Merge branch 'main' into admin/drop-python3.8

README.md

@@ -1,6 +1,6 @@
 # AICSImageIO
 
-[![Build Status](https://github.com/AllenCellModeling/aicsimageio/workflows/Build%20Main/badge.svg)](https://github.com/AllenCellModeling/aicsimageio/actions)
+[![Build Status](https://github.com/AllenCellModeling/aicsimageio/actions/workflows/build-main.yml/badge.svg)](https://github.com/AllenCellModeling/aicsimageio/actions)
 [![Documentation](https://github.com/AllenCellModeling/aicsimageio/workflows/Documentation/badge.svg)](https://AllenCellModeling.github.io/aicsimageio/)
 [![Code Coverage](https://codecov.io/gh/AllenCellModeling/aicsimageio/branch/main/graph/badge.svg)](https://app.codecov.io/gh/AllenCellModeling/aicsimageio/branch/main)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4906608.svg)](https://doi.org/10.5281/zenodo.4906608)

aicsimageio/__init__.py

@@ -13,7 +13,7 @@
 __email__ = "[email protected], [email protected], [email protected]"
 # Do not edit this string manually, always use bumpversion
 # Details in CONTRIBUTING.md
-__version__ = "4.12.1"
+__version__ = "4.13.0"
 
 
 def get_module_version() -> str:

aicsimageio/readers/nd2_reader.py

@@ -85,6 +85,14 @@ def _xarr_reformat(self, delayed: bool) -> xr.DataArray:
                 xarr.attrs[constants.METADATA_UNPROCESSED][
                     "frame"
                 ] = rdr.frame_metadata(self.current_scene_index)
+
+            # include OME metadata as attrs of returned xarray.DataArray if possible
+            # (not possible with `nd2` version < 0.7.0; see PR #521)
+            try:
+                xarr.attrs[constants.METADATA_PROCESSED] = self.ome_metadata
+            except NotImplementedError:
+                pass
+
         return xarr.isel({nd2.AXIS.POSITION: 0}, missing_dims="ignore")
 
     @property

aicsimageio/readers/ome_tiff_reader.py

@@ -10,7 +10,7 @@
 from fsspec.implementations.local import LocalFileSystem
 from fsspec.spec import AbstractFileSystem
 from ome_types import OME, from_xml
-from pydantic.error_wrappers import ValidationError
+from pydantic import ValidationError
 from tifffile.tifffile import TiffFile, TiffFileError, TiffTags
 from xmlschema import XMLSchemaValidationError
 from xmlschema.exceptions import XMLSchemaValueError
@@ -185,7 +185,7 @@ def __init__(
 
         # Get ome-types object and warn of other behaviors
         with self._fs.open(self._path) as open_resource:
-            with TiffFile(open_resource, is_mmstack=False) as tiff:
+            with TiffFile(open_resource) as tiff:
                 # Get and store OME
                 self._ome = self._get_ome(
                     tiff.pages[0].description, self.clean_metadata
@@ -308,7 +308,7 @@ def _read_delayed(self) -> xr.DataArray:
             The file could not be read or is not supported.
         """
         with self._fs.open(self._path) as open_resource:
-            with TiffFile(open_resource, is_mmstack=False) as tiff:
+            with TiffFile(open_resource) as tiff:
                 # Get unprocessed metadata from tags
                 tiff_tags = self._get_tiff_tags(tiff)
 
@@ -353,7 +353,7 @@ def _read_immediate(self) -> xr.DataArray:
             The file could not be read or is not supported.
         """
         with self._fs.open(self._path) as open_resource:
-            with TiffFile(open_resource, is_mmstack=False) as tiff:
+            with TiffFile(open_resource) as tiff:
                 # Get unprocessed metadata from tags
                 tiff_tags = self._get_tiff_tags(tiff)
 

aicsimageio/readers/tiff_glob_reader.py

@@ -117,7 +117,7 @@ def _is_supported_image(
     ) -> bool:
         try:
             with fs.open(path) as open_resource:
-                with TiffFile(open_resource, is_mmstack=False):
+                with TiffFile(open_resource):
                     return True
 
         except (TiffFileError, TypeError):
@@ -256,7 +256,7 @@ def indexer(x: str) -> pd.Series:
 
         if single_file_shape is None:
             with self._fs.open(self._path) as open_resource:
-                with TiffFile(open_resource, is_mmstack=False) as tiff:
+                with TiffFile(open_resource) as tiff:
                     self._single_file_shape = tiff.series[0].shape
 
         else:
@@ -299,9 +299,7 @@ def _read_delayed(self) -> xr.DataArray:
         scene_files = scene_files.drop(self.scene_glob_character, axis=1)
         scene_nunique = scene_files.nunique()
 
-        tiff_tags = self._get_tiff_tags(
-            TiffFile(scene_files.filename.iloc[0], is_mmstack=False)
-        )
+        tiff_tags = self._get_tiff_tags(TiffFile(scene_files.filename.iloc[0]))
 
         group_dims = [
             x for x in scene_files.columns if x not in ["filename", *self.chunk_dims]
@@ -366,9 +364,7 @@ def _read_delayed(self) -> xr.DataArray:
             dims = list(expanded_blocks_sizes.keys())
 
         else:  # assemble array in a single chunk
-            zarr_im = imread(
-                scene_files.filename.tolist(), aszarr=True, level=0, is_mmstack=False
-            )
+            zarr_im = imread(scene_files.filename.tolist(), aszarr=True, level=0)
             darr = da.from_zarr(zarr_im).rechunk(-1)
             darr = darr.reshape(reshape_sizes)
             darr = darr.transpose(axes_order)
@@ -407,9 +403,7 @@ def _read_immediate(self) -> xr.DataArray:
         scene_files = scene_files.drop(self.scene_glob_character, axis=1)
         scene_nunique = scene_files.nunique()
 
-        tiff_tags = self._get_tiff_tags(
-            TiffFile(scene_files.filename.iloc[0], is_mmstack=False)
-        )
+        tiff_tags = self._get_tiff_tags(TiffFile(scene_files.filename.iloc[0]))
 
         chunk_sizes = self._get_chunk_sizes(scene_nunique)
 

aicsimageio/readers/tiff_reader.py

@@ -126,7 +126,7 @@ def __init__(
     def scenes(self) -> Tuple[str, ...]:
         if self._scenes is None:
             with self._fs.open(self._path) as open_resource:
-                with TiffFile(open_resource, is_mmstack=False) as tiff:
+                with TiffFile(open_resource) as tiff:
                     # This is non-metadata tiff, just use available series indices
                     self._scenes = tuple(
                         metadata_utils.generate_ome_image_id(i)
@@ -186,7 +186,6 @@ def _get_image_data(
                 series=scene,
                 level=0,
                 chunkmode="page",
-                is_mmstack=False,
             ) as store:
                 arr = da.from_zarr(store)
                 arr = arr.transpose(transpose_indices)
@@ -456,7 +455,7 @@ def _read_delayed(self) -> xr.DataArray:
             The file could not be read or is not supported.
         """
         with self._fs.open(self._path) as open_resource:
-            with TiffFile(open_resource, is_mmstack=False) as tiff:
+            with TiffFile(open_resource) as tiff:
                 # Get dims from provided or guess
                 dims = self._get_dims_for_scene(tiff)
 
@@ -509,7 +508,7 @@ def _read_immediate(self) -> xr.DataArray:
             The file could not be read or is not supported.
         """
         with self._fs.open(self._path) as open_resource:
-            with TiffFile(open_resource, is_mmstack=False) as tiff:
+            with TiffFile(open_resource) as tiff:
                 # Get dims from provided or guess
                 dims = self._get_dims_for_scene(tiff)
 
@@ -577,7 +576,7 @@ def _get_pixel_size(
 ) -> Tuple[Optional[float], Optional[float], Optional[float]]:
     """Return the pixel size in microns (z,y,x) for the given series in a tiff path."""
 
-    with TiffFile(path_or_file, is_mmstack=False) as tiff:
+    with TiffFile(path_or_file) as tiff:
         tags = tiff.series[series_index].pages[0].tags
 
     if tiff.is_imagej:

aicsimageio/tests/readers/extra_readers/test_nd2_reader.py

@@ -31,7 +31,8 @@
     "expected_dtype, "
     "expected_dims_order, "
     "expected_channel_names, "
-    "expected_physical_pixel_sizes",
+    "expected_physical_pixel_sizes, "
+    "expected_metadata_type",
     [
         pytest.param(
             "example.txt",
@@ -42,6 +43,7 @@
             None,
             None,
             None,
+            None,
             marks=pytest.mark.xfail(raises=exceptions.UnsupportedFileFormatError),
         ),
         pytest.param(
@@ -53,6 +55,7 @@
             "TCYX",
             ["20phase", "20xDiO"],
             (1, 50, 50),
+            dict,
         ),
         (
             "ND2_jonas_header_test2.nd2",
@@ -63,6 +66,7 @@
             "CTZYX",
             ["Jonas_DIC"],
             (0.5, 0.12863494437945, 0.12863494437945),
+            OME,
         ),
         (
             "ND2_maxime_BF007.nd2",
@@ -73,6 +77,7 @@
             "CYX",
             ["405/488/561/633nm"],
             (1.0, 0.158389678930686, 0.158389678930686),
+            OME,
         ),
         (
             "ND2_dims_p4z5t3c2y32x32.nd2",
@@ -83,6 +88,7 @@
             "TZCYX",
             ["Widefield Green", "Widefield Red"],
             (1.0, 0.652452890023035, 0.652452890023035),
+            OME,
         ),
         (
             "ND2_dims_c2y32x32.nd2",
@@ -93,6 +99,7 @@
             "CYX",
             ["Widefield Green", "Widefield Red"],
             (1.0, 0.652452890023035, 0.652452890023035),
+            OME,
         ),
         (
             "ND2_dims_p1z5t3c2y32x32.nd2",
@@ -103,6 +110,7 @@
             "TZCYX",
             ["Widefield Green", "Widefield Red"],
             (1.0, 0.652452890023035, 0.652452890023035),
+            OME,
         ),
         (
             "ND2_dims_p2z5t3-2c4y32x32.nd2",
@@ -113,6 +121,7 @@
             "TZCYX",
             ["Widefield Green", "Widefield Red", "Widefield Far-Red", "Brightfield"],
             (1.0, 0.652452890023035, 0.652452890023035),
+            OME,
         ),
         (
             "ND2_dims_t3c2y32x32.nd2",
@@ -123,6 +132,7 @@
             "TCYX",
             ["Widefield Green", "Widefield Red"],
             (1.0, 0.652452890023035, 0.652452890023035),
+            OME,
         ),
         (
             "ND2_dims_rgb_t3p2c2z3x64y64.nd2",
@@ -133,6 +143,7 @@
             "TZCYXS",
             ["Brightfield", "Brightfield"],
             (0.01, 0.34285714285714286, 0.34285714285714286),
+            OME,
         ),
         (
             "ND2_dims_rgb.nd2",
@@ -143,6 +154,7 @@
             "CYXS",
             ["Brightfield"],
             (1.0, 0.34285714285714286, 0.34285714285714286),
+            OME,
         ),
     ],
 )
@@ -156,6 +168,7 @@ def test_nd2_reader(
     expected_dims_order: str,
     expected_channel_names: List[str],
     expected_physical_pixel_sizes: Tuple[float, float, float],
+    expected_metadata_type: Union[type, Tuple[Union[type, Tuple[Any, ...]], ...]],
 ) -> None:
     # Construct full filepath
     uri = get_resource_full_path(filename, host)
@@ -172,7 +185,7 @@ def test_nd2_reader(
         expected_dims_order=expected_dims_order,
         expected_channel_names=expected_channel_names,
         expected_physical_pixel_sizes=expected_physical_pixel_sizes,
-        expected_metadata_type=dict,
+        expected_metadata_type=expected_metadata_type,
     )
 
 
@@ -196,7 +209,7 @@ def test_nd2_reader(
             dimensions.DEFAULT_DIMENSION_ORDER,
             ["Jonas_DIC"],
             (0.5, 0.12863494437945, 0.12863494437945),
-            dict,
+            OME,
         ),
     ],
 )

cookiecutter.yaml

@@ -6,5 +6,5 @@ default_context:
     project_slug: "aicsimageio"
     project_short_description: "Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python"
     pypi_username: "aicspypi"
-    version: "4.12.1"
+    version: "4.13.0"
     open_source_license: "BSD license"

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.12.1
+current_version = 4.13.0
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)
 serialize = {major}.{minor}.{patch}
 commit = True

setup.py

@@ -36,7 +36,7 @@ def run(self):
     ],
     "nd2": ["nd2[legacy]>=0.6.0"],
     "dv": ["mrc>=0.2.0"],
-    "bfio": ["bfio>=2.3.0", "tifffile<2022.4.22"],
+    "bfio": ["bfio==2.3.0", "tifffile<2022.4.22"],
     # "czi": [  # excluded for licensing reasons
     #     "fsspec>=2022.8.0",
     #     "aicspylibczi>=3.1.1",
@@ -110,10 +110,10 @@ def run(self):
     "PyYAML>=6.0",
     "wrapt>=1.12",
     "resource-backed-dask-array>=0.1.0",
-    "tifffile>=2021.8.30",
+    "tifffile>=2021.8.30,<2023.3.15",
     "xarray>=0.16.1",
     "xmlschema",  # no pin because it's pulled in from OME types
-    "zarr>=2.6,<3",
+    "zarr>=2.6,<2.16.0",
 ]
 
 extra_requirements = {
@@ -170,6 +170,6 @@ def run(self):
     url="https://github.com/AllenCellModeling/aicsimageio",
     # Do not edit this string manually, always use bumpversion
     # Details in CONTRIBUTING.md
-    version="4.12.1",
+    version="4.13.0",
     zip_safe=False,
 )