Fix label direct mode for installation without numba

.github/workflows/reusable_pip_test.yml

@@ -27,6 +27,10 @@ jobs:
         env:
           PIP_CONSTRAINT: napari-from-github/resources/constraints/constraints_py3.9.txt
 
+      - name: uninstall numba
+        run: |
+          pip uninstall -y numba
+
       - name: Test
         uses: aganders3/headless-gui@v1
         with:

napari/_qt/_tests/test_qt_viewer.py

@@ -749,7 +749,9 @@ def test_label_colors_matching_widget_auto(
 
 @skip_local_popups
 @skip_on_win_ci
-@pytest.mark.parametrize("use_selection", [True, False])
+@pytest.mark.parametrize(
+    "use_selection", [True, False], ids=["selected", "all"]
+)
 @pytest.mark.parametrize("dtype", [np.uint64, np.uint16, np.uint8, np.int16])
 def test_label_colors_matching_widget_direct(
     qtbot, qt_viewer_with_controls, use_selection, dtype
@@ -786,12 +788,14 @@ def test_label_colors_matching_widget_direct(
         color_box_color, middle_pixel = _update_data(
             layer, label, qtbot, qt_viewer_with_controls, dtype
         )
-        assert np.allclose(color_box_color, middle_pixel, atol=1), label
-        assert np.allclose(
+        npt.assert_almost_equal(
+            color_box_color, middle_pixel, err_msg=f"{label=}"
+        )
+        npt.assert_almost_equal(
             color_box_color,
             layer.color.get(label, layer.color[None]) * 255,
-            atol=1,
-        ), label
+            err_msg=f"{label=}",
+        )
 
 
 def test_axes_labels(make_napari_viewer):
@@ -1006,6 +1010,7 @@ def test_all_supported_dtypes(qt_viewer):
 
 
 def test_more_than_uint16_colors(qt_viewer):
+    pytest.importorskip("numba")
     # this test is slow (10s locally)
     data = np.zeros((10, 10), dtype=np.uint32)
     colors = {

napari/layers/labels/_tests/test_labels.py

@@ -1468,6 +1468,7 @@ def test_is_default_color():
 
 def test_large_labels_direct_color():
     """Make sure direct color works with large label ranges"""
+    pytest.importorskip('numba')
     data = np.array([[0, 1], [2**16, 2**20]], dtype=np.uint32)
     colors = {1: 'white', 2**16: 'green', 2**20: 'magenta'}
     layer = Labels(data)

napari/utils/colormaps/_tests/test_colormap.py

@@ -11,6 +11,7 @@
 from napari.utils.colormaps.colormap import (
     MAPPING_OF_UNKNOWN_VALUE,
     DirectLabelColormap,
+    _labels_raw_to_texture_direct_numpy,
 )
 from napari.utils.colormaps.colormap_utils import label_colormap
 
@@ -430,3 +431,25 @@ def test_direct_colormap_negative_values():
     # Map multiple values
     mapped = cmap.map(np.array([-1, -2], dtype=np.int8))
     npt.assert_array_equal(mapped, np.array([[1, 0, 0, 1], [0, 1, 0, 1]]))
+
+
+def test_direct_colormap_negative_values_numpy():
+    color_dict = {
+        -1: np.array([1, 0, 0, 1]),
+        -2: np.array([0, 1, 0, 1]),
+        None: np.array([0, 0, 0, 1]),
+    }
+    cmap = DirectLabelColormap(color_dict=color_dict)
+
+    res = _labels_raw_to_texture_direct_numpy(
+        np.array([-1, -2, 5], dtype=np.int8), cmap
+    )
+    npt.assert_array_equal(res, [1, 2, 0])
+
+    cmap.selection = -2
+    cmap.use_selection = True
+
+    res = _labels_raw_to_texture_direct_numpy(
+        np.array([-1, -2, 5], dtype=np.int8), cmap
+    )
+    npt.assert_array_equal(res, [0, 1, 0])

napari/utils/colormaps/colormap.py

@@ -534,7 +534,12 @@ def _get_typed_dict_mapping(self, data_dtype: np.dtype) -> 'typed.Dict':
     @cached_property
     def _array_map(self):
         """Create an array to map labels to texture values of smaller dtype."""
-        max_value = max(x for x in self.color_dict if x is not None)
+
+        max_value = max(
+            (abs(x) for x in self.color_dict if x is not None), default=0
+        )
+        if any(x < 0 for x in self.color_dict if x is not None):
+            max_value *= 2
         if max_value > 2**16:
             raise RuntimeError(  # pragma: no cover
                 "Cannot use numpy implementation for large values of labels "
@@ -827,10 +832,15 @@ def _labels_raw_to_texture_direct_numpy(
 
     See `_cast_labels_data_to_texture_dtype_direct` for more details.
     """
+    if direct_colormap.use_selection:
+        return (data == direct_colormap.selection).astype(np.uint8)
     mapper = direct_colormap._array_map
-
-    if data.dtype.itemsize > 2:
+    if any(x < 0 for x in direct_colormap.color_dict if x is not None):
+        half_shape = mapper.shape[0] // 2 - 1
+        data = np.clip(data, -half_shape, half_shape)
+    else:
         data = np.clip(data, 0, mapper.shape[0] - 1)
+
     return mapper[data]