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Commit251d333

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Merge pull request#242 from p-j-smith/feat/hist-bin-params
Add widgets for setting histogram bins
2 parents0501fab +8fe7c7f commit251d333

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4 files changed

+96
-11
lines changed

4 files changed

+96
-11
lines changed

‎docs/changelog.rst‎

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Original file line numberDiff line numberDiff line change
@@ -1,6 +1,12 @@
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Changelog
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=========
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4+
2.1.0
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-----
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New features
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~~~~~~~~~~~~
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- Added a GUI element to manually set the number of bins in the histogram widgets.
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2.0.3
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-----
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Bug fixes

‎src/napari_matplotlib/histogram.py‎

Lines changed: 76 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,10 @@
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fromnapari.layers._multiscale_dataimportMultiScaleData
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fromqtpy.QtWidgetsimport (
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QComboBox,
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QFormLayout,
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QGroupBox,
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QLabel,
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QSpinBox,
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QVBoxLayout,
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QWidget,
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)
@@ -22,15 +25,32 @@
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_COLORS= {"r":"tab:red","g":"tab:green","b":"tab:blue"}
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25-
def_get_bins(data:npt.NDArray[Any])->npt.NDArray[Any]:
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def_get_bins(
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data:npt.NDArray[Any],
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num_bins:int=100,
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)->npt.NDArray[Any]:
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"""Create evenly spaced bins with a given interval.
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Parameters
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----------
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data : napari.layers.Layer.data
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Napari layer data.
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num_bins : integer, optional
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Number of evenly-spaced bins to create. Defaults to 100.
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Returns
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-------
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bin_edges : numpy.ndarray
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Array of evenly spaced bin edges.
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"""
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ifdata.dtype.kindin {"i","u"}:
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# Make sure integer data types have integer sized bins
28-
step=np.ceil(np.ptp(data)/100)
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step=np.ceil(np.ptp(data)/num_bins)
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returnnp.arange(np.min(data),np.max(data)+step,step)
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else:
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# For other data types, just have 100 evenly spaced bins
32-
# (and101 bin edges)
33-
returnnp.linspace(np.min(data),np.max(data),101)
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# For other data types we can use exactly `num_bins` bins
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# (and`num_bins` + 1 bin edges)
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returnnp.linspace(np.min(data),np.max(data),num_bins+1)
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classHistogramWidget(SingleAxesWidget):
@@ -47,6 +67,30 @@ def __init__(
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parent:QWidget|None=None,
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):
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super().__init__(napari_viewer,parent=parent)
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num_bins_widget=QSpinBox()
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num_bins_widget.setRange(1,100_000)
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num_bins_widget.setValue(101)
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num_bins_widget.setWrapping(False)
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num_bins_widget.setKeyboardTracking(False)
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# Set bins widget layout
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bins_selection_layout=QFormLayout()
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bins_selection_layout.addRow("num bins",num_bins_widget)
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# Group the widgets and add to main layout
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params_widget_group=QGroupBox("Params")
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params_widget_group_layout=QVBoxLayout()
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params_widget_group_layout.addLayout(bins_selection_layout)
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params_widget_group.setLayout(params_widget_group_layout)
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self.layout().addWidget(params_widget_group)
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# Add callbacks
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num_bins_widget.valueChanged.connect(self._draw)
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# Store widgets for later usage
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self.num_bins_widget=num_bins_widget
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self._update_layers(None)
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self.viewer.events.theme.connect(self._on_napari_theme_changed)
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@@ -60,6 +104,13 @@ def on_update_layers(self) -> None:
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self._update_contrast_lims
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)
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ifnotself.layers:
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return
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# Reset the num bins based on new layer data
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layer_data=self._get_layer_data(self.layers[0])
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self._set_widget_nums_bins(data=layer_data)
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def_update_contrast_lims(self)->None:
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forlim,lineinzip(
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self.layers[0].contrast_limits,self._contrast_lines,strict=False
@@ -68,11 +119,13 @@ def _update_contrast_lims(self) -> None:
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self.figure.canvas.draw()
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71-
defdraw(self)->None:
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"""
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Clear the axes and histogram the currently selected layer/slice.
74-
"""
75-
layer:Image=self.layers[0]
122+
def_set_widget_nums_bins(self,data:npt.NDArray[Any])->None:
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"""Update num_bins widget with bins determined from the image data"""
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bins=_get_bins(data)
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self.num_bins_widget.setValue(bins.size-1)
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def_get_layer_data(self,layer:napari.layers.Layer)->npt.NDArray[Any]:
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"""Get the data associated with a given layer"""
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data=layer.data
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78131
ifisinstance(layer.data,MultiScaleData):
@@ -87,9 +140,21 @@ def draw(self) -> None:
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# Read data into memory if it's a dask array
88141
data=np.asarray(data)
89142

143+
returndata
144+
145+
defdraw(self)->None:
146+
"""
147+
Clear the axes and histogram the currently selected layer/slice.
148+
"""
149+
layer:Image=self.layers[0]
150+
data=self._get_layer_data(layer)
151+
90152
# Important to calculate bins after slicing 3D data, to avoid reading
91153
# whole cube into memory.
92-
bins=_get_bins(data)
154+
bins=_get_bins(
155+
data,
156+
num_bins=self.num_bins_widget.value(),
157+
)
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94159
iflayer.rgb:
95160
# Histogram RGB channels independently
19.4 KB
Loading

‎src/napari_matplotlib/tests/test_histogram.py‎

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Original file line numberDiff line numberDiff line change
@@ -10,6 +10,20 @@
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)
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13+
@pytest.mark.mpl_image_compare
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deftest_histogram_2D_bins(make_napari_viewer,astronaut_data):
15+
viewer=make_napari_viewer()
16+
viewer.theme="light"
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viewer.add_image(astronaut_data[0],**astronaut_data[1])
18+
widget=HistogramWidget(viewer)
19+
viewer.window.add_dock_widget(widget)
20+
widget.num_bins_widget.setValue(25)
21+
fig=widget.figure
22+
# Need to return a copy, as original figure is too eagerley garbage
23+
# collected by the widget
24+
returndeepcopy(fig)
25+
26+
1327
@pytest.mark.mpl_image_compare
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deftest_histogram_2D(make_napari_viewer,astronaut_data):
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viewer=make_napari_viewer()

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