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 = ImageStack.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 = physical_coordinate_calculator.\
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 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 each tile of the return ImageStack
"""
stack = ImageStack.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])
coords_array = [
coords[PhysicalCoordinateTypes.X_MIN],
coords[PhysicalCoordinateTypes.X_MAX],
coords[PhysicalCoordinateTypes.Y_MIN],
coords[PhysicalCoordinateTypes.Y_MAX],
coords[PhysicalCoordinateTypes.Z_MIN],
coords[PhysicalCoordinateTypes.Z_MAX]
]
for _round in stack.axis_labels(Axes.ROUND):
for ch in stack.axis_labels(Axes.CH):
for z in stack.axis_labels(Axes.ZPLANE):
coordinate_selector = {
Axes.ROUND.value: _round,
Axes.CH.value: ch,
Axes.ZPLANE.value: z,
}
stack._coordinates.loc[coordinate_selector] = np.array(
coords_array)
return stack
