Merge pull request #123 from fmi-faim/issue-122

Issue 122

pyproject.toml

@@ -58,6 +58,11 @@ cov-report = [
   "- coverage combine",
   "coverage report",
 ]
+cov-html = [
+  "test-cov",
+  "- coverage combine",
+  "coverage html",
+]
 cov = [
   "test-cov",
   "cov-report",

src/faim_ipa/hcs/converter.py

@@ -43,7 +43,6 @@ def __init__(
         self,
         ngff_plate: NGFFPlate,
         yx_binning: int = 1,
-        stitching_yx_chunk_size_factor: int = 1,
         warp_func: Callable = stitching_utils.translate_tiles_2d,
         fuse_func: Callable = stitching_utils.fuse_mean,
         client: Client = None,
@@ -67,7 +66,6 @@ def __init__(
         ), "yx_binning must be an integer >= 1."
         self._ngff_plate = ngff_plate
         self._yx_binning = yx_binning
-        self._stitching_yx_chunk_size_factor = stitching_yx_chunk_size_factor
         self._warp_func = warp_func
         self._fuse_func = fuse_func
         self._client = client
@@ -159,6 +157,7 @@ def run(
                 plate,
                 well_acquisition,
                 well_sub_group,
+                add_to_well_images=not build_acquisition_mask,
             )
             group = well_group[well_sub_group]
             self._write_stitched_image(
@@ -365,11 +364,21 @@ def _stitch_well_image(
         )
         return image_da
 
-    def _create_well_group(self, plate, well_acquisition, well_sub_group):
+    def _create_well_group(
+        self, plate, well_acquisition, well_sub_group, add_to_well_images=True
+    ):
         row, col = well_acquisition.get_row_col()
         well_group = plate.require_group(row).require_group(col)
         well_group.require_group(well_sub_group)
-        write_well_metadata(well_group, [{"path": well_sub_group}])
+        if add_to_well_images:
+            zattrs = well_group.attrs.asdict()
+            if "well" in zattrs.keys() and "images" in zattrs["well"].keys():
+                existing_images = well_group.attrs.asdict()["well"]["images"]
+            else:
+                existing_images = []
+            write_well_metadata(
+                well_group, existing_images + [{"path": well_sub_group}]
+            )
         return well_group
 
     @staticmethod

tests/hcs/test_converter.py

@@ -181,6 +181,30 @@ def test__create_well_group(tmp_dir, plate_acquisition, hcs_plate):
     assert exists(join(tmp_dir, "plate_name.zarr", "D", "08", "0"))
     assert isinstance(well_group, zarr.Group)
 
+    mask_group = converter._create_well_group(
+        plate=zarr_plate,
+        well_acquisition=plate_acquisition.get_well_acquisitions()[0],
+        well_sub_group="0/mask",
+        add_to_well_images=False,
+    )
+    assert exists(join(tmp_dir, "plate_name.zarr", "D", "08", "0", "mask"))
+    assert isinstance(mask_group, zarr.Group)
+
+    assert mask_group.attrs.asdict()["well"]["images"] == [{"path": "0"}]
+
+    another_group = converter._create_well_group(
+        plate=zarr_plate,
+        well_acquisition=plate_acquisition.get_well_acquisitions()[0],
+        well_sub_group="0/another",
+        add_to_well_images=True,
+    )
+    assert exists(join(tmp_dir, "plate_name.zarr", "D", "08", "0", "another"))
+    assert isinstance(another_group, zarr.Group)
+    assert another_group.attrs.asdict()["well"]["images"] == [
+        {"path": "0"},
+        {"path": "0/another"},
+    ]
+
 
 def test__stitch_well_image_2d(tmp_dir, plate_acquisition_2d, hcs_plate):
     converter = ConvertToNGFFPlate(hcs_plate)