Merge pull request #29 from matplotlib/slice

Add SliceSelector

Author: dstansby

examples/slice.py

@@ -0,0 +1,15 @@
+"""
+1D slices
+=========
+"""
+import napari
+
+viewer = napari.Viewer()
+viewer.open_sample("napari", "kidney")
+
+viewer.window.add_plugin_dock_widget(
+    plugin_name="napari-matplotlib", widget_name="1D slice"
+)
+
+if __name__ == "__main__":
+    napari.run()

src/napari_matplotlib/__init__.py

@@ -6,3 +6,4 @@
 
 from .histogram import *  # NoQA
 from .scatter import *  # NoQA
+from .slice import *  # NoQA

src/napari_matplotlib/base.py

@@ -83,7 +83,7 @@ def setup_callbacks(self) -> None:
 
     def update_layers(self, event: napari.utils.events.Event) -> None:
         """
-        Update the currently selected layers and re-draw.
+        Update the layers attribute with currently selected layers and re-draw.
         """
         self.layers = list(self.viewer.layers.selection)
         self._draw()

src/napari_matplotlib/napari.yaml

@@ -10,9 +10,16 @@ contributions:
       python_name: napari_matplotlib:ScatterWidget
       title: Make a scatter plot
 
+    - id: napari-matplotlib.slice
+      python_name: napari_matplotlib:SliceWidget
+      title: Plot a 1D slice
+
   widgets:
     - command: napari-matplotlib.histogram
       display_name: Histogram
 
     - command: napari-matplotlib.scatter
       display_name: Scatter
+
+    - command: napari-matplotlib.slice
+      display_name: 1D slice

src/napari_matplotlib/slice.py

@@ -0,0 +1,118 @@
+from typing import Dict, Tuple
+
+import napari
+import numpy as np
+from qtpy.QtWidgets import QComboBox, QHBoxLayout, QLabel, QSpinBox
+
+from napari_matplotlib.base import NapariMPLWidget
+
+__all__ = ["SliceWidget"]
+
+_dims_sel = ["x", "y"]
+_dims = ["x", "y", "z"]
+
+
+class SliceWidget(NapariMPLWidget):
+    """
+    Plot a 1D slice along a given dimension.
+    """
+
+    n_layers_input = 1
+
+    def __init__(self, napari_viewer: napari.viewer.Viewer):
+        # Setup figure/axes
+        super().__init__(napari_viewer)
+        self.axes = self.canvas.figure.subplots()
+
+        button_layout = QHBoxLayout()
+        self.layout().addLayout(button_layout)
+
+        self.dim_selector = QComboBox()
+        button_layout.addWidget(QLabel("Slice axis:"))
+        button_layout.addWidget(self.dim_selector)
+        self.dim_selector.addItems(_dims)
+
+        self.slice_selectors = {}
+        for d in _dims_sel:
+            self.slice_selectors[d] = QSpinBox()
+            button_layout.addWidget(QLabel(f"{d}:"))
+            button_layout.addWidget(self.slice_selectors[d])
+
+        # Setup callbacks
+        # Re-draw when any of the combon/spin boxes are updated
+        self.dim_selector.currentTextChanged.connect(self._draw)
+        for d in _dims_sel:
+            self.slice_selectors[d].textChanged.connect(self._draw)
+
+        self.update_layers(None)
+
+    @property
+    def layer(self):
+        return self.layers[0]
+
+    @property
+    def current_dim(self) -> str:
+        """
+        Currently selected slice dimension.
+        """
+        return self.dim_selector.currentText()
+
+    @property
+    def current_dim_index(self) -> int:
+        """
+        Currently selected slice dimension index.
+        """
+        # Note the reversed list because in napari the z-axis is the first
+        # numpy axis
+        return _dims[::-1].index(self.current_dim)
+
+    @property
+    def selector_values(self) -> Dict[str, int]:
+        return {d: self.slice_selectors[d].value() for d in _dims_sel}
+
+    def update_slice_selectors(self) -> None:
+        """
+        Update range and enabled status of the slice selectors, and the value
+        of the z slice selector.
+        """
+        # Update min/max
+        for i, dim in enumerate(_dims_sel):
+            self.slice_selectors[dim].setRange(0, self.layer.data.shape[i])
+
+    def get_xy(self) -> Tuple[np.ndarray, np.ndarray]:
+        """
+        Get data for plotting.
+        """
+        x = np.arange(self.layer.data.shape[self.current_dim_index])
+
+        vals = self.selector_values
+        vals.update({"z": self.current_z})
+
+        slices = []
+        for d in _dims:
+            if d == self.current_dim:
+                # Select all data along this axis
+                slices.append(slice(None))
+            else:
+                # Select specific index
+                val = vals[d]
+                slices.append(slice(val, val + 1))
+
+        # Reverse since z is the first axis in napari
+        slices = slices[::-1]
+        y = self.layer.data[tuple(slices)].ravel()
+
+        return x, y
+
+    def clear(self) -> None:
+        self.axes.cla()
+
+    def draw(self) -> None:
+        """
+        Clear axes and draw a 1D plot.
+        """
+        x, y = self.get_xy()
+
+        self.axes.plot(x, y)
+        self.axes.set_xlabel(self.current_dim)
+        self.axes.set_title(self.layer.name)

src/napari_matplotlib/tests/test_slice.py

@@ -0,0 +1,10 @@
+import numpy as np
+
+from napari_matplotlib import SliceWidget
+
+
+def test_scatter(make_napari_viewer):
+    # Smoke test adding a histogram widget
+    viewer = make_napari_viewer()
+    viewer.add_image(np.random.random((100, 100, 100)))
+    SliceWidget(viewer)