BROKEN add test for multiplexing beyond-parsing workflow (ref #199)

tests/test_workflows_multiplexing.py

@@ -21,8 +21,15 @@
 from fractal_tasks_core.create_zarr_structure_multiplex import (
     create_zarr_structure_multiplex,
 )
+from fractal_tasks_core.replicate_zarr_structure import (
+    replicate_zarr_structure,
+)  # noqa
 from fractal_tasks_core.yokogawa_to_zarr import yokogawa_to_zarr
 
+# from fractal_tasks_core.maximum_intensity_projection import (
+#    maximum_intensity_projection,
+# )  # noqa
+
 
 single_cycle_channel_parameters = {
     "A01_C01": {
@@ -99,3 +106,75 @@ def test_workflow_multiplexing(
 
     check_file_number(zarr_path=image_zarr_0)
     check_file_number(zarr_path=image_zarr_1)
+
+
+def test_workflow_multiplexing_MIP(
+    tmp_path: Path, zenodo_images_multiplex: Sequence[Path]
+):
+
+    # Init
+    img_paths = [
+        cycle_folder / "*.png" for cycle_folder in zenodo_images_multiplex
+    ]
+    zarr_path = tmp_path / "tmp_out/*.zarr"
+    zarr_path_mip = tmp_path / "tmp_out_mip/*.zarr"
+    metadata = {}
+
+    # Create zarr structure
+    debug(img_paths)
+    metadata_update = create_zarr_structure_multiplex(
+        input_paths=img_paths,
+        output_path=zarr_path,
+        channel_parameters=channel_parameters,
+        num_levels=num_levels,
+        coarsening_xy=coarsening_xy,
+        metadata_table="mrf_mlf",
+    )
+    metadata.update(metadata_update)
+    debug(metadata)
+
+    # Yokogawa to zarr
+    for component in metadata["image"]:
+        yokogawa_to_zarr(
+            input_paths=[zarr_path],
+            output_path=zarr_path,
+            metadata=metadata,
+            component=component,
+        )
+    debug(metadata)
+
+    # Replicate
+    metadata_update = replicate_zarr_structure(
+        input_paths=[zarr_path],
+        output_path=zarr_path_mip,
+        metadata=metadata,
+        project_to_2D=True,
+        suffix="mip",
+    )
+    metadata.update(metadata_update)
+    debug(metadata)
+
+    """
+    # MIP
+    for component in metadata["image"]:
+        maximum_intensity_projection(
+            input_paths=[zarr_path_mip],
+            output_path=zarr_path_mip,
+            metadata=metadata,
+            component=component,
+        )
+
+
+    # OME-NGFF JSON validation
+    image_zarr_0 = Path(zarr_path.parent / metadata["image"][0])
+    image_zarr_1 = Path(zarr_path.parent / metadata["image"][1])
+    well_zarr = image_zarr_0.parent
+    plate_zarr = image_zarr_0.parents[2]
+    validate_schema(path=str(image_zarr_0), type="image")
+    validate_schema(path=str(image_zarr_1), type="image")
+    validate_schema(path=str(well_zarr), type="well")
+    validate_schema(path=str(plate_zarr), type="plate")
+
+    check_file_number(zarr_path=image_zarr_0)
+    check_file_number(zarr_path=image_zarr_1)
+    """