Merge branch 'master' of https://github.com/soltesz-lab/neural_geometry

Author: iraikov

geometry.py

@@ -84,7 +84,18 @@ def transform_volume(transform, u, v, l, rotate=None):
 
     return xyz
 
+def get_layer_extents(layer_extents, layer):
+    min_u, max_u = 0.0, 0.0
+    min_v, max_v = 0.0, 0.0
+    min_l, max_l = 0.0, 0.0
+    for current_layer, extent in viewitems(layer_extents):
+        if current_layer == layer:
+            min_u, max_u = extent[0][0], extent[1][0]
+            min_v, max_v = extent[0][1], extent[1][1]
+            min_l, max_l = extent[0][2], extent[1][2]
+    return ((min_u, max_u), (min_v, max_v), (min_l, max_l))
 
+    
 def get_total_extents(layer_extents):
 
     min_u = float('inf')

linear_volume.py

@@ -470,7 +470,7 @@ def point_position(self, su, sv, sl, resolution=0.01, return_extent=True):
         else:
             return pos
 
-    def mplot_surface(self, ures=8, vres=8, **kwargs):
+    def mplot_surface(self, ures=8, vres=8, figax=False, **kwargs):
         """Plot the enclosing surfaces of the volume using Mayavi's `mesh()` function
 
         Parameters
@@ -514,13 +514,18 @@ def mplot_surface(self, ures=8, vres=8, **kwargs):
         meshpts1 = self.ev(hru, hrv, np.max(self.l))
         meshpts2 = self.ev(hru, hrv, np.min(self.l))
 
-        m1 = mlab.mesh(*meshpts1, **kwargs)
-        m2 = mlab.mesh(*meshpts2, **kwargs)
+        if figax is None:
+            m1 = mlab.mesh(*meshpts1, **kwargs)
+            m2 = mlab.mesh(*meshpts2, **kwargs)
 
-        # Turn off perspective
-        fig = mlab.gcf()
-        fig.scene.camera.trait_set(parallel_projection=1)
-        return fig
+            # Turn off perspective
+            fig = mlab.gcf()
+            fig.scene.camera.trait_set(parallel_projection=1)
+            return fig
+        else:
+            fig, ax = figax
+            m1 = ax.plot_surface(*meshpts1, **kwargs)
+            m2 = ax.plot_surface(*meshpts2, **kwargs)
 
     def mplot_volume(self, ures=8, vres=8, **kwargs):
         """Plot the volume using Mayavi's `scalar_scatter()` function