try to use optimized codepath through ome-types (#478)

* try to use optimized codepath through ome-types

* update test

* fix lint

* remove recently deprecated iteritems

Author: toloudis

aicsimageio/readers/ome_tiff_reader.py

@@ -68,7 +68,7 @@ def _get_ome(ome_xml: str, clean_metadata: bool = True) -> OME:
         if clean_metadata:
             ome_xml = metadata_utils.clean_ome_xml_for_known_issues(ome_xml)
 
-        return from_xml(ome_xml)
+        return from_xml(ome_xml, parser="lxml")
 
     @staticmethod
     def _is_supported_image(

aicsimageio/readers/tiff_glob_reader.py

@@ -408,7 +408,7 @@ def _read_immediate(self) -> xr.DataArray:
         chunk_sizes = self._get_chunk_sizes(scene_nunique)
 
         unpack_sizes = OrderedDict(
-            [(d, s) for d, s in scene_nunique.iteritems() if d in chunk_sizes.keys()]
+            [(d, s) for d, s in scene_nunique.items() if d in chunk_sizes.keys()]
         )
 
         reshape_sizes = tuple(unpack_sizes.values()) + tuple(

aicsimageio/tests/writers/test_ome_tiff_writer.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import urllib
 from typing import Callable, List, Optional, Tuple, Union
 
+import lxml
 import numpy as np
 import pytest
 from ome_types import to_xml
@@ -166,7 +166,7 @@ def test_ome_tiff_writer_no_meta(
             "bad ome string",
             "TCZYX",
             # raised from within ome-types
-            marks=pytest.mark.xfail(raises=urllib.error.URLError),
+            marks=pytest.mark.xfail(raises=lxml.etree.XMLSyntaxError),
         ),
     ],
 )

aicsimageio/writers/ome_tiff_writer.py

@@ -255,7 +255,7 @@ def save(
             )
         # else if string, then construct OME from string
         elif isinstance(ome_xml, str):
-            ome_xml = from_xml(ome_xml)
+            ome_xml = from_xml(ome_xml, parser="lxml")
 
         # if we do not have an OME object now, something is wrong
         if not isinstance(ome_xml, OME):

setup.py

@@ -105,7 +105,7 @@ def run(self):
     "imagecodecs>=2020.5.30",
     "lxml>=4.6,<5",
     "numpy>=1.16,<2",
-    "ome-types>=0.2",
+    "ome-types>=0.3.3",
     "ome-zarr>=0.6.1",
     "wrapt>=1.12",
     "resource-backed-dask-array>=0.1.0",