ENH: Add manual value limits to OrthoSlicer3D

Pass kwargs to OrthoSlicer3D from SpatialImage.orthoview()

Author: effigies

nibabel/spatialimages.py

@@ -663,7 +663,7 @@ def __getitem__(self):
                         "array data with `img.dataobj[slice]` or "
                         "`img.get_data()[slice]`")
 
-    def orthoview(self):
+    def orthoview(self, **kwargs):
         """Plot the image using OrthoSlicer3D
 
         Returns
@@ -678,4 +678,4 @@ def orthoview(self):
         the figure.
         """
         return OrthoSlicer3D(self.dataobj, self.affine,
-                             title=self.get_filename())
+                             title=self.get_filename(), **kwargs)

nibabel/viewers.py

@@ -42,7 +42,7 @@ class OrthoSlicer3D(object):
     """
     # Skip doctest above b/c not all systems have mpl installed
 
-    def __init__(self, data, affine=None, axes=None, title=None):
+    def __init__(self, data, affine=None, axes=None, title=None, vlim=None):
         """
         Parameters
         ----------
@@ -61,6 +61,9 @@ def __init__(self, data, affine=None, axes=None, title=None):
         title : str or None, optional
             The title to display. Can be None (default) to display no
             title.
+        vlim : array-like or None, optional
+            Value limits to display image and time series. Can be None
+            (default) to derive limits from data.
         """
         # Use these late imports of matplotlib so that we have some hope that
         # the test functions are the first to set the matplotlib backend. The
@@ -90,7 +93,7 @@ def __init__(self, data, affine=None, axes=None, title=None):
         self._volume_dims = data.shape[3:]
         self._current_vol_data = data[:, :, :, 0] if data.ndim > 3 else data
         self._data = data
-        self._clim = np.percentile(data, (1., 99.))
+        self._clim = np.percentile(data, (1., 99.)) if vlim is None else vlim
         del data
 
         if axes is None:  # make the axes
@@ -183,8 +186,11 @@ def __init__(self, data, affine=None, axes=None, title=None):
             ax.set_xticks(np.unique(np.linspace(0, self.n_volumes - 1,
                                                 5).astype(int)))
             ax.set_xlim(x[0], x[-1])
-            yl = [self._data.min(), self._data.max()]
-            yl = [l + s * np.diff(lims)[0] for l, s in zip(yl, [-1.01, 1.01])]
+            if vlim is None:
+                yl = [self._data.min(), self._data.max()]
+                yl = [l + s * np.diff(lims)[0] for l, s in zip(yl, [-1.01, 1.01])]
+            else:
+                yl = vlim
             patch = mpl_patch.Rectangle([-0.5, yl[0]], 1., np.diff(yl)[0],
                                         fill=True, facecolor=(0, 1, 0),
                                         edgecolor=(0, 1, 0), alpha=0.25)