diff --git a/docs/changelog.rst b/docs/changelog.rst
index 54e6bba..60dd72b 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -1,6 +1,12 @@
Changelog
=========
+2.1.0
+-----
+New features
+~~~~~~~~~~~~
+- Added a GUI element to manually set the number of bins in the histogram widgets.
+
2.0.3
-----
Bug fixes
diff --git a/src/napari_matplotlib/histogram.py b/src/napari_matplotlib/histogram.py
index 2881cf7..acdd840 100644
--- a/src/napari_matplotlib/histogram.py
+++ b/src/napari_matplotlib/histogram.py
@@ -8,7 +8,10 @@
from napari.layers._multiscale_data import MultiScaleData
from qtpy.QtWidgets import (
QComboBox,
+ QFormLayout,
+ QGroupBox,
QLabel,
+ QSpinBox,
QVBoxLayout,
QWidget,
)
@@ -22,15 +25,32 @@
_COLORS = {"r": "tab:red", "g": "tab:green", "b": "tab:blue"}
-def _get_bins(data: npt.NDArray[Any]) -> npt.NDArray[Any]:
+def _get_bins(
+ data: npt.NDArray[Any],
+ num_bins: int = 100,
+) -> npt.NDArray[Any]:
+ """Create evenly spaced bins with a given interval.
+
+ Parameters
+ ----------
+ data : napari.layers.Layer.data
+ Napari layer data.
+ num_bins : integer, optional
+ Number of evenly-spaced bins to create. Defaults to 100.
+
+ Returns
+ -------
+ bin_edges : numpy.ndarray
+ Array of evenly spaced bin edges.
+ """
if data.dtype.kind in {"i", "u"}:
# Make sure integer data types have integer sized bins
- step = np.ceil(np.ptp(data) / 100)
+ step = np.ceil(np.ptp(data) / num_bins)
return np.arange(np.min(data), np.max(data) + step, step)
else:
- # For other data types, just have 100 evenly spaced bins
- # (and 101 bin edges)
- return np.linspace(np.min(data), np.max(data), 101)
+ # For other data types we can use exactly `num_bins` bins
+ # (and `num_bins` + 1 bin edges)
+ return np.linspace(np.min(data), np.max(data), num_bins + 1)
class HistogramWidget(SingleAxesWidget):
@@ -47,6 +67,30 @@ def __init__(
parent: QWidget | None = None,
):
super().__init__(napari_viewer, parent=parent)
+
+ num_bins_widget = QSpinBox()
+ num_bins_widget.setRange(1, 100_000)
+ num_bins_widget.setValue(101)
+ num_bins_widget.setWrapping(False)
+ num_bins_widget.setKeyboardTracking(False)
+
+ # Set bins widget layout
+ bins_selection_layout = QFormLayout()
+ bins_selection_layout.addRow("num bins", num_bins_widget)
+
+ # Group the widgets and add to main layout
+ params_widget_group = QGroupBox("Params")
+ params_widget_group_layout = QVBoxLayout()
+ params_widget_group_layout.addLayout(bins_selection_layout)
+ params_widget_group.setLayout(params_widget_group_layout)
+ self.layout().addWidget(params_widget_group)
+
+ # Add callbacks
+ num_bins_widget.valueChanged.connect(self._draw)
+
+ # Store widgets for later usage
+ self.num_bins_widget = num_bins_widget
+
self._update_layers(None)
self.viewer.events.theme.connect(self._on_napari_theme_changed)
@@ -60,6 +104,13 @@ def on_update_layers(self) -> None:
self._update_contrast_lims
)
+ if not self.layers:
+ return
+
+ # Reset the num bins based on new layer data
+ layer_data = self._get_layer_data(self.layers[0])
+ self._set_widget_nums_bins(data=layer_data)
+
def _update_contrast_lims(self) -> None:
for lim, line in zip(
self.layers[0].contrast_limits, self._contrast_lines, strict=False
@@ -68,11 +119,13 @@ def _update_contrast_lims(self) -> None:
self.figure.canvas.draw()
- def draw(self) -> None:
- """
- Clear the axes and histogram the currently selected layer/slice.
- """
- layer: Image = self.layers[0]
+ def _set_widget_nums_bins(self, data: npt.NDArray[Any]) -> None:
+ """Update num_bins widget with bins determined from the image data"""
+ bins = _get_bins(data)
+ self.num_bins_widget.setValue(bins.size - 1)
+
+ def _get_layer_data(self, layer: napari.layers.Layer) -> npt.NDArray[Any]:
+ """Get the data associated with a given layer"""
data = layer.data
if isinstance(layer.data, MultiScaleData):
@@ -87,9 +140,21 @@ def draw(self) -> None:
# Read data into memory if it's a dask array
data = np.asarray(data)
+ return data
+
+ def draw(self) -> None:
+ """
+ Clear the axes and histogram the currently selected layer/slice.
+ """
+ layer: Image = self.layers[0]
+ data = self._get_layer_data(layer)
+
# Important to calculate bins after slicing 3D data, to avoid reading
# whole cube into memory.
- bins = _get_bins(data)
+ bins = _get_bins(
+ data,
+ num_bins=self.num_bins_widget.value(),
+ )
if layer.rgb:
# Histogram RGB channels independently
diff --git a/src/napari_matplotlib/tests/baseline/test_histogram_2D_bins.png b/src/napari_matplotlib/tests/baseline/test_histogram_2D_bins.png
new file mode 100644
index 0000000..98e3cde
Binary files /dev/null and b/src/napari_matplotlib/tests/baseline/test_histogram_2D_bins.png differ
diff --git a/src/napari_matplotlib/tests/test_histogram.py b/src/napari_matplotlib/tests/test_histogram.py
index 1ceca51..435973b 100644
--- a/src/napari_matplotlib/tests/test_histogram.py
+++ b/src/napari_matplotlib/tests/test_histogram.py
@@ -10,6 +10,20 @@
)
+@pytest.mark.mpl_image_compare
+def test_histogram_2D_bins(make_napari_viewer, astronaut_data):
+ viewer = make_napari_viewer()
+ viewer.theme = "light"
+ viewer.add_image(astronaut_data[0], **astronaut_data[1])
+ widget = HistogramWidget(viewer)
+ viewer.window.add_dock_widget(widget)
+ widget.num_bins_widget.setValue(25)
+ fig = widget.figure
+ # Need to return a copy, as original figure is too eagerley garbage
+ # collected by the widget
+ return deepcopy(fig)
+
+
@pytest.mark.mpl_image_compare
def test_histogram_2D(make_napari_viewer, astronaut_data):
viewer = make_napari_viewer()
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