RF: Handle overlay in .orthoview()

Author: rmarkello

nibabel/spatialimages.py

@@ -589,9 +589,14 @@ def __getitem__(self, idx):
             "slicing image array data with `img.dataobj[slice]` or "
             "`img.get_fdata()[slice]`")
 
-    def orthoview(self):
+    def orthoview(self, overlay=None, **kwargs):
         """Plot the image using OrthoSlicer3D
 
+        Parameters
+        ----------
+        overlay : ``spatialimage`` instance
+            Image to be plotted as overlay. Default: None
+
         Returns
         -------
         viewer : instance of OrthoSlicer3D
@@ -603,8 +608,12 @@ def orthoview(self):
         consider using viewer.show() (equivalently plt.show()) to show
         the figure.
         """
-        return OrthoSlicer3D(self.dataobj, self.affine,
-                             title=self.get_filename())
+        ortho = OrthoSlicer3D(self.dataobj, self.affine,
+                              title=self.get_filename())
+        if overlay is not None:
+            ortho.set_overlay(overlay, **kwargs)
+
+        return ortho
 
     def as_reoriented(self, ornt):
         """Apply an orientation change and return a new image

nibabel/viewers.py

@@ -332,7 +332,29 @@ def alpha(self, alpha):
         self._alpha = alpha
         self.draw()
 
-    def set_overlay(self, data, affine=None, threshold=None, cmap='viridis'):
+    def set_overlay(self, data, affine=None, threshold=None, cmap='viridis',
+                    alpha=0.7):
+        """ Sets `data` as overlay for currently plotted image
+
+        Parameters
+        ----------
+        data : array-like
+            The data that will be overlayed on the slicer. Should have 3+
+            dimensions.
+        affine : array-like or None, optional
+            Affine transform for the provided data. This is used to determine
+            how the data should be sliced for plotting into the sagittal,
+            coronal, and axial view axes. If this does not match the currently
+            plotted slicer the provided data will be resampled.
+        threshold : float or None, optional
+            Threshold for overlay data; values below this threshold will not
+            be displayed. Default: None
+        cmap : str, optional
+            The Colormap instance or registered colormap name used to map
+            scalar data to colors. Default: 'viridis'
+        alpha : [0, 1] float, optional
+            Set the alpha value used for blending. Default: 0.7
+        """
         if affine is None:
             try:  # did we get an image?
                 affine = data.affine
@@ -385,8 +407,7 @@ def set_overlay(self, data, affine=None, threshold=None, cmap='viridis'):
 
         # set transparency and new cmap
         self._overlay.cmap = cmap
-        for im in self._overlay._ims:
-            im.set_alpha(0.7)
+        self._overlay.alpha = alpha
 
         # no double cross-hairs (they get confused when we have linked orthos)
         for cross in self._overlay._crosshairs: