from datetime import datetime, timezone from pathlib import Path from typing import Callable, Tuple, Union import cv2 import h5py import numpy as np import pytest import zarr from numpydantic.interface.hdf5 import H5ArrayPath from numpydantic.interface.zarr import ZarrArrayPath @pytest.fixture(scope="function") def hdf5_array( request, tmp_output_dir_func ) -> Callable[[Tuple[int, ...], Union[np.dtype, type]], H5ArrayPath]: hdf5_file = tmp_output_dir_func / "h5f.h5" def _hdf5_array( shape: Tuple[int, ...] = (10, 10), dtype: Union[np.dtype, type] = float, compound: bool = False, ) -> H5ArrayPath: array_path = "/" + "_".join([str(s) for s in shape]) + "__" + dtype.__name__ if not compound: if dtype is str: data = np.random.random(shape).astype(bytes) elif dtype is datetime: data = np.empty(shape, dtype="S32") data.fill(datetime.now(timezone.utc).isoformat().encode("utf-8")) else: data = np.random.random(shape).astype(dtype) h5path = H5ArrayPath(hdf5_file, array_path) else: if dtype is str: dt = np.dtype([("data", np.dtype("S10")), ("extra", "i8")]) data = np.array([("hey", 0)] * np.prod(shape), dtype=dt).reshape(shape) elif dtype is datetime: dt = np.dtype([("data", np.dtype("S32")), ("extra", "i8")]) data = np.array( [(datetime.now(timezone.utc).isoformat().encode("utf-8"), 0)] * np.prod(shape), dtype=dt, ).reshape(shape) else: dt = np.dtype([("data", dtype), ("extra", "i8")]) data = np.zeros(shape, dtype=dt) h5path = H5ArrayPath(hdf5_file, array_path, "data") with h5py.File(hdf5_file, "w") as h5f: _ = h5f.create_dataset(array_path, data=data) return h5path return _hdf5_array @pytest.fixture(scope="function") def zarr_nested_array(tmp_output_dir_func) -> ZarrArrayPath: """Zarr array within a nested array""" file = tmp_output_dir_func / "nested.zarr" path = "a/b/c" root = zarr.open(str(file), mode="w") array = root.zeros(path, shape=(100, 100), chunks=(10, 10)) return ZarrArrayPath(file=file, path=path) @pytest.fixture(scope="function") def zarr_array(tmp_output_dir_func) -> Path: file = tmp_output_dir_func / "array.zarr" array = zarr.open(str(file), mode="w", shape=(100, 100), chunks=(10, 10)) array[:] = 0 return file @pytest.fixture(scope="function") def avi_video(tmp_output_dir_func) -> Callable[[Tuple[int, int], int, bool], Path]: video_path = tmp_output_dir_func / "test.avi" def _make_video(shape=(100, 50), frames=10, is_color=True) -> Path: writer = cv2.VideoWriter( str(video_path), cv2.VideoWriter_fourcc(*"RGBA"), # raw video for testing purposes 30, (shape[1], shape[0]), is_color, ) if is_color: shape = (*shape, 3) for i in range(frames): # make fresh array every time bc opencv eats them array = np.zeros(shape, dtype=np.uint8) if not is_color: array[i, i] = i else: array[i, i, :] = i writer.write(array) writer.release() return video_path return _make_video