def coordinates(self) -> Mapping[Coordinates, ArrayLike[Number]]:
xrange = self._wrapped_tile.coordinates[Coordinates.X]
yrange = self._wrapped_tile.coordinates[Coordinates.Y]
return_coords = {
Coordinates.X: np.linspace(xrange[0], xrange[1], self.tile_shape[Axes.X]),
Coordinates.Y: np.linspace(yrange[0], yrange[1], self.tile_shape[Axes.Y]),
}
if Coordinates.Z in self._wrapped_tile.coordinates:
zrange = self._wrapped_tile.coordinates[Coordinates.Z]
zplane_coord = _get_physical_coordinates_of_z_plane(zrange)
return_coords[Coordinates.Z] = [zplane_coord]
return return_coords
def imagestack_with_coords_factory(stack_shape: OrderedDict,
coords: OrderedDict) -> ImageStack:
"""
Create an ImageStack of given shape and assigns the given x,y,z
min/max physical coordinates to each tile.
Parameters
----------
stack_shape: OrderedDict
Dict[Axes, int] defining the size of each dimension for an ImageStack
coords: OrderedDict
Dict[PhysicalCoordinateTypes, float] defining the min/max values of physical
coordinates to assign to the Imagestack
"""
stack = synthetic_stack(
num_round=stack_shape[Axes.ROUND],
num_ch=stack_shape[Axes.CH],
num_z=stack_shape[Axes.ZPLANE],
tile_height=stack_shape[Axes.Y],
tile_width=stack_shape[Axes.X],
)
stack.xarray[Coordinates.X.value] = xr.DataArray(np.linspace(
coords[PhysicalCoordinateTypes.X_MIN],
coords[PhysicalCoordinateTypes.X_MAX],
stack.xarray.sizes[Axes.X.value]),
dims=Axes.X.value)
stack.xarray[Coordinates.Y.value] = xr.DataArray(np.linspace(
coords[PhysicalCoordinateTypes.Y_MIN],
coords[PhysicalCoordinateTypes.Y_MAX],
stack.xarray.sizes[Axes.Y.value]),
dims=Axes.Y.value)
z_coord = _get_physical_coordinates_of_z_plane(
(coords[PhysicalCoordinateTypes.Z_MIN],
coords[PhysicalCoordinateTypes.Z_MAX]))
stack.xarray[Coordinates.Z.value] = xr.DataArray(np.zeros(
stack.xarray.sizes[Axes.ZPLANE.value]),
dims=Axes.ZPLANE.value)
for z in stack.axis_labels(Axes.ZPLANE):
stack.xarray[Coordinates.Z.value].loc[z] = z_coord
return stack
def coordinates(self) -> Mapping[Coordinates, ArrayLike[Number]]:
return_coords: MutableMapping[Coordinates, ArrayLike[Number]] = dict()
for axis, coord in ((Axes.X, Coordinates.X), (Axes.Y, Coordinates.Y)):
coordinate_range = self._tile.coordinates[coord]
if not isinstance(coordinate_range, tuple):
raise ValueError("x-y coordinates for a tile must be a range expressed as a tuple.")
return_coords[coord] = np.linspace(
coordinate_range[0], coordinate_range[1], self.tile_shape[axis])
if Coordinates.Z in self._tile.coordinates:
zrange = self._tile.coordinates[Coordinates.Z]
if isinstance(zrange, tuple):
zplane_coord = _get_physical_coordinates_of_z_plane(zrange)
return_coords[Coordinates.Z] = [zplane_coord]
else:
return_coords[Coordinates.Z] = zrange
return return_coords