Renamed _construct.pyx to _build_rag.pyx and some code corrections

doc/examples/plot_rag_meancolor.py

@@ -3,9 +3,9 @@
 RAG Thresholding
 ================
 
-This examples constructs a Region Adjacency Graph and merges region which are
+This examples constructs a Region Adjacency Graph (RAG) and merges regions which are
 similar in color. We construct a RAG and define edges as the difference in
-mean color. We the join regions with similar mean color.
+mean color. We then join regions with similar mean color.
 
 """
 

skimage/graph/_build_rag.pyx

@@ -8,9 +8,9 @@ def construct_rag_meancolor_3d(img, arr):
     difference in mean color of regions as edge weights.
 
     Given an image and its segmentation, this method constructs the
-    corresponsing Region Adjacency Graph (RAG).Each node in the RAG
-    represents a contiguous pixels with in `img` the same label in
-    `arr`
+    corresponsing Region Adjacency Graph (RAG). Each node in the RAG
+    represents contiguous pixels with in `img` with the same label in
+    `arr`. There is an edge between each pair of adjacent regions.
 
     Parameters
     ----------
@@ -25,29 +25,29 @@ def construct_rag_meancolor_3d(img, arr):
         The region adjacency graph.
     """
 
-    cdef Py_ssize_t l, b, h, i, j, k
+    cdef Py_ssize_t depth,width,height, i, j, k
     cdef cnp.int32_t current, next
-    l = arr.shape[0]
-    b = arr.shape[1]
-    h = arr.shape[2]
+    width = arr.shape[0]
+    height = arr.shape[1]
+    depth = arr.shape[2]
 
     g = rag.RAG()
 
     i = 0
-    while i < l - 1:
+    for i in range(width-1):
         j = 0
-        while j < b - 1:
+        for j in range(height-1):
             k = 0
-            while k < h - 1:
+            for k in range(depth-1):
                 current = arr[i, j, k]
 
                 try:
-                    g.node[current]['pixel_count'] += 1
-                    g.node[current]['total_color'] += img[i, j]
+                    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]['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]
@@ -85,12 +85,12 @@ def construct_rag_meancolor_3d(img, arr):
         i += 1
 
     for n in g.nodes():
-        g.node[n]['mean_color'] = g.node[n][
-            'total_color'] / g.node[n]['pixel_count']
+        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))
+        diff = g.node[x]['mean color'] - g.node[y]['mean color']
+        g[x][y]['weight'] = np.linalg.norm(diff)
 
     return g
 
@@ -100,9 +100,9 @@ def construct_rag_meancolor_2d(img, arr):
     difference in mean color of regions as edge weights.
 
     Given an image and its segmentation, this method constructs the
-    corresponsing Region Adjacency Graph (RAG).Each node in the RAG
-    represents a contiguous pixels with in `img` the same label in
-    `arr`
+    corresponsing Region Adjacency Graph (RAG). Each node in the RAG
+    represents contiguous pixels with in `img` with the same label in
+    `arr`. There is an edge between each pair of adjacent regions.
 
     Parameters
     ----------
@@ -117,26 +117,26 @@ def construct_rag_meancolor_2d(img, arr):
         The region adjacency graph.
     """
 
-    cdef Py_ssize_t l, b, h, i, j, k
+    cdef Py_ssize_t width, height, h, i, j, k
     cdef cnp.int32_t current, next
-    l = arr.shape[0]
-    b = arr.shape[1]
+    width = arr.shape[0]
+    height = arr.shape[1]
 
     g = rag.RAG()
 
     i = 0
-    while i < l - 1:
+    for i in range(width-1):
         j = 0
-        while j < b - 1:
+        for j in range(height-1):
             current = arr[i, j]
 
             try:
-                g.node[current]['pixel_count'] += 1
-                g.node[current]['total_color'] += img[i, j]
+                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]['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]
@@ -156,11 +156,11 @@ def construct_rag_meancolor_2d(img, arr):
         i += 1
 
     for n in g.nodes():
-        g.node[n]['mean_color'] = g.node[n][
-            'total_color'] / g.node[n]['pixel_count']
+        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))
+        diff = g.node[x]['mean color'] - g.node[y]['mean color']
+        g[x][y]['weight'] = np.linalg.norm(diff)
 
     return g

skimage/graph/graph_cut.py

@@ -11,7 +11,7 @@ def threshold_cut(label, rag, thresh):
 
     Parameters
     ----------
-    label : (width, height, 3) or (width, height, depth, 3) ndarray
+    label : (width, height) or (width, height, 3) ndarray
         The array of labels.
     rag : RAG
         The region adjacency graph.

skimage/graph/rag.py

@@ -1,7 +1,7 @@
 import networkx as nx
 from skimage import util
-from ._construct import construct_rag_meancolor_2d
-from ._construct import construct_rag_meancolor_3d
+from ._build_rag import construct_rag_meancolor_2d
+from ._build_rag import construct_rag_meancolor_3d
 
 
 class RAG(nx.Graph):

skimage/graph/setup.py

@@ -17,7 +17,7 @@ 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)
+    cython(['_build_rag.pyx'], working_path=base_path)
 
 
     config.add_extension('_spath', sources=['_spath.c'],
@@ -26,7 +26,7 @@ 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'],
+    config.add_extension('_build_rag', sources=['_build_rag.c'],
                          include_dirs=[get_numpy_include_dirs()])