diff --git a/docs/source/_static/coordinate_system_builder.html b/docs/source/_static/coordinate_system_builder.html
new file mode 100644
index 000000000..7e7ed183c
--- /dev/null
+++ b/docs/source/_static/coordinate_system_builder.html
@@ -0,0 +1,1132 @@
+
+
+
+
+ AIND Coordinate System Builder
+
+
+
+
+
+
+
+
+
+
Loading brain mesh…
+
+
+
+
+
+
diff --git a/docs/source/aind_data_schema_models/modalities.md b/docs/source/aind_data_schema_models/modalities.md
index 33a654594..75efe770e 100644
--- a/docs/source/aind_data_schema_models/modalities.md
+++ b/docs/source/aind_data_schema_models/modalities.md
@@ -23,6 +23,7 @@ Modalities
| `MAPSEQ` | `Multiplexed analysis of projections by sequencing` | `MAPseq` |
| `MERFISH` | `Multiplexed error-robust fluorescence in situ hybridization` | `merfish` |
| `MRI` | `Magnetic resonance imaging` | `MRI` |
+| `ONE_PHOTON` | `One-photon imaging` | `one-photon` |
| `POPHYS` | `Planar optical physiology` | `pophys` |
| `SCRNASEQ` | `Single cell RNA sequencing` | `scRNAseq` |
| `SLAP2` | `Random access projection microscopy` | `slap2` |
diff --git a/docs/source/components/configs.md b/docs/source/components/configs.md
index daf60a9e9..239431de5 100644
--- a/docs/source/components/configs.md
+++ b/docs/source/components/configs.md
@@ -122,7 +122,7 @@ Description of an N-D image
| `channel_name` | `str` | Channel name |
| `dimensions_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Dimensions unit |
| `image_to_acquisition_transform` | List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#affine)] | Image to acquisition transform (Position, rotation, and scale of the image. Note that depth should be in the planes.) |
-| `dimensions` | Optional[[Scale](coordinates.md#scale)] | Dimensions |
+| `dimensions` | Optional[[Scale](coordinates.md#scale) or [Rectangle](geometry.md#rectangle)] | Dimensions |
### ImageSPIM
@@ -139,7 +139,7 @@ Description of an N-D image acquired with SPIM
| `channel_name` | `str` | Channel name |
| `dimensions_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Dimensions unit |
| `image_to_acquisition_transform` | List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#affine)] | Image to acquisition transform (Position, rotation, and scale of the image. Note that depth should be in the planes.) |
-| `dimensions` | Optional[[Scale](coordinates.md#scale)] | Dimensions |
+| `dimensions` | Optional[[Scale](coordinates.md#scale) or [Rectangle](geometry.md#rectangle)] | Dimensions |
### ImagingConfig
@@ -371,7 +371,7 @@ Description of an N-D image acquired in a specific imaging plane
| `channel_name` | `str` | Channel name |
| `dimensions_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Dimensions unit |
| `image_to_acquisition_transform` | List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#affine)] | Image to acquisition transform (Position, rotation, and scale of the image. Note that depth should be in the planes.) |
-| `dimensions` | Optional[[Scale](coordinates.md#scale)] | Dimensions |
+| `dimensions` | Optional[[Scale](coordinates.md#scale) or [Rectangle](geometry.md#rectangle)] | Dimensions |
### PlanarImageStack
@@ -389,7 +389,7 @@ Description of a stack of images acquired in a specific imaging plane
| `channel_name` | `str` | Channel name |
| `dimensions_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Dimensions unit |
| `image_to_acquisition_transform` | List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#affine)] | Image to acquisition transform (Position, rotation, and scale of the image. Note that depth should be in the planes.) |
-| `dimensions` | Optional[[Scale](coordinates.md#scale)] | Dimensions |
+| `dimensions` | Optional[[Scale](coordinates.md#scale) or [Rectangle](geometry.md#rectangle)] | Dimensions |
### Plane
diff --git a/docs/source/components/coordinates.md b/docs/source/components/coordinates.md
index 2578065b7..2c0139df1 100644
--- a/docs/source/components/coordinates.md
+++ b/docs/source/components/coordinates.md
@@ -23,9 +23,10 @@ Definition an atlas
| `size_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Size unit |
| `resolution` | `List[float]` | Resolution |
| `resolution_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Resolution unit |
-| `origin` | [Origin](../aind_data_schema_models/coordinates.md#origin) | Origin (Defines the position of (0,0,0) in the coordinate system) |
+| `origin` | [MouseAnatomyModel](../aind_data_schema_models/external.md#mouseanatomymodel) | Origin (Defines the position of (0,0,0) in the coordinate system) |
| `axes` | List[[Axis](#axis)] | Axis names (Axis names and directions) |
| `axis_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Size unit |
+| `handedness` | Optional[[Handedness](#handedness)] | Handedness (Whether the coordinate system is right-handed or left-handed) |
### AtlasCoordinate
@@ -36,6 +37,7 @@ A point in an Atlas
|-------|------|-------------|
| `coordinate_system` | [Atlas](#atlas) | Atlas |
| `translation` | `List[float]` | Translation parameters |
+| `frame` | [TransformFrame](#transformframe) | Reference frame |
### Axis
@@ -50,14 +52,25 @@ Linked direction and axis
### CoordinateSystem
-Definition of a coordinate system relative to a brain
+Definition of a coordinate system
| Field | Type | Title (Description) |
|-------|------|-------------|
| `name` | `str` | Name |
-| `origin` | [Origin](../aind_data_schema_models/coordinates.md#origin) | Origin (Defines the position of (0,0,0) in the coordinate system) |
+| `origin` | [MouseAnatomyModel](../aind_data_schema_models/external.md#mouseanatomymodel) | Origin (Defines the position of (0,0,0) in the coordinate system) |
| `axes` | List[[Axis](#axis)] | Axis names (Axis names and directions) |
| `axis_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Size unit |
+| `handedness` | Optional[[Handedness](#handedness)] | Handedness (Whether the coordinate system is right-handed or left-handed) |
+
+
+### Handedness
+
+Coordinate system handedness
+
+| Name | Value |
+|------|-------|
+| `RIGHT` | `right` |
+| `LEFT` | `left` |
### NonlinearTransform
@@ -73,14 +86,30 @@ Definition of a nonlinear transform
Rotation
-Rotations are applied as Euler angles in order X/Y/Z
+Rotations are applied as Euler angles in the specified axis order.
-Angles follow right-hand rule, with positive angles rotating counter-clockwise.
+The default convention is fixed global axes, right-hand rule (positive angles rotate
+counter-clockwise when looking toward the origin from the positive axis),
+xyz axis order, pivoting around the global origin.
| Field | Type | Title (Description) |
|-------|------|-------------|
| `angles` | `List[float]` | Angles and axes in 3D space (Right-hand rule, positive angles rotate CCW) |
| `angles_unit` | [AngleUnit](../aind_data_schema_models/units.md#angleunit) | Angle unit |
+| `axis_order` | `str` | Axis order (Order of rotation axes as a string (e.g. 'xyz', 'zyx'). Must match the length of angles.) |
+| `frame` | [TransformFrame](#transformframe) | Reference frame (Whether to rotate around global axes or local axes (which rotate with the device)) |
+| `rotation_direction` | [RotationDirection](#rotationdirection) | Rotation direction (Right-hand rule: positive angles rotate CCW when looking toward the origin from the positive axis) |
+| `pivot` | [TransformFrame](#transformframe) | Rotation pivot (Whether to rotate around the global origin or the local origin of the device) |
+
+
+### RotationDirection
+
+Rotation direction convention
+
+| Name | Value |
+|------|-------|
+| `RIGHT_HAND` | `right_hand` |
+| `LEFT_HAND` | `left_hand` |
### Scale
@@ -90,6 +119,17 @@ Scale
| Field | Type | Title (Description) |
|-------|------|-------------|
| `scale` | `List[float]` | Scale parameters |
+| `pivot` | Optional[[TransformFrame](#transformframe)] | Scale pivot (Whether to scale around the global origin or the local origin of the device) |
+
+
+### TransformFrame
+
+Reference frame for applying transforms
+
+| Name | Value |
+|------|-------|
+| `GLOBAL` | `global` |
+| `LOCAL` | `local` |
### Translation
@@ -99,5 +139,6 @@ Translation
| Field | Type | Title (Description) |
|-------|------|-------------|
| `translation` | `List[float]` | Translation parameters |
+| `frame` | [TransformFrame](#transformframe) | Reference frame |
diff --git a/docs/source/components/devices.md b/docs/source/components/devices.md
index 6e2b5f4b5..843e5ab67 100644
--- a/docs/source/components/devices.md
+++ b/docs/source/components/devices.md
@@ -35,12 +35,13 @@ Description of an air puff device
### Arena
-Description of a rectangular arena
+Description of an arena
| Field | Type | Title (Description) |
|-------|------|-------------|
-| `size` | [Scale](coordinates.md#scale) | 3D Size |
-| `size_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Size unit |
+| `size` | [Scale](coordinates.md#scale) | **[DEPRECATED]** Use shape. 3D Size |
+| `size_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | **[DEPRECATED]** Use shape. Size unit |
+| `shape` | Optional[[Rectangle](geometry.md#rectangle) or [Circle](geometry.md#circle)] | Shape of the arena |
| `objects_in_arena` | List[[Device](#device)] | Objects in arena |
| `name` | `str` | Device name |
| `serial_number` | `Optional[str]` | Serial number |
@@ -319,8 +320,9 @@ Description of an enclosure
| Field | Type | Title (Description) |
|-------|------|-------------|
-| `size` | [Scale](coordinates.md#scale) | Size |
-| `size_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Size unit |
+| `size` | [Scale](coordinates.md#scale) | **[DEPRECATED]** Use shape. Size |
+| `size_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | **[DEPRECATED]** Use shape. Size unit |
+| `shape` | Optional[[Rectangle](geometry.md#rectangle) or [Circle](geometry.md#circle)] | Shape of the enclosure |
| `internal_material` | `Optional[str]` | Internal material |
| `external_material` | `str` | External material |
| `grounded` | `bool` | Grounded |
diff --git a/docs/source/components/geometry.md b/docs/source/components/geometry.md
new file mode 100644
index 000000000..1eb1bd794
--- /dev/null
+++ b/docs/source/components/geometry.md
@@ -0,0 +1,25 @@
+# Geometry
+
+## Model definitions
+
+### Circle
+
+Circle geometry
+
+| Field | Type | Title (Description) |
+|-------|------|-------------|
+| `radius` | `float` | Radius |
+| `radius_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Radius unit |
+
+
+### Rectangle
+
+Rectangle geometry
+
+| Field | Type | Title (Description) |
+|-------|------|-------------|
+| `width` | `float` | Width |
+| `height` | `float` | Height |
+| `size_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Size unit |
+
+
diff --git a/docs/source/coordinate_systems.md b/docs/source/coordinate_systems.md
index fede177f6..8b336fb65 100644
--- a/docs/source/coordinate_systems.md
+++ b/docs/source/coordinate_systems.md
@@ -121,3 +121,22 @@ CoordinateSystem(
The device is now defined in the instrument coordinate system, but at a physically impossible location overlapping the mouse. Now draw a second picture, which is the actual location of your monitor relative to the mouse. In our case, lets assume that this monitor is facing the mouse's right eye, at a 45 degree angle to the axis of the mouse's body (i.e. the eye to monitor vector is perpendicular to the monitor surface.), and at a viewing distance of 100 mm.
Now we calculate the transforms needed to correctly position the device in the acquisition coordinate system. First we translate the monitor to the correct position by applying `Translation(translation=70.7, 70.7, 0)`. Then, we rotate *clockwise* around the Z axis by applying `Rotation(angles=[0, 0, -45], angles_unit=AngleUnit.DEG)`.
+
+## Interactive Coordinate System Builder
+
+The builder below lets you set up your instrument coordinate system, add a probe or monitor device, and construct the transform list interactively. The 3D viewport shows a semi-transparent brain mesh with the device rendered in its final position. When you are satisfied, copy the generated Python code from the Export panel.
+
+```{raw} html
+
+
+ Open builder in full screen ↗
+
+
+
+```
+
diff --git a/src/aind_data_schema/components/configs.py b/src/aind_data_schema/components/configs.py
index 58b55a335..41595074e 100644
--- a/src/aind_data_schema/components/configs.py
+++ b/src/aind_data_schema/components/configs.py
@@ -23,7 +23,7 @@
from pydantic import Field, field_validator, model_validator
from pydantic_core.core_schema import ValidationInfo
-from aind_data_schema.base import AwareDatetimeWithDefault, DataModel, DiscriminatedList, GenericModel
+from aind_data_schema.base import AwareDatetimeWithDefault, DataModel, Discriminated, DiscriminatedList, GenericModel
from aind_data_schema.components.coordinates import (
TRANSFORM_TYPES,
AtlasCoordinate,
@@ -32,6 +32,7 @@
Translation,
)
from aind_data_schema.components.devices import DevicePosition
+from aind_data_schema.components.geometry import Rectangle
from aind_data_schema.components.identifiers import Code
from aind_data_schema.components.wrappers import AssetPath
@@ -265,7 +266,7 @@ class Image(DataModel):
description="Position, rotation, and scale of the image. Note that depth should be in the planes.",
)
- dimensions: Optional[Scale] = Field(default=None, title="Dimensions")
+ dimensions: Optional[Discriminated[Scale | Rectangle]] = Field(default=None, title="Dimensions")
class ImageSPIM(Image):
diff --git a/src/aind_data_schema/components/coordinates.py b/src/aind_data_schema/components/coordinates.py
index be136d5a4..041f333a3 100644
--- a/src/aind_data_schema/components/coordinates.py
+++ b/src/aind_data_schema/components/coordinates.py
@@ -1,17 +1,41 @@
"""Classes to define device positions, orientations, and coordinates"""
import math
-from typing import List, Union
+from enum import Enum
+from typing import List, Optional, Union
+import warnings
from aind_data_schema_models.atlas import AtlasName
from aind_data_schema_models.coordinates import AxisName, Direction, Origin
from aind_data_schema_models.units import AngleUnit, SizeUnit
-from pydantic import Field
+from aind_data_schema_models.mouse_anatomy import MouseAnatomyModel
+from pydantic import Field, field_validator, model_validator
from aind_data_schema.base import DataModel, DiscriminatedList
from aind_data_schema.components.wrappers import AssetPath
+class TransformFrame(str, Enum):
+ """Reference frame for applying transforms"""
+
+ GLOBAL = "global"
+ LOCAL = "local"
+
+
+class RotationDirection(str, Enum):
+ """Rotation direction convention"""
+
+ RIGHT_HAND = "right_hand"
+ LEFT_HAND = "left_hand"
+
+
+class Handedness(str, Enum):
+ """Coordinate system handedness"""
+
+ RIGHT = "right"
+ LEFT = "left"
+
+
class Axis(DataModel):
"""Linked direction and axis"""
@@ -27,6 +51,11 @@ class Scale(DataModel):
"""Scale"""
scale: List[float] = Field(..., title="Scale parameters")
+ pivot: Optional[TransformFrame] = Field(
+ default=TransformFrame.GLOBAL,
+ title="Scale pivot",
+ description="Whether to scale around the global origin or the local origin of the device",
+ )
def to_matrix(self) -> List[List[float]]:
"""Return the affine scale matrix for arbitrary sized lists
@@ -36,6 +65,12 @@ def to_matrix(self) -> List[List[float]]:
List[List[float]]
Affine scale matrix
"""
+ warnings.warn(
+ "to_matrix() is not valid when frame or pivot are set to local values "
+ "and will be removed in a future version.",
+ DeprecationWarning,
+ stacklevel=2,
+ )
size = len(self.scale)
scale_matrix = [[1.0 if i == j else 0.0 for j in range(size + 1)] for i in range(size + 1)]
@@ -50,6 +85,10 @@ class Translation(DataModel):
"""Translation"""
translation: List[float] = Field(..., title="Translation parameters")
+ frame: TransformFrame = Field(
+ default=TransformFrame.GLOBAL,
+ title="Reference frame",
+ )
def to_matrix(self) -> List[List[float]]:
"""Return the affine translation matrix for arbitrary sized lists.
@@ -59,6 +98,12 @@ def to_matrix(self) -> List[List[float]]:
List[List[float]]
Affine transform matrix.
"""
+ warnings.warn(
+ "to_matrix() is not valid when frame or pivot are set to local values "
+ "and will be removed in a future version.",
+ DeprecationWarning,
+ stacklevel=2,
+ )
size = len(self.translation)
@@ -75,15 +120,46 @@ def to_matrix(self) -> List[List[float]]:
class Rotation(DataModel):
"""Rotation
- Rotations are applied as Euler angles in order X/Y/Z
+ Rotations are applied as Euler angles in the specified axis order.
- Angles follow right-hand rule, with positive angles rotating counter-clockwise.
+ The default convention is fixed global axes, right-hand rule (positive angles rotate
+ counter-clockwise when looking toward the origin from the positive axis),
+ xyz axis order, pivoting around the global origin.
"""
angles: List[float] = Field(
..., title="Angles and axes in 3D space", description="Right-hand rule, positive angles rotate CCW"
)
angles_unit: AngleUnit = Field(default=AngleUnit.DEG, title="Angle unit")
+ axis_order: str = Field(
+ default="xyz",
+ title="Axis order",
+ description="Order of rotation axes as a string (e.g. 'xyz', 'zyx'). Must match the length of angles.",
+ )
+ frame: TransformFrame = Field(
+ default=TransformFrame.GLOBAL,
+ title="Reference frame",
+ description="Whether to rotate around global axes or local axes (which rotate with the device)",
+ )
+ rotation_direction: RotationDirection = Field(
+ default=RotationDirection.RIGHT_HAND,
+ title="Rotation direction",
+ description="Right-hand rule: positive angles rotate CCW when looking toward the origin from the positive axis",
+ )
+ pivot: TransformFrame = Field(
+ default=TransformFrame.GLOBAL,
+ title="Rotation pivot",
+ description="Whether to rotate around the global origin or the local origin of the device",
+ )
+
+ @field_validator("axis_order")
+ @classmethod
+ def validate_axis_order(cls, v: str) -> str:
+ """Validate that axis_order only contains valid axis characters and is lowercase"""
+ valid_chars = set("xyzXYZ")
+ if not v or not all(c in valid_chars for c in v):
+ raise ValueError(f"axis_order must only contain axis characters (x, y, z), got '{v}'")
+ return v.lower()
def to_matrix(self) -> List[List[float]]:
"""Return the affine rotation matrix for arbitrary sized lists.
@@ -93,6 +169,12 @@ def to_matrix(self) -> List[List[float]]:
List[List[float]]
Affine rotation matrix.
"""
+ warnings.warn(
+ "to_matrix() is not valid when frame or pivot are set to local values "
+ "and will be removed in a future version.",
+ DeprecationWarning,
+ stacklevel=2,
+ )
try:
from scipy.spatial.transform import Rotation as R
except ImportError: # pragma: no cover
@@ -105,7 +187,17 @@ def to_matrix(self) -> List[List[float]]:
angles = [angle if self.angles_unit == AngleUnit.RAD else math.radians(angle) for angle in self.angles]
# Create the rotation matrix
- order = "xyz"[: len(self.angles)]
+ # Apply left-hand rule by negating angles
+ if self.rotation_direction == RotationDirection.LEFT_HAND:
+ angles = [-a for a in angles]
+
+ # Use specified axis order, truncated to the number of angles
+ order = self.axis_order[: len(self.angles)]
+
+ # Intrinsic rotations use uppercase axis letters in scipy
+ if self.frame == TransformFrame.LOCAL:
+ order = order.upper()
+
rotation = R.from_euler(order, angles)
rotation_matrix = rotation.as_matrix().tolist()
@@ -131,6 +223,12 @@ def to_matrix(self) -> List[List[float]]:
List[List[float]]
Affine transform matrix
"""
+ warnings.warn(
+ "to_matrix() is not valid when frame or pivot are set to local values "
+ "and will be removed in a future version.",
+ DeprecationWarning,
+ stacklevel=2,
+ )
return self.affine_transform
@classmethod
@@ -147,6 +245,12 @@ def compose(cls, transform: List[Union[Translation, Rotation, Scale, "Affine"]])
Affine
Composed transform
"""
+ warnings.warn(
+ "compose() is not valid when frame or pivot are set to local values "
+ "and will be removed in a future version.",
+ DeprecationWarning,
+ stacklevel=2,
+ )
try:
import numpy as np
except ImportError: # pragma: no cover
@@ -194,13 +298,33 @@ class NonlinearTransform(DataModel):
class CoordinateSystem(DataModel):
- """Definition of a coordinate system relative to a brain"""
+ """Definition of a coordinate system"""
name: str = Field(..., title="Name")
- origin: Origin = Field(..., title="Origin", description="Defines the position of (0,0,0) in the coordinate system")
+ origin: Origin | MouseAnatomyModel = Field(
+ ..., title="Origin", description="Defines the position of (0,0,0) in the coordinate system"
+ )
axes: List[Axis] = Field(..., title="Axis names", description="Axis names and directions")
axis_unit: SizeUnit = Field(..., title="Size unit")
+ handedness: Optional[Handedness] = Field(
+ default=None,
+ title="Handedness",
+ description="Whether the coordinate system is right-handed or left-handed",
+ )
+
+ @model_validator(mode="after")
+ def warn_depth_axis(self) -> "CoordinateSystem":
+ """Warn if using a DEPTH axis, which is deprecated in favor of
+ standard 3-axis coordinate systems with a Z axis for depth"""
+ if any(axis.name == AxisName.DEPTH for axis in self.axes):
+ warnings.warn(
+ f"CoordinateSystem '{self.name}' uses a DEPTH axis, which is deprecated. "
+ "Use a standard 3-axis coordinate system instead.",
+ DeprecationWarning,
+ stacklevel=2,
+ )
+ return self
class Atlas(CoordinateSystem):
diff --git a/src/aind_data_schema/components/devices.py b/src/aind_data_schema/components/devices.py
index fcbda70da..b4f7844ec 100644
--- a/src/aind_data_schema/components/devices.py
+++ b/src/aind_data_schema/components/devices.py
@@ -44,6 +44,7 @@
from aind_data_schema.base import DataModel, Discriminated, GenericModel
from aind_data_schema.components.coordinates import TRANSFORM_TYPES, AxisName, CoordinateSystem, Scale
+from aind_data_schema.components.geometry import Circle, Rectangle
from aind_data_schema.components.identifiers import Software
logger = logging.getLogger(__name__)
@@ -535,8 +536,9 @@ class PockelsCell(Device):
class Enclosure(Device):
"""Description of an enclosure"""
- size: Scale = Field(..., title="Size")
- size_unit: SizeUnit = Field(..., title="Size unit")
+ size: Scale = Field(..., title="Size", deprecated="Use shape")
+ size_unit: SizeUnit = Field(..., title="Size unit", deprecated="Use shape")
+ shape: Optional[Discriminated[Rectangle | Circle]] = Field(default=None, title="Shape of the enclosure")
internal_material: Optional[str] = Field(default=None, title="Internal material")
external_material: str = Field(..., title="External material")
grounded: bool = Field(..., title="Grounded")
@@ -589,10 +591,11 @@ class Treadmill(Device):
class Arena(Device):
- """Description of a rectangular arena"""
+ """Description of an arena"""
- size: Scale = Field(..., title="3D Size")
- size_unit: SizeUnit = Field(..., title="Size unit")
+ size: Scale = Field(..., title="3D Size", deprecated="Use shape")
+ size_unit: SizeUnit = Field(..., title="Size unit", deprecated="Use shape")
+ shape: Optional[Discriminated[Circle | Rectangle]] = Field(default=None, title="Shape of the arena")
objects_in_arena: List[Device] = Field(default=[], title="Objects in arena")
diff --git a/src/aind_data_schema/components/geometry.py b/src/aind_data_schema/components/geometry.py
new file mode 100644
index 000000000..a9e66c642
--- /dev/null
+++ b/src/aind_data_schema/components/geometry.py
@@ -0,0 +1,21 @@
+"""Classes to define geometry"""
+
+from aind_data_schema_models.units import SizeUnit
+from pydantic import Field
+
+from aind_data_schema.base import DataModel
+
+
+class Rectangle(DataModel):
+ """Rectangle geometry"""
+
+ width: float = Field(..., title="Width")
+ height: float = Field(..., title="Height")
+ size_unit: SizeUnit = Field(..., title="Size unit")
+
+
+class Circle(DataModel):
+ """Circle geometry"""
+
+ radius: float = Field(..., title="Radius")
+ radius_unit: SizeUnit = Field(..., title="Radius unit")
diff --git a/tests/test_coordinates.py b/tests/test_coordinates.py
index 2d082b904..b1f3e2a2e 100644
--- a/tests/test_coordinates.py
+++ b/tests/test_coordinates.py
@@ -1,6 +1,7 @@
"""Tests for the coordinates module"""
import unittest
+import warnings
import numpy as np
from aind_data_schema_models.atlas import AtlasName
@@ -12,10 +13,14 @@
Atlas,
Axis,
AxisName,
+ CoordinateSystem,
Direction,
+ Handedness,
Origin,
Rotation,
+ RotationDirection,
Scale,
+ TransformFrame,
Translation,
)
@@ -23,6 +28,14 @@
class TestScale(unittest.TestCase):
"""Tests for the Scale class"""
+ def setUp(self):
+ """Set up for tests"""
+ warnings.simplefilter("ignore", DeprecationWarning)
+
+ def tearDown(self):
+ """Tear down after tests"""
+ warnings.resetwarnings()
+
def test_to_matrix_default_order(self):
"""Test to_matrix method with default axis order"""
scale = Scale(scale=[2, 3, 4])
@@ -43,6 +56,14 @@ def test_to_matrix_partial_axes(self):
class TestTranslation(unittest.TestCase):
"""Tests for the Translation class"""
+ def setUp(self):
+ """Set up for tests"""
+ warnings.simplefilter("ignore", DeprecationWarning)
+
+ def tearDown(self):
+ """Tear down after tests"""
+ warnings.resetwarnings()
+
def test_to_matrix_default_order(self):
"""Test to_matrix method with default axis order"""
translation = Translation(translation=[2, 3, 4])
@@ -59,6 +80,14 @@ def test_to_matrix_partial_axes(self):
class TestRotation(unittest.TestCase):
"""Tests for the Rotation class"""
+ def setUp(self):
+ """Set up for tests"""
+ warnings.simplefilter("ignore", DeprecationWarning)
+
+ def tearDown(self):
+ """Tear down after tests"""
+ warnings.resetwarnings()
+
def test_to_matrix_default_order(self):
"""Test to_matrix method with default axis order"""
@@ -107,6 +136,14 @@ def test_to_matrix_no_rotation(self):
class TestAffineWithAffineTransforms(unittest.TestCase):
"""Additional tests for the Affine class with Affine transforms"""
+ def setUp(self):
+ """Set up for tests"""
+ warnings.simplefilter("ignore", DeprecationWarning)
+
+ def tearDown(self):
+ """Tear down after tests"""
+ warnings.resetwarnings()
+
def test_compose_with_single_affine(self):
"""Test compose method with a single Affine transform"""
affine = Affine(
@@ -178,6 +215,159 @@ def test_compose_with_multiple_affine_transforms(self):
expected_matrix = np.matmul(affine1.affine_transform, affine2.affine_transform).tolist()
self.assertEqual(composed_transform.affine_transform, expected_matrix)
+
+class TestTranslationFrame(unittest.TestCase):
+ """Tests for Translation frame field"""
+
+ def setUp(self):
+ """Set up for tests"""
+ warnings.simplefilter("ignore", DeprecationWarning)
+
+ def tearDown(self):
+ """Tear down after tests"""
+ warnings.resetwarnings()
+
+ def test_default_frame_is_global(self):
+ """Test that the default frame is global"""
+ t = Translation(translation=[1, 2, 3])
+ self.assertEqual(t.frame, TransformFrame.GLOBAL)
+
+ def test_local_frame(self):
+ """Test that local frame is stored correctly"""
+ t = Translation(translation=[1, 2, 3], frame=TransformFrame.LOCAL)
+ self.assertEqual(t.frame, TransformFrame.LOCAL)
+
+ def test_matrix_unaffected_by_frame(self):
+ """Test that the matrix output is the same regardless of frame"""
+ t_global = Translation(translation=[1, 2, 3], frame=TransformFrame.GLOBAL)
+ t_local = Translation(translation=[1, 2, 3], frame=TransformFrame.LOCAL)
+ self.assertEqual(t_global.to_matrix(), t_local.to_matrix())
+
+
+class TestRotationNewFields(unittest.TestCase):
+ """Tests for new Rotation fields"""
+
+ def setUp(self):
+ """Set up for tests"""
+ warnings.simplefilter("ignore", DeprecationWarning)
+
+ def tearDown(self):
+ """Tear down after tests"""
+ warnings.resetwarnings()
+
+ def test_default_fields(self):
+ """Test that default field values are correct"""
+ r = Rotation(angles=[45, 0, 0])
+ self.assertEqual(r.frame, TransformFrame.GLOBAL)
+ self.assertEqual(r.rotation_direction, RotationDirection.RIGHT_HAND)
+ self.assertEqual(r.pivot, TransformFrame.GLOBAL)
+ self.assertEqual(r.axis_order, "xyz")
+
+ def test_custom_axis_order(self):
+ """Test rotation matrix with a custom axis order"""
+ r = Rotation(angles=[45, 30, 15], axis_order="zyx")
+ self.assertEqual(r.axis_order, "zyx")
+ expected = R.from_euler("zyx", [45, 30, 15], degrees=True).as_matrix().tolist()
+ expected = [row + [0.0] for row in expected] + [[0.0, 0.0, 0.0, 1.0]]
+ self.maxDiff = None
+ self.assertEqual(r.to_matrix(), expected)
+
+ def test_axis_order_normalized_to_lowercase(self):
+ """Test that axis_order is normalized to lowercase"""
+ r = Rotation(angles=[45, 0, 0], axis_order="XYZ")
+ self.assertEqual(r.axis_order, "xyz")
+
+ def test_invalid_axis_order_raises(self):
+ """Test that an invalid axis_order raises an exception"""
+ with self.assertRaises(Exception):
+ Rotation(angles=[45, 0, 0], axis_order="abc")
+
+ def test_left_hand_rule_negates_angles(self):
+ """Test that left-hand rule negates angles relative to right-hand"""
+ angles = [30, 45, 60]
+ r_right = Rotation(angles=angles, rotation_direction=RotationDirection.RIGHT_HAND)
+ r_left = Rotation(angles=angles, rotation_direction=RotationDirection.LEFT_HAND)
+ expected_left = R.from_euler("xyz", [-30, -45, -60], degrees=True).as_matrix().tolist()
+ expected_left = [row + [0.0] for row in expected_left] + [[0.0, 0.0, 0.0, 1.0]]
+ self.maxDiff = None
+ self.assertNotEqual(r_right.to_matrix(), r_left.to_matrix())
+ self.assertEqual(r_left.to_matrix(), expected_left)
+
+ def test_local_frame_differs_from_global(self):
+ """Test that local (intrinsic) frame produces a different matrix than global (extrinsic)"""
+ angles = [30, 45, 60]
+ r_global = Rotation(angles=angles, frame=TransformFrame.GLOBAL)
+ r_local = Rotation(angles=angles, frame=TransformFrame.LOCAL)
+ expected_global = R.from_euler("xyz", angles, degrees=True).as_matrix().tolist()
+ expected_local = R.from_euler("XYZ", angles, degrees=True).as_matrix().tolist()
+ expected_global = [row + [0.0] for row in expected_global] + [[0.0, 0.0, 0.0, 1.0]]
+ expected_local = [row + [0.0] for row in expected_local] + [[0.0, 0.0, 0.0, 1.0]]
+ self.maxDiff = None
+ self.assertEqual(r_global.to_matrix(), expected_global)
+ self.assertEqual(r_local.to_matrix(), expected_local)
+ self.assertNotEqual(r_global.to_matrix(), r_local.to_matrix())
+
+ def test_pivot_field_stored(self):
+ """Test that pivot field is stored correctly"""
+ r = Rotation(angles=[0, 0, 90], pivot=TransformFrame.LOCAL)
+ self.assertEqual(r.pivot, TransformFrame.LOCAL)
+
+
+class TestCoordinateSystemHandedness(unittest.TestCase):
+ """Tests for CoordinateSystem handedness field"""
+
+ def setUp(self):
+ """Set up for tests"""
+ warnings.simplefilter("ignore", DeprecationWarning)
+
+ def tearDown(self):
+ """Tear down after tests"""
+ warnings.resetwarnings()
+
+ def test_default_handedness_is_none(self):
+ """Test that handedness defaults to None"""
+ cs = CoordinateSystem(
+ name="TEST",
+ origin=Origin.BREGMA,
+ axis_unit=SizeUnit.MM,
+ axes=[
+ Axis(name=AxisName.AP, direction=Direction.PA),
+ Axis(name=AxisName.ML, direction=Direction.LR),
+ Axis(name=AxisName.SI, direction=Direction.SI),
+ ],
+ )
+ self.assertIsNone(cs.handedness)
+
+ def test_right_handedness(self):
+ """Test setting right handedness"""
+ cs = CoordinateSystem(
+ name="TEST_R",
+ origin=Origin.BREGMA,
+ axis_unit=SizeUnit.MM,
+ handedness=Handedness.RIGHT,
+ axes=[
+ Axis(name=AxisName.AP, direction=Direction.PA),
+ Axis(name=AxisName.ML, direction=Direction.LR),
+ Axis(name=AxisName.SI, direction=Direction.SI),
+ ],
+ )
+ self.assertEqual(cs.handedness, Handedness.RIGHT)
+
+ def test_left_handedness(self):
+ """Test setting left handedness"""
+ cs = CoordinateSystem(
+ name="TEST_L",
+ origin=Origin.BREGMA,
+ axis_unit=SizeUnit.MM,
+ handedness=Handedness.LEFT,
+ axes=[
+ Axis(name=AxisName.AP, direction=Direction.PA),
+ Axis(name=AxisName.ML, direction=Direction.LR),
+ Axis(name=AxisName.SI, direction=Direction.SI),
+ ],
+ )
+ self.assertEqual(cs.handedness, Handedness.LEFT)
+
def test_compose_with_affine_and_other_transforms(self):
"""Test compose method with an Affine transform and other transforms"""
affine = Affine(
@@ -272,5 +462,96 @@ def test_validate_atlas_valid(self):
self.assertIsNotNone(atlas)
+class TestDeprecationWarnings(unittest.TestCase):
+ """Tests that deprecation warnings are raised"""
+
+ def test_scale_to_matrix_warns(self):
+ """Test that Scale.to_matrix raises a DeprecationWarning"""
+ scale = Scale(scale=[2, 3, 4])
+ with self.assertWarns(DeprecationWarning):
+ scale.to_matrix()
+
+ def test_translation_to_matrix_warns(self):
+ """Test that Translation.to_matrix raises a DeprecationWarning"""
+ translation = Translation(translation=[1, 2, 3])
+ with self.assertWarns(DeprecationWarning):
+ translation.to_matrix()
+
+ def test_rotation_to_matrix_warns(self):
+ """Test that Rotation.to_matrix raises a DeprecationWarning"""
+ rotation = Rotation(angles=[90, 0, 0])
+ with self.assertWarns(DeprecationWarning):
+ rotation.to_matrix()
+
+ def test_affine_to_matrix_warns(self):
+ """Test that Affine.to_matrix raises a DeprecationWarning"""
+ affine = Affine(
+ affine_transform=[[1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]]
+ )
+ with self.assertWarns(DeprecationWarning):
+ affine.to_matrix()
+
+ def test_affine_compose_warns(self):
+ """Test that Affine.compose raises a DeprecationWarning"""
+ translation = Translation(translation=[1, 2, 3])
+ with self.assertWarns(DeprecationWarning):
+ Affine.compose([translation])
+
+ def test_depth_axis_warns(self):
+ """Test that constructing a CoordinateSystem with a DEPTH axis raises a DeprecationWarning"""
+ with self.assertWarns(DeprecationWarning):
+ CoordinateSystem(
+ name="TEST_DEPTH",
+ origin=Origin.BREGMA,
+ axis_unit=SizeUnit.MM,
+ axes=[
+ Axis(name=AxisName.AP, direction=Direction.PA),
+ Axis(name=AxisName.ML, direction=Direction.LR),
+ Axis(name=AxisName.SI, direction=Direction.SI),
+ Axis(name=AxisName.DEPTH, direction=Direction.UD),
+ ],
+ )
+
+ def test_no_warning_without_depth_axis(self):
+ """Test that no DeprecationWarning is raised when DEPTH axis is absent"""
+ with warnings.catch_warnings(record=True) as w:
+ warnings.simplefilter("always", DeprecationWarning)
+ CoordinateSystem(
+ name="TEST_NO_DEPTH",
+ origin=Origin.BREGMA,
+ axis_unit=SizeUnit.MM,
+ axes=[
+ Axis(name=AxisName.AP, direction=Direction.PA),
+ Axis(name=AxisName.ML, direction=Direction.LR),
+ Axis(name=AxisName.SI, direction=Direction.SI),
+ ],
+ )
+ depth_warnings = [x for x in w if "DEPTH" in str(x.message)]
+ self.assertEqual(len(depth_warnings), 0)
+
+
+class TestCoordinateSystemMouseAnatomyOrigin(unittest.TestCase):
+ """Tests for CoordinateSystem with MouseAnatomyModel as origin"""
+
+ def test_mouse_anatomy_origin(self):
+ """Test that CoordinateSystem accepts a MouseAnatomyModel as origin"""
+ from aind_data_schema_models.mouse_anatomy import MouseAnatomy
+
+ cs = CoordinateSystem(
+ name="TEST_MOUSE_ANATOMY",
+ origin=MouseAnatomy.FRONTONASAL_SUTURE,
+ axis_unit=SizeUnit.MM,
+ axes=[
+ Axis(name=AxisName.AP, direction=Direction.PA),
+ Axis(name=AxisName.ML, direction=Direction.LR),
+ Axis(name=AxisName.SI, direction=Direction.SI),
+ ],
+ )
+ self.assertEqual(cs.origin, MouseAnatomy.FRONTONASAL_SUTURE)
+
+ cs_roundtrip = CoordinateSystem.model_validate(cs.model_dump())
+ self.assertEqual(cs_roundtrip.origin, MouseAnatomy.FRONTONASAL_SUTURE)
+
+
if __name__ == "__main__":
unittest.main()
diff --git a/tests/test_geometry.py b/tests/test_geometry.py
new file mode 100644
index 000000000..ecfe9ee23
--- /dev/null
+++ b/tests/test_geometry.py
@@ -0,0 +1,42 @@
+"""Tests for the geometry module"""
+
+import unittest
+
+from aind_data_schema_models.units import SizeUnit
+
+from aind_data_schema.components.geometry import Circle, Rectangle
+
+
+class TestRectangle(unittest.TestCase):
+ """Tests for the Rectangle class"""
+
+ def test_create_rectangle(self):
+ """Test creating a rectangle with specific dimensions and units"""
+ rect = Rectangle(width=10.0, height=5.0, size_unit=SizeUnit.MM)
+ self.assertEqual(rect.width, 10.0)
+ self.assertEqual(rect.height, 5.0)
+ self.assertEqual(rect.size_unit, SizeUnit.MM)
+
+ def test_different_units(self):
+ """Test creating a rectangle with different units"""
+ rect = Rectangle(width=1.0, height=2.0, size_unit=SizeUnit.UM)
+ self.assertEqual(rect.size_unit, SizeUnit.UM)
+
+
+class TestCircle(unittest.TestCase):
+ """Tests for the Circle class"""
+
+ def test_create_circle(self):
+ """Test creating a circle with specific radius and units"""
+ circle = Circle(radius=3.0, radius_unit=SizeUnit.MM)
+ self.assertEqual(circle.radius, 3.0)
+ self.assertEqual(circle.radius_unit, SizeUnit.MM)
+
+ def test_different_units(self):
+ """Test creating a circle with different units"""
+ circle = Circle(radius=500.0, radius_unit=SizeUnit.UM)
+ self.assertEqual(circle.radius_unit, SizeUnit.UM)
+
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/uv.lock b/uv.lock
new file mode 100644
index 000000000..15dcd071a
--- /dev/null
+++ b/uv.lock
@@ -0,0 +1,2320 @@
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+ "python_full_version < '3.11'",
+]
+
+[[package]]
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+[[package]]
+name = "aind-data-schema"
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