Temp fix for napari bug, add test to catch it (#177)

* add test that fails :(

* disable axis labels for now due to napari bug

Author: brisvag

src/blik/reader.py

@@ -42,7 +42,7 @@ def _construct_positions_layer(
             "metadata": {"experiment_id": exp_id, "p_id": p_id, "source": source},
             "out_of_slice_display": True,
             "projection_mode": "all",
-            "axis_labels": ('z', 'y', 'x'),
+            # "axis_labels": ('z', 'y', 'x'),
             "units": 'angstrom',
             **pt_kwargs,
         },
@@ -71,7 +71,7 @@ def _construct_orientations_layer(
             "vector_style": "arrow",
             "out_of_slice_display": True,
             "projection_mode": "all",
-            "axis_labels": ('z', 'y', 'x'),
+            # "axis_labels": ('z', 'y', 'x'),
             "units": 'angstrom',
         },
         "vectors",
@@ -179,7 +179,7 @@ def read_image(image):
             "blending": "translucent",
             "plane": {"thickness": 5},
             "projection_mode": "mean",
-            "axis_labels": ('z', 'y', 'x'),
+            # "axis_labels": ('z', 'y', 'x'),
             "units": 'angstrom',
         },
         "image",
@@ -212,7 +212,7 @@ def read_surface_picks(path):
             "edge_color": "surface_id",
             "shape_type": "path",
             "ndim": 3,
-            "axis_labels": ('z', 'y', 'x'),
+            # "axis_labels": ('z', 'y', 'x'),
             "units": 'angstrom',
         },
         "shapes",
@@ -236,7 +236,7 @@ def read_surface(path):
             "scale": scale,
             # TODO: needs to exposed in napari
             # colormap=colormap
-            "axis_labels": ('z', 'y', 'x'),
+            # "axis_labels": ('z', 'y', 'x'),
             "units": 'angstrom',
         },
         "surface",

src/blik/widgets/main_widget.py

@@ -79,7 +79,7 @@ def _attach_callbacks_to_viewer(wdg):
         # pixels are 1 A. We put 0.1nm cause it's more readable with multiples
         viewer.scale_bar.unit = "0.1nm"
         viewer.scale_bar.visible = True
-        viewer.dims.axis_labels = ['z', 'y', 'x']
+        # viewer.dims.axis_labels = ['z', 'y', 'x']
 
 
 def _connect_layers(viewer, e):
@@ -175,7 +175,7 @@ def new(
                     np.zeros(lay.data.shape, dtype=np.int32),
                     name=f"{exp_id} - segmentation",
                     scale=lay.scale,
-                    axis_labels=('z', 'y', 'x'),
+                    # axis_labels=('z', 'y', 'x'),
                     units='angstrom',
                     metadata={
                         "experiment_id": exp_id,
@@ -207,7 +207,7 @@ def new(
                     edge_color_cycle=np.random.rand(30, 3),
                     edge_color="surface_id",
                     ndim=3,
-                    axis_labels=('z', 'y', 'x'),
+                    # axis_labels=('z', 'y', 'x'),
                     units='angstrom',
                 )
 
@@ -222,7 +222,7 @@ def new(
                     metadata={"experiment_id": exp_id},
                     face_color_cycle=np.random.rand(30, 3),
                     ndim=3,
-                    axis_labels=('z', 'y', 'x'),
+                    # axis_labels=('z', 'y', 'x'),
                     units='angstrom',
                 )
 

tests/test_reader.py

@@ -28,3 +28,9 @@ def test_construct_empty_layers():
     assert pts[2] == "points"
     vec = layer_data_list[1]
     assert vec[2] == "vectors"
+
+
+def test_napari_read(star_file, mrc_file, make_napari_viewer):
+    v = make_napari_viewer()
+    v.open(star_file, plugin='blik')
+    v.open(mrc_file, plugin='blik')