import itertools from tempfile import NamedTemporaryFile from skimage.io import imread, imsave, use_plugin, reset_plugins import numpy as np from skimage._shared.testing import (assert_array_equal, assert_array_almost_equal, parametrize, fetch) from skimage._shared import testing def setup(): use_plugin('tifffile') np.random.seed(0) def teardown(): reset_plugins() def test_imread_uint16(): expected = np.load(fetch('data/chessboard_GRAY_U8.npy')) img = imread(fetch('data/chessboard_GRAY_U16.tif')) assert img.dtype == np.uint16 assert_array_almost_equal(img, expected) def test_imread_uint16_big_endian(): expected = np.load(fetch('data/chessboard_GRAY_U8.npy')) img = imread(fetch('data/chessboard_GRAY_U16B.tif')) assert img.dtype == np.uint16 assert_array_almost_equal(img, expected) def test_imread_multipage_rgb_tif(): img = imread(fetch('data/multipage_rgb.tif')) assert img.shape == (2, 10, 10, 3), img.shape def test_tifffile_kwarg_passthrough (): img = imread(fetch('data/multipage.tif'), key=[1], multifile=False, multifile_close=True, fastij=True, is_ome=True) assert img.shape == (15, 10), img.shape def test_imread_handle(): expected = np.load(fetch('data/chessboard_GRAY_U8.npy')) with open(fetch('data/chessboard_GRAY_U16.tif'), 'rb') as fh: img = imread(fh) assert img.dtype == np.uint16 assert_array_almost_equal(img, expected) class TestSave: def roundtrip(self, dtype, x): f = NamedTemporaryFile(suffix='.tif') fname = f.name f.close() imsave(fname, x, check_contrast=False) y = imread(fname) assert_array_equal(x, y) shapes = ((10, 10), (10, 10, 3), (10, 10, 4)) dtypes = (np.uint8, np.uint16, np.float32, np.int16, np.float64) @parametrize("shape, dtype", itertools.product(shapes, dtypes)) def test_imsave_roundtrip(self, shape, dtype): x = np.random.rand(*shape) if not np.issubdtype(dtype, np.floating): x = (x * np.iinfo(dtype).max).astype(dtype) else: x = x.astype(dtype) self.roundtrip(dtype, x)