Add basic tests for convert_2D_segmentation_to_3D

Author: jluethi

pyproject.toml

@@ -18,7 +18,7 @@ dependencies = [
 # Optional dependencies (e.g. for `pip install -e ".[dev]"`, see
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies)
 [project.optional-dependencies]
-dev = ["devtools", "pytest", "requests", "build", "jsonschema"]
+dev = ["devtools", "pytest", "requests", "build", "jsonschema", "pooch"]
 test = ["pytest", "pytest-cov"]
 
 # Build options (see https://peps.python.org/pep-0517)

src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json

@@ -118,7 +118,7 @@
         ],
         "additionalProperties": false
       },
-      "docs_info": "## convert_2D_segmentation_to_3D\nConvert 2D segmentation to 3D segmentation.\n\nThis task loads the 2D segmentation, replicates it along the Z slice and\nstores it back into the 3D OME-Zarr image.\n\nThis is a temporary workaround task, as long as we store 2D data in\na separate OME-Zarr file from the 3D data. If the 2D & 3D OME-Zarr images\nhave different suffixes in their name, use `image_suffix_2D_to_remove` &\n`image_suffix_3D_to_add`. If their base names are different, this task\ndoes not support processing them at the moment.\n"
+      "docs_info": "## convert_2D_segmentation_to_3D\nConvert 2D segmentation to 3D segmentation.\n\nThis task loads the 2D segmentation, replicates it along the Z slice and\nstores it back into the 3D OME-Zarr image.\n\nThis is a temporary workaround task, as long as we store 2D data in\na separate OME-Zarr file from the 3D data. If the 2D & 3D OME-Zarr images\nhave different suffixes in their name, use `image_suffix_2D_to_remove` &\n`image_suffix_3D_to_add`. If their base names are different, this task\ndoes not support processing them at the moment.\n\nIt makes the assumption that the 3D OME-Zarrs are stored in the same place \nas the 2D OME-Zarrs (same based folder).\n"
     }
   ],
   "has_args_schemas": true,

src/fractal_helper_tasks/convert_2D_segmentation_to_3D.py

@@ -113,6 +113,9 @@ def convert_2D_segmentation_to_3D(
     `image_suffix_3D_to_add`. If their base names are different, this task
     does not support processing them at the moment.
 
+    It makes the assumption that the 3D OME-Zarrs are stored in the same place
+    as the 2D OME-Zarrs (same based folder).
+
     Args:
         zarr_url: Path or url to the individual OME-Zarr image to be processed.
             (standard argument for Fractal tasks, managed by Fractal server).

tests/conftest.py

@@ -0,0 +1,73 @@
+import os
+import shutil
+from pathlib import Path
+
+import pooch
+import pytest
+
+
+@pytest.fixture(scope="session")
+def testdata_path() -> Path:
+    TEST_DIR = Path(__file__).parent
+    return TEST_DIR / "data/"
+
+
+@pytest.fixture(scope="session")
+def zenodo_zarr(testdata_path: Path) -> list[str]:
+    """
+    This takes care of multiple steps:
+
+    1. Download/unzip two Zarr containers (3D and MIP) from Zenodo, via pooch
+    2. Copy the two Zarr containers into tests/data
+    3. Modify the Zarrs in tests/data, to add whatever is not in Zenodo
+    """
+
+    # 1 Download Zarrs from Zenodo
+    DOI = "10.5281/zenodo.10257149"
+    DOI_slug = DOI.replace("/", "_").replace(".", "_")
+    platenames = ["plate.zarr", "plate_mip.zarr"]
+    rootfolder = testdata_path / DOI_slug
+    folders = [rootfolder / plate for plate in platenames]
+
+    registry = {
+        "20200812-CardiomyocyteDifferentiation14-Cycle1.zarr.zip": None,
+        "20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr.zip": None,
+    }
+    base_url = f"doi:{DOI}"
+    POOCH = pooch.create(
+        pooch.os_cache("pooch") / DOI_slug,
+        base_url,
+        registry=registry,
+        retry_if_failed=10,
+        allow_updates=False,
+    )
+
+    for ind, file_name in enumerate(
+        [
+            "20200812-CardiomyocyteDifferentiation14-Cycle1.zarr",
+            "20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr",
+        ]
+    ):
+        # 1) Download/unzip a single Zarr from Zenodo
+        file_paths = POOCH.fetch(
+            f"{file_name}.zip", processor=pooch.Unzip(extract_dir=file_name)
+        )
+        zarr_full_path = file_paths[0].split(file_name)[0] + file_name
+        print(zarr_full_path)
+        folder = folders[ind]
+
+        # 2) Copy the downloaded Zarr into tests/data
+        if os.path.isdir(str(folder)):
+            shutil.rmtree(str(folder))
+        shutil.copytree(Path(zarr_full_path) / file_name, folder)
+    return [str(f) for f in folders]
+
+
+@pytest.fixture(scope="function")
+def tmp_zenodo_zarr(zenodo_zarr: list[str], tmpdir: Path) -> list[str]:
+    """Generates a copy of the zenodo zarrs in a tmpdir"""
+    zenodo_mip_path = str(tmpdir / Path(zenodo_zarr[1]).name)
+    zenodo_path = str(tmpdir / Path(zenodo_zarr[0]).name)
+    shutil.copytree(zenodo_zarr[0], zenodo_path)
+    shutil.copytree(zenodo_zarr[1], zenodo_mip_path)
+    return [zenodo_path, zenodo_mip_path]

tests/data/.gitignore

@@ -0,0 +1 @@
+10_5281_zenodo_10257149

tests/test_convert_2d_to_3d_segmentation.py

@@ -0,0 +1,31 @@
+"""Test copy 2D to 3D segmentation."""
+
+import dask.array as da
+import zarr
+
+from fractal_helper_tasks.convert_2D_segmentation_to_3D import (
+    convert_2D_segmentation_to_3D,
+)
+
+
+def test_2d_to_3d(tmp_zenodo_zarr: list[str]):
+    zarr_url = f"{tmp_zenodo_zarr[1]}/B/03/0"
+    label_name = "nuclei"
+
+    convert_2D_segmentation_to_3D(
+        zarr_url=zarr_url,
+        label_name=label_name,
+    )
+    zarr_3D_label_url = f"{tmp_zenodo_zarr[0]}/B/03/0/labels/{label_name}"
+    # Check that the label has been copied correctly
+    with zarr.open(zarr_3D_label_url, mode="rw+") as zarr_img:
+        zarr_3D = da.from_zarr(zarr_img[0])
+        assert zarr_3D.shape == (2, 540, 1280)
+
+
+# TODO: Add custom ROI tables to be copied to 3D
+
+# TODO: Add test with new label name, new table names
+
+# TODO: Create a version of the test data where image suffixes need to be
+# changed, run tests on those