tests

brainlit/BrainLine/tests/test_apply_ilastik.py

@@ -14,6 +14,35 @@
 from datetime import date
 
 
+@pytest.fixture(scope="session")
+def axon_data_dir(tmp_path_factory):
+    data_dir = tmp_path_factory.mktemp("data")
+    brain_dir = data_dir / "braintest"
+    brain_dir.mkdir()
+    val_dir = brain_dir / "val"
+    val_dir.mkdir()
+
+    labels = np.ones((2, 10, 10, 10), dtype=np.uint16)
+    labels[0, 0, 0, :] = 2
+    labels_path = val_dir / "subvol-image_3channel_Labels.h5"
+    with h5py.File(str(labels_path), "w") as f:
+        dset = f.create_dataset("exported_data", data=labels)
+
+    im_probs = np.zeros((2, 10, 10, 10))
+    im_probs[0, 0, 0, :5] = 0.9
+    path = val_dir / "subvol_Probabilities.h5"
+    with h5py.File(path, "w") as f:
+        f.create_dataset("exported_data", data=im_probs)
+
+    im = np.zeros((3, 10, 10, 10))
+    im[0, 0, 0, :5] = 0.9
+    path = val_dir / "subvol.h5"
+    with h5py.File(path, "w") as f:
+        f.create_dataset("image_3channel", data=im)
+
+    return data_dir
+
+
 # ApplyIlastik
 
 
@@ -34,7 +63,7 @@ def test_processsubvols_none(axon_data_dir):
         apl.process_subvols()
 
     # brainr1
-    val_dir = axon_data_dir / "brain8557"
+    val_dir = axon_data_dir / "brainr1"
     val_dir.mkdir()
     val_dir = val_dir / "val"
     val_dir.mkdir()
@@ -50,7 +79,7 @@ def test_processsubvols_none(axon_data_dir):
         apl.process_subvols()
 
     # brainr2
-    val_dir = axon_data_dir / "brain8555"
+    val_dir = axon_data_dir / "brainr2"
     val_dir.mkdir()
     val_dir = val_dir / "val"
     val_dir.mkdir()
@@ -89,35 +118,6 @@ def test_move_results(axon_data_dir):
 # Other methods
 
 
-@pytest.fixture(scope="session")
-def axon_data_dir(tmp_path_factory):
-    data_dir = tmp_path_factory.mktemp("data")
-    brain_dir = data_dir / "braintest"
-    brain_dir.mkdir()
-    val_dir = brain_dir / "val"
-    val_dir.mkdir()
-
-    labels = np.ones((2, 10, 10, 10), dtype=np.uint16)
-    labels[0, 0, 0, :] = 2
-    labels_path = val_dir / "subvol-image_3channel_Labels.h5"
-    with h5py.File(str(labels_path), "w") as f:
-        dset = f.create_dataset("exported_data", data=labels)
-
-    im_probs = np.zeros((2, 10, 10, 10))
-    im_probs[0, 0, 0, :5] = 0.9
-    path = val_dir / "subvol_Probabilities.h5"
-    with h5py.File(path, "w") as f:
-        f.create_dataset("exported_data", data=im_probs)
-
-    im = np.zeros((3, 10, 10, 10))
-    im[0, 0, 0, :5] = 0.9
-    path = val_dir / "subvol.h5"
-    with h5py.File(path, "w") as f:
-        f.create_dataset("image_3channel", data=im)
-
-    return data_dir
-
-
 def test_plot_results_axon(axon_data_dir):
     data_dir_str = str(axon_data_dir)
 

brainlit/BrainLine/tests/test_util.py

@@ -15,6 +15,17 @@ def make_data_dir(tmp_path_factory):
     return data_dir
 
 
+@pytest.fixture(scope="session")
+def make_bad_datafile(make_data_dir):
+    data_dir = make_data_dir
+    bad_data_file = data_dir / "bad_data.json"
+    bad_type = {"object_type": "invalid", "brain2paths": {}}
+    with open(bad_data_file, "w") as f:
+        json.dump(bad_type, f)
+
+    return bad_data_file
+
+
 @pytest.fixture(scope="session")
 def ontology_path():
     ontology_json_path = (
@@ -48,10 +59,22 @@ def test_find_atlas_level_label(ontology_path):
     assert new_label == 8
 
 
-def test_download_subvolumes(make_data_dir):
-    # Axon
+def test_download_subvolumes(make_data_dir, make_bad_datafile):
     data_dir = make_data_dir  # tmp_path_factory.mktemp("data")
-    layer_names = ["average_10um"] * 3
+    layer_names = ["average_10um", "average_10um", "zero"]
+
+    # Data file with bad object_fype
+    bad_data_file = make_bad_datafile
+    with pytest.raises(ValueError):
+        util.download_subvolumes(
+            data_dir=data_dir,
+            brain_id="pytest",
+            layer_names=layer_names,
+            dataset_to_save="val",
+            data_file=bad_data_file,
+        )
+
+    # Axon
     data_file = (
         Path(os.path.abspath(__file__)).parents[3]
         / "docs"