Fix labels mapping cache by filling it with background, not 0 (napari…

…#6580) # References and relevant issues closes napari#6578 updates example to mitigate napari#6579 # Description As unknown values are mapped in direct mode to 0 then filing cache with 0 leads to the artifact reported in napari#6578. In this PR, the mapped cache is filled with the result of background mapping. --------- Co-authored-by: Juan Nunez-Iglesias <[email protected]>
jni · Jan 9, 2024 · 4a1b0b5 · 4a1b0b5
1 parent c4e79cb
commit 4a1b0b5
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diff --git a/examples/add_labels.py b/examples/add_labels.py
@@ -7,7 +7,6 @@
 
 .. tags:: layers, visualization-basic
 """
-
 from skimage import data
 from skimage.filters import threshold_otsu
 from skimage.measure import label
@@ -26,7 +25,7 @@
 cleared = remove_small_objects(clear_border(bw), 20)
 
 # label image regions
-label_image = label(cleared)
+label_image = label(cleared).astype("uint8")
 
 # initialise viewer with coins image
 viewer = napari.view_image(image, name='coins', rgb=False)

diff --git a/napari/layers/labels/_tests/test_labels.py b/napari/layers/labels/_tests/test_labels.py
@@ -23,6 +23,7 @@
 from napari.layers.labels._labels_utils import get_contours
 from napari.utils import Colormap
 from napari.utils.colormaps import label_colormap
+from napari.utils.colormaps.colormap import DirectLabelColormap
 
 
 def test_random_labels():
@@ -1685,6 +1686,35 @@ def test_copy():
     assert l1.data is l3.data
 
 
+@pytest.mark.parametrize(
+    "colormap,expected",
+    [
+        (label_colormap(49, 0.5), [0, 1]),
+        (
+            DirectLabelColormap(
+                color_dict={
+                    0: np.array([0, 0, 0, 0]),
+                    1: np.array([1, 0, 0, 1]),
+                    None: np.array([1, 1, 0, 1]),
+                }
+            ),
+            [1, 2],
+        ),
+    ],
+    ids=["auto", "direct"],
+)
+def test_draw(colormap, expected):
+    labels = Labels(np.zeros((30, 30), dtype=np.uint32))
+    labels.mode = "paint"
+    labels.colormap = colormap
+    labels.selected_label = 1
+    npt.assert_array_equal(np.unique(labels._slice.image.raw), [0])
+    npt.assert_array_equal(np.unique(labels._slice.image.view), expected[:1])
+    labels._draw(1, (15, 15), (15, 15))
+    npt.assert_array_equal(np.unique(labels._slice.image.raw), [0, 1])
+    npt.assert_array_equal(np.unique(labels._slice.image.view), expected)
+
+
 class TestLabels:
     @staticmethod
     def get_objects():

diff --git a/napari/layers/labels/labels.py b/napari/layers/labels/labels.py
@@ -992,9 +992,22 @@ def _setup_cache(self, labels):
         if self._cached_labels is not None:
             return
 
+        if isinstance(self._colormap, LabelColormap):
+            mapped_background = _cast_labels_data_to_texture_dtype_auto(
+                labels.dtype.type(self.colormap.background_value),
+                self._random_colormap,
+            )
+        else:  # direct
+            mapped_background = _cast_labels_data_to_texture_dtype_direct(
+                labels.dtype.type(self.colormap.background_value),
+                self._direct_colormap,
+            )
+
         self._cached_labels = np.zeros_like(labels)
-        self._cached_mapped_labels = np.zeros_like(
-            labels, dtype=self._get_cache_dtype(labels.dtype)
+        self._cached_mapped_labels = np.full(
+            shape=labels.shape,
+            fill_value=mapped_background,
+            dtype=self._get_cache_dtype(labels.dtype),
         )
 
     def _raw_to_displayed(