extent object for napari

extent.py

import numpy as np

from ..utils.events import EmitterGroup


class Extent:
    """Extent object holding minimum and maximum values of data.

    Parameters
    ----------
    transform : napari.utils.transforms.Transform, optional
        Transform from data to world coordinates.

    Attributes
    ----------
    events : EmitterGroup
        Event emitter group
    data : (2, D) np.ndarray
        Minimum and maximum values of the data in D dimensions
        in the original data coordinates.
    step : (D,) np.ndarray
        Step values for appropriately sampling data in world
        coordinates.
    world : (2, D) np.ndarray
        Minimum and maximum values of the data in D dimensions
        mapped into world coordinates.
    """

    def __init__(self, ndim, transform=None):

        # Events:
        self.events = EmitterGroup(
            source=self,
            auto_connect=True,
            data=None,
            step=None,
            world=None,
        )
        self._data = np.array([0, 0, 0])
        self._step = np.array([1, 1, 1])
        self._world = np.array([1, 1, 1])
        self._transform = transform

    @property
    def data(self):
        """np.ndarray: Minimum and maximum values in data coordinates."""
        return self._data

    @data.setter
    def data(self, data):
        self._data = data
        self._world = transform_extent(self._data, self._transform)
        self.events.world()

    @property
    def world(self):
        """np.ndarray: Minimum and maximum values in data coordinates."""
        return self._world

    @world.setter
    def world(self, world):
        self._world = world
        self._data = transform_extent(self._world, self._transform.inverse)
        self.events.world()

    @property
    def step(self):
        """np.ndarray: Values for sampling data in world coordinates."""
        return self._step

    @step.setter
    def step(self, step):
        self._step = step
        self.events.step()


def transform_extent(input_extent, transform):
    """Transform extent from one coordinate system to another.

    Note that the full nD bounding box is consider during the
    transformation of an extent from one coordinate system
    to another.

    Parameters
    ----------
    input_extent : (2, D) np.ndarray
        Minimum and maximum values of the data in D dimensions
        in either data coordinates or world coordinates.
    transform : napari.utils.transforms.Transform, optional
        Transform from either data to world coordinates or
        world to data coordinates.

    Returns
    ----------
    output_extent : (2, D) np.ndarray
        Minimum and maximum values of the data in D dimensions
        in either data coordinates or world coordinates after
        being transformed by the transform.
    """
    # Get full nD bounding box
    D = input_extent.shape[1]
    full_input_extent = np.array(np.meshgrid(*input_extent.T)).T.reshape(
        -1, D
    )
    full_output_extent = self._transform(full_input_extent)
    output_extent = np.array(
        [
            np.min(full_output_extent, axis=0),
            np.max(full_output_extent, axis=0),
        ]
    )
    return output_extent