From ba86e321c59edfd6cce9b240bc83ccb9aee32e16 Mon Sep 17 00:00:00 2001
From: Jan Eglinger <jan.eglinger@fmi.ch>
Date: Mon, 16 Oct 2023 21:36:42 +0200
Subject: [PATCH] mobie: expand test to cover add_labels_view

---
 tests/test_mobie.py | 55 ++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 47 insertions(+), 8 deletions(-)

diff --git a/tests/test_mobie.py b/tests/test_mobie.py
index 7a21964e..f8811d23 100644
--- a/tests/test_mobie.py
+++ b/tests/test_mobie.py
@@ -8,11 +8,16 @@
 )
 from mobie.metadata.project_metadata import add_dataset, create_project_metadata
 from mobie.validation import validate_project
+from skimage.measure import label
 
 from faim_hcs.io.MolecularDevicesImageXpress import parse_single_plane_multi_fields
 from faim_hcs.MetaSeriesUtils import get_well_image_CYX
-from faim_hcs.mobie import add_wells_to_project
-from faim_hcs.Zarr import build_zarr_scaffold, write_cyx_image_to_well
+from faim_hcs.mobie import add_labels_view, add_wells_to_project
+from faim_hcs.Zarr import (
+    build_zarr_scaffold,
+    write_cyx_image_to_well,
+    write_labels_to_group,
+)
 
 ROOT_DIR = Path(__file__).parent.parent
 
@@ -23,7 +28,12 @@ def files():
 
 
 @pytest.fixture
-def zarr_group(files, zarr_dir):
+def threshold():
+    return 10000
+
+
+@pytest.fixture
+def zarr_group(files, zarr_dir, threshold):
     plate = build_zarr_scaffold(
         root_dir=zarr_dir,
         files=files,
@@ -39,6 +49,12 @@ def zarr_group(files, zarr_dir):
         )
         field = plate[well[0]][str(int(well[1:]))][0]
         write_cyx_image_to_well(img, hists, ch_metadata, metadata, field)
+        labels = label(img > threshold)
+        write_labels_to_group(
+            labels=labels,
+            labels_name="simple_threshold",
+            parent_group=field,
+        )
     return plate
 
 
@@ -52,7 +68,7 @@ def zarr_dir(tmp_path_factory):
     return tmp_path_factory.mktemp("zarr")
 
 
-def test_add_wells_to_project(zarr_group, mobie_project_folder):
+def test_full_mobie_project(zarr_group, mobie_project_folder):
     # setup OME-ZARR folder
     # setup MoBIE project
     dataset_name = "mobie_test_dataset"
@@ -84,7 +100,23 @@ def test_add_wells_to_project(zarr_group, mobie_project_folder):
         view_name="default",
     )
 
-    # assert
+    # validate 1
+    validate_project(
+        root=mobie_project_folder,
+    )
+
+    # add_labels_view
+    add_labels_view(
+        plate=zarr_group,
+        dataset_folder=(mobie_project_folder / dataset_name),
+        well_group="0",
+        channel=0,
+        label_name="simple_threshold",
+        view_name="default",
+        extra_properties=("area", "bbox"),
+    )
+
+    # validate 2
     validate_project(
         root=mobie_project_folder,
     )
@@ -99,11 +131,18 @@ def test_add_wells_to_project(zarr_group, mobie_project_folder):
     assert "sourceDisplays" in json_data["views"]["default"]
     assert "sourceTransforms" in json_data["views"]["default"]
 
+    # wells table
     table_path: Path = (
         mobie_project_folder / dataset_name / "tables" / "wells" / "default.tsv"
     )
     assert table_path.exists()
 
-
-def test_add_labels_view():
-    pass
+    # segmentation table for E07
+    label_table_path: Path = (
+        mobie_project_folder
+        / dataset_name
+        / "tables"
+        / "E07_simple_threshold"
+        / "default.tsv"
+    )
+    assert label_table_path.exists()