test_spatial_image_ngff.py

import pytest

from ipfsspec import IPFSFileSystem
import xarray as xr
import zarr

from spatial_image_multiscale import Method, to_multiscale

from spatial_image_ngff import imwrite

IPFS_FS = IPFSFileSystem()
IPFS_CID = "bafybeibpqky6d335duxtkmwowcc6igt2q5qorqd7e5xqfoxlfxm4pozg74"


@pytest.fixture
def input_images():
    result = {}

    store = IPFS_FS.get_mapper(f"ipfs://{IPFS_CID}/input/cthead1.zarr")
    image_ds = xr.open_zarr(store)
    image_da = image_ds.cthead1
    result["cthead1"] = image_da

    store = IPFS_FS.get_mapper(f"ipfs://{IPFS_CID}/input/small_head.zarr")
    image_ds = xr.open_zarr(store)
    image_da = image_ds.small_head
    result["small_head"] = image_da

    return result


def verify_against_baseline(dataset_name, baseline_name, multiscale):
    for idx, scale in enumerate(multiscale):
        store = IPFS_FS.get_mapper(
            f"ipfs://{IPFS_CID}/baseline/{dataset_name}/{baseline_name}/{idx}"
        )
        image_ds = xr.open_zarr(store)
        baseline = image_ds[dataset_name]
        xr.testing.assert_equal(baseline, scale)


def test_imwrite(input_images):
    dataset_name = "cthead1"
    image = input_images[dataset_name]
    multiscale = to_multiscale(image, [4, 2])
    verify_against_baseline(dataset_name, "4_2", multiscale)

    store = zarr.storage.MemoryStore(dimension_separator='/')

    imwrite(multiscale, store)
    imwrite(multiscale, '/tmp/ngff.zarr')
    root = zarr.group(store=store)
    assert 'multiscales' in root.attrs
    multiscales = root.attrs['multiscales'][0]
    assert multiscales['name'] == dataset_name
    assert multiscales['version'] == "0.1"
    assert multiscales['datasets'][0]['path'] == f'0/{dataset_name}'
    assert multiscales['datasets'][1]['path'] == f'1/{dataset_name}'

    # dataset_name = "small_head"
    # image = input_images[dataset_name]
    # multiscale = to_multiscale(image, [3, 2, 2])
    # verify_against_baseline(dataset_name, "3_2_2", multiscale)