def test_OmeTiffWriter_compare_tile_plane_rgb_nl_large(tmp_path):
im_array = da.from_array(
np.random.randint(0, 255, (2**13, 2**13, 3), dtype=np.uint8),
chunks=(1024, 1024, 3),
)
reg_image = reg_image_loader(im_array, 0.5)
rts = RegTransformSeq(TFORM_FP)
ometiffwriter = OmeTiffWriter(reg_image, reg_transform_seq=rts)
ometiletiffwriter = OmeTiffTiledWriter(reg_image, reg_transform_seq=rts)
by_tile_fp = ometiletiffwriter.write_image_by_tile(
gen_project_name_str(),
output_dir=str(tmp_path),
)
by_plane_fp = ometiffwriter.write_image_by_plane(
gen_project_name_str(),
output_dir=str(tmp_path),
)
im_tile = imread(by_tile_fp)
im_plane = imread(by_plane_fp)
assert np.array_equal(im_tile, im_plane)
def test_OmeTiffWriter_compare_tile_plane_rgb_nl(
simple_transform_affine_nl, tmp_path
):
reg_image = reg_image_loader(
np.random.randint(0, 255, (1024, 1024, 3), dtype=np.uint8), 1
)
rts = RegTransformSeq(simple_transform_affine_nl)
ometiffwriter = OmeTiffWriter(reg_image, reg_transform_seq=rts)
ometiletiffwriter = OmeTiffTiledWriter(reg_image, reg_transform_seq=rts)
by_tile_fp = ometiletiffwriter.write_image_by_tile(
gen_project_name_str(),
output_dir=str(tmp_path),
)
by_plane_fp = ometiffwriter.write_image_by_plane(
gen_project_name_str(),
output_dir=str(tmp_path),
)
im_tile = imread(by_tile_fp)
im_plane = imread(by_plane_fp)
assert np.array_equal(im_tile, im_plane)
def test_OmeTiffWriter_by_tile(complex_transform, tmp_path):
reg_image = reg_image_loader(np.ones((4096, 4096), dtype=np.uint8), 0.5)
rts = RegTransformSeq(complex_transform)
ometiffwriter = OmeTiffTiledWriter(reg_image, reg_transform_seq=rts)
by_tile_fp = ometiffwriter.write_image_by_tile(
gen_project_name_str(),
output_dir=str(tmp_path),
zarr_temp_dir=tmp_path,
)
by_tile_image = reg_image_loader(by_tile_fp, 2)
assert by_tile_image.shape == (1, 1024, 1024)
def test_OmeTiffWriter_compare_tile_plane(simple_transform_affine, tmp_path):
reg_image = reg_image_loader(np.ones((1024, 1024), dtype=np.uint8), 1)
rts = RegTransformSeq(simple_transform_affine)
ometifftilewriter = OmeTiffTiledWriter(reg_image, reg_transform_seq=rts)
ometiffwriter = OmeTiffWriter(reg_image, reg_transform_seq=rts)
by_tile_fp = ometifftilewriter.write_image_by_tile(
gen_project_name_str(),
output_dir=str(tmp_path),
zarr_temp_dir=tmp_path,
)
by_tile_image = reg_image_loader(by_tile_fp, 2)
by_plane_fp = ometiffwriter.write_image_by_plane(
gen_project_name_str(),
output_dir=str(tmp_path),
)
by_plane_image = reg_image_loader(by_plane_fp, 2)
ch0_im_tile = by_tile_image.read_single_channel(0)
ch0_im_plane = by_plane_image.read_single_channel(0)
assert by_plane_image.shape == by_tile_image.shape
assert np.array_equal(ch0_im_tile, ch0_im_plane)