Changeset 7862:0d488ade72fc

Timestamp:

12/18/07 22:12:27 (5 years ago)

Author:

Robert Bradshaw <robertwb@…>

Branch:

default

Message:

3d plotting for graphs using plot3d (rather than tachyon directly)

Location:

sage/graphs

Files:

• graph.py (modified) (2 diffs)
• graph_fast.pyx (modified) (2 diffs)

sage/graphs/graph.py

@@ -2804 +2804 @@
                   color_by_label=color_by_label,
                   heights=heights).show(**kwds)
+
+
+    def plot3d_new(self, bgcolor=(1,1,1),
+                         vertex_colors=None, vertex_size=0.06, 
+                         edge_colors=None, edge_size=0.02,
+                         pos3d=None,
+                         iterations=50, color_by_label=False, **kwds):
+        from sage.plot.plot3d.all import Sphere, Line, Arrow
+        line = Arrow if self.is_directed() else Line
+        
+        verts = self.vertices()
+
+        if vertex_colors is None:
+            vertex_colors = { (1,0,0) : verts }
+        if pos3d is None:
+            pos3d = graph_fast.spring_layout_fast(self, dim=3, iterations=iterations)
+
+        if color_by_label:
+            if edge_colors is  None:
+                    # do the coloring
+                    edge_colors = self._color_by_label(format='rgbtuple')
+        elif edge_colors is None:
+            edge_colors = { (0,0,0) : self.edges() }
+
+        try:
+            graphic = 0
+            for color in vertex_colors:
+                for v in vertex_colors[color]:
+                    graphic += Sphere(vertex_size, color=color).translate(*pos3d[v])
+
+            for color in edge_colors:
+                for u, v, l in edge_colors[color]:
+                    graphic += line(pos3d[u], pos3d[v], edge_size, color=color, closed=False)
+
+            return graphic
+
+        except KeyError:
+            raise KeyError, "Oops! You haven't specified positions for all the vertices."
+        
+
 
     def transitive_closure(self):
@@ -4812 +4852 @@
         f.close()
         
-    def plot3d_new(self, bgcolor=(1,1,1),
-                         vertex_colors=None, vertex_size=0.06, 
-                         edge_colors=None, edge_size=0.02,
-                         pos3d=None,
-                         iterations=50, color_by_label=False, **kwds):
-        from math import sqrt
-        from sage.plot.plot3d.all import Sphere, Line
-        
-        c = [0,0,0]
-        r = []
-
-        verts = self.vertices()
-
-        if vertex_colors is None:
-            vertex_colors = { (1,0,0) : verts }
-        if pos3d is None:
-            pos3d = graph_fast.spring_layout_fast(self, dim=3, iterations=iterations)
-        try:
-            for v in verts:
-                c[0] += pos3d[v][0]
-                c[1] += pos3d[v][1]
-                c[2] += pos3d[v][2]
-        except KeyError:
-            raise KeyError, "Oops! You haven't specified positions for all the vertices."
-
-        order = self.order()
-        c[0] = c[0]/order
-        c[1] = c[1]/order
-        c[2] = c[2]/order
-        for v in verts:
-            pos3d[v][0] = pos3d[v][0] - c[0]
-            pos3d[v][1] = pos3d[v][1] - c[1]
-            pos3d[v][2] = pos3d[v][2] - c[2]
-            r.append(abs(sqrt((pos3d[v][0])**2 + (pos3d[v][1])**2 + (pos3d[v][2])**2)))
-        r = max(r)
-        if r == 0:
-            r = 1
-        for v in verts:
-            pos3d[v][0] = pos3d[v][0]/r
-            pos3d[v][1] = pos3d[v][1]/r
-            pos3d[v][2] = pos3d[v][2]/r
-
-        graphic = 0
-        for color in vertex_colors:
-            for v in vertex_colors[color]:
-                graphic += Sphere(vertex_size, color=color).translate(*pos3d[v])
-
-        if color_by_label:
-            if edge_colors is  None:
-                    # do the coloring
-                    edge_colors = self._color_by_label(format='rgbtuple')
-        elif edge_colors is None:
-            edge_colors = { (0,0,0) : self.edges() }
-
-        for color in edge_colors:
-            for u, v, l in edge_colors[color]:
-                graphic += Line(pos3d[u], pos3d[v], edge_size, color=color)
-
-        return graphic
         
     def plot3d(self, bgcolor=(1,1,1),

sage/graphs/graph_fast.pyx

@@ -60 +60 @@
     return pos
 
-def spring_layout_fast(G, iterations=50, dim=2, vpos=None):
+def spring_layout_fast(G, iterations=50, int dim=2, vpos=None, bint rescale=True):
     """
     Spring force model layout
@@ -117 +117 @@
     
     run_spring(iterations, dim, pos, elist, n)
+    
+    # recenter
+    cdef double* cen 
+    cdef double r, r2, max_r2 = 0
+    if rescale:
+        cen = <double *>sage_malloc(sizeof(double) * dim)
+        for x from 0 <= x < dim: cen[x] = 0
+        for i from 0 <= i < n:
+            for x from 0 <= x < dim:
+                cen[x] += pos[i*dim + x]
+        for x from 0 <= x < dim: cen[x] /= n
+        for i from 0 <= i < n:
+            r2 = 0
+            for x from 0 <= x < dim:
+                pos[i*dim + x] -= cen[x]
+                r2 += pos[i*dim + x] * pos[i*dim + x]
+            if r2 > max_r2:
+                max_r2 = r2
+        r = 1 if max_r2 == 0 else sqrt(max_r2)
+        for i from 0 <= i < n:
+            for x from 0 <= x < dim:
+                pos[i*dim + x] /= r
+        sage_free(cen)
     
     # put the data back into a position dictionary