Enable histogram

pyproject.toml

@@ -40,7 +40,7 @@ dependencies = [
     "napari-skimage-regionprops>=0.3.1",
     "scikit-image",
     "scipy",
-    "biaplotter>=0.1.0"
+    "biaplotter>=0.2.0"
 ]
 
 

src/napari_clusters_plotter/_new_plotter_widget.py

@@ -4,9 +4,12 @@
 import napari
 import numpy as np
 import pandas as pd
-from biaplotter.plotter import ArtistType, CanvasWidget
+from biaplotter.plotter import CanvasWidget
 from matplotlib.pyplot import cm as plt_colormaps
-from nap_plot_tools.cmap import cat10_mod_cmap
+from nap_plot_tools.cmap import (
+    cat10_mod_cmap,
+    cat10_mod_cmap_first_transparent,
+)
 from napari.utils.colormaps import ALL_COLORMAPS
 from qtpy import uic
 from qtpy.QtCore import Qt, Signal
@@ -17,7 +20,7 @@
 
 
 class PlottingType(Enum):
-    HISTOGRAM = auto()
+    HISTOGRAM2D = auto()
     SCATTER = auto()
 
 
@@ -41,6 +44,15 @@ def __init__(self, napari_viewer):
 
         self.plot_needs_update.connect(self._replot)
 
+        # Colormap reference to be indexed like this:
+        # reference[is_categorical, plot_type]
+        self.colormap_reference = {
+            (True, "HISTOGRAM2D"): cat10_mod_cmap_first_transparent,
+            (True, "SCATTER"): cat10_mod_cmap,
+            (False, "HISTOGRAM2D"): plt_colormaps.magma,
+            (False, "SCATTER"): plt_colormaps.magma,
+        }
+
     def _setup_ui(self, napari_viewer):
         """
         Helper function to set up the UI of the widget.
@@ -60,9 +72,7 @@ def _setup_ui(self, napari_viewer):
         self.layout.setAlignment(Qt.AlignTop)
 
         self.plotting_widget = CanvasWidget(napari_viewer, self)
-        self.plotting_widget.active_artist = self.plotting_widget.artists[
-            ArtistType.SCATTER
-        ]
+        self.plotting_widget.active_artist = "SCATTER"
 
         # Add plot and options as widgets
         self.layout.addWidget(self.plotting_widget)
@@ -71,9 +81,7 @@ def _setup_ui(self, napari_viewer):
         # Setting of Widget options
         self.hue: QComboBox = self.control_widget.hue_box
 
-        self.control_widget.plot_type_box.addItems(
-            [PlottingType.SCATTER.name, PlottingType.HISTOGRAM.name]
-        )
+        self.control_widget.plot_type_box.addItems(["SCATTER", "HISTOGRAM2D"])
 
         self.control_widget.cmap_box.addItems(list(ALL_COLORMAPS.keys()))
         self.control_widget.cmap_box.setCurrentIndex(
@@ -140,6 +148,11 @@ def _setup_callbacks(self):
         for selector in self.plotting_widget.selectors.values():
             selector.selection_applied_signal.connect(self._on_finish_draw)
 
+        # connect scatter/histogram switch
+        self.control_widget.plot_type_box.currentTextChanged.connect(
+            self._on_plot_type_changed
+        )
+
     def _on_finish_draw(self, color_indices: np.ndarray):
         """
         Called when user finsihes drawing. Will change the hue combo box to the
@@ -177,15 +190,11 @@ def _replot(self):
         x_data = features[self.x_axis].values
         y_data = features[self.y_axis].values
 
-        # check hue axis for categorical data
-        if self.hue_axis in self.categorical_columns:
-            self.plotting_widget.active_artist.overlay_colormap = (
-                cat10_mod_cmap
-            )
-        else:
-            self.plotting_widget.active_artist.overlay_colormap = (
-                plt_colormaps.magma
-            )
+        # select appropriate colormap for usecase
+        cmap = self.colormap_reference[
+            (self.hue_axis in self.categorical_columns, self.plotting_type)
+        ]
+        self.plotting_widget.active_artist.overlay_colormap = cmap
 
         # set the data and color indices in the active artist
         active_artist = self.plotting_widget.active_artist
@@ -219,25 +228,24 @@ def _on_frame_changed(self, event: napari.utils.events.Event):
             self.plotting_widget.active_artist.alpha = alpha
             self.plotting_widget.active_artist.size = size
 
-    def _checkbox_status_changed(self):
-        self._replot()
+    def _on_plot_type_changed(self):
+        """
+        Called when the plot type changes.
+        """
+        if self.plotting_type == PlottingType.HISTOGRAM2D.name:
+            self.plotting_widget.active_artist = "HISTOGRAM2D"
+            self.plotting_widget.active_artist.overlay_colormap = (
+                cat10_mod_cmap_first_transparent
+            )
 
-    def _plotting_type_changed(
-        self,
-    ):  # TODO NEED TO ADD WHICH VARIABLE STORES THE TYPE
-        if (
-            self.control_widget.plot_type_box.currentText()
-            == PlottingType.HISTOGRAM.name
-        ):
-            self.control_widget.bins_settings_container.setVisible(True)
-            self.control_widget.log_scale_container.setVisible(True)
-        elif (
-            self.control_widget.plot_type_box.currentText()
-            == PlottingType.SCATTER.name
-        ):
-            self.control_widget.bins_settings_container.setVisible(False)
-            self.control_widget.log_scale_container.setVisible(False)
+        elif self.plotting_type == PlottingType.SCATTER.name:
+            self.plotting_widget.active_artist = "SCATTER"
+            self.plotting_widget.active_artist.overlay_colormap = (
+                cat10_mod_cmap
+            )
+        self._replot()
 
+    def _checkbox_status_changed(self):
         self._replot()
 
     def _bin_number_set(self):
@@ -426,24 +434,21 @@ def _color_layer_by_value(self):
         """
 
         features = self._get_features()
-        color_indices = self.plotting_widget.active_artist.color_indices
-        norm = self.plotting_widget.active_artist._get_normalization(
-            color_indices
-        )
-        colors = self.plotting_widget.active_artist._get_rgba_colors(
-            color_indices, norm
+        active_artist = self.plotting_widget.active_artist
+        rgba_colors = active_artist.color_indices_to_rgba(
+            active_artist.color_indices
         )
 
         for selected_layer in self.viewer.layers.selection:
             layer_indices = features[
                 features["layer"] == selected_layer.name
             ].index
-            _apply_layer_color(selected_layer, colors[layer_indices])
+            _apply_layer_color(selected_layer, rgba_colors[layer_indices])
 
             # store latest cluster indeces in the features table
             if self.hue_axis == "MANUAL_CLUSTER_ID":
                 selected_layer.features["MANUAL_CLUSTER_ID"] = pd.Series(
-                    color_indices[layer_indices]
+                    active_artist.color_indices[layer_indices]
                 ).astype("category")
 
     def _reset(self):

src/napari_clusters_plotter/_tests/test_plotter.py

@@ -375,3 +375,36 @@ def test_temporal_highlighting(make_napari_viewer, create_sample_layers):
     # to highlight out-of and in-frame data points
     assert plotter_widget.plotting_widget.active_artist.alpha.min() == 0.25
     assert plotter_widget.plotting_widget.active_artist.size.min() == 35
+
+
+@pytest.mark.parametrize(
+    "create_sample_layers",
+    [
+        create_multi_point_layer,
+        create_multi_vectors_layer,
+        create_multi_surface_layer,
+        create_multi_shapes_layers,
+    ],
+)
+def test_histogram_support(make_napari_viewer, create_sample_layers):
+
+    from napari_clusters_plotter import PlotterWidget
+
+    viewer = make_napari_viewer()
+    layer, layer2 = create_sample_layers()
+
+    # add layers to viewer
+    viewer.add_layer(layer)
+    viewer.add_layer(layer2)
+    plotter_widget = PlotterWidget(viewer)
+    viewer.window.add_dock_widget(plotter_widget, area="right")
+
+    plotter_widget._selectors["x"].setCurrentText("feature3")
+    plotter_widget.plotting_type = "HISTOGRAM2D"
+
+    # select both layers
+    viewer.layers.selection.active = layer
+    assert "MANUAL_CLUSTER_ID" in layer.features.columns
+    assert "MANUAL_CLUSTER_ID" in layer2.features.columns
+
+    plotter_widget.plotting_type = "SCATTER"

src/napari_clusters_plotter/plotter_inputs.ui

@@ -211,7 +211,7 @@
           <item row="0" column="1">
            <widget class="QComboBox" name="plot_type_box">
             <property name="enabled">
-             <bool>false</bool>
+             <bool>true</bool>
             </property>
            </widget>
           </item>