diff --git a/nwb_linkml/src/nwb_linkml/adapters/dataset.py b/nwb_linkml/src/nwb_linkml/adapters/dataset.py index fb8b285..085864c 100644 --- a/nwb_linkml/src/nwb_linkml/adapters/dataset.py +++ b/nwb_linkml/src/nwb_linkml/adapters/dataset.py @@ -447,7 +447,7 @@ class DatasetAdapter(ClassAdapter): """ Orchestrator class for datasets - calls the set of applicable mapping classes """ - TYPE = Dataset + TYPE: Type = Dataset cls: Dataset diff --git a/nwb_linkml/src/nwb_linkml/adapters/group.py b/nwb_linkml/src/nwb_linkml/adapters/group.py index 6fe9703..53c5c6a 100644 --- a/nwb_linkml/src/nwb_linkml/adapters/group.py +++ b/nwb_linkml/src/nwb_linkml/adapters/group.py @@ -2,6 +2,8 @@ Adapter for NWB groups to linkml Classes """ +from typing import Type + from linkml_runtime.linkml_model import SlotDefinition from nwb_linkml.adapters.adapter import BuildResult @@ -16,7 +18,7 @@ class GroupAdapter(ClassAdapter): """ Adapt NWB Groups to LinkML Classes """ - TYPE = Group + TYPE: Type = Group cls: Group diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_base.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_base.py index 0766284..b87dee5 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_base.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_base.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: 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" @@ -118,8 +118,8 @@ class Image(NWBData): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -204,9 +204,9 @@ class TimeSeriesData(ConfiguredBaseModel): array: Optional[ Union[ NDArray[Shape["* num_times"], 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, * num_DIM4"], 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, * num_dim4"], Any], ] ] = Field(None) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_ecephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_ecephys.py index 9723157..4bf24a7 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_ecephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_ecephys.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_1_0.hdmf_common_table import DynamicTable, DynamicTableRegion - from .core_nwb_base import ( - TimeSeriesStartingTime, NWBDataInterface, + TimeSeriesStartingTime, TimeSeriesSync, TimeSeries, NWBContainer, ) +from ...hdmf_common.v1_1_0.hdmf_common_table import DynamicTable, DynamicTableRegion + metamodel_version = "None" version = "2.2.0" diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_epoch.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_epoch.py index 8586b33..70f543f 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_epoch.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_epoch.py @@ -54,9 +54,9 @@ if TYPE_CHECKING: from ...hdmf_common.v1_1_0.hdmf_common_table import ( + VectorIndex, VectorData, DynamicTable, - VectorIndex, ) from .core_nwb_base import TimeSeries diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_file.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_file.py index 863c4e2..b2ffd1d 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_file.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_file.py @@ -53,26 +53,26 @@ if TYPE_CHECKING: import numpy as np -from .core_nwb_misc import Units - from .core_nwb_device import Device 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_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 ( + DynamicTable, VectorIndex, VectorData, - DynamicTable, ) +from .core_nwb_misc import Units + from .core_nwb_ogen import OptogeneticStimulusSite diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_icephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_icephys.py index 8b4e86b..d73fc63 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_icephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_icephys.py @@ -61,9 +61,9 @@ from .core_nwb_base import ( ) from ...hdmf_common.v1_1_0.hdmf_common_table import ( + DynamicTable, VectorIndex, VectorData, - DynamicTable, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_image.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_image.py index bc18173..0cf42cf 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_image.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_image.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: 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" @@ -109,8 +109,8 @@ class GrayscaleImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -131,8 +131,8 @@ class RGBImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -153,8 +153,8 @@ class RGBAImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -291,8 +291,8 @@ class OpticalSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width, height"], float], - NDArray[Shape["3 width, height, depth"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height_depth"], float], ] ] = Field( None, diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_misc.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_misc.py index c1b8fec..72c5b83 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_misc.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_misc.py @@ -54,10 +54,10 @@ if TYPE_CHECKING: from ...hdmf_common.v1_1_0.hdmf_common_table import ( + VectorIndex, VectorData, DynamicTable, DynamicTableRegion, - VectorIndex, ) from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, TimeSeries @@ -313,7 +313,7 @@ class DecompositionSeriesBands(DynamicTable): band_name: Optional[List[str] | str] = Field( 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.""", ) @@ -359,7 +359,7 @@ class Units(DynamicTable): obs_intervals_index: Optional[str] = Field( 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.""") ) electrodes_index: Optional[str] = Field( diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_ogen.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_ogen.py index 910f69b..6636d32 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_ogen.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_ogen.py @@ -54,10 +54,10 @@ if TYPE_CHECKING: from .core_nwb_base import ( + TimeSeriesSync, NWBContainer, TimeSeries, TimeSeriesStartingTime, - TimeSeriesSync, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_ophys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_ophys.py index c3d498f..6bd1472 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_ophys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_ophys.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from .core_nwb_image import ImageSeriesExternalFile, ImageSeries - from .core_nwb_base import ( + NWBDataInterface, TimeSeriesStartingTime, TimeSeriesSync, - NWBDataInterface, TimeSeries, NWBContainer, ) +from .core_nwb_image import ImageSeriesExternalFile, ImageSeries + from ...hdmf_common.v1_1_0.hdmf_common_table import DynamicTable, DynamicTableRegion @@ -117,8 +117,8 @@ class TwoPhotonSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width|height"], float], - NDArray[Shape["3 width|height"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height"], float], ] ] = Field( None, @@ -179,7 +179,7 @@ class RoiResponseSeries(TimeSeries): name: str = Field(...) data: Union[ NDArray[Shape["* num_times"], float], - NDArray[Shape["* num_times, * num_ROIs"], float], + NDArray[Shape["* num_times, * num_rois"], float], ] = Field(..., description="""Signals from ROIs.""") rois: str = Field( ..., @@ -325,8 +325,8 @@ class ImagingPlaneManifold(ConfiguredBaseModel): ) array: Optional[ Union[ - NDArray[Shape["* height, * width, * depth, 3 x, y, z"], float], - NDArray[Shape["* height, * width, 3 x, y, z"], float], + NDArray[Shape["* height, * width, * depth, 3 x_y_z"], float], + NDArray[Shape["* height, * width, 3 x_y_z"], float], ] ] = Field(None) @@ -342,7 +342,7 @@ class ImagingPlaneOriginCoords(ConfiguredBaseModel): None, 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): @@ -356,7 +356,7 @@ class ImagingPlaneGridSpacing(ConfiguredBaseModel): None, 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): diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_retinotopy.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_retinotopy.py index 0320789..84b6ed7 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_retinotopy.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_retinotopy.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: import numpy as np -from .core_nwb_base import NWBData, NWBDataInterface +from .core_nwb_base import NWBDataInterface, NWBData from .core_nwb_image import GrayscaleImage @@ -162,8 +162,8 @@ class RetinotopyImage(GrayscaleImage): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -336,8 +336,8 @@ class ImagingRetinotopyFocalDepthImage(RetinotopyImage): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -372,8 +372,8 @@ class ImagingRetinotopyVasculatureImage(RetinotopyImage): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_base.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_base.py index b7471a3..f97e831 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_base.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_base.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: 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" @@ -118,8 +118,8 @@ class Image(NWBData): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -204,9 +204,9 @@ class TimeSeriesData(ConfiguredBaseModel): array: Optional[ Union[ NDArray[Shape["* num_times"], 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, * num_DIM4"], 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, * num_dim4"], Any], ] ] = Field(None) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_ecephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_ecephys.py index 99fea00..7c61201 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_ecephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_ecephys.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_1_2.hdmf_common_table import DynamicTable, DynamicTableRegion - from .core_nwb_base import ( - TimeSeriesStartingTime, NWBDataInterface, + TimeSeriesStartingTime, TimeSeriesSync, TimeSeries, NWBContainer, ) +from ...hdmf_common.v1_1_2.hdmf_common_table import DynamicTable, DynamicTableRegion + metamodel_version = "None" version = "2.2.1" diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_epoch.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_epoch.py index 4f781fd..c7d8b98 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_epoch.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_epoch.py @@ -54,9 +54,9 @@ if TYPE_CHECKING: from ...hdmf_common.v1_1_2.hdmf_common_table import ( + VectorIndex, VectorData, DynamicTable, - VectorIndex, ) from .core_nwb_base import TimeSeries diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_file.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_file.py index b7ec4fc..5e326ca 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_file.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_file.py @@ -53,26 +53,26 @@ if TYPE_CHECKING: import numpy as np -from .core_nwb_misc import Units - from .core_nwb_device import Device 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_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 ( + DynamicTable, VectorIndex, VectorData, - DynamicTable, ) +from .core_nwb_misc import Units + from .core_nwb_ogen import OptogeneticStimulusSite diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_icephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_icephys.py index 3371688..7388550 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_icephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_icephys.py @@ -61,9 +61,9 @@ from .core_nwb_base import ( ) from ...hdmf_common.v1_1_2.hdmf_common_table import ( + DynamicTable, VectorIndex, VectorData, - DynamicTable, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_image.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_image.py index 6170445..99d6f4c 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_image.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_image.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: 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" @@ -109,8 +109,8 @@ class GrayscaleImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -131,8 +131,8 @@ class RGBImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -153,8 +153,8 @@ class RGBAImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -291,8 +291,8 @@ class OpticalSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width, height"], float], - NDArray[Shape["3 width, height, depth"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height_depth"], float], ] ] = Field( None, diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_misc.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_misc.py index 39d5000..2dc81ae 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_misc.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_misc.py @@ -54,10 +54,10 @@ if TYPE_CHECKING: from ...hdmf_common.v1_1_2.hdmf_common_table import ( + VectorIndex, VectorData, DynamicTable, DynamicTableRegion, - VectorIndex, ) from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, TimeSeries @@ -313,7 +313,7 @@ class DecompositionSeriesBands(DynamicTable): band_name: Optional[List[str] | str] = Field( 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.""", ) @@ -359,7 +359,7 @@ class Units(DynamicTable): obs_intervals_index: Optional[str] = Field( 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.""") ) electrodes_index: Optional[str] = Field( diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_ogen.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_ogen.py index 921daf9..8a658dd 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_ogen.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_ogen.py @@ -54,10 +54,10 @@ if TYPE_CHECKING: from .core_nwb_base import ( + TimeSeriesSync, NWBContainer, TimeSeries, TimeSeriesStartingTime, - TimeSeriesSync, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_ophys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_ophys.py index f118d26..5accbce 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_ophys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_ophys.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from .core_nwb_image import ImageSeriesExternalFile, ImageSeries - from .core_nwb_base import ( + NWBDataInterface, TimeSeriesStartingTime, TimeSeriesSync, - NWBDataInterface, TimeSeries, NWBContainer, ) +from .core_nwb_image import ImageSeriesExternalFile, ImageSeries + from ...hdmf_common.v1_1_2.hdmf_common_table import DynamicTable, DynamicTableRegion @@ -117,8 +117,8 @@ class TwoPhotonSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width|height"], float], - NDArray[Shape["3 width|height"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height"], float], ] ] = Field( None, @@ -179,7 +179,7 @@ class RoiResponseSeries(TimeSeries): name: str = Field(...) data: Union[ NDArray[Shape["* num_times"], float], - NDArray[Shape["* num_times, * num_ROIs"], float], + NDArray[Shape["* num_times, * num_rois"], float], ] = Field(..., description="""Signals from ROIs.""") rois: str = Field( ..., @@ -325,8 +325,8 @@ class ImagingPlaneManifold(ConfiguredBaseModel): ) array: Optional[ Union[ - NDArray[Shape["* height, * width, * depth, 3 x, y, z"], float], - NDArray[Shape["* height, * width, 3 x, y, z"], float], + NDArray[Shape["* height, * width, * depth, 3 x_y_z"], float], + NDArray[Shape["* height, * width, 3 x_y_z"], float], ] ] = Field(None) @@ -342,7 +342,7 @@ class ImagingPlaneOriginCoords(ConfiguredBaseModel): None, 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): @@ -356,7 +356,7 @@ class ImagingPlaneGridSpacing(ConfiguredBaseModel): None, 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): diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_retinotopy.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_retinotopy.py index 73ed473..004c4d7 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_retinotopy.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_1/core_nwb_retinotopy.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: import numpy as np -from .core_nwb_base import NWBData, NWBDataInterface +from .core_nwb_base import NWBDataInterface, NWBData from .core_nwb_image import GrayscaleImage @@ -162,8 +162,8 @@ class RetinotopyImage(GrayscaleImage): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -336,8 +336,8 @@ class ImagingRetinotopyFocalDepthImage(RetinotopyImage): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -372,8 +372,8 @@ class ImagingRetinotopyVasculatureImage(RetinotopyImage): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_base.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_base.py index 910624d..b0ca8c1 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_base.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_base.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: 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" @@ -118,8 +118,8 @@ class Image(NWBData): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -204,9 +204,9 @@ class TimeSeriesData(ConfiguredBaseModel): array: Optional[ Union[ NDArray[Shape["* num_times"], 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, * num_DIM4"], 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, * num_dim4"], Any], ] ] = Field(None) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_ecephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_ecephys.py index 39cef94..700ce0d 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_ecephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_ecephys.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, DynamicTableRegion - from .core_nwb_base import ( - TimeSeriesStartingTime, NWBDataInterface, + TimeSeriesStartingTime, TimeSeriesSync, TimeSeries, NWBContainer, ) +from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, DynamicTableRegion + metamodel_version = "None" version = "2.2.2" diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_epoch.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_epoch.py index 0cd3e67..0eec394 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_epoch.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_epoch.py @@ -54,9 +54,9 @@ if TYPE_CHECKING: from ...hdmf_common.v1_1_3.hdmf_common_table import ( + VectorIndex, VectorData, DynamicTable, - VectorIndex, ) from .core_nwb_base import TimeSeries diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_file.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_file.py index f8fd528..7adbfcc 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_file.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_file.py @@ -53,26 +53,26 @@ if TYPE_CHECKING: import numpy as np -from .core_nwb_misc import Units - from .core_nwb_device import Device 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_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 ( + DynamicTable, VectorIndex, VectorData, - DynamicTable, ) +from .core_nwb_misc import Units + from .core_nwb_ogen import OptogeneticStimulusSite diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_icephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_icephys.py index f671534..198b6a4 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_icephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_icephys.py @@ -61,9 +61,9 @@ from .core_nwb_base import ( ) from ...hdmf_common.v1_1_3.hdmf_common_table import ( + DynamicTable, VectorIndex, VectorData, - DynamicTable, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_image.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_image.py index 5a7a945..97c3457 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_image.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_image.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: 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" @@ -109,8 +109,8 @@ class GrayscaleImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -131,8 +131,8 @@ class RGBImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -153,8 +153,8 @@ class RGBAImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -291,8 +291,8 @@ class OpticalSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width, height"], float], - NDArray[Shape["3 width, height, depth"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height_depth"], float], ] ] = Field( None, @@ -300,7 +300,7 @@ class OpticalSeries(ImageSeries): ) data: Union[ 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( ..., description="""Images presented to subject, either grayscale or RGB""" ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_misc.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_misc.py index 3a977e4..2419df2 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_misc.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_misc.py @@ -54,10 +54,10 @@ if TYPE_CHECKING: from ...hdmf_common.v1_1_3.hdmf_common_table import ( + VectorIndex, VectorData, DynamicTable, DynamicTableRegion, - VectorIndex, ) from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, TimeSeries @@ -313,7 +313,7 @@ class DecompositionSeriesBands(DynamicTable): band_name: Optional[List[str] | str] = Field( 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.""", ) @@ -359,7 +359,7 @@ class Units(DynamicTable): obs_intervals_index: Optional[str] = Field( 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.""") ) electrodes_index: Optional[str] = Field( diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_ogen.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_ogen.py index 7632919..b699a5d 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_ogen.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_ogen.py @@ -54,10 +54,10 @@ if TYPE_CHECKING: from .core_nwb_base import ( + TimeSeriesSync, NWBContainer, TimeSeries, TimeSeriesStartingTime, - TimeSeriesSync, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_ophys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_ophys.py index b62056c..fa61adc 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_ophys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_ophys.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from .core_nwb_image import ImageSeriesExternalFile, ImageSeries - from .core_nwb_base import ( + NWBDataInterface, TimeSeriesStartingTime, TimeSeriesSync, - NWBDataInterface, TimeSeries, NWBContainer, ) +from .core_nwb_image import ImageSeriesExternalFile, ImageSeries + from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, DynamicTableRegion @@ -117,8 +117,8 @@ class TwoPhotonSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width|height"], float], - NDArray[Shape["3 width|height"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height"], float], ] ] = Field( None, @@ -179,7 +179,7 @@ class RoiResponseSeries(TimeSeries): name: str = Field(...) data: Union[ NDArray[Shape["* num_times"], float], - NDArray[Shape["* num_times, * num_ROIs"], float], + NDArray[Shape["* num_times, * num_rois"], float], ] = Field(..., description="""Signals from ROIs.""") rois: str = Field( ..., diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_retinotopy.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_retinotopy.py index 501641f..e535818 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_retinotopy.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_2/core_nwb_retinotopy.py @@ -114,7 +114,7 @@ class ImagingRetinotopy(NWBDataInterface): 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.""", ) - 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'].""", ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_base.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_base.py index 936a875..2291a3e 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_base.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_base.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: 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" @@ -118,8 +118,8 @@ class Image(NWBData): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -204,9 +204,9 @@ class TimeSeriesData(ConfiguredBaseModel): array: Optional[ Union[ NDArray[Shape["* num_times"], 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, * num_DIM4"], 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, * num_dim4"], Any], ] ] = Field(None) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_ecephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_ecephys.py index ac10dec..26d9f34 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_ecephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_ecephys.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, DynamicTableRegion - from .core_nwb_base import ( - TimeSeriesStartingTime, NWBDataInterface, + TimeSeriesStartingTime, TimeSeriesSync, TimeSeries, NWBContainer, ) +from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, DynamicTableRegion + metamodel_version = "None" version = "2.2.4" diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_epoch.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_epoch.py index 4166313..8ec9f63 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_epoch.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_epoch.py @@ -54,9 +54,9 @@ if TYPE_CHECKING: from ...hdmf_common.v1_1_3.hdmf_common_table import ( + VectorIndex, VectorData, DynamicTable, - VectorIndex, ) from .core_nwb_base import TimeSeries diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_file.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_file.py index 7ada071..d3e1a13 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_file.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_file.py @@ -53,32 +53,32 @@ if TYPE_CHECKING: import numpy as np -from .core_nwb_misc import Units - from .core_nwb_device import Device 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 ( NWBContainer, NWBData, TimeSeries, - ProcessingModule, NWBDataInterface, + ProcessingModule, ) -from .core_nwb_ophys import ImagingPlane - -from .core_nwb_icephys import SweepTable, IntracellularElectrode +from .core_nwb_epoch import TimeIntervals from ...hdmf_common.v1_1_3.hdmf_common_table import ( + DynamicTable, VectorIndex, VectorData, - DynamicTable, ) +from .core_nwb_misc import Units + from .core_nwb_ogen import OptogeneticStimulusSite diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_icephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_icephys.py index eff8f65..ba990ac 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_icephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_icephys.py @@ -61,9 +61,9 @@ from .core_nwb_base import ( ) from ...hdmf_common.v1_1_3.hdmf_common_table import ( + DynamicTable, VectorIndex, VectorData, - DynamicTable, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_image.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_image.py index 1831f88..e23a743 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_image.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_image.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: 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" @@ -109,8 +109,8 @@ class GrayscaleImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -131,8 +131,8 @@ class RGBImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -153,8 +153,8 @@ class RGBAImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -291,8 +291,8 @@ class OpticalSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width, height"], float], - NDArray[Shape["3 width, height, depth"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height_depth"], float], ] ] = Field( None, @@ -300,7 +300,7 @@ class OpticalSeries(ImageSeries): ) data: Union[ 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( ..., description="""Images presented to subject, either grayscale or RGB""" ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_misc.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_misc.py index 183a762..6747904 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_misc.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_misc.py @@ -54,10 +54,10 @@ if TYPE_CHECKING: from ...hdmf_common.v1_1_3.hdmf_common_table import ( + VectorIndex, VectorData, DynamicTable, DynamicTableRegion, - VectorIndex, ) from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, TimeSeries @@ -313,7 +313,7 @@ class DecompositionSeriesBands(DynamicTable): band_name: Optional[List[str] | str] = Field( 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.""", ) @@ -359,7 +359,7 @@ class Units(DynamicTable): obs_intervals_index: Optional[str] = Field( 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.""") ) electrodes_index: Optional[str] = Field( diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_ogen.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_ogen.py index ab92e42..943343b 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_ogen.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_ogen.py @@ -54,10 +54,10 @@ if TYPE_CHECKING: from .core_nwb_base import ( + TimeSeriesSync, NWBContainer, TimeSeries, TimeSeriesStartingTime, - TimeSeriesSync, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_ophys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_ophys.py index 053e108..2b9b2d2 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_ophys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_ophys.py @@ -53,15 +53,6 @@ if TYPE_CHECKING: 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 ( TimeSeriesStartingTime, NWBContainer, @@ -70,6 +61,15 @@ from .core_nwb_base import ( 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" version = "2.2.4" @@ -122,8 +122,8 @@ class TwoPhotonSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width|height"], float], - NDArray[Shape["3 width|height"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height"], float], ] ] = Field( None, @@ -184,7 +184,7 @@ class RoiResponseSeries(TimeSeries): name: str = Field(...) data: Union[ NDArray[Shape["* num_times"], float], - NDArray[Shape["* num_times, * num_ROIs"], float], + NDArray[Shape["* num_times, * num_rois"], float], ] = Field(..., description="""Signals from ROIs.""") rois: str = Field( ..., diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_retinotopy.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_retinotopy.py index 7b4a04e..1638c17 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_retinotopy.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_4/core_nwb_retinotopy.py @@ -114,7 +114,7 @@ class ImagingRetinotopy(NWBDataInterface): 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.""", ) - 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'].""", ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_base.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_base.py index 9f5a179..dadf59e 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_base.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_base.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: 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" @@ -118,8 +118,8 @@ class Image(NWBData): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -204,9 +204,9 @@ class TimeSeriesData(ConfiguredBaseModel): array: Optional[ Union[ NDArray[Shape["* num_times"], 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, * num_DIM4"], 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, * num_dim4"], Any], ] ] = Field(None) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_ecephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_ecephys.py index 3c9489f..75c6b24 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_ecephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_ecephys.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, DynamicTableRegion - from .core_nwb_base import ( - TimeSeriesStartingTime, NWBDataInterface, + TimeSeriesStartingTime, TimeSeriesSync, TimeSeries, NWBContainer, ) +from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, DynamicTableRegion + metamodel_version = "None" version = "2.2.5" diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_epoch.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_epoch.py index 85e50f6..7fb6cef 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_epoch.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_epoch.py @@ -54,9 +54,9 @@ if TYPE_CHECKING: from ...hdmf_common.v1_1_3.hdmf_common_table import ( + VectorIndex, VectorData, DynamicTable, - VectorIndex, ) from .core_nwb_base import TimeSeries diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_file.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_file.py index 3c6eee7..e8f808c 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_file.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_file.py @@ -53,32 +53,32 @@ if TYPE_CHECKING: import numpy as np -from .core_nwb_misc import Units - from .core_nwb_device import Device 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 ( NWBContainer, NWBData, TimeSeries, - ProcessingModule, NWBDataInterface, + ProcessingModule, ) -from .core_nwb_ophys import ImagingPlane - -from .core_nwb_icephys import SweepTable, IntracellularElectrode +from .core_nwb_epoch import TimeIntervals from ...hdmf_common.v1_1_3.hdmf_common_table import ( + DynamicTable, VectorIndex, VectorData, - DynamicTable, ) +from .core_nwb_misc import Units + from .core_nwb_ogen import OptogeneticStimulusSite diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_icephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_icephys.py index 3c48641..3693b66 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_icephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_icephys.py @@ -61,9 +61,9 @@ from .core_nwb_base import ( ) from ...hdmf_common.v1_1_3.hdmf_common_table import ( + DynamicTable, VectorIndex, VectorData, - DynamicTable, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_image.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_image.py index 905c01b..4b0cf89 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_image.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_image.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: 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" @@ -109,8 +109,8 @@ class GrayscaleImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -131,8 +131,8 @@ class RGBImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -153,8 +153,8 @@ class RGBAImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -291,8 +291,8 @@ class OpticalSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width, height"], float], - NDArray[Shape["3 width, height, depth"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height_depth"], float], ] ] = Field( None, @@ -300,7 +300,7 @@ class OpticalSeries(ImageSeries): ) data: Union[ 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( ..., description="""Images presented to subject, either grayscale or RGB""" ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_misc.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_misc.py index b10ffc6..f5e25df 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_misc.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_misc.py @@ -54,10 +54,10 @@ if TYPE_CHECKING: from ...hdmf_common.v1_1_3.hdmf_common_table import ( + VectorIndex, VectorData, DynamicTable, DynamicTableRegion, - VectorIndex, ) from .core_nwb_base import TimeSeriesStartingTime, TimeSeriesSync, TimeSeries @@ -313,7 +313,7 @@ class DecompositionSeriesBands(DynamicTable): band_name: Optional[List[str] | str] = Field( 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.""", ) @@ -359,7 +359,7 @@ class Units(DynamicTable): obs_intervals_index: Optional[str] = Field( 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.""") ) electrodes_index: Optional[str] = Field( diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_ogen.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_ogen.py index 929719c..277e33a 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_ogen.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_ogen.py @@ -54,10 +54,10 @@ if TYPE_CHECKING: from .core_nwb_base import ( + TimeSeriesSync, NWBContainer, TimeSeries, TimeSeriesStartingTime, - TimeSeriesSync, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_ophys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_ophys.py index c207f5e..88676cd 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_ophys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_ophys.py @@ -53,15 +53,6 @@ if TYPE_CHECKING: 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 ( TimeSeriesStartingTime, NWBContainer, @@ -70,6 +61,15 @@ from .core_nwb_base import ( 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" version = "2.2.5" @@ -122,8 +122,8 @@ class TwoPhotonSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width|height"], float], - NDArray[Shape["3 width|height|depth"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height_depth"], float], ] ] = Field( None, @@ -184,7 +184,7 @@ class RoiResponseSeries(TimeSeries): name: str = Field(...) data: Union[ NDArray[Shape["* num_times"], float], - NDArray[Shape["* num_times, * num_ROIs"], float], + NDArray[Shape["* num_times, * num_rois"], float], ] = Field(..., description="""Signals from ROIs.""") rois: str = Field( ..., diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_retinotopy.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_retinotopy.py index c0adf23..91b167c 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_retinotopy.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_5/core_nwb_retinotopy.py @@ -114,7 +114,7 @@ class ImagingRetinotopy(NWBDataInterface): 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.""", ) - 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'].""", ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_base.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_base.py index 165a4d6..d7ba412 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_base.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_base.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: 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 @@ -120,8 +120,8 @@ class Image(NWBData): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -210,9 +210,9 @@ class TimeSeriesData(ConfiguredBaseModel): array: Optional[ Union[ NDArray[Shape["* num_times"], 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, * num_DIM4"], 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, * num_dim4"], Any], ] ] = Field(None) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_ecephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_ecephys.py index 80c9fa1..ae450e4 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_ecephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_ecephys.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, DynamicTableRegion - from .core_nwb_base import ( - TimeSeriesStartingTime, NWBDataInterface, + TimeSeriesStartingTime, TimeSeriesSync, TimeSeries, NWBContainer, ) +from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, DynamicTableRegion + metamodel_version = "None" version = "2.3.0" diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_epoch.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_epoch.py index 17002a4..fca2141 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_epoch.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_epoch.py @@ -54,9 +54,9 @@ if TYPE_CHECKING: from ...hdmf_common.v1_5_0.hdmf_common_table import ( + VectorIndex, VectorData, DynamicTable, - VectorIndex, ) from .core_nwb_base import TimeSeries diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_file.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_file.py index 9ca43e8..bdccafe 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_file.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_file.py @@ -53,27 +53,27 @@ if TYPE_CHECKING: import numpy as np -from .core_nwb_misc import Units - from .core_nwb_device import Device 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 ( NWBContainer, NWBData, TimeSeries, - ProcessingModule, 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 diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_icephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_icephys.py index 2e33891..4423d81 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_icephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_icephys.py @@ -61,9 +61,9 @@ from .core_nwb_base import ( ) from ...hdmf_common.v1_5_0.hdmf_common_table import ( + DynamicTable, VectorIndex, VectorData, - DynamicTable, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_image.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_image.py index 0387152..80dfacf 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_image.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_image.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: 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" @@ -109,8 +109,8 @@ class GrayscaleImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -131,8 +131,8 @@ class RGBImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -153,8 +153,8 @@ class RGBAImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -291,8 +291,8 @@ class OpticalSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width, height"], float], - NDArray[Shape["3 width, height, depth"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height_depth"], float], ] ] = Field( None, @@ -300,7 +300,7 @@ class OpticalSeries(ImageSeries): ) data: Union[ 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( ..., description="""Images presented to subject, either grayscale or RGB""" ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_misc.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_misc.py index f1de761..8c196cf 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_misc.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_misc.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_5_0.hdmf_common_table import ( - DynamicTableRegion, - VectorIndex, - VectorData, - DynamicTable, -) +from .core_nwb_base import TimeSeriesStartingTime, TimeSeries, TimeSeriesSync 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" @@ -341,7 +341,7 @@ class DecompositionSeriesBands(DynamicTable): band_name: Optional[List[str] | str] = Field( 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.""", ) @@ -384,7 +384,7 @@ class Units(DynamicTable): obs_intervals_index: Optional[str] = Field( 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.""") ) electrodes_index: Optional[str] = Field( diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_ogen.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_ogen.py index 4b04266..ee05ed6 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_ogen.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_ogen.py @@ -54,10 +54,10 @@ if TYPE_CHECKING: from .core_nwb_base import ( + TimeSeriesSync, NWBContainer, TimeSeries, TimeSeriesStartingTime, - TimeSeriesSync, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_ophys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_ophys.py index cb1fefc..0ea1827 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_ophys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_ophys.py @@ -53,15 +53,6 @@ if TYPE_CHECKING: 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 ( TimeSeriesStartingTime, NWBContainer, @@ -70,6 +61,15 @@ from .core_nwb_base import ( 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" version = "2.3.0" @@ -122,8 +122,8 @@ class TwoPhotonSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width|height"], float], - NDArray[Shape["3 width|height|depth"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height_depth"], float], ] ] = Field( None, @@ -184,7 +184,7 @@ class RoiResponseSeries(TimeSeries): name: str = Field(...) data: Union[ NDArray[Shape["* num_times"], float], - NDArray[Shape["* num_times, * num_ROIs"], float], + NDArray[Shape["* num_times, * num_rois"], float], ] = Field(..., description="""Signals from ROIs.""") rois: str = Field( ..., diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_retinotopy.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_retinotopy.py index ce18a7c..18428fd 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_retinotopy.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_3_0/core_nwb_retinotopy.py @@ -114,7 +114,7 @@ class ImagingRetinotopy(NWBDataInterface): 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.""", ) - 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'].""", ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_base.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_base.py index 0fe3f04..70d4dd6 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_base.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_base.py @@ -53,9 +53,9 @@ if TYPE_CHECKING: 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" @@ -151,8 +151,8 @@ class Image(NWBData): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -241,9 +241,9 @@ class TimeSeriesData(ConfiguredBaseModel): array: Optional[ Union[ NDArray[Shape["* num_times"], 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, * num_DIM4"], 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, * num_dim4"], Any], ] ] = Field(None) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_ecephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_ecephys.py index d6373a7..3b10db2 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_ecephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_ecephys.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, DynamicTableRegion - from .core_nwb_base import ( - TimeSeriesStartingTime, NWBDataInterface, + TimeSeriesStartingTime, TimeSeriesSync, TimeSeries, NWBContainer, ) +from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, DynamicTableRegion + metamodel_version = "None" version = "2.4.0" diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_epoch.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_epoch.py index 8c1af60..8a98b22 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_epoch.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_epoch.py @@ -54,9 +54,9 @@ if TYPE_CHECKING: from ...hdmf_common.v1_5_0.hdmf_common_table import ( + VectorIndex, VectorData, DynamicTable, - VectorIndex, ) from .core_nwb_base import TimeSeries diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_file.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_file.py index 758be41..b4e397e 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_file.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_file.py @@ -53,35 +53,35 @@ if TYPE_CHECKING: import numpy as np -from .core_nwb_misc import Units - from .core_nwb_icephys import ( - RepetitionsTable, - ExperimentalConditionsTable, - SimultaneousRecordingsTable, - IntracellularRecordingsTable, - SweepTable, SequentialRecordingsTable, + IntracellularRecordingsTable, + SimultaneousRecordingsTable, IntracellularElectrode, + ExperimentalConditionsTable, + SweepTable, + RepetitionsTable, ) from .core_nwb_device import Device from .core_nwb_ecephys import ElectrodeGroup -from .core_nwb_epoch import TimeIntervals +from .core_nwb_ophys import ImagingPlane from .core_nwb_base import ( NWBContainer, NWBData, TimeSeries, - ProcessingModule, 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 diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_icephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_icephys.py index 3f9d392..dad9e3e 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_icephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_icephys.py @@ -53,20 +53,20 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_5_0.hdmf_common_table import ( - DynamicTableRegion, - AlignedDynamicTable, - VectorIndex, - VectorData, - DynamicTable, -) - from .core_nwb_base import ( TimeSeriesStartingTime, - TimeSeriesReferenceVectorData, NWBContainer, TimeSeries, TimeSeriesSync, + TimeSeriesReferenceVectorData, +) + +from ...hdmf_common.v1_5_0.hdmf_common_table import ( + DynamicTable, + DynamicTableRegion, + VectorIndex, + VectorData, + AlignedDynamicTable, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_image.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_image.py index 3fe3751..138537d 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_image.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_image.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: 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" @@ -109,8 +109,8 @@ class GrayscaleImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -131,8 +131,8 @@ class RGBImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -153,8 +153,8 @@ class RGBAImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -293,8 +293,8 @@ class OpticalSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width, height"], float], - NDArray[Shape["3 width, height, depth"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height_depth"], float], ] ] = Field( None, @@ -302,7 +302,7 @@ class OpticalSeries(ImageSeries): ) data: Union[ 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( ..., description="""Images presented to subject, either grayscale or RGB""" ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_misc.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_misc.py index 2de3a45..e338d7e 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_misc.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_misc.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_5_0.hdmf_common_table import ( - DynamicTableRegion, - VectorIndex, - VectorData, - DynamicTable, -) +from .core_nwb_base import TimeSeriesStartingTime, TimeSeries, TimeSeriesSync 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" @@ -341,7 +341,7 @@ class DecompositionSeriesBands(DynamicTable): band_name: Optional[List[str] | str] = Field( 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.""", ) @@ -384,7 +384,7 @@ class Units(DynamicTable): obs_intervals_index: Optional[str] = Field( 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.""") ) electrodes_index: Optional[str] = Field( diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_ogen.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_ogen.py index 333d0e4..a4cc7a3 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_ogen.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_ogen.py @@ -54,10 +54,10 @@ if TYPE_CHECKING: from .core_nwb_base import ( + TimeSeriesSync, NWBContainer, TimeSeries, TimeSeriesStartingTime, - TimeSeriesSync, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_ophys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_ophys.py index 0867451..dc4280c 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_ophys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_ophys.py @@ -53,15 +53,6 @@ if TYPE_CHECKING: 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 ( TimeSeriesStartingTime, NWBContainer, @@ -70,6 +61,15 @@ from .core_nwb_base import ( 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" version = "2.4.0" @@ -122,8 +122,8 @@ class TwoPhotonSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width|height"], float], - NDArray[Shape["3 width|height|depth"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height_depth"], float], ] ] = Field( None, @@ -185,7 +185,7 @@ class RoiResponseSeries(TimeSeries): name: str = Field(...) data: Union[ NDArray[Shape["* num_times"], float], - NDArray[Shape["* num_times, * num_ROIs"], float], + NDArray[Shape["* num_times, * num_rois"], float], ] = Field(..., description="""Signals from ROIs.""") rois: str = Field( ..., diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_retinotopy.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_retinotopy.py index 0509485..88d3f4c 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_retinotopy.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_4_0/core_nwb_retinotopy.py @@ -114,7 +114,7 @@ class ImagingRetinotopy(NWBDataInterface): 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.""", ) - 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'].""", ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_base.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_base.py index 196940c..2143bd6 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_base.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_base.py @@ -53,9 +53,9 @@ if TYPE_CHECKING: 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" @@ -151,8 +151,8 @@ class Image(NWBData): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -258,9 +258,9 @@ class TimeSeriesData(ConfiguredBaseModel): array: Optional[ Union[ NDArray[Shape["* num_times"], 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, * num_DIM4"], 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, * num_dim4"], Any], ] ] = Field(None) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_behavior.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_behavior.py index 59f40b6..77f5f81 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_behavior.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_behavior.py @@ -159,8 +159,8 @@ class SpatialSeriesData(ConfiguredBaseModel): Union[ NDArray[Shape["* num_times"], float], NDArray[Shape["* num_times, 1 x"], float], - NDArray[Shape["* num_times, 2 x,y"], float], - NDArray[Shape["* num_times, 3 x,y,z"], float], + NDArray[Shape["* num_times, 2 x_y"], float], + NDArray[Shape["* num_times, 3 x_y_z"], float], ] ] = Field(None) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_ecephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_ecephys.py index 801174d..f6347ac 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_ecephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_ecephys.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, DynamicTableRegion - from .core_nwb_base import ( - TimeSeriesStartingTime, NWBDataInterface, + TimeSeriesStartingTime, TimeSeriesSync, TimeSeries, NWBContainer, ) +from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, DynamicTableRegion + metamodel_version = "None" version = "2.5.0" diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_epoch.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_epoch.py index 099a19b..3a1d5fe 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_epoch.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_epoch.py @@ -54,12 +54,12 @@ if TYPE_CHECKING: from ...hdmf_common.v1_5_0.hdmf_common_table import ( + VectorIndex, VectorData, DynamicTable, - VectorIndex, ) -from .core_nwb_base import TimeSeriesReferenceVectorData, TimeSeries +from .core_nwb_base import TimeSeries, TimeSeriesReferenceVectorData metamodel_version = "None" diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_file.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_file.py index 87181f0..dde706a 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_file.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_file.py @@ -53,36 +53,36 @@ if TYPE_CHECKING: import numpy as np -from .core_nwb_misc import Units - from .core_nwb_icephys import ( - RepetitionsTable, - ExperimentalConditionsTable, - SimultaneousRecordingsTable, - IntracellularRecordingsTable, - SweepTable, SequentialRecordingsTable, + IntracellularRecordingsTable, + SimultaneousRecordingsTable, IntracellularElectrode, + ExperimentalConditionsTable, + SweepTable, + RepetitionsTable, ) from .core_nwb_device import Device from .core_nwb_ecephys import ElectrodeGroup -from .core_nwb_epoch import TimeIntervals +from .core_nwb_ophys import ImagingPlane from .core_nwb_base import ( NWBContainer, NWBData, TimeSeries, Images, - ProcessingModule, 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 diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_icephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_icephys.py index 4e6e0f1..86e6749 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_icephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_icephys.py @@ -53,20 +53,20 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_5_0.hdmf_common_table import ( - DynamicTableRegion, - AlignedDynamicTable, - VectorIndex, - VectorData, - DynamicTable, -) - from .core_nwb_base import ( TimeSeriesStartingTime, - TimeSeriesReferenceVectorData, NWBContainer, TimeSeries, TimeSeriesSync, + TimeSeriesReferenceVectorData, +) + +from ...hdmf_common.v1_5_0.hdmf_common_table import ( + DynamicTable, + DynamicTableRegion, + VectorIndex, + VectorData, + AlignedDynamicTable, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_image.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_image.py index 9ed4d15..6ddd8ad 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_image.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_image.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: 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" @@ -109,8 +109,8 @@ class GrayscaleImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -131,8 +131,8 @@ class RGBImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -153,8 +153,8 @@ class RGBAImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -293,8 +293,8 @@ class OpticalSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width, height"], float], - NDArray[Shape["3 width, height, depth"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height_depth"], float], ] ] = Field( None, @@ -302,7 +302,7 @@ class OpticalSeries(ImageSeries): ) data: Union[ 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( ..., description="""Images presented to subject, either grayscale or RGB""" ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_misc.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_misc.py index a3b4271..2dec894 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_misc.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_misc.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_5_0.hdmf_common_table import ( - DynamicTableRegion, - VectorIndex, - VectorData, - DynamicTable, -) +from .core_nwb_base import TimeSeriesStartingTime, TimeSeries, TimeSeriesSync 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" @@ -341,7 +341,7 @@ class DecompositionSeriesBands(DynamicTable): band_name: Optional[List[str] | str] = Field( 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.""", ) @@ -384,7 +384,7 @@ class Units(DynamicTable): obs_intervals_index: Optional[str] = Field( 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.""") ) electrodes_index: Optional[str] = Field( diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_ogen.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_ogen.py index ae74333..b82ecde 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_ogen.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_ogen.py @@ -54,10 +54,10 @@ if TYPE_CHECKING: from .core_nwb_base import ( + TimeSeriesSync, NWBContainer, TimeSeries, TimeSeriesStartingTime, - TimeSeriesSync, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_ophys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_ophys.py index 4f7c349..757b2c8 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_ophys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_ophys.py @@ -53,15 +53,6 @@ if TYPE_CHECKING: 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 ( TimeSeriesStartingTime, NWBContainer, @@ -70,6 +61,15 @@ from .core_nwb_base import ( 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" version = "2.5.0" @@ -122,8 +122,8 @@ class TwoPhotonSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width|height"], float], - NDArray[Shape["3 width|height|depth"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height_depth"], float], ] ] = Field( None, @@ -185,7 +185,7 @@ class RoiResponseSeries(TimeSeries): name: str = Field(...) data: Union[ NDArray[Shape["* num_times"], float], - NDArray[Shape["* num_times, * num_ROIs"], float], + NDArray[Shape["* num_times, * num_rois"], float], ] = Field(..., description="""Signals from ROIs.""") rois: str = Field( ..., diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_retinotopy.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_retinotopy.py index 094eb44..93a4bb9 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_retinotopy.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_5_0/core_nwb_retinotopy.py @@ -114,7 +114,7 @@ class ImagingRetinotopy(NWBDataInterface): 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.""", ) - 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'].""", ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_base.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_base.py index 79f6947..eef37a8 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_base.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_base.py @@ -53,9 +53,9 @@ if TYPE_CHECKING: 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" @@ -151,8 +151,8 @@ class Image(NWBData): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -258,9 +258,9 @@ class TimeSeriesData(ConfiguredBaseModel): array: Optional[ Union[ NDArray[Shape["* num_times"], 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, * num_DIM4"], 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, * num_dim4"], Any], ] ] = Field(None) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_behavior.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_behavior.py index 0f30adc..c81d141 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_behavior.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_behavior.py @@ -159,8 +159,8 @@ class SpatialSeriesData(ConfiguredBaseModel): Union[ NDArray[Shape["* num_times"], float], NDArray[Shape["* num_times, 1 x"], float], - NDArray[Shape["* num_times, 2 x,y"], float], - NDArray[Shape["* num_times, 3 x,y,z"], float], + NDArray[Shape["* num_times, 2 x_y"], float], + NDArray[Shape["* num_times, 3 x_y_z"], float], ] ] = Field(None) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_ecephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_ecephys.py index 05299ef..8b62b44 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_ecephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_ecephys.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, DynamicTableRegion - from .core_nwb_base import ( - TimeSeriesStartingTime, NWBDataInterface, + TimeSeriesStartingTime, TimeSeriesSync, TimeSeries, NWBContainer, ) +from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, DynamicTableRegion + metamodel_version = "None" version = "2.6.0-alpha" diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_epoch.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_epoch.py index ad88cf7..194d436 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_epoch.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_epoch.py @@ -54,12 +54,12 @@ if TYPE_CHECKING: from ...hdmf_common.v1_5_0.hdmf_common_table import ( + VectorIndex, VectorData, DynamicTable, - VectorIndex, ) -from .core_nwb_base import TimeSeriesReferenceVectorData, TimeSeries +from .core_nwb_base import TimeSeries, TimeSeriesReferenceVectorData metamodel_version = "None" diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_file.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_file.py index 4041fbb..9296cef 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_file.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_file.py @@ -53,36 +53,36 @@ if TYPE_CHECKING: import numpy as np -from .core_nwb_misc import Units - from .core_nwb_icephys import ( - RepetitionsTable, - ExperimentalConditionsTable, - SimultaneousRecordingsTable, - IntracellularRecordingsTable, - SweepTable, SequentialRecordingsTable, + IntracellularRecordingsTable, + SimultaneousRecordingsTable, IntracellularElectrode, + ExperimentalConditionsTable, + SweepTable, + RepetitionsTable, ) from .core_nwb_device import Device from .core_nwb_ecephys import ElectrodeGroup -from .core_nwb_epoch import TimeIntervals +from .core_nwb_ophys import ImagingPlane from .core_nwb_base import ( NWBContainer, NWBData, TimeSeries, Images, - ProcessingModule, 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 diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_icephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_icephys.py index 0d69cde..13ec765 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_icephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_icephys.py @@ -53,20 +53,20 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_5_0.hdmf_common_table import ( - DynamicTableRegion, - AlignedDynamicTable, - VectorIndex, - VectorData, - DynamicTable, -) - from .core_nwb_base import ( TimeSeriesStartingTime, - TimeSeriesReferenceVectorData, NWBContainer, TimeSeries, TimeSeriesSync, + TimeSeriesReferenceVectorData, +) + +from ...hdmf_common.v1_5_0.hdmf_common_table import ( + DynamicTable, + DynamicTableRegion, + VectorIndex, + VectorData, + AlignedDynamicTable, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_image.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_image.py index f91e99b..223b0dc 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_image.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_image.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: 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" @@ -109,8 +109,8 @@ class GrayscaleImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -131,8 +131,8 @@ class RGBImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -153,8 +153,8 @@ class RGBAImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -293,8 +293,8 @@ class OpticalSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width, height"], float], - NDArray[Shape["3 width, height, depth"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height_depth"], float], ] ] = Field( None, @@ -302,7 +302,7 @@ class OpticalSeries(ImageSeries): ) data: Union[ 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( ..., description="""Images presented to subject, either grayscale or RGB""" ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_misc.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_misc.py index 0e20c78..c8f379c 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_misc.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_misc.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_5_0.hdmf_common_table import ( - DynamicTableRegion, - VectorIndex, - VectorData, - DynamicTable, -) +from .core_nwb_base import TimeSeriesStartingTime, TimeSeries, TimeSeriesSync 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" @@ -341,7 +341,7 @@ class DecompositionSeriesBands(DynamicTable): band_name: Optional[List[str] | str] = Field( 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.""", ) @@ -384,7 +384,7 @@ class Units(DynamicTable): obs_intervals_index: Optional[str] = Field( 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.""") ) electrodes_index: Optional[str] = Field( diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_ogen.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_ogen.py index afa9c99..f8b60d7 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_ogen.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_ogen.py @@ -54,10 +54,10 @@ if TYPE_CHECKING: from .core_nwb_base import ( + TimeSeriesSync, NWBContainer, TimeSeries, TimeSeriesStartingTime, - TimeSeriesSync, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_ophys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_ophys.py index 25ce31f..f993dfe 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_ophys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_ophys.py @@ -53,15 +53,6 @@ if TYPE_CHECKING: 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 ( TimeSeriesStartingTime, NWBContainer, @@ -70,6 +61,15 @@ from .core_nwb_base import ( 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" version = "2.6.0-alpha" @@ -195,8 +195,8 @@ class TwoPhotonSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width|height"], float], - NDArray[Shape["3 width|height|depth"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height_depth"], float], ] ] = Field( None, @@ -258,7 +258,7 @@ class RoiResponseSeries(TimeSeries): name: str = Field(...) data: Union[ NDArray[Shape["* num_times"], float], - NDArray[Shape["* num_times, * num_ROIs"], float], + NDArray[Shape["* num_times, * num_rois"], float], ] = Field(..., description="""Signals from ROIs.""") rois: str = Field( ..., diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_retinotopy.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_retinotopy.py index 6ba2d7e..8785997 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_retinotopy.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_6_0_alpha/core_nwb_retinotopy.py @@ -114,7 +114,7 @@ class ImagingRetinotopy(NWBDataInterface): 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.""", ) - 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'].""", ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_base.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_base.py index 46d1599..d4e8399 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_base.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_base.py @@ -53,9 +53,9 @@ if TYPE_CHECKING: 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" @@ -151,8 +151,8 @@ class Image(NWBData): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -258,9 +258,9 @@ class TimeSeriesData(ConfiguredBaseModel): array: Optional[ Union[ NDArray[Shape["* num_times"], 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, * num_DIM4"], 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, * num_dim4"], Any], ] ] = Field(None) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_behavior.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_behavior.py index f6c95b3..7781093 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_behavior.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_behavior.py @@ -159,8 +159,8 @@ class SpatialSeriesData(ConfiguredBaseModel): Union[ NDArray[Shape["* num_times"], float], NDArray[Shape["* num_times, 1 x"], float], - NDArray[Shape["* num_times, 2 x,y"], float], - NDArray[Shape["* num_times, 3 x,y,z"], float], + NDArray[Shape["* num_times, 2 x_y"], float], + NDArray[Shape["* num_times, 3 x_y_z"], float], ] ] = Field(None) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_ecephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_ecephys.py index caf7b3f..c110d26 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_ecephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_ecephys.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_8_0.hdmf_common_table import DynamicTable, DynamicTableRegion - from .core_nwb_base import ( - TimeSeriesStartingTime, NWBDataInterface, + TimeSeriesStartingTime, TimeSeriesSync, TimeSeries, NWBContainer, ) +from ...hdmf_common.v1_8_0.hdmf_common_table import DynamicTable, DynamicTableRegion + metamodel_version = "None" version = "2.7.0" diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_epoch.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_epoch.py index 540c115..3213dc6 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_epoch.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_epoch.py @@ -54,12 +54,12 @@ if TYPE_CHECKING: from ...hdmf_common.v1_8_0.hdmf_common_table import ( + VectorIndex, VectorData, DynamicTable, - VectorIndex, ) -from .core_nwb_base import TimeSeriesReferenceVectorData, TimeSeries +from .core_nwb_base import TimeSeries, TimeSeriesReferenceVectorData metamodel_version = "None" diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_file.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_file.py index 103ebf0..ffac815 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_file.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_file.py @@ -53,36 +53,36 @@ if TYPE_CHECKING: import numpy as np -from .core_nwb_misc import Units - from .core_nwb_icephys import ( - RepetitionsTable, - ExperimentalConditionsTable, - SimultaneousRecordingsTable, - IntracellularRecordingsTable, - SweepTable, SequentialRecordingsTable, + IntracellularRecordingsTable, + SimultaneousRecordingsTable, IntracellularElectrode, + ExperimentalConditionsTable, + SweepTable, + RepetitionsTable, ) from .core_nwb_device import Device from .core_nwb_ecephys import ElectrodeGroup -from .core_nwb_epoch import TimeIntervals +from .core_nwb_ophys import ImagingPlane from .core_nwb_base import ( NWBContainer, NWBData, TimeSeries, Images, - ProcessingModule, 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 diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_icephys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_icephys.py index 46d7517..f6ac233 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_icephys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_icephys.py @@ -53,20 +53,20 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_8_0.hdmf_common_table import ( - DynamicTableRegion, - AlignedDynamicTable, - VectorIndex, - VectorData, - DynamicTable, -) - from .core_nwb_base import ( TimeSeriesStartingTime, - TimeSeriesReferenceVectorData, NWBContainer, TimeSeries, TimeSeriesSync, + TimeSeriesReferenceVectorData, +) + +from ...hdmf_common.v1_8_0.hdmf_common_table import ( + DynamicTable, + DynamicTableRegion, + VectorIndex, + VectorData, + AlignedDynamicTable, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_image.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_image.py index 9931d79..71b5633 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_image.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_image.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: 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" @@ -109,8 +109,8 @@ class GrayscaleImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -131,8 +131,8 @@ class RGBImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -153,8 +153,8 @@ class RGBAImage(Image): array: Optional[ Union[ NDArray[Shape["* x, * y"], float], - NDArray[Shape["* x, * y, 3 r, g, b"], float], - NDArray[Shape["* x, * y, 4 r, g, b, a"], float], + NDArray[Shape["* x, * y, 3 r_g_b"], float], + NDArray[Shape["* x, * y, 4 r_g_b_a"], float], ] ] = Field(None) @@ -293,8 +293,8 @@ class OpticalSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width, height"], float], - NDArray[Shape["3 width, height, depth"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height_depth"], float], ] ] = Field( None, @@ -302,7 +302,7 @@ class OpticalSeries(ImageSeries): ) data: Union[ 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( ..., description="""Images presented to subject, either grayscale or RGB""" ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_misc.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_misc.py index 18ed3da..7a875cb 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_misc.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_misc.py @@ -53,16 +53,16 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_8_0.hdmf_common_table import ( - DynamicTableRegion, - VectorIndex, - VectorData, - DynamicTable, -) +from .core_nwb_base import TimeSeriesStartingTime, TimeSeries, TimeSeriesSync from .core_nwb_ecephys import ElectrodeGroup -from .core_nwb_base import TimeSeriesStartingTime, TimeSeries, TimeSeriesSync +from ...hdmf_common.v1_8_0.hdmf_common_table import ( + DynamicTable, + DynamicTableRegion, + VectorIndex, + VectorData, +) metamodel_version = "None" @@ -341,7 +341,7 @@ class DecompositionSeriesBands(DynamicTable): band_name: Optional[List[str] | str] = Field( 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.""", ) @@ -384,7 +384,7 @@ class Units(DynamicTable): obs_intervals_index: Optional[str] = Field( 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.""") ) electrodes_index: Optional[str] = Field( diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_ogen.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_ogen.py index df23c11..0598f78 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_ogen.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_ogen.py @@ -54,10 +54,10 @@ if TYPE_CHECKING: from .core_nwb_base import ( + TimeSeriesSync, NWBContainer, TimeSeries, TimeSeriesStartingTime, - TimeSeriesSync, ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_ophys.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_ophys.py index 43f8486..19057e2 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_ophys.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_ophys.py @@ -53,15 +53,6 @@ if TYPE_CHECKING: import numpy as np -from .core_nwb_image import ImageSeriesExternalFile, ImageSeries - -from ...hdmf_common.v1_8_0.hdmf_common_table import ( - DynamicTableRegion, - VectorData, - VectorIndex, - DynamicTable, -) - from .core_nwb_base import ( TimeSeriesStartingTime, NWBContainer, @@ -70,6 +61,15 @@ from .core_nwb_base import ( TimeSeriesSync, ) +from .core_nwb_image import ImageSeries, ImageSeriesExternalFile + +from ...hdmf_common.v1_8_0.hdmf_common_table import ( + DynamicTable, + DynamicTableRegion, + VectorIndex, + VectorData, +) + metamodel_version = "None" version = "2.7.0" @@ -195,8 +195,8 @@ class TwoPhotonSeries(ImageSeries): ) field_of_view: Optional[ Union[ - NDArray[Shape["2 width|height"], float], - NDArray[Shape["3 width|height|depth"], float], + NDArray[Shape["2 width_height"], float], + NDArray[Shape["3 width_height_depth"], float], ] ] = Field( None, @@ -258,7 +258,7 @@ class RoiResponseSeries(TimeSeries): name: str = Field(...) data: Union[ NDArray[Shape["* num_times"], float], - NDArray[Shape["* num_times, * num_ROIs"], float], + NDArray[Shape["* num_times, * num_rois"], float], ] = Field(..., description="""Signals from ROIs.""") rois: str = Field( ..., diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_retinotopy.py b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_retinotopy.py index f412900..037a70c 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_retinotopy.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_7_0/core_nwb_retinotopy.py @@ -114,7 +114,7 @@ class ImagingRetinotopy(NWBDataInterface): 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.""", ) - 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'].""", ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/v1_5_0/hdmf_common_sparse.py b/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/v1_5_0/hdmf_common_sparse.py index 960f611..379c961 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/v1_5_0/hdmf_common_sparse.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/v1_5_0/hdmf_common_sparse.py @@ -104,13 +104,13 @@ class CSRMatrix(Container): None, description="""The shape (number of rows, number of columns) of this sparse matrix.""", ) - indices: NDArray[Shape["* number of non-zero values"], int] = Field( + indices: NDArray[Shape["* number_of_non_zero_values"], int] = Field( ..., description="""The column indices.""" ) - indptr: NDArray[Shape["* number of rows in the matrix + 1"], int] = Field( + indptr: NDArray[Shape["* number_of_rows_in_the_matrix_1"], int] = Field( ..., description="""The row index pointer.""" ) - data: NDArray[Shape["* number of non-zero values"], Any] = Field( + data: NDArray[Shape["* number_of_non_zero_values"], Any] = Field( ..., description="""The non-zero values in the matrix.""" ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/v1_5_0/hdmf_common_table.py b/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/v1_5_0/hdmf_common_table.py index 0524910..438670a 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/v1_5_0/hdmf_common_table.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/v1_5_0/hdmf_common_table.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: import numpy as np -from .hdmf_common_base import Container, Data +from .hdmf_common_base import Data, Container metamodel_version = "None" diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/v1_8_0/hdmf_common_sparse.py b/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/v1_8_0/hdmf_common_sparse.py index 1ae0e72..49e0252 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/v1_8_0/hdmf_common_sparse.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/v1_8_0/hdmf_common_sparse.py @@ -104,13 +104,13 @@ class CSRMatrix(Container): None, description="""The shape (number of rows, number of columns) of this sparse matrix.""", ) - indices: NDArray[Shape["* number of non-zero values"], int] = Field( + indices: NDArray[Shape["* number_of_non_zero_values"], int] = Field( ..., description="""The column indices.""" ) - indptr: NDArray[Shape["* number of rows in the matrix + 1"], int] = Field( + indptr: NDArray[Shape["* number_of_rows_in_the_matrix_1"], int] = Field( ..., description="""The row index pointer.""" ) - data: NDArray[Shape["* number of non-zero values"], Any] = Field( + data: NDArray[Shape["* number_of_non_zero_values"], Any] = Field( ..., description="""The non-zero values in the matrix.""" ) diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/v1_8_0/hdmf_common_table.py b/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/v1_8_0/hdmf_common_table.py index de599a6..211fe46 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/v1_8_0/hdmf_common_table.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/v1_8_0/hdmf_common_table.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: import numpy as np -from .hdmf_common_base import Container, Data +from .hdmf_common_base import Data, Container metamodel_version = "None" diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_experimental/v0_1_0/hdmf_experimental_resources.py b/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_experimental/v0_1_0/hdmf_experimental_resources.py index eef67d2..5a84cab 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_experimental/v0_1_0/hdmf_experimental_resources.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_experimental/v0_1_0/hdmf_experimental_resources.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: 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 metamodel_version = "None" diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_experimental/v0_5_0/hdmf_experimental_resources.py b/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_experimental/v0_5_0/hdmf_experimental_resources.py index 393ce36..4450d21 100644 --- a/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_experimental/v0_5_0/hdmf_experimental_resources.py +++ b/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_experimental/v0_5_0/hdmf_experimental_resources.py @@ -53,7 +53,7 @@ if TYPE_CHECKING: import numpy as np -from ...hdmf_common.v1_8_0.hdmf_common_base import Container, Data +from ...hdmf_common.v1_8_0.hdmf_common_base import Data, Container metamodel_version = "None"