aind_data_schema package#
Subpackages#
- aind_data_schema.core package
- Submodules
- aind_data_schema.core.acquisition module
- aind_data_schema.core.data_description module
- aind_data_schema.core.instrument module
- aind_data_schema.core.metadata module
- aind_data_schema.core.mri_session module
- aind_data_schema.core.procedures module
- aind_data_schema.core.processing module
- aind_data_schema.core.rig module
- aind_data_schema.core.session module
- aind_data_schema.core.subject module
- Module contents
- aind_data_schema.imaging package
- aind_data_schema.models package
- Submodules
- aind_data_schema.models.coordinates module
- aind_data_schema.models.devices module
- aind_data_schema.models.harp_types module
Behavior
CameraController
ClockSynchronizer
Cuttlefish
GenericHarpDevice
HarpDeviceType
HarpDeviceType.BEHAVIOR
HarpDeviceType.CAMERA_CONTROLLER
HarpDeviceType.CLOCK_SYNCHRONIZER
HarpDeviceType.CUTTLEFISH
HarpDeviceType.GENERIC_HARP_DEVICE
HarpDeviceType.INPUT_EXPANDER
HarpDeviceType.LICKETY_SPLIT
HarpDeviceType.LOAD_CELLS
HarpDeviceType.OLFACTOMETER
HarpDeviceType.ONE_OF
HarpDeviceType.SNIFF_DETECTOR
HarpDeviceType.SOUND_CARD
HarpDeviceType.STEPPER_DRIVER
HarpDeviceType.SYNCHRONIZER
HarpDeviceType.TIMESTAMP_GENERATOR_1
HarpDeviceType.TIMESTAMP_GENERATOR_3
HarpDeviceType.TREADMILL
InputExpander
LicketySplit
LoadCells
Olfactometer
SniffDetector
SoundCard
StepperDriver
Synchronizer
TimestampGeneratorGen1
TimestampGeneratorGen3
Treadmill
- aind_data_schema.models.modalities module
- aind_data_schema.models.organizations module
- aind_data_schema.models.pid_names module
- aind_data_schema.models.platforms module
- aind_data_schema.models.process_names module
ProcessName
ProcessName.ANALYSIS
ProcessName.COMPRESSION
ProcessName.DENOISING
ProcessName.DFF_ESTIMATION
ProcessName.EPHYS_CURATION
ProcessName.EPHYS_POSTPROCESSING
ProcessName.EPHYS_PREPROCESSING
ProcessName.EPHYS_VISUALIZATION
ProcessName.FIDUCIAL_SEGMENTATION
ProcessName.FILE_CONVERSION
ProcessName.FLUORESCENCE_EVENT_DETECTION
ProcessName.IMAGE_ATLAS_ALIGNMENT
ProcessName.IMAGE_BACKGROUND_SUBTRACTION
ProcessName.IMAGE_CELL_QUANTIFICATION
ProcessName.IMAGE_CELL_SEGMENTATION
ProcessName.IMAGE_DESTRIPING
ProcessName.IMAGE_FLATFIELD_CORRECTION
ProcessName.IMAGE_IMPORTING
ProcessName.IMAGE_THRESHOLDING
ProcessName.IMAGE_TILE_ALIGNMENT
ProcessName.IMAGE_TILE_FUSING
ProcessName.IMAGE_TILE_PROJECTION
ProcessName.MANUAL_ANNOTATION
ProcessName.NEUROPIL_SUBTRACTION
ProcessName.OTHER
ProcessName.QUALITY_CONTROL_AND_ASSESSMENT
ProcessName.REGISTRATION_TO_TEMPLATE
ProcessName.SKULL_STRIPPING
ProcessName.SPATIAL_TIMESERIES_DEMIXING
ProcessName.SPIKE_SORTING
ProcessName.VIDEO_MOTION_CORRECTION
ProcessName.VIDEO_PLANE_DECROSSTALK
ProcessName.VIDEO_ROI_CLASSIFICATION
ProcessName.VIDEO_ROI_SEGMENTATION
ProcessName.VIDEO_ROI_TIMESERIES_EXTRACTION
- aind_data_schema.models.reagent module
- aind_data_schema.models.registry module
- aind_data_schema.models.species module
- aind_data_schema.models.stimulus module
- aind_data_schema.models.units module
- Module contents
- aind_data_schema.utils package
Submodules#
aind_data_schema.base module#
generic base class with supporting validators and fields for basic AIND schema
- class aind_data_schema.base.AindCoreModel(*, describedBy: str, schema_version: str[str])#
Bases:
AindModel
Generic base class to hold common fields/validators/etc for all basic AIND schema
- classmethod default_filename()#
Returns standard filename in snakecase
- describedBy: str#
- model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}#
A dictionary of computed field names and their corresponding ComputedFieldInfo objects.
- model_config: ClassVar[ConfigDict] = {'extra': 'forbid', 'use_enum_values': True}#
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- model_fields: ClassVar[dict[str, FieldInfo]] = {'describedBy': FieldInfo(annotation=str, required=True), 'schema_version': FieldInfo(annotation=str, required=True, title='Version', description='schema version', frozen=True, metadata=[_PydanticGeneralMetadata(pattern='^\\d+.\\d+.\\d+$')])}#
Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].
This replaces Model.__fields__ from Pydantic V1.
- model_post_init(__context: Any) None #
This function is meant to behave like a BaseModel method to initialise private attributes.
It takes context as an argument since that’s what pydantic-core passes when calling it.
- Parameters:
self – The BaseModel instance.
__context – The context.
- schema_version: str#
- write_standard_file(output_directory: Path | None = None, prefix: str | None = None, suffix: str | None = None)#
Writes schema to standard json file :param output_directory: optional Path object for output directory.
Default: None
- Parameters:
prefix (Optional[str]) – optional str for intended filepath with extra naming convention Default: None
suffix (Optional[str]) – optional str for intended filepath with extra naming convention Default: None
- class aind_data_schema.base.AindGeneric(**extra_data: Any)#
Bases:
BaseModel
Base class for generic types that can be used in AIND schema
- model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}#
A dictionary of computed field names and their corresponding ComputedFieldInfo objects.
- model_config: ClassVar[ConfigDict] = {'extra': 'allow'}#
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- model_fields: ClassVar[dict[str, FieldInfo]] = {}#
Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].
This replaces Model.__fields__ from Pydantic V1.
- class aind_data_schema.base.AindModel#
Bases:
BaseModel
,Generic
[AindGenericType
]BaseModel that disallows extra fields
- model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}#
A dictionary of computed field names and their corresponding ComputedFieldInfo objects.
- model_config: ClassVar[ConfigDict] = {'extra': 'forbid', 'use_enum_values': True}#
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- model_fields: ClassVar[dict[str, FieldInfo]] = {}#
Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].
This replaces Model.__fields__ from Pydantic V1.
Module contents#
imports for AindModel subclasses