feature/ome-metadata-xslt-spec (#289)

* Write generic function for XSLT transformation

* Add prop def for ome meta for aicsimage and reader

* Passthrough impl for OmeTiffReader

* Add basic tests for all readers

* Add lxml to deps

* Bump min ome-types

* Change docstring of NotImplError

aicsimageio/aics_image.py

@@ -8,6 +8,7 @@
 import dask.array as da
 import numpy as np
 import xarray as xr
+from ome_types import OME
 
 from . import dimensions, exceptions, transforms, types
 from .formats import FORMAT_IMPLEMENTATIONS
@@ -663,6 +664,23 @@ def metadata(self) -> Any:
         """
         return self.reader.metadata
 
+    @property
+    def ome_metadata(self) -> OME:
+        """
+        Returns
+        -------
+        metadata: OME
+            The original metadata transformed into the OME specfication.
+            This likely isn't a complete transformation but is guarenteed to
+            be a valid transformation.
+
+        Raises
+        ------
+        NotImplementedError
+            No metadata transformer available.
+        """
+        return self.reader.ome_metadata
+
     @property
     def channel_names(self) -> List[str]:
         """

aicsimageio/metadata/utils.py

@@ -2,14 +2,20 @@
 # -*- coding: utf-8 -*-
 
 import logging
+import os
 import re
-import xml.etree.ElementTree as ET
 from copy import deepcopy
+from pathlib import Path
 from typing import Dict, Optional, Union
+from xml.etree import ElementTree as ET
 
+import lxml.etree
 import numpy as np
+from ome_types import OME, from_xml
 from ome_types.model.simple_types import PixelType
 
+from ..types import PathLike
+
 ###############################################################################
 
 log = logging.getLogger(__name__)
@@ -36,6 +42,64 @@
 ###############################################################################
 
 
+def transform_metadata_with_xslt(
+    tree: ET.Element,
+    xslt: PathLike,
+) -> OME:
+    """
+    Given an in-memory metadata Element and a path to an XSLT file, convert
+    metadata to OME.
+
+    Parameters
+    ----------
+    tree: ET.Element
+        The metadata tree to convert.
+    xslt: PathLike
+        Path to the XSLT file.
+
+    Returns
+    -------
+    ome: OME
+        The generated / translated OME metadata.
+
+    Notes
+    -----
+    This function will briefly update your processes current working directory
+    to the directory that stores the XSLT file.
+    """
+    # Store current process directory
+    process_dir = Path().cwd()
+
+    # Make xslt path absolute
+    xslt_abs_path = Path(xslt).resolve(strict=True).absolute()
+
+    # Try the transform
+    try:
+        # We switch directories so that whatever sub-moduled in XSLT
+        # main file can have local references to supporting transforms.
+        # i.e. the main XSLT file imports a transformers for specific sections
+        # of the metadata (camera, experiment, etc.)
+        os.chdir(xslt_abs_path.parent)
+
+        # Parse template and generate transform function
+        template = lxml.etree.parse(str(xslt_abs_path))
+        transform = lxml.etree.XSLT(template)
+
+        # Convert from stdlib ET to lxml ET
+        tree_str = ET.tostring(tree)
+        lxml_tree = lxml.etree.fromstring(tree_str)
+        ome_etree = transform(lxml_tree)
+
+        # Dump generated etree to string and read with ome-types
+        ome = from_xml(str(ome_etree))
+
+    # Regardless of error or succeed, move back to original process dir
+    finally:
+        os.chdir(process_dir)
+
+    return ome
+
+
 def generate_ome_image_id(image_id: Union[str, int]) -> str:
     """
     Naively generates the standard OME image ID using a provided ID.

aicsimageio/readers/ome_tiff_reader.py

@@ -391,6 +391,10 @@ def _read_immediate(self) -> xr.DataArray:
                     tiff_tags,
                 )
 
+    @property
+    def ome_metadata(self) -> OME:
+        return self.metadata
+
     @property
     def physical_pixel_sizes(self) -> PhysicalPixelSizes:
         """

aicsimageio/readers/reader.py

@@ -9,6 +9,7 @@
 import numpy as np
 import xarray as xr
 from fsspec.spec import AbstractFileSystem
+from ome_types import OME
 
 from .. import constants, exceptions, transforms, types
 from ..dimensions import DEFAULT_DIMENSION_ORDER, DimensionNames, Dimensions
@@ -697,6 +698,23 @@ def metadata(self) -> Any:
 
         return self._metadata
 
+    @property
+    def ome_metadata(self) -> OME:
+        """
+        Returns
+        -------
+        metadata: OME
+            The original metadata transformed into the OME specfication.
+            This likely isn't a complete transformation but is guarenteed to
+            be a valid transformation.
+
+        Raises
+        ------
+        NotImplementedError
+            No metadata transformer available.
+        """
+        raise NotImplementedError()
+
     @property
     def channel_names(self) -> Optional[List[str]]:
         """

aicsimageio/tests/metadata/__init__.py

@@ -0,0 +1,2 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-

aicsimageio/tests/metadata/test_utils.py

@@ -0,0 +1,54 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import pytest
+from ome_types import OME
+
+from aicsimageio import AICSImage
+
+from ..conftest import get_resource_full_path, host
+
+###############################################################################
+
+
+@host
+@pytest.mark.parametrize(
+    "filename",
+    [
+        # DefaultReader
+        pytest.param(
+            "example.png",
+            marks=pytest.mark.raises(execeptions=NotImplementedError),
+        ),
+        # TiffReader
+        pytest.param(
+            "s_1_t_10_c_3_z_1.tiff",
+            marks=pytest.mark.raises(execeptions=NotImplementedError),
+        ),
+        # OmeTiffReader
+        ("actk.ome.tiff"),
+        # LifReader
+        pytest.param(
+            "tiled.lif",
+            marks=pytest.mark.raises(execeptions=NotImplementedError),
+        ),
+        # CziReader
+        pytest.param(
+            "s_1_t_1_c_1_z_1.czi",
+            marks=pytest.mark.raises(execeptions=NotImplementedError),
+        ),
+        pytest.param(
+            "RGB-8bit.czi",
+            marks=pytest.mark.raises(execeptions=NotImplementedError),
+        ),
+    ],
+)
+def test_ome_metadata(filename: str, host: str) -> None:
+    # Get full filepath
+    uri = get_resource_full_path(filename, host)
+
+    # Init image
+    img = AICSImage(uri)
+
+    # Test the transform
+    assert isinstance(img.ome_metadata, OME)

setup.py

@@ -68,8 +68,9 @@
     "dask[array]>=2021.4.1",
     "fsspec>=2021.4.0",
     "imagecodecs>=2020.5.30",
+    "lxml~=4.6.3",
     "numpy~=1.16",
-    "ome-types~=0.2.4",
+    "ome-types~=0.2.7",
     "tifffile>=2021.6.6",
     "toolz~=0.11.0",
     "xarray~=0.16.1",