aind_data_schema.imaging package#
Submodules#
aind_data_schema.imaging.tile module#
“ Models related to imaging tiles and their transformations
- pydantic model aind_data_schema.imaging.tile.AcquisitionTile#
Bases:
Tile
Description of acquisition tile
Show JSON schema
{ "title": "AcquisitionTile", "description": "Description of acquisition tile", "type": "object", "properties": { "coordinate_transformations": { "items": { "discriminator": { "mapping": { "affine": "#/$defs/Affine3dTransform", "rotation": "#/$defs/Rotation3dTransform", "scale": "#/$defs/Scale3dTransform", "translation": "#/$defs/Translation3dTransform" }, "propertyName": "type" }, "oneOf": [ { "$ref": "#/$defs/Scale3dTransform" }, { "$ref": "#/$defs/Translation3dTransform" }, { "$ref": "#/$defs/Rotation3dTransform" }, { "$ref": "#/$defs/Affine3dTransform" } ] }, "title": "Tile coordinate transformations", "type": "array" }, "file_name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "File name" }, "channel": { "$ref": "#/$defs/Channel" }, "notes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Notes" }, "imaging_angle": { "default": 0, "title": "Imaging angle", "type": "integer" }, "imaging_angle_unit": { "allOf": [ { "$ref": "#/$defs/AngleUnit" } ], "default": "degrees", "title": "Imaging angle unit" } }, "$defs": { "Affine3dTransform": { "additionalProperties": false, "description": "Values to be vector-added to a 3D position. Often needed to specify a Tile's origin.", "properties": { "type": { "const": "affine", "default": "affine", "title": "Type" }, "affine_transform": { "items": { "anyOf": [ { "type": "number" }, { "type": "string" } ] }, "maxItems": 12, "minItems": 12, "title": "Affine transform matrix values (top 3x4 matrix)", "type": "array" } }, "required": [ "affine_transform" ], "title": "Affine3dTransform", "type": "object" }, "AngleUnit": { "description": "Enumeration of Angle Measurements", "enum": [ "radians", "degrees" ], "title": "AngleUnit", "type": "string" }, "Channel": { "additionalProperties": false, "description": "Description of a channel", "properties": { "channel_name": { "title": "Channel", "type": "string" }, "light_source_name": { "description": "Must match device name", "title": "Light source name", "type": "string" }, "filter_names": { "description": "Must match device names", "items": { "type": "string" }, "title": "Filter names", "type": "array" }, "detector_name": { "description": "Must match device name", "title": "Detector name", "type": "string" }, "additional_device_names": { "default": [], "items": { "type": "string" }, "title": "Additional device names", "type": "array" }, "excitation_wavelength": { "maximum": 1000, "minimum": 300, "title": "Wavelength", "type": "integer" }, "excitation_wavelength_unit": { "allOf": [ { "$ref": "#/$defs/SizeUnit" } ], "default": "nanometer", "title": "Laser wavelength unit" }, "excitation_power": { "maximum": 2000.0, "title": "Laser power", "type": "number" }, "excitation_power_unit": { "allOf": [ { "$ref": "#/$defs/PowerUnit" } ], "default": "milliwatt", "title": "Laser power unit" }, "filter_wheel_index": { "title": "Filter wheel index", "type": "integer" }, "dilation": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Dilation (pixels)" }, "dilation_unit": { "allOf": [ { "$ref": "#/$defs/SizeUnit" } ], "default": "pixel", "title": "Dilation unit" }, "description": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Description" } }, "required": [ "channel_name", "light_source_name", "filter_names", "detector_name", "excitation_wavelength", "excitation_power", "filter_wheel_index" ], "title": "Channel", "type": "object" }, "PowerUnit": { "description": "Unit for power, set or measured", "enum": [ "microwatt", "milliwatt", "percent" ], "title": "PowerUnit", "type": "string" }, "Rotation3dTransform": { "additionalProperties": false, "description": "Values to be vector-added to a 3D position. Often needed to specify a device or tile's origin.", "properties": { "type": { "const": "rotation", "default": "rotation", "title": "Type" }, "rotation": { "items": { "anyOf": [ { "type": "number" }, { "type": "string" } ] }, "maxItems": 9, "minItems": 9, "title": "3D rotation matrix values (3x3) ", "type": "array" } }, "required": [ "rotation" ], "title": "Rotation3dTransform", "type": "object" }, "Scale3dTransform": { "additionalProperties": false, "description": "Values to be vector-multiplied with a 3D position, equivalent to the diagonals of a 3x3 transform matrix.\nRepresents voxel spacing if used as the first applied coordinate transform.", "properties": { "type": { "const": "scale", "default": "scale", "title": "Type" }, "scale": { "items": { "anyOf": [ { "type": "number" }, { "type": "string" } ] }, "maxItems": 3, "minItems": 3, "title": "3D scale parameters", "type": "array" } }, "required": [ "scale" ], "title": "Scale3dTransform", "type": "object" }, "SizeUnit": { "description": "Enumeration of Length Measurements", "enum": [ "meter", "centimeter", "millimeter", "micrometer", "nanometer", "inch", "pixel" ], "title": "SizeUnit", "type": "string" }, "Translation3dTransform": { "additionalProperties": false, "description": "Values to be vector-added to a 3D position. Often needed to specify a device or tile's origin.", "properties": { "type": { "const": "translation", "default": "translation", "title": "Type" }, "translation": { "items": { "anyOf": [ { "type": "number" }, { "type": "string" } ] }, "maxItems": 3, "minItems": 3, "title": "3D translation parameters", "type": "array" } }, "required": [ "translation" ], "title": "Translation3dTransform", "type": "object" } }, "additionalProperties": false, "required": [ "coordinate_transformations", "channel" ] }
- Config:
extra: str = forbid
use_enum_values: bool = True
- Fields:
- field imaging_angle: int = 0#
- field notes: str | None = None#
- pydantic model aind_data_schema.imaging.tile.Channel#
Bases:
AindModel
Description of a channel
Show JSON schema
{ "title": "Channel", "description": "Description of a channel", "type": "object", "properties": { "channel_name": { "title": "Channel", "type": "string" }, "light_source_name": { "description": "Must match device name", "title": "Light source name", "type": "string" }, "filter_names": { "description": "Must match device names", "items": { "type": "string" }, "title": "Filter names", "type": "array" }, "detector_name": { "description": "Must match device name", "title": "Detector name", "type": "string" }, "additional_device_names": { "default": [], "items": { "type": "string" }, "title": "Additional device names", "type": "array" }, "excitation_wavelength": { "maximum": 1000, "minimum": 300, "title": "Wavelength", "type": "integer" }, "excitation_wavelength_unit": { "allOf": [ { "$ref": "#/$defs/SizeUnit" } ], "default": "nanometer", "title": "Laser wavelength unit" }, "excitation_power": { "maximum": 2000.0, "title": "Laser power", "type": "number" }, "excitation_power_unit": { "allOf": [ { "$ref": "#/$defs/PowerUnit" } ], "default": "milliwatt", "title": "Laser power unit" }, "filter_wheel_index": { "title": "Filter wheel index", "type": "integer" }, "dilation": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Dilation (pixels)" }, "dilation_unit": { "allOf": [ { "$ref": "#/$defs/SizeUnit" } ], "default": "pixel", "title": "Dilation unit" }, "description": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Description" } }, "$defs": { "PowerUnit": { "description": "Unit for power, set or measured", "enum": [ "microwatt", "milliwatt", "percent" ], "title": "PowerUnit", "type": "string" }, "SizeUnit": { "description": "Enumeration of Length Measurements", "enum": [ "meter", "centimeter", "millimeter", "micrometer", "nanometer", "inch", "pixel" ], "title": "SizeUnit", "type": "string" } }, "additionalProperties": false, "required": [ "channel_name", "light_source_name", "filter_names", "detector_name", "excitation_wavelength", "excitation_power", "filter_wheel_index" ] }
- Config:
extra: str = forbid
use_enum_values: bool = True
- Fields:
- field additional_device_names: List[str] = []#
- field channel_name: str [Required]#
- field description: str | None = None#
- field detector_name: str [Required]#
Must match device name
- field dilation: int | None = None#
- field excitation_power: float [Required]#
- Constraints:
le = 2000
- field excitation_wavelength: int [Required]#
- Constraints:
ge = 300
le = 1000
- field filter_names: List[str] [Required]#
Must match device names
- field filter_wheel_index: int [Required]#
- field light_source_name: str [Required]#
Must match device name
- pydantic model aind_data_schema.imaging.tile.Tile#
Bases:
AindModel
Description of an image tile
Show JSON schema
{ "title": "Tile", "description": "Description of an image tile", "type": "object", "properties": { "coordinate_transformations": { "items": { "discriminator": { "mapping": { "affine": "#/$defs/Affine3dTransform", "rotation": "#/$defs/Rotation3dTransform", "scale": "#/$defs/Scale3dTransform", "translation": "#/$defs/Translation3dTransform" }, "propertyName": "type" }, "oneOf": [ { "$ref": "#/$defs/Scale3dTransform" }, { "$ref": "#/$defs/Translation3dTransform" }, { "$ref": "#/$defs/Rotation3dTransform" }, { "$ref": "#/$defs/Affine3dTransform" } ] }, "title": "Tile coordinate transformations", "type": "array" }, "file_name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "File name" } }, "$defs": { "Affine3dTransform": { "additionalProperties": false, "description": "Values to be vector-added to a 3D position. Often needed to specify a Tile's origin.", "properties": { "type": { "const": "affine", "default": "affine", "title": "Type" }, "affine_transform": { "items": { "anyOf": [ { "type": "number" }, { "type": "string" } ] }, "maxItems": 12, "minItems": 12, "title": "Affine transform matrix values (top 3x4 matrix)", "type": "array" } }, "required": [ "affine_transform" ], "title": "Affine3dTransform", "type": "object" }, "Rotation3dTransform": { "additionalProperties": false, "description": "Values to be vector-added to a 3D position. Often needed to specify a device or tile's origin.", "properties": { "type": { "const": "rotation", "default": "rotation", "title": "Type" }, "rotation": { "items": { "anyOf": [ { "type": "number" }, { "type": "string" } ] }, "maxItems": 9, "minItems": 9, "title": "3D rotation matrix values (3x3) ", "type": "array" } }, "required": [ "rotation" ], "title": "Rotation3dTransform", "type": "object" }, "Scale3dTransform": { "additionalProperties": false, "description": "Values to be vector-multiplied with a 3D position, equivalent to the diagonals of a 3x3 transform matrix.\nRepresents voxel spacing if used as the first applied coordinate transform.", "properties": { "type": { "const": "scale", "default": "scale", "title": "Type" }, "scale": { "items": { "anyOf": [ { "type": "number" }, { "type": "string" } ] }, "maxItems": 3, "minItems": 3, "title": "3D scale parameters", "type": "array" } }, "required": [ "scale" ], "title": "Scale3dTransform", "type": "object" }, "Translation3dTransform": { "additionalProperties": false, "description": "Values to be vector-added to a 3D position. Often needed to specify a device or tile's origin.", "properties": { "type": { "const": "translation", "default": "translation", "title": "Type" }, "translation": { "items": { "anyOf": [ { "type": "number" }, { "type": "string" } ] }, "maxItems": 3, "minItems": 3, "title": "3D translation parameters", "type": "array" } }, "required": [ "translation" ], "title": "Translation3dTransform", "type": "object" } }, "additionalProperties": false, "required": [ "coordinate_transformations" ] }
- Config:
extra: str = forbid
use_enum_values: bool = True
- Fields:
- field coordinate_transformations: List[Scale3dTransform | aind_data_schema.models.coordinates.Translation3dTransform | aind_data_schema.models.coordinates.Rotation3dTransform | aind_data_schema.models.coordinates.Affine3dTransform[Scale3dTransform | Translation3dTransform | Rotation3dTransform | Affine3dTransform]] [Required]#
- field file_name: str | None = None#
Module contents#
imports for imaging subpackage