Feature/add writers

.gitignore

@@ -50,9 +50,6 @@ coverage.xml
 .hypothesis/
 .pytest_cache/
 
-# Unit test files
-bioio/tests/resources/
-
 # Translations
 *.mo
 *.pot

CONTRIBUTING.md

@@ -25,7 +25,7 @@ Ready to contribute? Here's how to set up `bioio` for local development.
 
     ```bash
     cd bioio/
-    just setup-dev
+    just install
     ```
 
 4. Create a branch for local development:

Justfile

@@ -23,6 +23,7 @@ clean:
 # install with all deps
 install:
 	pip install -e .[lint,test,docs,dev]
+	pre-commit install
 
 # lint, format, and check all files
 lint:
@@ -37,12 +38,6 @@ build:
 	just lint
 	just test
 
-# install dependencies, setup pre-commit, download test resources
-setup-dev:
-	just install
-	pre-commit install
-	python scripts/download_test_resources.py
-
 # generate Sphinx HTML documentation
 generate-docs:
 	rm -f docs/bioio*.rst

bioio/bio_image.py

@@ -11,6 +11,7 @@
 import xarray as xr
 from ome_types import OME
 
+from .ome_utils import generate_ome_channel_id
 from .plugins import plugins_by_ext
 
 ###############################################################################
@@ -176,36 +177,6 @@ def determine_reader(
             ),
         )
 
-    @staticmethod
-    def _generate_ome_channel_id(image_id: str, channel_id: Union[str, int]) -> str:
-        """
-        Naively generates the standard OME channel ID using a provided ID.
-
-        Parameters
-        ----------
-        image_id: str
-            An image id to pull the image specific index from.
-            See: `generate_ome_image_id` for more details.
-        channel_id: Union[str, int]
-            A string or int representing the ID for a channel.
-            In the context of the usage of this function, this is usually used with the
-            index of the channel.
-
-        Returns
-        -------
-        ome_channel_id: str
-            The OME standard for channel IDs.
-
-        Notes
-        -----
-        ImageIds are usually: "Image:0", "Image:1", or "Image:N",
-        ChannelIds are usually the combination of image index + channel index --
-        "Channel:0:0" for the first channel of the first image for example.
-        """
-        # Remove the prefix 'Image:' to get just the index
-        image_index = image_id.replace("Image:", "")
-        return f"Channel:{image_index}:{channel_id}"
-
     def __init__(
         self,
         image: biob.types.ImageLike,
@@ -349,7 +320,7 @@ def _transform_data_array_to_bioio_image_standard(
         # Add channel coordinate plane because it is required in BioImage
         if biob.dimensions.DimensionNames.Channel not in coords:
             coords[biob.dimensions.DimensionNames.Channel] = [
-                BioImage._generate_ome_channel_id(
+                generate_ome_channel_id(
                     image_id=self.current_scene,
                     channel_id=0,
                 )

bioio/ome_utils.py

@@ -0,0 +1,137 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import logging
+import typing
+
+import numpy as np
+from ome_types.model.simple_types import PixelType
+
+###############################################################################
+
+log = logging.getLogger(__name__)
+
+###############################################################################
+
+
+def generate_ome_channel_id(image_id: str, channel_id: typing.Union[str, int]) -> str:
+    """
+    Naively generates the standard OME channel ID using a provided ID.
+
+    Parameters
+    ----------
+    image_id: str
+        An image id to pull the image specific index from.
+        See: `generate_ome_image_id` for more details.
+    channel_id: Union[str, int]
+        A string or int representing the ID for a channel.
+        In the context of the usage of this function, this is usually used with the
+        index of the channel.
+
+    Returns
+    -------
+    ome_channel_id: str
+        The OME standard for channel IDs.
+
+    Notes
+    -----
+    ImageIds are usually: "Image:0", "Image:1", or "Image:N",
+    ChannelIds are usually the combination of image index + channel index --
+    "Channel:0:0" for the first channel of the first image for example.
+    """
+    # Remove the prefix 'Image:' to get just the index
+    image_index = image_id.replace("Image:", "")
+    return f"Channel:{image_index}:{channel_id}"
+
+
+def generate_ome_image_id(image_id: typing.Union[str, int]) -> str:
+    """
+    Naively generates the standard OME image ID using a provided ID.
+
+    Parameters
+    ----------
+    image_id: Union[str, int]
+        A string or int representing the ID for an image.
+        In the context of the usage of this function, this is usually used with the
+        index of the scene / image.
+
+    Returns
+    -------
+    ome_image_id: str
+        The OME standard for image IDs.
+    """
+    return f"Image:{image_id}"
+
+
+def dtype_to_ome_type(npdtype: np.dtype) -> PixelType:
+    """
+    Convert numpy dtype to OME PixelType
+
+    Parameters
+    ----------
+    npdtype: numpy.dtype
+        A numpy datatype.
+
+    Returns
+    -------
+    ome_type: PixelType
+        One of the supported OME Pixels types
+
+    Raises
+    ------
+    ValueError
+        No matching pixel type for provided numpy type.
+    """
+    ometypedict = {
+        np.dtype(np.int8): PixelType.INT8,
+        np.dtype(np.int16): PixelType.INT16,
+        np.dtype(np.int32): PixelType.INT32,
+        np.dtype(np.uint8): PixelType.UINT8,
+        np.dtype(np.uint16): PixelType.UINT16,
+        np.dtype(np.uint32): PixelType.UINT32,
+        np.dtype(np.float32): PixelType.FLOAT,
+        np.dtype(np.float64): PixelType.DOUBLE,
+        np.dtype(np.complex64): PixelType.COMPLEXFLOAT,
+        np.dtype(np.complex128): PixelType.COMPLEXDOUBLE,
+    }
+    ptype = ometypedict.get(npdtype)
+    if ptype is None:
+        raise ValueError(f"Ome utils can't resolve pixel type: {npdtype.name}")
+    return ptype
+
+
+def ome_to_numpy_dtype(ome_type: PixelType) -> np.dtype:
+    """
+    Convert OME PixelType to numpy dtype
+
+    Parameters
+    ----------
+    ome_type: PixelType
+        One of the supported OME Pixels types
+
+    Returns
+    -------
+    npdtype: numpy.dtype
+        A numpy datatype.
+
+    Raises
+    ------
+    ValueError
+        No matching numpy type for the provided pixel type.
+    """
+    ometypedict: typing.Dict[PixelType, np.dtype] = {
+        PixelType.INT8: np.dtype(np.int8),
+        PixelType.INT16: np.dtype(np.int16),
+        PixelType.INT32: np.dtype(np.int32),
+        PixelType.UINT8: np.dtype(np.uint8),
+        PixelType.UINT16: np.dtype(np.uint16),
+        PixelType.UINT32: np.dtype(np.uint32),
+        PixelType.FLOAT: np.dtype(np.float32),
+        PixelType.DOUBLE: np.dtype(np.float64),
+        PixelType.COMPLEXFLOAT: np.dtype(np.complex64),
+        PixelType.COMPLEXDOUBLE: np.dtype(np.complex128),
+    }
+    nptype = ometypedict.get(ome_type)
+    if nptype is None:
+        raise ValueError(f"Ome utils can't resolve pixel type: {ome_type.value}")
+    return nptype

bioio/tests/conftest.py

@@ -16,19 +16,40 @@
       https://docs.pytest.org/en/latest/plugins.html#requiring-loading-plugins-in-a-test-module-or-conftest-file
 """
 
+import logging
 import pathlib
 import typing
 
+import dask.array as da
+import numpy as np
 import pytest
 
-LOCAL_RESOURCES_DIR = pathlib.Path(__file__).parent / "resources"
-LOCAL_RESOURCES_WRITE_DIR = pathlib.Path(__file__).parent / "writer_products"
+###############################################################################
 
+log = logging.getLogger(__name__)
 
-def get_resource_full_path(filename: str) -> typing.Union[str, pathlib.Path]:
-    return LOCAL_RESOURCES_DIR / filename
+###############################################################################
 
 
 @pytest.fixture
-def data_dir() -> pathlib.Path:
-    return pathlib.Path(__file__).parent / "data"
+def sample_text_file(tmp_path: pathlib.Path) -> pathlib.Path:
+    example_file = tmp_path / "temp-example.txt"
+    example_file.write_text("just some example text here")
+    return example_file
+
+
+def np_random_from_shape(
+    shape: typing.Tuple[int, ...], **kwargs: typing.Any
+) -> np.ndarray:
+    return np.random.randint(255, size=shape, **kwargs)
+
+
+def da_random_from_shape(
+    shape: typing.Tuple[int, ...], **kwargs: typing.Any
+) -> da.Array:
+    return da.random.randint(255, size=shape, **kwargs)
+
+
+array_constructor = pytest.mark.parametrize(
+    "array_constructor", [np_random_from_shape, da_random_from_shape]
+)

bioio/tests/test_bio_image.py

@@ -1,30 +1,21 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import pathlib
+
 import bioio_base as biob
 import pytest
 
 from bioio import BioImage
 
-from .conftest import get_resource_full_path
+
+def test_bioimage_with_text_file(sample_text_file: pathlib.Path) -> None:
+    with pytest.raises(biob.exceptions.UnsupportedFileFormatError):
+        BioImage(sample_text_file)
 
 
-@pytest.mark.parametrize(
-    "filename",
-    [
-        pytest.param(
-            "example.txt",
-            marks=pytest.mark.xfail(raises=biob.exceptions.UnsupportedFileFormatError),
-        ),
-        pytest.param(
-            "does-not-exist-klafjjksdafkjl.bad",
-            marks=pytest.mark.xfail(raises=FileNotFoundError),
-        ),
-    ],
-)
-def test_bioimage(
-    filename: str,
-) -> None:
+def test_bioimage_with_missing_file(tmp_path: pathlib.Path) -> None:
     # Construct full filepath
-    uri = get_resource_full_path(filename)
-    BioImage(uri)
+    uri = tmp_path / "does-not-exist-klafjjksdafkjl.bad"
+    with pytest.raises(FileNotFoundError):
+        BioImage(uri)

bioio/tests/writers/__init__.py

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