_times, * num_ROIs"], float], NDArray[Shape["* num_times, * num_rois"], float],
] = Field(..., description="""Signals from ROIs.""") ] = Field(..., description="""Signals from ROIs.""")
rois: str = Field( rois: str = Field(
..., ...,

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_retinotopy.py
View file

@ -114,7 +114,7 @@ class ImagingRetinotopy(NWBDataInterface):
None, None,
description="""Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""", description="""Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""",
) )
axis_descriptions: NDArray[Shape["2 axis_1, axis_2"], str] = Field( axis_descriptions: NDArray[Shape["2 axis_1_axis_2"], str] = Field(
..., ...,
description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""", description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""",
) )

14
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_base.py
View file

@ -53,9 +53,9 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_table import VectorData, DynamicTable from ...hdmf_common.v1_5_0.hdmf_common_base import Data, Container
from ...hdmf_common.v1_5_0.hdmf_common_base import Container, Data from ...hdmf_common.v1_5_0.hdmf_common_table import VectorData, DynamicTable
metamodel_version = "None" metamodel_version = "None"
@ -151,8 +151,8 @@ class Image(NWBData):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -241,9 +241,9 @@ class TimeSeriesData(ConfiguredBaseModel):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* num_times"], Any], NDArray[Shape["* num_times"], Any],
NDArray[Shape["* num_times, * num_DIM2"], Any], NDArray[Shape["* num_times, * num_dim2"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3, * num_DIM4"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3, * num_dim4"], Any],
] ]
] = Field(None) ] = Field(None)

6
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_ecephys.py
View file

@ -53,16 +53,16 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, DynamicTableRegion
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime,
NWBDataInterface, NWBDataInterface,
TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
TimeSeries, TimeSeries,
NWBContainer, NWBContainer,
) )
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.4.0" version = "2.4.0"

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_epoch.py
View file

@ -54,9 +54,9 @@ if TYPE_CHECKING:
from ...hdmf_common.v1_5_0.hdmf_common_table import ( from ...hdmf_common.v1_5_0.hdmf_common_table import (
VectorIndex,
VectorData, VectorData,
DynamicTable, DynamicTable,
VectorIndex,
) )
from .core_nwb_base import TimeSeries from .core_nwb_base import TimeSeries

22
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_file.py
View file

@ -53,35 +53,35 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_misc import Units
from .core_nwb_icephys import ( from .core_nwb_icephys import (
RepetitionsTable,
ExperimentalConditionsTable,
SimultaneousRecordingsTable,
IntracellularRecordingsTable,
SweepTable,
SequentialRecordingsTable, SequentialRecordingsTable,
IntracellularRecordingsTable,
SimultaneousRecordingsTable,
IntracellularElectrode, IntracellularElectrode,
ExperimentalConditionsTable,
SweepTable,
RepetitionsTable,
) )
from .core_nwb_device import Device from .core_nwb_device import Device
from .core_nwb_ecephys import ElectrodeGroup from .core_nwb_ecephys import ElectrodeGroup
from .core_nwb_epoch import TimeIntervals from .core_nwb_ophys import ImagingPlane
from .core_nwb_base import ( from .core_nwb_base import (
NWBContainer, NWBContainer,
NWBData, NWBData,
TimeSeries, TimeSeries,
ProcessingModule,
NWBDataInterface, NWBDataInterface,
ProcessingModule,
) )
from .core_nwb_ophys import ImagingPlane from .core_nwb_epoch import TimeIntervals
from ...hdmf_common.v1_5_0.hdmf_common_table import VectorData, DynamicTable from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, VectorData
from .core_nwb_misc import Units
from .core_nwb_ogen import OptogeneticStimulusSite from .core_nwb_ogen import OptogeneticStimulusSite

18
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_icephys.py
View file

@ -53,20 +53,20 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTableRegion,
AlignedDynamicTable,
VectorIndex,
VectorData,
DynamicTable,
)
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesReferenceVectorData,
NWBContainer, NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesSync, TimeSeriesSync,
TimeSeriesReferenceVectorData,
)
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorIndex,
VectorData,
AlignedDynamicTable,
) )

20
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_image.py
View file

@ -53,7 +53,7 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, Image, TimeSeries from .core_nwb_base import Image, TimeSeriesStartingTime, TimeSeriesSync, TimeSeries
metamodel_version = "None" metamodel_version = "None"
@ -109,8 +109,8 @@ class GrayscaleImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -131,8 +131,8 @@ class RGBImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -153,8 +153,8 @@ class RGBAImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -293,8 +293,8 @@ class OpticalSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width, height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width, height, depth"], float], NDArray[Shape["3 width_height_depth"], float],
] ]
] = Field( ] = Field(
None, None,
@ -302,7 +302,7 @@ class OpticalSeries(ImageSeries):
) )
data: Union[ data: Union[
NDArray[Shape["* frame, * x, * y"], float], NDArray[Shape["* frame, * x, * y"], float],
NDArray[Shape["* frame, * x, * y, 3 r, g, b"], float], NDArray[Shape["* frame, * x, * y, 3 r_g_b"], float],
] = Field( ] = Field(
..., description="""Images presented to subject, either grayscale or RGB""" ..., description="""Images presented to subject, either grayscale or RGB"""
) )

18
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_misc.py
View file

@ -53,16 +53,16 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_table import ( from .core_nwb_base import TimeSeriesStartingTime, TimeSeries, TimeSeriesSync
DynamicTableRegion,
VectorIndex,
VectorData,
DynamicTable,
)
from .core_nwb_ecephys import ElectrodeGroup from .core_nwb_ecephys import ElectrodeGroup
from .core_nwb_base import TimeSeriesStartingTime, TimeSeries, TimeSeriesSync from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorIndex,
VectorData,
)
metamodel_version = "None" metamodel_version = "None"
@ -341,7 +341,7 @@ class DecompositionSeriesBands(DynamicTable):
band_name: Optional[List[str] | str] = Field( band_name: Optional[List[str] | str] = Field(
default_factory=list, description="""Name of the band, e.g. theta.""" default_factory=list, description="""Name of the band, e.g. theta."""
) )
band_limits: NDArray[Shape["* num_bands, 2 low, high"], float] = Field( band_limits: NDArray[Shape["* num_bands, 2 low_high"], float] = Field(
..., ...,
description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""", description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""",
) )
@ -384,7 +384,7 @@ class Units(DynamicTable):
obs_intervals_index: Optional[str] = Field( obs_intervals_index: Optional[str] = Field(
None, description="""Index into the obs_intervals dataset.""" None, description="""Index into the obs_intervals dataset."""
) )
obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start|end"], float]] = ( obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start_end"], float]] = (
Field(None, description="""Observation intervals for each unit.""") Field(None, description="""Observation intervals for each unit.""")
) )
electrodes_index: Optional[str] = Field( electrodes_index: Optional[str] = Field(

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_ogen.py
View file

@ -54,10 +54,10 @@ if TYPE_CHECKING:
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesSync,
NWBContainer, NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync,
) )

24
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_ophys.py
View file

@ -53,15 +53,6 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_image import ImageSeriesExternalFile, ImageSeries
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTableRegion,
VectorData,
VectorIndex,
DynamicTable,
)
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime, TimeSeriesStartingTime,
NWBContainer, NWBContainer,
@ -70,6 +61,15 @@ from .core_nwb_base import (
TimeSeriesSync, TimeSeriesSync,
) )
from .core_nwb_image import ImageSeries, ImageSeriesExternalFile
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorIndex,
VectorData,
)
metamodel_version = "None" metamodel_version = "None"
version = "2.4.0" version = "2.4.0"
@ -122,8 +122,8 @@ class TwoPhotonSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width|height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width|height|depth"], float], NDArray[Shape["3 width_height_depth"], float],
] ]
] = Field( ] = Field(
None, None,
@ -185,7 +185,7 @@ class RoiResponseSeries(TimeSeries):
name: str = Field(...) name: str = Field(...)
data: Union[ data: Union[
NDArray[Shape["* num_times"], float], NDArray[Shape["* num_times"], float],
NDArray[Shape["* num_times, * num_ROIs"], float], NDArray[Shape["* num_times, * num_rois"], float],
] = Field(..., description="""Signals from ROIs.""") ] = Field(..., description="""Signals from ROIs.""")
rois: str = Field( rois: str = Field(
..., ...,

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_retinotopy.py
View file

@ -114,7 +114,7 @@ class ImagingRetinotopy(NWBDataInterface):
None, None,
description="""Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""", description="""Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""",
) )
axis_descriptions: NDArray[Shape["2 axis_1, axis_2"], str] = Field( axis_descriptions: NDArray[Shape["2 axis_1_axis_2"], str] = Field(
..., ...,
description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""", description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""",
) )

14
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_base.py
View file

@ -53,9 +53,9 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_table import VectorData, DynamicTable from ...hdmf_common.v1_5_0.hdmf_common_base import Data, Container
from ...hdmf_common.v1_5_0.hdmf_common_base import Container, Data from ...hdmf_common.v1_5_0.hdmf_common_table import VectorData, DynamicTable
metamodel_version = "None" metamodel_version = "None"
@ -151,8 +151,8 @@ class Image(NWBData):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -258,9 +258,9 @@ class TimeSeriesData(ConfiguredBaseModel):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* num_times"], Any], NDArray[Shape["* num_times"], Any],
NDArray[Shape["* num_times, * num_DIM2"], Any], NDArray[Shape["* num_times, * num_dim2"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3, * num_DIM4"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3, * num_dim4"], Any],
] ]
] = Field(None) ] = Field(None)

4
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_behavior.py
View file

@ -159,8 +159,8 @@ class SpatialSeriesData(ConfiguredBaseModel):
Union[ Union[
NDArray[Shape["* num_times"], float], NDArray[Shape["* num_times"], float],
NDArray[Shape["* num_times, 1 x"], float], NDArray[Shape["* num_times, 1 x"], float],
NDArray[Shape["* num_times, 2 x,y"], float], NDArray[Shape["* num_times, 2 x_y"], float],
NDArray[Shape["* num_times, 3 x,y,z"], float], NDArray[Shape["* num_times, 3 x_y_z"], float],
] ]
] = Field(None) ] = Field(None)

6
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_ecephys.py
View file

@ -53,16 +53,16 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, DynamicTableRegion
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime,
NWBDataInterface, NWBDataInterface,
TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
TimeSeries, TimeSeries,
NWBContainer, NWBContainer,
) )
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.5.0" version = "2.5.0"

4
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_epoch.py
View file

@ -54,12 +54,12 @@ if TYPE_CHECKING:
from ...hdmf_common.v1_5_0.hdmf_common_table import ( from ...hdmf_common.v1_5_0.hdmf_common_table import (
VectorIndex,
VectorData, VectorData,
DynamicTable, DynamicTable,
VectorIndex,
) )
from .core_nwb_base import TimeSeriesReferenceVectorData, TimeSeries from .core_nwb_base import TimeSeries, TimeSeriesReferenceVectorData
metamodel_version = "None" metamodel_version = "None"

22
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_file.py
View file

@ -53,36 +53,36 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_misc import Units
from .core_nwb_icephys import ( from .core_nwb_icephys import (
RepetitionsTable,
ExperimentalConditionsTable,
SimultaneousRecordingsTable,
IntracellularRecordingsTable,
SweepTable,
SequentialRecordingsTable, SequentialRecordingsTable,
IntracellularRecordingsTable,
SimultaneousRecordingsTable,
IntracellularElectrode, IntracellularElectrode,
ExperimentalConditionsTable,
SweepTable,
RepetitionsTable,
) )
from .core_nwb_device import Device from .core_nwb_device import Device
from .core_nwb_ecephys import ElectrodeGroup from .core_nwb_ecephys import ElectrodeGroup
from .core_nwb_epoch import TimeIntervals from .core_nwb_ophys import ImagingPlane
from .core_nwb_base import ( from .core_nwb_base import (
NWBContainer, NWBContainer,
NWBData, NWBData,
TimeSeries, TimeSeries,
Images, Images,
ProcessingModule,
NWBDataInterface, NWBDataInterface,
ProcessingModule,
) )
from .core_nwb_ophys import ImagingPlane from .core_nwb_epoch import TimeIntervals
from ...hdmf_common.v1_5_0.hdmf_common_table import VectorData, DynamicTable from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, VectorData
from .core_nwb_misc import Units
from .core_nwb_ogen import OptogeneticStimulusSite from .core_nwb_ogen import OptogeneticStimulusSite

18
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_icephys.py
View file

@ -53,20 +53,20 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTableRegion,
AlignedDynamicTable,
VectorIndex,
VectorData,
DynamicTable,
)
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesReferenceVectorData,
NWBContainer, NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesSync, TimeSeriesSync,
TimeSeriesReferenceVectorData,
)
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorIndex,
VectorData,
AlignedDynamicTable,
) )

20
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_image.py
View file

@ -53,7 +53,7 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, Image, TimeSeries from .core_nwb_base import Image, TimeSeriesStartingTime, TimeSeriesSync, TimeSeries
metamodel_version = "None" metamodel_version = "None"
@ -109,8 +109,8 @@ class GrayscaleImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -131,8 +131,8 @@ class RGBImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -153,8 +153,8 @@ class RGBAImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -293,8 +293,8 @@ class OpticalSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width, height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width, height, depth"], float], NDArray[Shape["3 width_height_depth"], float],
] ]
] = Field( ] = Field(
None, None,
@ -302,7 +302,7 @@ class OpticalSeries(ImageSeries):
) )
data: Union[ data: Union[
NDArray[Shape["* frame, * x, * y"], float], NDArray[Shape["* frame, * x, * y"], float],
NDArray[Shape["* frame, * x, * y, 3 r, g, b"], float], NDArray[Shape["* frame, * x, * y, 3 r_g_b"], float],
] = Field( ] = Field(
..., description="""Images presented to subject, either grayscale or RGB""" ..., description="""Images presented to subject, either grayscale or RGB"""
) )

18
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_misc.py
View file

@ -53,16 +53,16 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_table import ( from .core_nwb_base import TimeSeriesStartingTime, TimeSeries, TimeSeriesSync
DynamicTableRegion,
VectorIndex,
VectorData,
DynamicTable,
)
from .core_nwb_ecephys import ElectrodeGroup from .core_nwb_ecephys import ElectrodeGroup
from .core_nwb_base import TimeSeriesStartingTime, TimeSeries, TimeSeriesSync from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorIndex,
VectorData,
)
metamodel_version = "None" metamodel_version = "None"
@ -341,7 +341,7 @@ class DecompositionSeriesBands(DynamicTable):
band_name: Optional[List[str] | str] = Field( band_name: Optional[List[str] | str] = Field(
default_factory=list, description="""Name of the band, e.g. theta.""" default_factory=list, description="""Name of the band, e.g. theta."""
) )
band_limits: NDArray[Shape["* num_bands, 2 low, high"], float] = Field( band_limits: NDArray[Shape["* num_bands, 2 low_high"], float] = Field(
..., ...,
description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""", description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""",
) )
@ -384,7 +384,7 @@ class Units(DynamicTable):
obs_intervals_index: Optional[str] = Field( obs_intervals_index: Optional[str] = Field(
None, description="""Index into the obs_intervals dataset.""" None, description="""Index into the obs_intervals dataset."""
) )
obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start|end"], float]] = ( obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start_end"], float]] = (
Field(None, description="""Observation intervals for each unit.""") Field(None, description="""Observation intervals for each unit.""")
) )
electrodes_index: Optional[str] = Field( electrodes_index: Optional[str] = Field(

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_ogen.py
View file

@ -54,10 +54,10 @@ if TYPE_CHECKING:
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesSync,
NWBContainer, NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync,
) )

24
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_ophys.py
View file

@ -53,15 +53,6 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_image import ImageSeriesExternalFile, ImageSeries
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTableRegion,
VectorData,
VectorIndex,
DynamicTable,
)
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime, TimeSeriesStartingTime,
NWBContainer, NWBContainer,
@ -70,6 +61,15 @@ from .core_nwb_base import (
TimeSeriesSync, TimeSeriesSync,
) )
from .core_nwb_image import ImageSeries, ImageSeriesExternalFile
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorIndex,
VectorData,
)
metamodel_version = "None" metamodel_version = "None"
version = "2.5.0" version = "2.5.0"
@ -122,8 +122,8 @@ class TwoPhotonSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width|height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width|height|depth"], float], NDArray[Shape["3 width_height_depth"], float],
] ]
] = Field( ] = Field(
None, None,
@ -185,7 +185,7 @@ class RoiResponseSeries(TimeSeries):
name: str = Field(...) name: str = Field(...)
data: Union[ data: Union[
NDArray[Shape["* num_times"], float], NDArray[Shape["* num_times"], float],
NDArray[Shape["* num_times, * num_ROIs"], float], NDArray[Shape["* num_times, * num_rois"], float],
] = Field(..., description="""Signals from ROIs.""") ] = Field(..., description="""Signals from ROIs.""")
rois: str = Field( rois: str = Field(
..., ...,

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_retinotopy.py
View file

@ -114,7 +114,7 @@ class ImagingRetinotopy(NWBDataInterface):
None, None,
description="""Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""", description="""Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""",
) )
axis_descriptions: NDArray[Shape["2 axis_1, axis_2"], str] = Field( axis_descriptions: NDArray[Shape["2 axis_1_axis_2"], str] = Field(
..., ...,
description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""", description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""",
) )

14
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_base.py
View file

@ -53,9 +53,9 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_table import VectorData, DynamicTable from ...hdmf_common.v1_5_0.hdmf_common_base import Data, Container
from ...hdmf_common.v1_5_0.hdmf_common_base import Container, Data from ...hdmf_common.v1_5_0.hdmf_common_table import VectorData, DynamicTable
metamodel_version = "None" metamodel_version = "None"
@ -151,8 +151,8 @@ class Image(NWBData):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -258,9 +258,9 @@ class TimeSeriesData(ConfiguredBaseModel):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* num_times"], Any], NDArray[Shape["* num_times"], Any],
NDArray[Shape["* num_times, * num_DIM2"], Any], NDArray[Shape["* num_times, * num_dim2"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3, * num_DIM4"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3, * num_dim4"], Any],
] ]
] = Field(None) ] = Field(None)

4
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_behavior.py
View file

@ -159,8 +159,8 @@ class SpatialSeriesData(ConfiguredBaseModel):
Union[ Union[
NDArray[Shape["* num_times"], float], NDArray[Shape["* num_times"], float],
NDArray[Shape["* num_times, 1 x"], float], NDArray[Shape["* num_times, 1 x"], float],
NDArray[Shape["* num_times, 2 x,y"], float], NDArray[Shape["* num_times, 2 x_y"], float],
NDArray[Shape["* num_times, 3 x,y,z"], float], NDArray[Shape["* num_times, 3 x_y_z"], float],
] ]
] = Field(None) ] = Field(None)

6
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_ecephys.py
View file

@ -53,16 +53,16 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, DynamicTableRegion
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime,
NWBDataInterface, NWBDataInterface,
TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
TimeSeries, TimeSeries,
NWBContainer, NWBContainer,
) )
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.6.0-alpha" version = "2.6.0-alpha"

4
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_epoch.py
View file

@ -54,12 +54,12 @@ if TYPE_CHECKING:
from ...hdmf_common.v1_5_0.hdmf_common_table import ( from ...hdmf_common.v1_5_0.hdmf_common_table import (
VectorIndex,
VectorData, VectorData,
DynamicTable, DynamicTable,
VectorIndex,
) )
from .core_nwb_base import TimeSeriesReferenceVectorData, TimeSeries from .core_nwb_base import TimeSeries, TimeSeriesReferenceVectorData
metamodel_version = "None" metamodel_version = "None"

22
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_file.py
View file

@ -53,36 +53,36 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_misc import Units
from .core_nwb_icephys import ( from .core_nwb_icephys import (
RepetitionsTable,
ExperimentalConditionsTable,
SimultaneousRecordingsTable,
IntracellularRecordingsTable,
SweepTable,
SequentialRecordingsTable, SequentialRecordingsTable,
IntracellularRecordingsTable,
SimultaneousRecordingsTable,
IntracellularElectrode, IntracellularElectrode,
ExperimentalConditionsTable,
SweepTable,
RepetitionsTable,
) )
from .core_nwb_device import Device from .core_nwb_device import Device
from .core_nwb_ecephys import ElectrodeGroup from .core_nwb_ecephys import ElectrodeGroup
from .core_nwb_epoch import TimeIntervals from .core_nwb_ophys import ImagingPlane
from .core_nwb_base import ( from .core_nwb_base import (
NWBContainer, NWBContainer,
NWBData, NWBData,
TimeSeries, TimeSeries,
Images, Images,
ProcessingModule,
NWBDataInterface, NWBDataInterface,
ProcessingModule,
) )
from .core_nwb_ophys import ImagingPlane from .core_nwb_epoch import TimeIntervals
from ...hdmf_common.v1_5_0.hdmf_common_table import VectorData, DynamicTable from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, VectorData
from .core_nwb_misc import Units
from .core_nwb_ogen import OptogeneticStimulusSite from .core_nwb_ogen import OptogeneticStimulusSite

18
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_icephys.py
View file

@ -53,20 +53,20 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTableRegion,
AlignedDynamicTable,
VectorIndex,
VectorData,
DynamicTable,
)
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesReferenceVectorData,
NWBContainer, NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesSync, TimeSeriesSync,
TimeSeriesReferenceVectorData,
)
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorIndex,
VectorData,
AlignedDynamicTable,
) )

20
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_image.py
View file

@ -53,7 +53,7 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, Image, TimeSeries from .core_nwb_base import Image, TimeSeriesStartingTime, TimeSeriesSync, TimeSeries
metamodel_version = "None" metamodel_version = "None"
@ -109,8 +109,8 @@ class GrayscaleImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -131,8 +131,8 @@ class RGBImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -153,8 +153,8 @@ class RGBAImage(Image):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -293,8 +293,8 @@ class OpticalSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width, height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width, height, depth"], float], NDArray[Shape["3 width_height_depth"], float],
] ]
] = Field( ] = Field(
None, None,
@ -302,7 +302,7 @@ class OpticalSeries(ImageSeries):
) )
data: Union[ data: Union[
NDArray[Shape["* frame, * x, * y"], float], NDArray[Shape["* frame, * x, * y"], float],
NDArray[Shape["* frame, * x, * y, 3 r, g, b"], float], NDArray[Shape["* frame, * x, * y, 3 r_g_b"], float],
] = Field( ] = Field(
..., description="""Images presented to subject, either grayscale or RGB""" ..., description="""Images presented to subject, either grayscale or RGB"""
) )

18
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_misc.py
View file

@ -53,16 +53,16 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_table import ( from .core_nwb_base import TimeSeriesStartingTime, TimeSeries, TimeSeriesSync
DynamicTableRegion,
VectorIndex,
VectorData,
DynamicTable,
)
from .core_nwb_ecephys import ElectrodeGroup from .core_nwb_ecephys import ElectrodeGroup
from .core_nwb_base import TimeSeriesStartingTime, TimeSeries, TimeSeriesSync from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorIndex,
VectorData,
)
metamodel_version = "None" metamodel_version = "None"
@ -341,7 +341,7 @@ class DecompositionSeriesBands(DynamicTable):
band_name: Optional[List[str] | str] = Field( band_name: Optional[List[str] | str] = Field(
default_factory=list, description="""Name of the band, e.g. theta.""" default_factory=list, description="""Name of the band, e.g. theta."""
) )
band_limits: NDArray[Shape["* num_bands, 2 low, high"], float] = Field( band_limits: NDArray[Shape["* num_bands, 2 low_high"], float] = Field(
..., ...,
description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""", description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""",
) )
@ -384,7 +384,7 @@ class Units(DynamicTable):
obs_intervals_index: Optional[str] = Field( obs_intervals_index: Optional[str] = Field(
None, description="""Index into the obs_intervals dataset.""" None, description="""Index into the obs_intervals dataset."""
) )
obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start|end"], float]] = ( obs_intervals: Optional[NDArray[Shape["* num_intervals, 2 start_end"], float]] = (
Field(None, description="""Observation intervals for each unit.""") Field(None, description="""Observation intervals for each unit.""")
) )
electrodes_index: Optional[str] = Field( electrodes_index: Optional[str] = Field(

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_ogen.py
View file

@ -54,10 +54,10 @@ if TYPE_CHECKING:
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesSync,
NWBContainer, NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync,
) )

24
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_ophys.py
View file

@ -53,15 +53,6 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_image import ImageSeriesExternalFile, ImageSeries
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTableRegion,
VectorData,
VectorIndex,
DynamicTable,
)
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime, TimeSeriesStartingTime,
NWBContainer, NWBContainer,
@ -70,6 +61,15 @@ from .core_nwb_base import (
TimeSeriesSync, TimeSeriesSync,
) )
from .core_nwb_image import ImageSeries, ImageSeriesExternalFile
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorIndex,
VectorData,
)
metamodel_version = "None" metamodel_version = "None"
version = "2.6.0-alpha" version = "2.6.0-alpha"
@ -195,8 +195,8 @@ class TwoPhotonSeries(ImageSeries):
) )
field_of_view: Optional[ field_of_view: Optional[
Union[ Union[
NDArray[Shape["2 width|height"], float], NDArray[Shape["2 width_height"], float],
NDArray[Shape["3 width|height|depth"], float], NDArray[Shape["3 width_height_depth"], float],
] ]
] = Field( ] = Field(
None, None,
@ -258,7 +258,7 @@ class RoiResponseSeries(TimeSeries):
name: str = Field(...) name: str = Field(...)
data: Union[ data: Union[
NDArray[Shape["* num_times"], float], NDArray[Shape["* num_times"], float],
NDArray[Shape["* num_times, * num_ROIs"], float], NDArray[Shape["* num_times, * num_rois"], float],
] = Field(..., description="""Signals from ROIs.""") ] = Field(..., description="""Signals from ROIs.""")
rois: str = Field( rois: str = Field(
..., ...,

2
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_retinotopy.py
View file

@ -114,7 +114,7 @@ class ImagingRetinotopy(NWBDataInterface):
None, None,
description="""Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""", description="""Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""",
) )
axis_descriptions: NDArray[Shape["2 axis_1, axis_2"], str] = Field( axis_descriptions: NDArray[Shape["2 axis_1_axis_2"], str] = Field(
..., ...,
description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""", description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""",
) )

14
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_base.py
View file

@ -53,9 +53,9 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_8_0.hdmf_common_table import VectorData, DynamicTable from ...hdmf_common.v1_8_0.hdmf_common_base import Data, Container
from ...hdmf_common.v1_8_0.hdmf_common_base import Container, Data from ...hdmf_common.v1_8_0.hdmf_common_table import VectorData, DynamicTable
metamodel_version = "None" metamodel_version = "None"
@ -151,8 +151,8 @@ class Image(NWBData):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y"], float],
NDArray[Shape["* x, * y, 3 r, g, b"], float], NDArray[Shape["* x, * y, 3 r_g_b"], float],
NDArray[Shape["* x, * y, 4 r, g, b, a"], float], NDArray[Shape["* x, * y, 4 r_g_b_a"], float],
] ]
] = Field(None) ] = Field(None)
@ -258,9 +258,9 @@ class TimeSeriesData(ConfiguredBaseModel):
array: Optional[ array: Optional[
Union[ Union[
NDArray[Shape["* num_times"], Any], NDArray[Shape["* num_times"], Any],
NDArray[Shape["* num_times, * num_DIM2"], Any], NDArray[Shape["* num_times, * num_dim2"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3"], Any],
NDArray[Shape["* num_times, * num_DIM2, * num_DIM3, * num_DIM4"], Any], NDArray[Shape["* num_times, * num_dim2, * num_dim3, * num_dim4"], Any],
] ]
] = Field(None) ] = Field(None)

4
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_behavior.py
View file

@ -159,8 +159,8 @@ class SpatialSeriesData(ConfiguredBaseModel):
Union[ Union[
NDArray[Shape["* num_times"], float], NDArray[Shape["* num_times"], float],
NDArray[Shape["* num_times, 1 x"], float], NDArray[Shape["* num_times, 1 x"], float],
NDArray[Shape["* num_times, 2 x,y"], float], NDArray[Shape["* num_times, 2 x_y"], float],
NDArray[Shape["* num_times, 3 x,y,z"], float], NDArray[Shape["* num_times, 3 x_y_z"], float],
] ]
] = Field(None) ] = Field(None)

6
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_ecephys.py
View file

@ -53,16 +53,16 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_8_0.hdmf_common_table import DynamicTable, DynamicTableRegion
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime,
NWBDataInterface, NWBDataInterface,
TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
TimeSeries, TimeSeries,
NWBContainer, NWBContainer,
) )
from ...hdmf_common.v1_8_0.hdmf_common_table import DynamicTable, DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.7.0" version = "2.7.0"

4
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_epoch.py
View file

@ -54,12 +54,12 @@ if TYPE_CHECKING:
from ...hdmf_common.v1_8_0.hdmf_common_table import ( from ...hdmf_common.v1_8_0.hdmf_common_table import (
VectorIndex,
VectorData, VectorData,
DynamicTable, DynamicTable,
VectorIndex,
) )
from .core_nwb_base import TimeSeriesReferenceVectorData, TimeSeries from .core_nwb_base import TimeSeries, TimeSeriesReferenceVectorData
metamodel_version = "None" metamodel_version = "None"

22
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_file.py
View file

@ -53,36 +53,36 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from .core_nwb_misc import Units
from .core_nwb_icephys import ( from .core_nwb_icephys import (
RepetitionsTable,
ExperimentalConditionsTable,
SimultaneousRecordingsTable,
IntracellularRecordingsTable,
SweepTable,
SequentialRecordingsTable, SequentialRecordingsTable,
IntracellularRecordingsTable,
SimultaneousRecordingsTable,
IntracellularElectrode, IntracellularElectrode,
ExperimentalConditionsTable,
SweepTable,
RepetitionsTable,
) )
from .core_nwb_device import Device from .core_nwb_device import Device
from .core_nwb_ecephys import ElectrodeGroup from .core_nwb_ecephys import ElectrodeGroup
from .core_nwb_epoch import TimeIntervals from .core_nwb_ophys import ImagingPlane
from .core_nwb_base import ( from .core_nwb_base import (
NWBContainer, NWBContainer,
NWBData, NWBData,
TimeSeries, TimeSeries,
Images, Images,
ProcessingModule,
NWBDataInterface, NWBDataInterface,
ProcessingModule,
) )
from .core_nwb_ophys import ImagingPlane from .core_nwb_epoch import TimeIntervals
from ...hdmf_common.v1_8_0.hdmf_common_table import VectorData, DynamicTable from ...hdmf_common.v1_8_0.hdmf_common_table import DynamicTable, VectorData
from .core_nwb_misc import Units
from .core_nwb_ogen import OptogeneticStimulusSite from .core_nwb_ogen import OptogeneticStimulusSite

18
nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_icephys.py
View file

@ -53,20 +53,20 @@ if TYPE_CHECKING:
import numpy as np import numpy as np
from ...hdmf_common.v1_8_0.hdmf_common_table import (
DynamicTableRegion,
AlignedDynamicTable,
VectorIndex,
VectorData,
DynamicTable,
)
from .core_nwb_base import ( from .core_nwb_base import (
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesReferenceVectorData,
NWBContainer, NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesSync, TimeSeriesSync,
TimeSeriesReferenceVectorData,
)
from ...hdmf_common.v1_8_0.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorIndex,
VectorData,
AlignedDynamicTable,
) )

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