Mapping values to foci.

surfer/viz.py

@@ -1570,7 +1570,7 @@ def add_morphometry(self, measure, grayscale=False, hemi=None,
 
     def add_foci(self, coords, coords_as_verts=False, map_surface=None,
                  scale_factor=1, color="white", alpha=1, name=None,
-                 hemi=None):
+                 hemi=None, allow_data=False, data=None):
         """Add spherical foci, possibly mapping to displayed surf.
 
         The foci spheres can be displayed at the coordinates given, or
@@ -1588,8 +1588,8 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
             whether the coords parameter should be interpreted as vertex ids
         map_surface : Freesurfer surf or None
             surface to map coordinates through, or None to use raw coords
-        scale_factor : float
-            Controls the size of the foci spheres (relative to 1cm).
+        scale_factor : int
+            controls the size of the foci spheres
         color : matplotlib color code
             HTML name, RBG tuple, or hex code
         alpha : float in [0, 1]
@@ -1600,6 +1600,14 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
             If None, it is assumed to belong to the hemipshere being
             shown. If two hemispheres are being shown, an error will
             be thrown.
+        allow_data : bool | False
+            If True, will plot foci using quiver3d instead of points3d to allow
+            mapping data to spheres.
+        data : numpy array
+            1D array the same size as the number of foci. Spheres will be
+            colorcoded acording to data values, whereas spheres' sizes will be
+            coded using the absolute values of data.
+
         """
         from matplotlib.colors import colorConverter
         hemi = self._check_hemi(hemi)
@@ -1614,8 +1622,7 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
             foci_coords = np.atleast_2d(coords)
         else:
             foci_surf = Surface(self.subject_id, hemi, map_surface,
-                                subjects_dir=self.subjects_dir,
-                                units=self._units)
+                                subjects_dir=self.subjects_dir)
             foci_surf.load_geometry()
             foci_vtxs = utils.find_closest_vertices(foci_surf.coords, coords)
             foci_coords = self.geo[hemi].coords[foci_vtxs]
@@ -1630,12 +1637,16 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
 
         views = self._toggle_render(False)
         fl = []
-        if self._units == 'm':
-            scale_factor = scale_factor / 1000.
         for brain in self._brain_list:
             if brain['hemi'] == hemi:
-                fl.append(brain['brain'].add_foci(foci_coords, scale_factor,
-                                                  color, alpha, name))
+                if allow_data:
+                    vtxs = utils.find_closest_vertices(self.geo[hemi].coords, foci_coords)
+                    fl.append(brain['brain'].add_foci_data(foci_coords,
+                                                           scale_factor, color, alpha, name, data,
+                                                           self.geo[hemi].nn[vtxs, :]))
+                else:
+                    fl.append(brain['brain'].add_foci(foci_coords,
+                                                      scale_factor, color, alpha, name))
         self.foci_dict[name] = fl
         self._toggle_render(True, views)
 
@@ -1737,6 +1748,45 @@ def add_text(self, x, y, text, name, color=None, opacity=1.0,
         if justification is not None:
             text.property.justification = justification
 
+    def add_text3d(self, x, y, z, text, name, color=None, opacity=1.0,
+                 row=-1, col=-1, font_size=None, justification=None):
+        """ Add a text to the visualization
+
+        Parameters
+        ----------
+        x : Float
+            x coordinate
+        y : Float
+            y coordinate
+        z : Float
+            z coordinate
+        text : str
+            Text to add
+        name : str
+            Name of the text (text label can be updated using update_text())
+        color : Tuple
+            Color of the text. Default is the foreground color set during
+            initialization (default is black or white depending on the
+            background color).
+        opacity : Float
+            Opacity of the text. Default: 1.0
+        row : int
+            Row index of which brain to use
+        col : int
+            Column index of which brain to use
+        """
+        if name in self.texts_dict:
+            self.texts_dict[name]['text'].remove()
+        text = self.brain_matrix[row, col].add_text3d(x, y, z, text,
+                                                    name, color, opacity)
+        self.texts_dict[name] = dict(row=row, col=col, text=text)
+        if font_size is not None:
+            text.property.font_size = font_size
+            text.actor.text_scale_mode = 'viewport'
+        if justification is not None:
+            text.property.justification = justification
+
+
     def update_text(self, text, name, row=-1, col=-1):
         """Update text label
 
@@ -3290,6 +3340,27 @@ def add_foci(self, foci_coords, scale_factor, color, alpha, name):
                 scale_factor=(10. * scale_factor), color=color, opacity=alpha)
         return points
 
+    def add_foci_data(self, foci_coords, scale_factor, color, alpha, name,data, normals):
+        """Add spherical foci with attached data, possibly mapping to displayed surf"""
+        # Create the visualization
+        hemi = self.hemi
+        if data == None:
+            u = np.array(normals[:,0])
+            v = np.array(normals[:,1])
+            w = np.array(normals[:,2])
+        else:
+            u = self.geo[hemi].nn[:,0] * np.abs(data)
+            v = self.geo[hemi].nn[:,1] * np.abs(data)
+            w = self.geo[hemi].nn[:,2] * np.abs(data)
+        with warnings.catch_warnings(record=True):  # traits
+            points = mlab.quiver3d(foci_coords[:, 0],foci_coords[:, 1],foci_coords[:, 2],
+                u,v,w, scalars = data, colormap='coolwarm', mode='sphere',
+                name=name, figure=self._f, scale_factor=(10. * scale_factor),
+                color=color, opacity=alpha)
+            points.glyph.color_mode = 'color_by_scalar'
+            points.glyph.glyph_source.glyph_source.center = [0, 0, 0]
+        return points
+
     def add_contour_overlay(self, scalar_data, min=None, max=None,
                             n_contours=7, line_width=1.5, lut=None,
                             colorbar=True):
@@ -3325,6 +3396,14 @@ def add_text(self, x, y, text, name, color=None, opacity=1.0):
                              opacity=opacity, figure=self._f)
             return text
 
+    def add_text3d(self, x, y, z, text, name, color=None, opacity=1.0):
+        """ Add a text in 3D to the visualization"""
+        color = self._fg_color if color is None else color
+        with warnings.catch_warnings(record=True):
+            text = mlab.text3d(x, y, z, text, name=name, color=color,
+                             opacity=opacity, figure=self._f)
+            return text
+
     def remove_data(self, layer_id):
         """Remove data shown with .add_data()"""
         data = self.data.pop(layer_id)