Improve multiple colors behavior in relevant layers (napari#782)

* Allow a single point to be added as 1D

* Added possible color configs to test

* Basic color tests for add_points

* Basic mechanism of color handling

* Mock data for tests

* Added color transformation and appropriate tests

* Moved transform function and its tests

* Improved tests

* Refactored Points layer object

* Minor test addition

* Test modifications

* Points layer uses ColorArray

* Point layer is now integrated with ColorArray colors, tests of it pass

* Fixed hex conversion, all tests pass

* Added test, fixed small bug with tiling

* edge_ and face_color save last used color

* added transparent color option

* Moved color-handling files to their own folder

* Renamed utils

* Removed old util module

* Fixed point selection bug

* Fixed faulty import

* Fixed numpy 1.17 deprecation becoming hard error in 1.18

* Fix numpy deprecation again

* Resolve conflict

* Fixed comments in PR and logic errors

* Refactoring according to comments, test should pass

* Fixed default face_color value

* Working on standardization color, half-way through

* More extensive work on standardize_color

* All tests besides the RGBA one pass

* Color tests pass

* Removing .rgba from the wild

* Removed .rgba isntances from relevant parts

* Got rid of ColorArray in layers

* Fixed tests to pass without ColorArray

* Last fixes for tests

* Moved tiling and transformation methods to their own utils module

* Various fixes from review

* Better param names

* More basic color manipulation fixes

* Applying suggestions

* Reverting old changes

* Remove support for list or tuple of arrays

* Transparent color is now working

* Better explain the logic behind combobox

* Fixed merge conflicts

* Formatting and other minor changes

* Added explicit copy flag, tests do not warn anymore

* Formatting

napari/_qt/layers/qt_points_layer.py

@@ -8,7 +8,7 @@
     QFrame,
     QHBoxLayout,
 )
-from vispy.color import Color
+
 from .qt_base_layer import QtLayerControls
 from ...layers.points._constants import Mode, Symbol
 from ..qt_mode_buttons import QtModeRadioButton, QtModePushButton
@@ -170,22 +170,42 @@ def _on_size_change(self, event=None):
             self.sizeSlider.setValue(int(value))
 
     def _on_edge_color_change(self, event=None):
+        """Change element's edge color based on user-provided value.
+
+        The new color (read from layer.current_edge_color) is a string -
+        either the color's name or its hex representation. This color has
+        already been verified by "transform_color". This value has to be
+        looked up in the color list of the layer and displayed in the
+        combobox. If it's not in the combobox the method will add it and
+        then display it, for future use.
+        """
+        color = self.layer.current_edge_color
         with self.layer.events.edge_color.blocker():
-            index = self.edgeComboBox.findText(
-                self.layer.current_edge_color, Qt.MatchFixedString
-            )
+            index = self.edgeComboBox.findText(color, Qt.MatchFixedString)
+            if index == -1:
+                self.edgeComboBox.addItem(color)
+                index = self.edgeComboBox.findText(color, Qt.MatchFixedString)
             self.edgeComboBox.setCurrentIndex(index)
-        color = Color(self.layer.current_edge_color).hex
-        self.edgeColorSwatch.setStyleSheet("background-color: " + color)
+        self.edgeColorSwatch.setStyleSheet(f"background-color: {color}")
 
     def _on_face_color_change(self, event=None):
+        """Change element's face color based user-provided value.
+
+        The new color (read from layer.current_face_color) is a string -
+        either the color's name or its hex representation. This color has
+        already been verified by "transform_color". This value has to be
+        looked up in the color list of the layer and displayed in the
+        combobox. If it's not in the combobox the method will add it and
+        then display it, for future use.
+        """
+        color = self.layer.current_face_color
         with self.layer.events.face_color.blocker():
-            index = self.faceComboBox.findText(
-                self.layer.current_face_color, Qt.MatchFixedString
-            )
+            index = self.faceComboBox.findText(color, Qt.MatchFixedString)
+            if index == -1:
+                self.faceComboBox.addItem(color)
+                index = self.faceComboBox.findText(color, Qt.MatchFixedString)
             self.faceComboBox.setCurrentIndex(index)
-        color = Color(self.layer.current_face_color).hex
-        self.faceColorSwatch.setStyleSheet("background-color: " + color)
+        self.faceColorSwatch.setStyleSheet(f"background-color: {color}")
 
     def _on_editable_change(self, event=None):
         self.select_button.setEnabled(self.layer.editable)

napari/_qt/tests/test_qt_layerlist.py

@@ -1,8 +1,10 @@
 import numpy as np
+from vispy.color import get_color_dict
 
 from napari.components import LayerList
 from napari.layers import Image
 from napari._qt.qt_layerlist import QtLayerList, QtDivider
+from napari.utils.colormaps.standardize_color import hex_to_name
 
 
 def check_layout_layers(layout, layers):
@@ -206,3 +208,16 @@ def test_reordering_layers(qtbot):
     assert view.vbox_layout.count() == 2 * (len(layers) + 1)
     assert check_layout_layers(view.vbox_layout, layers)
     assert check_layout_dividers(view.vbox_layout, len(layers))
+
+
+def test_hex_to_name_is_updated():
+    fail_msg = (
+        "If this test fails then vispy have probably updated their color dictionary, located "
+        "in vispy.color.get_color_dict. This not necessarily a bad thing, but make sure that "
+        "nothing terrible has happened due to this change."
+    )
+    new_hex_to_name = {
+        f"{v.lower()}ff": k for k, v in get_color_dict().items()
+    }
+    new_hex_to_name["#00000000"] = 'transparent'
+    assert new_hex_to_name == hex_to_name, fail_msg

napari/_vispy/vispy_points_layer.py

@@ -2,6 +2,7 @@
 from vispy.scene.visuals import Line, Compound
 from .markers import Markers
 from vispy.visuals.transforms import ChainTransform
+
 from .vispy_base_layer import VispyBaseLayer
 
 
@@ -51,15 +52,11 @@ def _on_data_change(self, event=None):
             self._on_highlight_change()
 
         if len(self.layer._data_view) > 0:
-            edge_color = [
-                self.layer.edge_color[i] for i in self.layer._indices_view
-            ]
-            face_color = [
-                self.layer.face_color[i] for i in self.layer._indices_view
-            ]
+            edge_color = self.layer.edge_color[self.layer._indices_view]
+            face_color = self.layer.face_color[self.layer._indices_view]
         else:
-            edge_color = 'white'
-            face_color = 'white'
+            edge_color = np.array([[0.0, 0.0, 0.0, 1.0]], dtype=np.float32)
+            face_color = np.array([[1.0, 1.0, 1.0, 1.0]], dtype=np.float32)
 
         # Set vispy data, noting that the order of the points needs to be
         # reversed to make the most recently added point appear on top
@@ -97,14 +94,13 @@ def _on_highlight_change(self, event=None):
             if data.ndim == 1:
                 data = np.expand_dims(data, axis=0)
             size = self.layer._size_view[self.layer._highlight_index]
-            face_color = [
-                self.layer.face_color[i]
-                for i in self.layer._indices_view[self.layer._highlight_index]
+            face_color = self.layer.face_color[
+                self.layer._indices_view[self.layer._highlight_index]
             ]
         else:
             data = np.zeros((1, self.layer.dims.ndisplay))
             size = 0
-            face_color = 'white'
+            face_color = np.array([[1.0, 1.0, 1.0, 1.0]], dtype=np.float32)
 
         self.node._subvisuals[1].set_data(
             data[:, ::-1] + 0.5,

napari/components/tests/test_multichannel.py

@@ -1,7 +1,8 @@
 import numpy as np
 import dask.array as da
 from napari.components import ViewerModel
-from napari.utils import colormaps
+from napari.utils.colormaps import colormaps
+
 
 base_colormaps = colormaps.CYMRGB
 two_colormaps = colormaps.MAGENTA_GREEN

napari/components/viewer_model.py

@@ -1,8 +1,9 @@
-import numpy as np
 from math import inf
 import itertools
 from xml.etree.ElementTree import Element, tostring
 
+import numpy as np
+
 from .dims import Dims
 from .layerlist import LayerList
 from .. import layers
@@ -616,10 +617,10 @@ def add_points(
             broadcastable to the same shape as the data.
         edge_width : float
             Width of the symbol edge in pixels.
-        edge_color : str
-            Color of the point marker border.
-        face_color : str
-            Color of the point marker body.
+        edge_color : str, array-like
+            Color of the point marker border. Numeric color values should be RGB(A).
+        face_color : str, array-like
+            Color of the point marker body. Numeric color values should be RGB(A).
         n_dimensional : bool
             If True, renders points not just in central plane but also in all
             n-dimensions according to specified point marker size.

napari/layers/labels/tests/test_label_utils.py

@@ -5,10 +5,10 @@
 
 def test_interpolate_coordinates():
     # test when number of interpolated points > 1
-    old_coord = np.asarray([0, 1])
-    new_coord = np.asarray([0, 10])
+    old_coord = np.array([0, 1])
+    new_coord = np.array([0, 10])
     coords = interpolate_coordinates(old_coord, new_coord, brush_size=3)
-    expected_coords = np.asarray(
+    expected_coords = np.array(
         [
             [0, 1.75],
             [0, 2.5],