feat: init

test/model/metadata_sources/test_zarr_metadata.py

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+import pytest
+
+SPACE_UNITS = [
+    "angstrom",
+    "attometer",
+    "centimeter",
+    "decimeter",
+    "exameter",
+    "femtometer",
+    "foot",
+    "gigameter",
+    "hectometer",
+    "inch",
+    "kilometer",
+    "megameter",
+    "meter",
+    "micrometer",
+    "mile",
+    "millimeter",
+    "nanometer",
+    "parsec",
+    "petameter",
+    "picometer",
+    "terameter",
+    "yard",
+    "yoctometer",
+    "yottameter",
+    "zeptometer",
+    "zettameter",
+]
+
+TIME_UNITS = [
+    "attosecond",
+    "centisecond",
+    "day",
+    "decisecond",
+    "exasecond",
+    "femtosecond",
+    "gigasecond",
+    "hectosecond",
+    "hour",
+    "kilosecond",
+    "megasecond",
+    "microsecond",
+    "millisecond",
+    "minute",
+    "nanosecond",
+    "petasecond",
+    "picosecond",
+    "second",
+    "terasecond",
+    "yoctosecond",
+    "yottasecond",
+    "zeptosecond",
+    "zettasecond",
+]
+
+
+@pytest.fixture
+def dummy_metadata(dummy_model):
+    from navigate.model.metadata_sources.zarr_metadata import OMEZarrMetadata
+
+    # Create metadata
+    md = OMEZarrMetadata()
+
+    md.configuration = dummy_model.configuration
+
+    return md
+
+
+def test_axes(dummy_metadata):
+
+    axes = dummy_metadata._axes
+
+    # Check length
+    assert (len(axes) > 1) and (len(axes) < 6)
+
+    # Check list types and count
+    time_count = 0
+    space_count = 0
+    channel_count = 0
+    custom_count = 0
+    for d in axes:
+        if d["type"] == "time":
+            assert d["unit"] in TIME_UNITS
+            time_count += 1
+        elif d["type"] == "space":
+            assert d["unit"] in SPACE_UNITS
+            space_count += 1
+        elif d["type"] == "channel":
+            channel_count += 1
+        else:
+            custom_count += 1
+
+    assert (space_count > 1) and (space_count < 4)
+    assert time_count < 2
+    assert ((channel_count < 2) and (custom_count == 0)) or (
+        (channel_count == 0) and (custom_count < 2)
+    )
+
+    # Check order
+    order_type = [x["type"] for x in axes]
+    if "time" in order_type:
+        # Time must be first, if present
+        assert order_type.index("time") == 0
+    if "channel" in order_type:
+        # Channel must be before all the space axes, if present
+        ci = order_type.index("channel")
+        for i, el in enumerate(order_type):
+            if el == "space":
+                assert i > ci
+
+    # Skip zyx order spec as the naming of axes is not enforcable.
+
+
+def test_stage_positions_to_translation_transform(dummy_metadata):
+    import random
+
+    pos = [random.random() for _ in range(5)]
+
+    translation = dummy_metadata._stage_positions_to_translation_transform(*pos)
+
+    axes = dummy_metadata._axes
+
+    assert len(translation) == len(axes)
+
+
+def test_scale_transform(dummy_metadata):
+    scale = dummy_metadata._scale_transform()
+
+    axes = dummy_metadata._axes
+
+    assert len(scale) == len(axes)
+
+
+def test_coordinate_transformations(dummy_metadata):
+    import random
+
+    pos = [random.random() for _ in range(5)]
+
+    translation = dummy_metadata._stage_positions_to_translation_transform(*pos)
+    scale = dummy_metadata._scale_transform()
+
+    assert len(dummy_metadata._coordinate_transformations(scale)) == 1
+
+    combo = dummy_metadata._coordinate_transformations(scale, translation)
+    assert len(combo) == 2
+    assert combo[0]["type"] == "scale" and combo[1]["type"] == "translation"
+
+    with pytest.raises(UserWarning):
+        dummy_metadata._coordinate_transformations(translation=translation)
+
+
+def test_multiscale_metadata(dummy_metadata):
+    """https://ngff.openmicroscopy.org/0.4/#multiscale-md"""
+    import numpy as np
+    import random
+
+    resolutions = np.array([[1, 1, 1], [2, 2, 1], [4, 4, 1], [8, 8, 1]], dtype=int)
+    paths = [f"path{i}" for i in range(resolutions.shape[0])]
+    view = {k: random.random() for k in ["x", "y", "z", "theta", "f"]}
+
+    msd = dummy_metadata.multiscales_dict("test", paths, resolutions, view)
+
+    # Each "multiscales" dictionary MUST contain the field "axes"
+    assert "axes" in msd.keys()
+
+    # Each "multiscales" dictionary MUST contain the field "datasets"
+    assert "datasets" in msd.keys()
+    # Each dictionary in "datasets" MUST contain the field "path",
+    # whose value contains the path to the array for this resolution
+    # relative to the current zarr group. The "path"s MUST be ordered
+    # from largest (i.e. highest resolution) to smallest.
+    # Each "datasets" dictionary MUST have the same number of dimensions
+    # and MUST NOT have more than 5 dimensions.
+
+    # Each "multiscales" dictionary SHOULD contain the field "name"
+    assert "name" in msd.keys()
+
+    # Each "multiscales" dictionary MAY contain the field "coordinateTransformations"
+    assert "coordinateTransformations" in msd.keys()
+
+    # It SHOULD contain the field "version"
+    assert "version" in msd.keys()
+
+    # Each "multiscales" dictionary SHOULD contain the field "type", which gives
+    # the type of downscaling method used to generate the multiscale image pyramid.
+    # It SHOULD contain the field "metadata", which contains a dictionary with
+    # additional information about the downscaling method.