From 2b10d9817944de7cac622a00f73a96876913584d Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Mon, 16 Jun 2014 02:04:42 +0530
Subject: [PATCH] Added mean color RAG construction code

---
 skimage/graph/_construct.pyx | 126 +++++++++++++++++++++++++++++++++++
 skimage/graph/graph.py       |  23 +++++++
 skimage/graph/setup.py       |   5 ++
 3 files changed, 154 insertions(+)
 create mode 100644 skimage/graph/_construct.pyx
 create mode 100644 skimage/graph/graph.py

diff --git a/skimage/graph/_construct.pyx b/skimage/graph/_construct.pyx
new file mode 100644
index 00000000..3b91fe64
--- /dev/null
+++ b/skimage/graph/_construct.pyx
@@ -0,0 +1,126 @@
+import networkx as nx
+cimport numpy as cnp
+import numpy as np
+
+
+def construct_rag_meancolor_3d( img, arr):
+    cdef Py_ssize_t l, b, h, i, j, k
+    cdef cnp.int32_t current, next
+    l = arr.shape[0]
+    b = arr.shape[1]
+    h = arr.shape[2]
+
+    g = nx.Graph()
+
+    i = 0
+    while i < l - 1:
+        j = 0
+        while j < b - 1:
+            k = 0
+            while k < h - 1:
+                current = arr[i, j, k]
+        
+                try :
+                    g.node[current]['pixel_count'] += 1
+                    g.node[current]['total_color'] += img[i,j]
+                except KeyError:
+                    g.add_node(current)
+                    g.node[current]['pixel_count'] = 1
+                    g.node[current]['total_color'] = img[i,j].astype(np.long)
+                    g.node[current]['labels'] = [arr[i,j]]
+
+                next = arr[i + 1, j, k]
+                if current != next:
+                    g.add_edge(current, next)
+
+                next = arr[i, j + 1, k]
+                if current != next:
+                    g.add_edge(current, next)
+
+                next = arr[i + 1, j + 1, k]
+                if current != next:
+                    g.add_edge(current, next)
+
+                next = arr[i + 1, j, k + 1]
+                if current != next:
+                    g.add_edge(current, next)
+
+                next = arr[i, j + 1, k + 1]
+                if current != next:
+                    g.add_edge(current, next)
+
+                next = arr[i + 1, j + 1, k + 1]
+                if current != next:
+                    g.add_edge(current, next)
+
+                next = arr[i, j, k + 1]
+                if current != next:
+                    g.add_edge(current, next)
+
+
+                k += 1
+
+            j += 1
+
+        i += 1
+
+
+    for n in g.nodes():
+        g.node[n]['mean_color'] = g.node[n]['total_color']/g.node[n]['pixel_count']
+
+    for x,y in g.edges_iter() :
+        diff = g.node[x]['mean_color'] - g.node[y]['mean_color']
+        g[x][y]['weight'] = np.sqrt(diff.dot(diff))
+
+    return g
+
+
+def construct_rag_meancolor_2d(img, arr):
+    cdef Py_ssize_t l, b, h, i, j, k
+    cdef cnp.int32_t current, next
+    l = arr.shape[0]
+    b = arr.shape[1]
+
+    g = nx.Graph()
+
+    i = 0
+    while i < l - 1:
+        j = 0
+        while j < b - 1:
+            current = arr[i, j]
+
+            try :
+                g.node[current]['pixel_count'] += 1
+                g.node[current]['total_color'] += img[i,j]
+            except KeyError:
+                g.add_node(current)
+                g.node[current]['pixel_count'] = 1
+                g.node[current]['total_color'] = img[i,j].astype(np.long)
+                g.node[current]['labels'] = [arr[i,j]]
+
+            next = arr[i + 1, j]
+            if current != next:
+                g.add_edge(current, next)
+
+            next = arr[i, j + 1]
+            if current != next:
+                g.add_edge(current, next)
+
+            next = arr[i + 1, j + 1]
+            if current != next:
+                g.add_edge(current, next)
+
+            j += 1
+
+        i += 1
+
+
+    for n in g.nodes():
+        g.node[n]['mean_color'] = g.node[n]['total_color']/g.node[n]['pixel_count']
+
+    for x,y in g.edges_iter() :
+        diff = g.node[x]['mean_color'] - g.node[y]['mean_color']
+        g[x][y]['weight'] = np.sqrt(diff.dot(diff))
+
+
+    return g
diff --git a/skimage/graph/graph.py b/skimage/graph/graph.py
new file mode 100644
index 00000000..2597e985
--- /dev/null
+++ b/skimage/graph/graph.py
@@ -0,0 +1,23 @@
+import netwrokx as nx
+
+class Graph(nx.Graph):
+
+    def merge_nodes(i,j):
+        if not self.has_edge(i, j):
+            raise ValueError('Cant merge non adjacent nodes')
+
+        # print "before ",self.order()
+        for x in self.neighbors(i):
+            if x == j:
+                continue
+            w1 = self.get_edge_data(x, i)['weight']
+            w2 = -1
+            if self.has_edge(x, j):
+                w2 = self.get_edge_data(x, j)['weight']
+
+            w = max(w1, w2)
+
+            self.add_edge(x, j, weight=w)
+
+        self.node[j]['labels'] += self.node[i]['labels'] 
+        self.remove_node(i)
diff --git a/skimage/graph/setup.py b/skimage/graph/setup.py
index 463d2739..252eeed2 100644
--- a/skimage/graph/setup.py
+++ b/skimage/graph/setup.py
@@ -17,6 +17,8 @@ def configuration(parent_package='', top_path=None):
     cython(['_spath.pyx'], working_path=base_path)
     cython(['_mcp.pyx'], working_path=base_path)
     cython(['heap.pyx'], working_path=base_path)
+    cython(['_construct.pyx'], working_path=base_path)
+
 
     config.add_extension('_spath', sources=['_spath.c'],
                          include_dirs=[get_numpy_include_dirs()])
@@ -24,6 +26,9 @@ def configuration(parent_package='', top_path=None):
                          include_dirs=[get_numpy_include_dirs()])
     config.add_extension('heap', sources=['heap.c'],
                          include_dirs=[get_numpy_include_dirs()])
+    config.add_extension('_construct', sources=['_construct.c'],
+                         include_dirs=[get_numpy_include_dirs()])
+
 
     return config