def test_read_block_2d(self):
"""
Read 2d uncompressed block.
Reads thew whole uncompressed image and compares received
raster against reference images.
"""
# Image to test
image_path = get_test_image_path("czi", "pJP31mCherry.czi")
# Reference channel images
channel_image_paths = [
get_test_image_path(
"czi",
"pJP31mCherry.grey/pJP31mCherry_b0t0z0c0x0-512y0-512.bmp"),
get_test_image_path(
"czi",
"pJP31mCherry.grey/pJP31mCherry_b0t0z0c1x0-512y0-512.bmp"),
get_test_image_path(
"czi",
"pJP31mCherry.grey/pJP31mCherry_b0t0z0c2x0-512y0-512.bmp")
]
slide = slideio.open_slide(image_path, "CZI")
self.assertTrue(slide is not None)
scene = slide.get_scene(0)
self.assertTrue(scene is not None)
for channel_index in range(scene.num_channels):
image_raster = scene.read_block(channel_indices=[channel_index])
reference_raster = cv.imread(channel_image_paths[channel_index],
cv.IMREAD_GRAYSCALE)
self.assertTrue(np.array_equal(image_raster, reference_raster))
def test_read_block_4d(self):
"""
Read 4d uncompressed block.
Reads thew whole uncompressed image and compares received
raster against reference images.
"""
# Image to test
image_path = get_test_image_path("czi", "pJP31mCherry.czi")
slide = slideio.open_slide(image_path, "CZI")
self.assertTrue(slide is not None)
scene = slide.get_scene(0)
self.assertTrue(scene is not None)
slices = (2, 5)
frames = (0, 1)
for channel_index in range(scene.num_channels):
image_raster = scene.read_block(channel_indices=[channel_index],
slices=slices,
frames=frames)
image_shape = image_raster.shape
self.assertEqual(image_shape, (3, 512, 512))
for slice_index in range(slices[0], slices[1]):
slice_raster = image_raster[slice_index - slices[0], :, :]
slice_shape = slice_raster.shape
self.assertEqual(slice_shape, (512, 512))
ref_image_name = "pJP31mCherry.grey/pJP31mCherry_b0t0z" + \
str(slice_index) + "c" + str(channel_index) + \
"x0-512y0-512.bmp"
ref_image_path = get_test_image_path("czi", ref_image_name)
reference_raster = cv.imread(ref_image_path,
cv.IMREAD_GRAYSCALE)
self.assertTrue(np.array_equal(slice_raster, reference_raster))
def test_3chnl_png16b_metadata(self):
"""Opens 3 channel 16 bit png file and checks metadata."""
image_path = get_test_image_path(
"gdal",
"img_2448x2448_3x16bit_SRC_RGB_ducks.png"
)
slide = slideio.open_slide(image_path, "GDAL")
self.assertTrue(slide is not None)
num_scenes = slide.num_scenes
self.assertEqual(num_scenes, 1)
self.assertEqual(image_path, slide.file_path)
scene = slide.get_scene(0)
self.assertTrue(scene is not None)
self.assertEqual(image_path, scene.file_path)
self.assertEqual(3, scene.num_channels)
scene_rect = scene.rect
self.assertEqual(0, scene_rect[0])
self.assertEqual(0, scene_rect[1])
self.assertEqual(2448, scene_rect[2])
self.assertEqual(2448, scene_rect[3])
for channel_index in range(scene.num_channels):
channel_type = scene.get_channel_data_type(channel_index)
self.assertEqual(channel_type, np.uint16)
compression = scene.compression
self.assertEqual(compression, slideio.Compression.Png)
res = scene.resolution
self.assertEqual(0, res[0])
self.assertEqual(0, res[1])
def test_readblock_png8bit_with(self):
"""
8 bit png image.
Reads 8b png images and checks the raster.
by calculation of raster statistics for
specific rectangles
"""
image_path = get_test_image_path(
"gdal",
"img_1024x600_3x8bit_RGB_color_bars_CMYKWRGB.png"
)
with slideio.open_slide(image_path, "GDAL") as slide:
self.assertTrue(slide is not None)
with slide.get_scene(0) as scene:
block_rect = (260, 500, 100, 100)
# read 3 channel block
raster = scene.read_block(block_rect)
mean, stddev = cv.meanStdDev(raster)
self.assertEqual(mean[0], 255)
self.assertEqual(stddev[0], 0)
self.assertEqual(mean[1], 255)
self.assertEqual(stddev[1], 0)
self.assertEqual(mean[2], 0)
self.assertEqual(stddev[2], 0)
# read one channel block
raster = scene.read_block(block_rect, channel_indices=[1])
mean, stddev = cv.meanStdDev(raster)
self.assertEqual(mean[0], 255)
self.assertEqual(stddev[0], 0)
def test_3chnl_jpeg_metadata(self):
"""Opens 3 channel jpeg file and checks metadata."""
image_path = get_test_image_path(
"gdal",
"Airbus_Pleiades_50cm_8bit_RGB_Yogyakarta.jpg"
)
slide = slideio.open_slide(image_path, "GDAL")
self.assertTrue(slide is not None)
num_scenes = slide.num_scenes
self.assertEqual(num_scenes, 1)
self.assertEqual(image_path, slide.file_path)
scene = slide.get_scene(0)
self.assertTrue(scene is not None)
self.assertEqual(image_path, scene.file_path)
self.assertEqual(3, scene.num_channels)
scene_rect = scene.rect
self.assertEqual(0, scene_rect[0])
self.assertEqual(0, scene_rect[1])
self.assertEqual(5494, scene_rect[2])
self.assertEqual(5839, scene_rect[3])
for channel_index in range(scene.num_channels):
channel_type = scene.get_channel_data_type(channel_index)
self.assertEqual(channel_type, np.uint8)
compression = scene.compression
self.assertEqual(compression, slideio.Compression.Jpeg)
res = scene.resolution
self.assertEqual(0, res[0])
self.assertEqual(0, res[1])
def test_file_metadata2(self):
"""
Checks image metadata.
Opens 6 channel uncompressed czi file and checks metadata.
"""
image_path = get_test_image_path("czi", "08_18_2018_enc_1001_633.czi")
channel_names = ["646", "655", "664", "673", "682", "691"]
slide = slideio.open_slide(image_path, "CZI")
self.assertTrue(slide is not None)
num_scenes = slide.num_scenes
self.assertEqual(num_scenes, 1)
self.assertEqual(image_path, slide.file_path)
scene = slide.get_scene(0)
self.assertTrue(scene is not None)
self.assertEqual(image_path, scene.file_path)
self.assertEqual(6, scene.num_channels)
scene_rect = scene.rect
self.assertEqual(0, scene_rect[0])
self.assertEqual(0, scene_rect[1])
self.assertEqual(1000, scene_rect[2])
self.assertEqual(1000, scene_rect[3])
self.assertEqual(63, scene.magnification)
for channel_index in range(scene.num_channels):
channel_type = scene.get_channel_data_type(channel_index)
self.assertEqual(channel_type, np.uint16)
compression = scene.compression
self.assertEqual(compression, slideio.Compression.Uncompressed)
channel_name = scene.get_channel_name(channel_index)
self.assertEqual(channel_name, channel_names[channel_index])
res = scene.resolution
correct_res = 6.7475572821478794e-8
self.assertEqual(correct_res, pytest.approx(res[0]))
self.assertEqual(correct_res, pytest.approx(res[1]))
def test_file_metadata(self):
"""
Checks image metadata.
Opens 3 channel uncompressed czi file and checks metadata.
"""
image_path = get_test_image_path("czi", "pJP31mCherry.czi")
slide = slideio.open_slide(image_path, "CZI")
self.assertTrue(slide is not None)
num_scenes = slide.num_scenes
self.assertEqual(num_scenes, 1)
self.assertEqual(image_path, slide.file_path)
scene = slide.get_scene(0)
self.assertTrue(scene is not None)
self.assertEqual(image_path, scene.file_path)
self.assertEqual(3, scene.num_channels)
scene_rect = scene.rect
self.assertEqual(0, scene_rect[0])
self.assertEqual(0, scene_rect[1])
self.assertEqual(512, scene_rect[2])
self.assertEqual(512, scene_rect[3])
self.assertEqual(100, scene.magnification)
raw_metadata = slide.raw_metadata
self.assertTrue(raw_metadata.startswith("<ImageDocument>"))
for channel_index in range(scene.num_channels):
channel_type = scene.get_channel_data_type(channel_index)
self.assertEqual(channel_type, np.uint8)
compression = scene.compression
self.assertEqual(compression, slideio.Compression.Uncompressed)
res = scene.resolution
correct_res = 9.76783e-8
self.assertEqual(correct_res, pytest.approx(res[0]))
self.assertEqual(correct_res, pytest.approx(res[1]))
def test_core_not_existing_driver(self):
"""
Test for calling of not-existing driver.
Checks if slideio throws RuntimeError
exception during opening of not existing file.
"""
image_path = get_test_image_path(
"GDAL", "img_2448x2448_3x8bit_SRC_RGB_ducks.png")
with pytest.raises(RuntimeError):
slideio.open_slide(image_path, "AAAA")
def test_corrupted_image(self):
"""
Raise an error for corrupted images.
Tries to open and read a corrupted image.
slideio shall raise an exception.
"""
# Image to test
image_path = get_test_image_path("czi", "corrupted.czi")
with pytest.raises(RuntimeError):
slideio.open_slide(image_path, "CZI")
def test_image_similarity_equal(self):
"""Similarity score of equal images shall be 1."""
image_path = get_test_image_path(
"gdal", "img_2448x2448_3x8bit_SRC_RGB_ducks.png")
with slideio.open_slide(image_path, "GDAL") as slide:
with slide.get_scene(0) as scene:
img1 = scene.read_block()
img2 = scene.read_block()
score = slideio.compare_images(img1, img2)
self.assertEqual(score, 1)
blank_image = np.zeros(img1.shape, np.uint8)
score = slideio.compare_images(img1, blank_image)
self.assertLess(score, 0.5)
blur = cv.blur(img2, (20, 20))
score = slideio.compare_images(img1, blur)
self.assertLess(score, 0.98)
self.assertGreater(score, 0.8)