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# ==========================================================================
#
# Copyright NumFOCUS
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0.txt
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# ==========================================================================*/
# also test the import callback feature
import sys
import os
import numpy as np
import pathlib
import itk
filename = sys.argv[1]
# xarray conversion
try:
import xarray as xr
print("Testing xarray conversion")
image = itk.imread(filename)
image.SetSpacing((0.1, 0.2))
image.SetOrigin((30.0, 44.0))
theta = np.radians(30)
cosine = np.cos(theta)
sine = np.sin(theta)
rotation = np.array(((cosine, -sine), (sine, cosine)))
image.SetDirection(rotation)
image["MyMeta"] = 4.0
data_array = itk.xarray_from_image(image)
# Default name
assert data_array.name == "image"
image.SetObjectName("test_image")
data_array = itk.xarray_from_image(image)
assert data_array.name == "test_image"
assert data_array.dims[0] == "y"
assert data_array.dims[1] == "x"
assert data_array.dims[2] == "c"
assert np.array_equal(data_array.values, itk.array_from_image(image))
assert len(data_array.coords["x"]) == 256
assert len(data_array.coords["y"]) == 256
assert len(data_array.coords["c"]) == 3
assert data_array.coords["x"][0] == 30.0
assert data_array.coords["x"][1] == 30.1
assert data_array.coords["y"][0] == 44.0
assert data_array.coords["y"][1] == 44.2
assert data_array.coords["c"][0] == 0
assert data_array.coords["c"][1] == 1
assert data_array.attrs["direction"][0, 0] == cosine
assert data_array.attrs["direction"][0, 1] == sine
assert data_array.attrs["direction"][1, 0] == -sine
assert data_array.attrs["direction"][1, 1] == cosine
assert data_array.attrs["MyMeta"] == 4.0
round_trip = itk.image_from_xarray(data_array)
assert round_trip.GetObjectName() == "test_image"
assert np.array_equal(itk.array_from_image(round_trip), itk.array_from_image(image))
spacing = round_trip.GetSpacing()
assert np.isclose(spacing[0], 0.1)
assert np.isclose(spacing[1], 0.2)
origin = round_trip.GetOrigin()
assert np.isclose(origin[0], 30.0)
assert np.isclose(origin[1], 44.0)
direction = round_trip.GetDirection()
assert np.isclose(direction(0, 0), cosine)
assert np.isclose(direction(0, 1), -sine)
assert np.isclose(direction(1, 0), sine)
assert np.isclose(direction(1, 1), cosine)
assert round_trip["MyMeta"] == 4.0
wrong_order = data_array.swap_dims({"y": "z"})
try:
round_trip = itk.image_from_xarray(wrong_order)
assert False
except ValueError:
pass
# Check empty array
empty_array = np.array([], dtype=np.uint8)
empty_array.shape = (0, 0, 0)
empty_image = itk.image_from_array(empty_array)
empty_da = itk.xarray_from_image(empty_image)
empty_image_round = itk.image_from_xarray(empty_da)
# Check order
arr = np.random.randint(0, 255, size=(4, 5, 6), dtype=np.uint8)
data_array = xr.DataArray(arr, dims=["z", "y", "x"])
image = itk.image_from_xarray(data_array)
assert np.allclose(arr, itk.array_view_from_image(image))
assert np.allclose(arr.shape, itk.array_view_from_image(image).shape)
data_array = xr.DataArray(arr, dims=["x", "y", "z"])
image = itk.image_from_xarray(data_array)
assert np.allclose(arr.transpose(), itk.array_view_from_image(image))
assert np.allclose(arr.shape[::-1], itk.array_view_from_image(image).shape)
data_array = xr.DataArray(arr, dims=["y", "x", "c"])
image = itk.image_from_xarray(data_array)
assert np.allclose(arr, itk.array_view_from_image(image))
assert np.allclose(arr.shape, itk.array_view_from_image(image).shape)
data_array = xr.DataArray(arr, dims=["c", "x", "y"])
image = itk.image_from_xarray(data_array)
assert np.allclose(arr.transpose(), itk.array_view_from_image(image))
assert np.allclose(arr.shape[::-1], itk.array_view_from_image(image).shape)
# Test in-place "view" where xarray data is valid only as long as ITK image
data_array = itk.xarray_from_image(image, view=True)
assert data_array.name == image.GetObjectName()
# verify we can run a computation on xarray data
assert 0 <= data_array.min().compute() <= 255
data_array = xr.DataArray(arr, dims=["q", "x", "y"])
try:
image = itk.image_from_xarray(data_array)
assert False
except ValueError:
pass
if "(<itkCType unsigned char>, 4)" in itk.Image.GetTypesAsList():
arr = np.random.randint(0, 255, size=(4, 5, 6, 3), dtype=np.uint8)
data_array = xr.DataArray(arr, dims=["t", "z", "y", "x"])
image = itk.image_from_xarray(data_array)
assert np.allclose(arr, itk.array_view_from_image(image))
assert np.allclose(arr.shape, itk.array_view_from_image(image).shape)
except ImportError:
print("xarray not imported. Skipping xarray conversion tests")
pass
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