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Commitdc1f3bb

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Merge pull request#148 from jo-mueller/add-feature-histogram
added a Feature Histogram Widget
2 parents3a8261a +e1ccfb1 commitdc1f3bb

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10 files changed

+231
-12
lines changed

10 files changed

+231
-12
lines changed

‎baseline/test_feature_histogram2.png

12.6 KB
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‎docs/changelog.rst

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,11 @@
11
Changelog
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=========
3-
1.0.3
3+
1.1.0
44
-----
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Additions
6+
~~~~~~~~~
7+
- Added a widget to draw a histogram of features.
8+
59
Changes
610
~~~~~~~
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- The slice widget is now limited to slicing along the x/y dimensions. Support

‎docs/user_guide.rst

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Original file line numberDiff line numberDiff line change
@@ -30,6 +30,7 @@ These widgets plot the data stored in the ``.features`` attribute of individual
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Currently available are:
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- 2D scatter plots of two features against each other.
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- Histograms of individual features.
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To use these:
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‎src/napari_matplotlib/features.py

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,9 @@
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fromnapari.layersimportLabels,Points,Shapes,Tracks,Vectors
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FEATURES_LAYER_TYPES= (
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Labels,
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Points,
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Shapes,
7+
Tracks,
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Vectors,
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)

‎src/napari_matplotlib/histogram.py

Lines changed: 114 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,15 @@
1-
fromtypingimportOptional
1+
fromtypingimportAny,List,Optional,Tuple
22

33
importnapari
44
importnumpyasnp
5-
fromqtpy.QtWidgetsimportQWidget
5+
importnumpy.typingasnpt
6+
fromqtpy.QtWidgetsimportQComboBox,QLabel,QVBoxLayout,QWidget
67

78
from .baseimportSingleAxesWidget
9+
from .featuresimportFEATURES_LAYER_TYPES
810
from .utilimportInterval
911

10-
__all__= ["HistogramWidget"]
12+
__all__= ["HistogramWidget","FeaturesHistogramWidget"]
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_COLORS= {"r":"tab:red","g":"tab:green","b":"tab:blue"}
1315

@@ -61,3 +63,112 @@ def draw(self) -> None:
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self.axes.hist(data.ravel(),bins=bins,label=layer.name)
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6365
self.axes.legend()
66+
67+
68+
classFeaturesHistogramWidget(SingleAxesWidget):
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"""
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Display a histogram of selected feature attached to selected layer.
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"""
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n_layers_input=Interval(1,1)
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# All layers that have a .features attributes
75+
input_layer_types=FEATURES_LAYER_TYPES
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77+
def__init__(
78+
self,
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napari_viewer:napari.viewer.Viewer,
80+
parent:Optional[QWidget]=None,
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):
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super().__init__(napari_viewer,parent=parent)
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84+
self.layout().addLayout(QVBoxLayout())
85+
self._key_selection_widget=QComboBox()
86+
self.layout().addWidget(QLabel("Key:"))
87+
self.layout().addWidget(self._key_selection_widget)
88+
89+
self._key_selection_widget.currentTextChanged.connect(
90+
self._set_axis_keys
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)
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self._update_layers(None)
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95+
@property
96+
defx_axis_key(self)->Optional[str]:
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"""Key to access x axis data from the FeaturesTable"""
98+
returnself._x_axis_key
99+
100+
@x_axis_key.setter
101+
defx_axis_key(self,key:Optional[str])->None:
102+
self._x_axis_key=key
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self._draw()
104+
105+
def_set_axis_keys(self,x_axis_key:str)->None:
106+
"""Set both axis keys and then redraw the plot"""
107+
self._x_axis_key=x_axis_key
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self._draw()
109+
110+
def_get_valid_axis_keys(self)->List[str]:
111+
"""
112+
Get the valid axis keys from the layer FeatureTable.
113+
114+
Returns
115+
-------
116+
axis_keys : List[str]
117+
The valid axis keys in the FeatureTable. If the table is empty
118+
or there isn't a table, returns an empty list.
119+
"""
120+
iflen(self.layers)==0ornot (hasattr(self.layers[0],"features")):
121+
return []
122+
else:
123+
returnself.layers[0].features.keys()
124+
125+
def_get_data(self)->Tuple[Optional[npt.NDArray[Any]],str]:
126+
"""Get the plot data.
127+
128+
Returns
129+
-------
130+
data : List[np.ndarray]
131+
List contains X and Y columns from the FeatureTable. Returns
132+
an empty array if nothing to plot.
133+
x_axis_name : str
134+
The title to display on the x axis. Returns
135+
an empty string if nothing to plot.
136+
"""
137+
ifnothasattr(self.layers[0],"features"):
138+
# if the selected layer doesn't have a featuretable,
139+
# skip draw
140+
returnNone,""
141+
142+
feature_table=self.layers[0].features
143+
144+
if (len(feature_table)==0)or (self.x_axis_keyisNone):
145+
returnNone,""
146+
147+
data=feature_table[self.x_axis_key]
148+
x_axis_name=self.x_axis_key.replace("_"," ")
149+
150+
returndata,x_axis_name
151+
152+
defon_update_layers(self)->None:
153+
"""
154+
Called when the layer selection changes by ``self.update_layers()``.
155+
"""
156+
# reset the axis keys
157+
self._x_axis_key=None
158+
159+
# Clear combobox
160+
self._key_selection_widget.clear()
161+
self._key_selection_widget.addItems(self._get_valid_axis_keys())
162+
163+
defdraw(self)->None:
164+
"""Clear the axes and histogram the currently selected layer/slice."""
165+
data,x_axis_name=self._get_data()
166+
167+
ifdataisNone:
168+
return
169+
170+
self.axes.hist(data,bins=50,edgecolor="white",linewidth=0.3)
171+
172+
# set ax labels
173+
self.axes.set_xlabel(x_axis_name)
174+
self.axes.set_ylabel("Counts [#]")

‎src/napari_matplotlib/napari.yaml

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Original file line numberDiff line numberDiff line change
@@ -14,6 +14,10 @@ contributions:
1414
python_name:napari_matplotlib:FeaturesScatterWidget
1515
title:Make a scatter plot of layer features
1616

17+
-id:napari-matplotlib.features_histogram
18+
python_name:napari_matplotlib:FeaturesHistogramWidget
19+
title:Plot feature histograms
20+
1721
-id:napari-matplotlib.slice
1822
python_name:napari_matplotlib:SliceWidget
1923
title:Plot a 1D slice
@@ -28,5 +32,8 @@ contributions:
2832
-command:napari-matplotlib.features_scatter
2933
display_name:FeaturesScatter
3034

35+
-command:napari-matplotlib.features_histogram
36+
display_name:FeaturesHistogram
37+
3138
-command:napari-matplotlib.slice
3239
display_name:1D slice

‎src/napari_matplotlib/scatter.py

Lines changed: 2 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,7 @@
55
fromqtpy.QtWidgetsimportQComboBox,QLabel,QVBoxLayout,QWidget
66

77
from .baseimportSingleAxesWidget
8+
from .featuresimportFEATURES_LAYER_TYPES
89
from .utilimportInterval
910

1011
__all__= ["ScatterBaseWidget","ScatterWidget","FeaturesScatterWidget"]
@@ -94,13 +95,7 @@ class FeaturesScatterWidget(ScatterBaseWidget):
9495

9596
n_layers_input=Interval(1,1)
9697
# All layers that have a .features attributes
97-
input_layer_types= (
98-
napari.layers.Labels,
99-
napari.layers.Points,
100-
napari.layers.Shapes,
101-
napari.layers.Tracks,
102-
napari.layers.Vectors,
103-
)
98+
input_layer_types=FEATURES_LAYER_TYPES
10499

105100
def__init__(
106101
self,

‎src/napari_matplotlib/tests/test_histogram.py

Lines changed: 93 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,13 @@
11
fromcopyimportdeepcopy
22

3+
importnumpyasnp
34
importpytest
45

5-
fromnapari_matplotlibimportHistogramWidget
6+
fromnapari_matplotlibimportFeaturesHistogramWidget,HistogramWidget
7+
fromnapari_matplotlib.tests.helpersimport (
8+
assert_figures_equal,
9+
assert_figures_not_equal,
10+
)
611

712

813
@pytest.mark.mpl_image_compare
@@ -28,3 +33,90 @@ def test_histogram_3D(make_napari_viewer, brain_data):
2833
# Need to return a copy, as original figure is too eagerley garbage
2934
# collected by the widget
3035
returndeepcopy(fig)
36+
37+
38+
deftest_feature_histogram(make_napari_viewer):
39+
n_points=1000
40+
random_points=np.random.random((n_points,3))*10
41+
feature1=np.random.random(n_points)
42+
feature2=np.random.normal(size=n_points)
43+
44+
viewer=make_napari_viewer()
45+
viewer.add_points(
46+
random_points,
47+
properties={"feature1":feature1,"feature2":feature2},
48+
name="points1",
49+
)
50+
viewer.add_points(
51+
random_points,
52+
properties={"feature1":feature1,"feature2":feature2},
53+
name="points2",
54+
)
55+
56+
widget=FeaturesHistogramWidget(viewer)
57+
viewer.window.add_dock_widget(widget)
58+
59+
# Check whether changing the selected key changes the plot
60+
widget._set_axis_keys("feature1")
61+
fig1=deepcopy(widget.figure)
62+
63+
widget._set_axis_keys("feature2")
64+
assert_figures_not_equal(widget.figure,fig1)
65+
66+
# check whether selecting a different layer produces the same plot
67+
viewer.layers.selection.clear()
68+
viewer.layers.selection.add(viewer.layers[1])
69+
assert_figures_equal(widget.figure,fig1)
70+
71+
72+
@pytest.mark.mpl_image_compare
73+
deftest_feature_histogram2(make_napari_viewer):
74+
importnumpyasnp
75+
76+
np.random.seed(0)
77+
n_points=1000
78+
random_points=np.random.random((n_points,3))*10
79+
feature1=np.random.random(n_points)
80+
feature2=np.random.normal(size=n_points)
81+
82+
viewer=make_napari_viewer()
83+
viewer.add_points(
84+
random_points,
85+
properties={"feature1":feature1,"feature2":feature2},
86+
name="points1",
87+
)
88+
viewer.add_points(
89+
random_points,
90+
properties={"feature1":feature1,"feature2":feature2},
91+
name="points2",
92+
)
93+
94+
widget=FeaturesHistogramWidget(viewer)
95+
viewer.window.add_dock_widget(widget)
96+
widget._set_axis_keys("feature1")
97+
98+
fig=FeaturesHistogramWidget(viewer).figure
99+
returndeepcopy(fig)
100+
101+
102+
deftest_change_layer(make_napari_viewer,brain_data,astronaut_data):
103+
viewer=make_napari_viewer()
104+
widget=HistogramWidget(viewer)
105+
106+
viewer.add_image(brain_data[0],**brain_data[1])
107+
viewer.add_image(astronaut_data[0],**astronaut_data[1])
108+
109+
# Select first layer
110+
viewer.layers.selection.clear()
111+
viewer.layers.selection.add(viewer.layers[0])
112+
fig1=deepcopy(widget.figure)
113+
114+
# Re-selecting first layer should produce identical plot
115+
viewer.layers.selection.clear()
116+
viewer.layers.selection.add(viewer.layers[0])
117+
assert_figures_equal(widget.figure,fig1)
118+
119+
# Plotting the second layer should produce a different plot
120+
viewer.layers.selection.clear()
121+
viewer.layers.selection.add(viewer.layers[1])
122+
assert_figures_not_equal(widget.figure,fig1)

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