diff --git a/tests/__init__.py b/tests/__init__.py index 3baa9d7..4e3ed45 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -6,7 +6,7 @@ import tiledb from tiledb.bioimg import ATTR_NAME -from tiledb.cc import WebpInputFormat +from tiledb.libtiledb import WebpInputFormat from tiledb.bioimg.helpers import merge_ned_ranges import xml.etree.ElementTree as ET diff --git a/tests/integration/converters/test_ome_tiff.py b/tests/integration/converters/test_ome_tiff.py index 52d7085..0f4ec57 100644 --- a/tests/integration/converters/test_ome_tiff.py +++ b/tests/integration/converters/test_ome_tiff.py @@ -12,7 +12,7 @@ from tiledb.bioimg.converters.ome_tiff import OMETiffConverter from tiledb.bioimg.helpers import open_bioimg from tiledb.bioimg.openslide import TileDBOpenSlide -from tiledb.cc import WebpInputFormat +from tiledb.libtiledb import WebpInputFormat def test_ome_tiff_converter(tmp_path): diff --git a/tests/integration/converters/test_ome_tiff_experimental.py b/tests/integration/converters/test_ome_tiff_experimental.py index 02f93f7..63eb4a1 100644 --- a/tests/integration/converters/test_ome_tiff_experimental.py +++ b/tests/integration/converters/test_ome_tiff_experimental.py @@ -7,7 +7,7 @@ from tiledb.bioimg.converters.ome_tiff import OMETiffConverter from tiledb.bioimg.helpers import open_bioimg from tiledb.bioimg.openslide import TileDBOpenSlide -from tiledb.cc import WebpInputFormat +from tiledb.libtiledb import WebpInputFormat # We need to expand on the test files. Most of the test files we have currently are not memory diff --git a/tests/integration/converters/test_ome_zarr.py b/tests/integration/converters/test_ome_zarr.py index cdb685b..5a5b88a 100644 --- a/tests/integration/converters/test_ome_zarr.py +++ b/tests/integration/converters/test_ome_zarr.py @@ -11,7 +11,7 @@ from tiledb.bioimg.converters.ome_zarr import OMEZarrConverter from tiledb.bioimg.helpers import iter_color, open_bioimg from tiledb.bioimg.openslide import TileDBOpenSlide -from tiledb.cc import WebpInputFormat +from tiledb.libtiledb import WebpInputFormat schemas = (get_schema(2220, 2967), get_schema(387, 463), get_schema(1280, 431)) diff --git a/tests/integration/converters/test_openslide.py b/tests/integration/converters/test_openslide.py index f49e39e..08d2b20 100644 --- a/tests/integration/converters/test_openslide.py +++ b/tests/integration/converters/test_openslide.py @@ -10,7 +10,7 @@ from tiledb.bioimg.converters.openslide import OpenSlideConverter from tiledb.bioimg.helpers import open_bioimg from tiledb.bioimg.openslide import TileDBOpenSlide -from tiledb.cc import WebpInputFormat +from tiledb.libtiledb import WebpInputFormat @pytest.mark.parametrize("preserve_axes", [False, True]) diff --git a/tests/integration/converters/test_png.py b/tests/integration/converters/test_png.py index c295b55..c16f6d2 100644 --- a/tests/integration/converters/test_png.py +++ b/tests/integration/converters/test_png.py @@ -10,7 +10,7 @@ from tiledb.bioimg.converters.png import PNGConverter from tiledb.bioimg.helpers import open_bioimg from tiledb.bioimg.openslide import TileDBOpenSlide -from tiledb.cc import WebpInputFormat +from tiledb.libtiledb import WebpInputFormat def create_synthetic_image( diff --git a/tiledb/bioimg/converters/base.py b/tiledb/bioimg/converters/base.py index 7da430e..0bff84f 100644 --- a/tiledb/bioimg/converters/base.py +++ b/tiledb/bioimg/converters/base.py @@ -37,7 +37,7 @@ register_group = None import tiledb -from tiledb.cc import WebpInputFormat +from tiledb.libtiledb import WebpInputFormat from .. import ATTR_NAME from ..helpers import ( diff --git a/tiledb/bioimg/converters/ome_tiff.py b/tiledb/bioimg/converters/ome_tiff.py index dff39af..7ea0a39 100644 --- a/tiledb/bioimg/converters/ome_tiff.py +++ b/tiledb/bioimg/converters/ome_tiff.py @@ -30,8 +30,8 @@ raise err from tiledb import VFS, Config, Ctx -from tiledb.cc import WebpInputFormat from tiledb.highlevel import _get_ctx +from tiledb.libtiledb import WebpInputFormat from .. import ATTR_NAME, EXPORT_TILE_SIZE, WHITE_RGBA from ..helpers import ( diff --git a/tiledb/bioimg/converters/ome_zarr.py b/tiledb/bioimg/converters/ome_zarr.py index 4375a71..172b8b0 100644 --- a/tiledb/bioimg/converters/ome_zarr.py +++ b/tiledb/bioimg/converters/ome_zarr.py @@ -32,8 +32,8 @@ raise err from tiledb import Config, Ctx -from tiledb.cc import WebpInputFormat from tiledb.highlevel import _get_ctx +from tiledb.libtiledb import WebpInputFormat from .. import WHITE_RGB from ..helpers import get_logger_wrapper, get_rgba, translate_config_to_s3fs diff --git a/tiledb/bioimg/converters/openslide.py b/tiledb/bioimg/converters/openslide.py index f07d0fe..b700633 100644 --- a/tiledb/bioimg/converters/openslide.py +++ b/tiledb/bioimg/converters/openslide.py @@ -8,8 +8,8 @@ from numpy._typing import NDArray from tiledb import Config, Ctx -from tiledb.cc import WebpInputFormat from tiledb.highlevel import _get_ctx +from tiledb.libtiledb import WebpInputFormat from ..helpers import cache_filepath, get_logger_wrapper, is_remote_protocol, iter_color from . import DEFAULT_SCRATCH_SPACE diff --git a/tiledb/bioimg/converters/png.py b/tiledb/bioimg/converters/png.py index f8dd5d6..295fde9 100644 --- a/tiledb/bioimg/converters/png.py +++ b/tiledb/bioimg/converters/png.py @@ -18,8 +18,8 @@ from PIL import Image from tiledb import VFS, Config, Ctx -from tiledb.cc import WebpInputFormat from tiledb.highlevel import _get_ctx +from tiledb.libtiledb import WebpInputFormat from ..helpers import get_logger_wrapper, iter_color from .axes import Axes diff --git a/tiledb/bioimg/helpers.py b/tiledb/bioimg/helpers.py index c1fb321..7cdc732 100644 --- a/tiledb/bioimg/helpers.py +++ b/tiledb/bioimg/helpers.py @@ -24,7 +24,7 @@ import tiledb from tiledb import Config, Ctx -from tiledb.cc import WebpInputFormat +from tiledb.libtiledb import WebpInputFormat from . import ATTR_NAME from .converters.axes import Axes, AxesMapper @@ -215,7 +215,7 @@ def iter_levels_meta( for o in group: with open_bioimg(o.uri, config=config, ctx=ctx) as array: try: - level = array.meta["level"] + level = int(array.meta["level"]) except KeyError as exc: raise RuntimeError( "Key: 'level' not found in array metadata. Make sure that levels have been "