Add regression test for lsm modality

tests/data/generate.py

@@ -0,0 +1,14 @@
+import os
+import tempfile
+
+import test_lsm
+import zarr
+
+from linc_convert.modalities.lsm import mosaic
+
+if __name__ == "__main__":
+    with tempfile.TemporaryDirectory() as tmp_dir:
+        test_lsm._write_test_data(tmp_dir)
+        output_zarr = os.path.join(tmp_dir, "output.zarr")
+        mosaic.convert(tmp_dir, output_zarr)
+        zarr.copy_all(zarr.open(output_zarr), zarr.open("data/lsm.zarr.zip", "w"))

tests/test_lsm.py

@@ -0,0 +1,75 @@
+import os
+from pathlib import Path
+from tempfile import TemporaryDirectory
+from unittest import TestCase
+
+import numpy as np
+import tifffile
+import zarr
+
+from linc_convert.modalities.lsm import mosaic
+
+
+def _compare_zarr_archives(path1, path2):
+    """
+    Compare two Zarr archives to check if they contain the same data.
+
+    Parameters
+    ----------
+    - path1 (str): Path to the first Zarr archive.
+    - path2 (str): Path to the second Zarr archive.
+
+    Returns
+    -------
+    - bool: True if both archives contain the same data, False otherwise.
+    """
+    # Open both Zarr groups
+    zarr1 = zarr.open(path1, mode="r")
+    zarr2 = zarr.open(path2, mode="r")
+
+    # Compare keys (dataset structure)
+    if zarr1.keys() != zarr2.keys():
+        return False
+    if zarr1.attrs != zarr2.attrs:
+        return False
+
+    # Compare each array in both archives
+    for key in zarr1.keys():
+        array1 = zarr1[key][:]
+        array2 = zarr2[key][:]
+
+        # Check for equality of the arrays
+        if not np.array_equal(array1, array2):
+            print(f"Mismatch found in dataset: {key}")
+            return False
+        if zarr1[key].attrs != zarr2[key].attrs:
+            return False
+
+    # If all checks pass
+    print("The Zarr archives are identical.")
+    return True
+
+
+def _write_test_data(directory):
+    root_path = Path(directory)
+    for z in range(1, 2, 1):
+        for y in range(1, 3, 1):
+            folder = root_path / f"test_z{z}_y{y}"
+            folder.mkdir(parents=True, exist_ok=True)
+            for plane in range(1, 4, 1):
+                for c in range(1, 3, 1):
+                    image = np.zeros((1024, 768)) + z * y * plane * c
+                    tifffile.imwrite(
+                        folder / f"test_z{z}_y{y}_plane{plane}_c{c}.tiff", image
+                    )
+
+
+class Test(TestCase):
+    def test_convert(self):
+        with TemporaryDirectory() as tmp_dir:
+            _write_test_data(tmp_dir)
+            output_zarr = os.path.join(tmp_dir, "output.zarr")
+            mosaic.convert(tmp_dir, output_zarr)
+            self.assertTrue(
+                _compare_zarr_archives(output_zarr, "tests/data/lsm.zarr.zip")
+            )