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[ENH] Heatmap: option to center color palette at 0 #4218

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Nov 29, 2019
Merged

[ENH] Heatmap: option to center color palette at 0 #4218

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33 changes: 24 additions & 9 deletions Orange/widgets/visualize/owheatmap.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -118,9 +118,12 @@ def color_palette_table(colors,
return np.c_[r, g, b]


def levels_with_thresholds(low, high, threshold_low, threshold_high):
def levels_with_thresholds(low, high, threshold_low, threshold_high, center_palette):
lt = low + (high - low) * threshold_low
ht = low + (high - low) * threshold_high
if center_palette:
ht = max(abs(lt), abs(ht))
lt = -max(abs(lt), abs(ht))
return lt, ht


Expand Down Expand Up @@ -317,6 +320,8 @@ class Outputs:
selected_data = Output("Selected Data", Table, default=True)
annotated_data = Output(ANNOTATED_DATA_SIGNAL_NAME, Table)

settings_version = 2

settingsHandler = settings.DomainContextHandler()

NoPosition, PositionTop, PositionBottom = 0, 1, 2
Expand All @@ -327,6 +332,7 @@ class Outputs:
gamma = settings.Setting(0)
threshold_low = settings.Setting(0.0)
threshold_high = settings.Setting(1.0)
center_palette = settings.Setting(False)

merge_kmeans = settings.Setting(False)
merge_kmeans_k = settings.Setting(50)
Expand Down Expand Up @@ -447,6 +453,9 @@ def __init__(self):

colorbox.layout().addLayout(form)

gui.checkBox(colorbox, self, 'center_palette', 'Center colors at 0',
callback=self.update_color_schema)

mergebox = gui.vBox(self.controlArea, "Merge",)
gui.checkBox(mergebox, self, "merge_kmeans", "Merge by k-means",
callback=self.update_sorting_examples)
Expand Down Expand Up @@ -982,7 +991,7 @@ def setup_scene(self, parts, data):

hw.set_levels(parts.levels)
hw.set_thresholds(self.threshold_low, self.threshold_high)
hw.set_color_table(palette)
hw.set_color_table(palette, self.center_palette)
hw.set_show_averages(self.averages)
hw.set_heatmap_data(X_part)

Expand Down Expand Up @@ -1057,7 +1066,7 @@ def setup_scene(self, parts, data):
parts.levels[0], parts.levels[1], self.threshold_low, self.threshold_high,
parent=widget)

legend.set_color_table(palette)
legend.set_color_table(palette, self.center_palette)
legend.setMinimumSize(QSizeF(100, 20))
legend.setVisible(self.legend)

Expand Down Expand Up @@ -1318,11 +1327,11 @@ def update_color_schema(self):
palette = self.color_palette()
for heatmap in self.heatmap_widgets():
heatmap.set_thresholds(self.threshold_low, self.threshold_high)
heatmap.set_color_table(palette)
heatmap.set_color_table(palette, self.center_palette)

for legend in self.legend_widgets():
legend.set_thresholds(self.threshold_low, self.threshold_high)
legend.set_color_table(palette)
legend.set_color_table(palette, self.center_palette)

def update_sorting_examples(self):
self.update_heatmaps()
Expand Down Expand Up @@ -1601,6 +1610,7 @@ def __init__(self, parent=None, data=None, **kwargs):

self.__levels = None
self.__threshold_low, self.__threshold_high = 0., 1.
self.__center_palette = False
self.__colortable = None
self.__data = data

Expand Down Expand Up @@ -1677,8 +1687,9 @@ def set_show_averages(self, show):
self.layout().invalidate()
self.update()

def set_color_table(self, table):
def set_color_table(self, table, center):
self.__colortable = table
self.__center_palette = center
self._update_pixmap()
self.update()

Expand All @@ -1699,7 +1710,8 @@ def _update_pixmap(self):
lut = None

ll, lh = self.__levels
ll, lh = levels_with_thresholds(ll, lh, self.__threshold_low, self.__threshold_high)
ll, lh = levels_with_thresholds(ll, lh, self.__threshold_low, self.__threshold_high,
self.__center_palette)

argb, _ = pg.makeARGB(
self.__data, lut=lut, levels=(ll, lh))
Expand Down Expand Up @@ -2058,6 +2070,7 @@ def __init__(self, low, high, threshold_low, threshold_high, parent=None):
self.high = high
self.threshold_low = threshold_low
self.threshold_high = threshold_high
self.center_palette = False
self.color_table = None

layout = QGraphicsLinearLayout(Qt.Vertical)
Expand All @@ -2084,8 +2097,9 @@ def __init__(self, low, high, threshold_low, threshold_high, parent=None):
layout.addItem(self.__pixitem)
self.__update()

def set_color_table(self, color_table):
def set_color_table(self, color_table, center):
self.color_table = color_table
self.center_palette = center
self.__update()

def set_thresholds(self, threshold_low, threshold_high):
Expand All @@ -2097,7 +2111,8 @@ def __update(self):
data = np.linspace(self.low, self.high, num=1000)
data = data.reshape((1, -1))
ll, lh = levels_with_thresholds(self.low, self.high,
self.threshold_low, self.threshold_high)
self.threshold_low, self.threshold_high,
self.center_palette)
argb, _ = pg.makeARGB(data, lut=self.color_table,
levels=(ll, lh))
qimg = pg.makeQImage(argb, transpose=False)
Expand Down
36 changes: 32 additions & 4 deletions Orange/widgets/visualize/tests/test_owheatmap.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,14 @@
from Orange.widgets.tests.base import WidgetTest, WidgetOutputsTestMixin, datasets


def image_row_colors(image):
colors = np.full((image.height(), 3), np.nan)
for r in range(image.height()):
c = image.pixelColor(0, r)
colors[r] = c.red(), c.green(), c.blue()
return colors


class TestOWHeatMap(WidgetTest, WidgetOutputsTestMixin):
@classmethod
def setUpClass(cls):
Expand Down Expand Up @@ -164,10 +172,7 @@ def test_use_enough_colors(self):
self.widget.update_color_schema()
heatmap_widget = self.widget.heatmap_widget_grid[0][0]
image = heatmap_widget.heatmap_item.pixmap().toImage()
colors = np.full((len(data), 3), np.nan)
for r in range(len(data)):
c = image.pixelColor(0, r)
colors[r] = c.red(), c.green(), c.blue()
colors = image_row_colors(image)
unique_colors = len(np.unique(colors, axis=0))
self.assertLessEqual(len(data)*self.widget.threshold_low, unique_colors)

Expand Down Expand Up @@ -209,6 +214,29 @@ def test_set_split_var(self):
self.assertIs(w.split_by_var, None)
self.assertEqual(len(w.heatmapparts.rows), 1)

def test_center_palette(self):
data = np.arange(2).reshape(-1, 1)
table = Table.from_numpy(Domain([ContinuousVariable("y")]), data)
self.send_signal(self.widget.Inputs.data, table)

cb_model = self.widget.color_cb.model()
ind = cb_model.indexFromItem(cb_model.findItems("Green-Black-Red")[0]).row()
self.widget.palette_index = ind

desired_uncentered = [[0, 255, 0],
[255, 0, 0]]

desired_centered = [[0, 0, 0],
[255, 0, 0]]

for center, desired in [(False, desired_uncentered), (True, desired_centered)]:
self.widget.center_palette = center
self.widget.update_color_schema()
heatmap_widget = self.widget.heatmap_widget_grid[0][0]
image = heatmap_widget.heatmap_item.pixmap().toImage()
colors = image_row_colors(image)
np.testing.assert_almost_equal(colors, desired)


if __name__ == "__main__":
unittest.main()