From 39dfcc414499f7a84ebf53900b93ae192f4eb54f Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Tue, 29 Jul 2014 01:05:10 +0530
Subject: [PATCH 01/21] Frist working copy of RAG draw

---
 doc/examples/plot_rag_draw.py | 21 ++++++++++++++
 skimage/graph/rag.py          | 53 +++++++++++++++++++++++++++++++++++
 2 files changed, 74 insertions(+)
 create mode 100644 doc/examples/plot_rag_draw.py

diff --git a/doc/examples/plot_rag_draw.py b/doc/examples/plot_rag_draw.py
new file mode 100644
index 00000000..22fb9e63
--- /dev/null
+++ b/doc/examples/plot_rag_draw.py
@@ -0,0 +1,21 @@
+from skimage import graph, data, io, segmentation, color
+from matplotlib import pyplot as plt
+
+
+img = data.coffee()
+
+labels = segmentation.slic(img, compactness=30, n_segments=400)
+
+g = graph.rag_mean_color(img, labels)
+
+out = graph.rag.rag_draw(labels, g, img)
+plt.figure()
+plt.title("RAG with all edges shown in green.")
+plt.imshow(out)
+
+out = graph.rag.rag_draw(labels, g, img, high_color=(1,0,0), thresh=30)
+plt.figure()
+plt.title("RAG with edge weights less than 30, color mapped between green and red.")
+plt.imshow(out)
+
+plt.show()
diff --git a/skimage/graph/rag.py b/skimage/graph/rag.py
index 5ef9a83b..42e4c4e3 100644
--- a/skimage/graph/rag.py
+++ b/skimage/graph/rag.py
@@ -13,6 +13,7 @@ import numpy as np
 from scipy.ndimage import filters
 from scipy import ndimage as nd
 import math
+from .. import draw, measure, segmentation
 
 
 def min_weight(graph, src, dst, n):
@@ -236,3 +237,55 @@ def rag_mean_color(image, labels, connectivity=2, mode='distance',
             raise ValueError("The mode '%s' is not recognised" % mode)
 
     return graph
+
+
+
+def rag_draw(labels, rag, img, border_color = (0,0,0), node_color = (1,1,0), 
+             low_color = (0,1,0), high_color=None, thresh=np.inf ):
+    rag = rag.copy()
+    rag_labels = labels.copy()
+    out = img.copy()
+    
+    low_color = np.array(low_color)
+    
+    if not high_color is None :
+        high_color = np.array(high_color)
+
+    # Handling the case where one node has multiple labels
+    offset = 1
+    for n, d in rag.nodes_iter(data=True):
+        for l in d['labels'] :
+            rag_labels[labels == l] = offset
+        offset += 1
+
+    regions = measure.regionprops(rag_labels)
+    for region in regions:
+        # Because we kept the offset as 1
+        rag.node[region['label'] - 1]['centroid'] = region['centroid']
+
+    if not border_color is None :
+        out = segmentation.mark_boundaries(out, rag_labels, color = border_color)
+
+    if not high_color is None :
+        max_weight = max([d['weight'] for x, y, d in rag.edges_iter(data=True) if d['weight'] < thresh ])
+        min_weight = min([d['weight'] for x, y, d in rag.edges_iter(data=True) if d['weight'] < thresh ])
+    
+    for n1,n2,data in rag.edges_iter(data=True):
+
+        if data['weight'] >=  thresh :
+            continue
+        r1, c1 = map(int, rag.node[n1]['centroid'])
+        r2, c2 = map(int, rag.node[n2]['centroid'])
+
+        line  = draw.line(r1, c1, r2, c2)
+                
+        if not high_color is None:
+            norm_weight = ( rag[n1][n2]['weight'] - min_weight ) / ( max_weight - min_weight )
+            out[line] = norm_weight*high_color + (1 - norm_weight)*low_color
+        else:
+            out[line] = low_color
+            
+        circle = draw.circle(r1,c1,2)
+        out[circle] = node_color
+
+    return out

From f4aa0fc8e16d8c3ec24759441b8150aea98c0240 Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Tue, 29 Jul 2014 02:36:20 +0530
Subject: [PATCH 02/21] Formatting

---
 doc/examples/plot_rag_draw.py |  7 ++---
 skimage/graph/rag.py          | 48 ++++++++++++++++++++---------------
 2 files changed, 31 insertions(+), 24 deletions(-)

diff --git a/doc/examples/plot_rag_draw.py b/doc/examples/plot_rag_draw.py
index 22fb9e63..e554e1a7 100644
--- a/doc/examples/plot_rag_draw.py
+++ b/doc/examples/plot_rag_draw.py
@@ -1,4 +1,4 @@
-from skimage import graph, data, io, segmentation, color
+from skimage import graph, data, segmentation
 from matplotlib import pyplot as plt
 
 
@@ -13,9 +13,10 @@ plt.figure()
 plt.title("RAG with all edges shown in green.")
 plt.imshow(out)
 
-out = graph.rag.rag_draw(labels, g, img, high_color=(1,0,0), thresh=30)
+out = graph.rag.rag_draw(labels, g, img, high_color=(1, 0, 0), thresh=30)
 plt.figure()
-plt.title("RAG with edge weights less than 30, color mapped between green and red.")
+plt.title("RAG with edge weights less than 30,\
+          color mapped between green and red.")
 plt.imshow(out)
 
 plt.show()
diff --git a/skimage/graph/rag.py b/skimage/graph/rag.py
index 42e4c4e3..5a3db12a 100644
--- a/skimage/graph/rag.py
+++ b/skimage/graph/rag.py
@@ -239,22 +239,21 @@ def rag_mean_color(image, labels, connectivity=2, mode='distance',
     return graph
 
 
-
-def rag_draw(labels, rag, img, border_color = (0,0,0), node_color = (1,1,0), 
-             low_color = (0,1,0), high_color=None, thresh=np.inf ):
+def rag_draw(labels, rag, img, border_color=(0, 0, 0), node_color = (1, 1, 0),
+             low_color = (0, 1, 0), high_color=None, thresh=np.inf):
     rag = rag.copy()
     rag_labels = labels.copy()
     out = img.copy()
-    
+
     low_color = np.array(low_color)
-    
-    if not high_color is None :
+
+    if not high_color is None:
         high_color = np.array(high_color)
 
     # Handling the case where one node has multiple labels
     offset = 1
     for n, d in rag.nodes_iter(data=True):
-        for l in d['labels'] :
+        for l in d['labels']:
             rag_labels[labels == l] = offset
         offset += 1
 
@@ -263,29 +262,36 @@ def rag_draw(labels, rag, img, border_color = (0,0,0), node_color = (1,1,0),
         # Because we kept the offset as 1
         rag.node[region['label'] - 1]['centroid'] = region['centroid']
 
-    if not border_color is None :
-        out = segmentation.mark_boundaries(out, rag_labels, color = border_color)
+    if not border_color is None:
+        out = segmentation.mark_boundaries(
+            out,
+            rag_labels,
+            color=border_color)
 
-    if not high_color is None :
-        max_weight = max([d['weight'] for x, y, d in rag.edges_iter(data=True) if d['weight'] < thresh ])
-        min_weight = min([d['weight'] for x, y, d in rag.edges_iter(data=True) if d['weight'] < thresh ])
-    
-    for n1,n2,data in rag.edges_iter(data=True):
+    if not high_color is None:
+        max_weight = max([d['weight'] for x, y, d in rag.edges_iter(data=True)
+                          if d['weight'] < thresh])
+        min_weight = min([d['weight'] for x, y, d in rag.edges_iter(data=True)
+                          if d['weight'] < thresh])
 
-        if data['weight'] >=  thresh :
+    for n1, n2, data in rag.edges_iter(data=True):
+
+        if data['weight'] >= thresh:
             continue
         r1, c1 = map(int, rag.node[n1]['centroid'])
         r2, c2 = map(int, rag.node[n2]['centroid'])
 
-        line  = draw.line(r1, c1, r2, c2)
-                
+        line = draw.line(r1, c1, r2, c2)
+
         if not high_color is None:
-            norm_weight = ( rag[n1][n2]['weight'] - min_weight ) / ( max_weight - min_weight )
-            out[line] = norm_weight*high_color + (1 - norm_weight)*low_color
+            norm_weight = (rag[n1][n2]['weight'] - min_weight) / (
+                max_weight - min_weight)
+            out[line] = norm_weight * high_color + \
+                (1 - norm_weight) * low_color
         else:
             out[line] = low_color
-            
-        circle = draw.circle(r1,c1,2)
+
+        circle = draw.circle(r1, c1, 2)
         out[circle] = node_color
 
     return out

From 5c662b447227ed422bdbf2b1ae51602d0c846780 Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Tue, 29 Jul 2014 03:12:22 +0530
Subject: [PATCH 03/21] Docstrings

---
 doc/examples/plot_rag_draw.py | 16 +++++++---
 skimage/graph/__init__.py     |  4 +++
 skimage/graph/rag.py          | 60 ++++++++++++++++++++++++++++++-----
 3 files changed, 67 insertions(+), 13 deletions(-)

diff --git a/doc/examples/plot_rag_draw.py b/doc/examples/plot_rag_draw.py
index e554e1a7..1c47743e 100644
--- a/doc/examples/plot_rag_draw.py
+++ b/doc/examples/plot_rag_draw.py
@@ -1,22 +1,28 @@
+"""
+===========
+RAG Drawing
+===========
+
+This example constructs a Region Adjacency Graph (RAG) and draws it with
+the `rag_draw` method.
+"""
 from skimage import graph, data, segmentation
 from matplotlib import pyplot as plt
 
 
 img = data.coffee()
-
 labels = segmentation.slic(img, compactness=30, n_segments=400)
-
 g = graph.rag_mean_color(img, labels)
 
-out = graph.rag.rag_draw(labels, g, img)
+out = graph.rag_draw(labels, g, img)
 plt.figure()
 plt.title("RAG with all edges shown in green.")
 plt.imshow(out)
 
-out = graph.rag.rag_draw(labels, g, img, high_color=(1, 0, 0), thresh=30)
+out = graph.rag_draw(labels, g, img, high_color=(1, 0, 0), thresh=30)
 plt.figure()
 plt.title("RAG with edge weights less than 30,\
           color mapped between green and red.")
-plt.imshow(out)
 
+plt.imshow(out)
 plt.show()
diff --git a/skimage/graph/__init__.py b/skimage/graph/__init__.py
index aca73bc4..2f1162d3 100644
--- a/skimage/graph/__init__.py
+++ b/skimage/graph/__init__.py
@@ -2,8 +2,11 @@ from .spath import shortest_path
 from .mcp import MCP, MCP_Geometric, MCP_Connect, MCP_Flexible, route_through_array
 from .rag import rag_mean_color, RAG
 from .graph_cut import cut_threshold, cut_normalized
+from .rag import rag_mean_color, RAG, rag_draw
+from .graph_cut import cut_threshold
 ncut = cut_normalized
 
+
 __all__ = ['shortest_path',
            'MCP',
            'MCP_Geometric',
@@ -14,4 +17,5 @@ __all__ = ['shortest_path',
            'cut_threshold',
            'cut_normalized',
            'ncut',
+           'rag_draw',
            'RAG']
diff --git a/skimage/graph/rag.py b/skimage/graph/rag.py
index 5a3db12a..d01d6e12 100644
--- a/skimage/graph/rag.py
+++ b/skimage/graph/rag.py
@@ -241,6 +241,52 @@ def rag_mean_color(image, labels, connectivity=2, mode='distance',
 
 def rag_draw(labels, rag, img, border_color=(0, 0, 0), node_color = (1, 1, 0),
              low_color = (0, 1, 0), high_color=None, thresh=np.inf):
+    """Draw a Region Adjacency Graph on an image.
+
+    Given a labelled image and its corresponding RAG, draw the nodes and edges
+    of the RAG on the image with the specified colors. Nodes are markes by
+    the centroids of the corresposning regions.
+
+    Parameters
+    ----------
+    labels : ndarray, shape(M, N, [..., P,])
+        The labelled image. This should have one dimension less than
+        `img`. If `image` has dimensions `(M, N, 3)` `labels` should have
+         dimensions `(M, N)`.
+    rag : RAG
+        The Region Adjacency Graph.
+    img : ndarray, shape(M, N, [..., P,] 3)
+        Input image.
+    border_color : length-3 sequence, optional
+        RGB color of the corder of regions. Specifying `None` won't draw
+        the border.
+    node_color : length-3 sequeunce, optional
+        RGB color of the centroid of nodes. Yellow by default.
+    low_color : length-3 sequeunce, optional
+        RGB color of the edges. If `high_color` is not specified, all edges
+        are draw with `low_color`. Green by default.
+    high_color : length-3 sequeunce, optional
+        RGB color of the edges with high weight. If specified, the edges are
+        color mapped between `low_color` and `high_color` depending on their
+        weight. Edges with low weights are more like `low_color` whereas edges
+        with high weights are more like `high_color`.
+    thresh : float, optiona;
+        Edges with weight below `thresh` are not drawn, or considered for color
+        mapping in case `high_color` is specified.
+
+    Returns
+    -------
+    out : ndarray, shape(M, N, [..., P,] 3)
+        The image with the RAG drawn.
+
+    Examples
+    --------
+    >>> from skimage import data, graph, segmentation
+    >>> img = data.lena()
+    >>> labels = segmentation.slic(img)
+    >>> g =  graph.rag_mean_color(img, labels)
+    >>> out = graph.rag_draw(labels, g, img)
+    """
     rag = rag.copy()
     rag_labels = labels.copy()
     out = img.copy()
@@ -251,6 +297,7 @@ def rag_draw(labels, rag, img, border_color=(0, 0, 0), node_color = (1, 1, 0),
         high_color = np.array(high_color)
 
     # Handling the case where one node has multiple labels
+    # offset is 1 so that regionprops does not ignore 0
     offset = 1
     for n, d in rag.nodes_iter(data=True):
         for l in d['labels']:
@@ -263,10 +310,7 @@ def rag_draw(labels, rag, img, border_color=(0, 0, 0), node_color = (1, 1, 0),
         rag.node[region['label'] - 1]['centroid'] = region['centroid']
 
     if not border_color is None:
-        out = segmentation.mark_boundaries(
-            out,
-            rag_labels,
-            color=border_color)
+        out = segmentation.mark_boundaries(out, rag_labels, color=border_color)
 
     if not high_color is None:
         max_weight = max([d['weight'] for x, y, d in rag.edges_iter(data=True)
@@ -284,10 +328,10 @@ def rag_draw(labels, rag, img, border_color=(0, 0, 0), node_color = (1, 1, 0),
         line = draw.line(r1, c1, r2, c2)
 
         if not high_color is None:
-            norm_weight = (rag[n1][n2]['weight'] - min_weight) / (
-                max_weight - min_weight)
-            out[line] = norm_weight * high_color + \
-                (1 - norm_weight) * low_color
+            norm_weight = ((rag[n1][n2]['weight'] - min_weight) /
+                           (max_weight - min_weight))
+            out[line] = (norm_weight * high_color +
+                         (1 - norm_weight) * low_color)
         else:
             out[line] = low_color
 

From 6928e5d9ef3c85fbd18ed6f008d55007947e4f36 Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Tue, 29 Jul 2014 03:15:24 +0530
Subject: [PATCH 04/21] Corrected docstrings

---
 skimage/graph/rag.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/skimage/graph/rag.py b/skimage/graph/rag.py
index d01d6e12..9368f558 100644
--- a/skimage/graph/rag.py
+++ b/skimage/graph/rag.py
@@ -251,15 +251,15 @@ def rag_draw(labels, rag, img, border_color=(0, 0, 0), node_color = (1, 1, 0),
     ----------
     labels : ndarray, shape(M, N, [..., P,])
         The labelled image. This should have one dimension less than
-        `img`. If `image` has dimensions `(M, N, 3)` `labels` should have
+        `img`. If `img` has dimensions `(M, N, 3)` `labels` should have
          dimensions `(M, N)`.
     rag : RAG
         The Region Adjacency Graph.
     img : ndarray, shape(M, N, [..., P,] 3)
         Input image.
     border_color : length-3 sequence, optional
-        RGB color of the corder of regions. Specifying `None` won't draw
-        the border.
+        RGB color of the border of regions. Specifying `None` won't draw
+        the border. Black by default.
     node_color : length-3 sequeunce, optional
         RGB color of the centroid of nodes. Yellow by default.
     low_color : length-3 sequeunce, optional

From 78caebf6d25b6bbba070b0d3b74abc26800dfa36 Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Tue, 29 Jul 2014 03:31:12 +0530
Subject: [PATCH 05/21] string wrap

---
 doc/examples/plot_rag_draw.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/examples/plot_rag_draw.py b/doc/examples/plot_rag_draw.py
index 1c47743e..51a33dbd 100644
--- a/doc/examples/plot_rag_draw.py
+++ b/doc/examples/plot_rag_draw.py
@@ -21,8 +21,8 @@ plt.imshow(out)
 
 out = graph.rag_draw(labels, g, img, high_color=(1, 0, 0), thresh=30)
 plt.figure()
-plt.title("RAG with edge weights less than 30,\
-          color mapped between green and red.")
+plt.title("RAG with edge weights less than 30, color "
+          "mapped between green and red.")
 
 plt.imshow(out)
 plt.show()

From 4005749a61f6022e3adc509b775f9d4c8a5a2c2d Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Tue, 5 Aug 2014 23:05:15 +0530
Subject: [PATCH 06/21] rebase and change API to support mpl colorspec

---
 doc/examples/plot_rag_draw.py | 13 ++---
 skimage/graph/__init__.py     |  2 +
 skimage/graph/rag.py          | 89 ++++++++++++++++++-----------------
 3 files changed, 56 insertions(+), 48 deletions(-)

diff --git a/doc/examples/plot_rag_draw.py b/doc/examples/plot_rag_draw.py
index 51a33dbd..21dbbc28 100644
--- a/doc/examples/plot_rag_draw.py
+++ b/doc/examples/plot_rag_draw.py
@@ -1,25 +1,26 @@
 """
-===========
-RAG Drawing
-===========
+=====================================
+Drawing Region Adjacency Graphs (RAGs)
+======================================
 
 This example constructs a Region Adjacency Graph (RAG) and draws it with
 the `rag_draw` method.
 """
 from skimage import graph, data, segmentation
-from matplotlib import pyplot as plt
+from matplotlib import pyplot as plt, colors
 
 
 img = data.coffee()
 labels = segmentation.slic(img, compactness=30, n_segments=400)
 g = graph.rag_mean_color(img, labels)
 
-out = graph.rag_draw(labels, g, img)
+out = graph.draw_rag(labels, g, img)
 plt.figure()
 plt.title("RAG with all edges shown in green.")
 plt.imshow(out)
 
-out = graph.rag_draw(labels, g, img, high_color=(1, 0, 0), thresh=30)
+cmap = colors.ListedColormap(['cyan', 'red'])
+out = graph.draw_rag(labels, g, img, colormap=cmap, thresh=30)
 plt.figure()
 plt.title("RAG with edge weights less than 30, color "
           "mapped between green and red.")
diff --git a/skimage/graph/__init__.py b/skimage/graph/__init__.py
index 2f1162d3..2cd422ba 100644
--- a/skimage/graph/__init__.py
+++ b/skimage/graph/__init__.py
@@ -3,6 +3,7 @@ from .mcp import MCP, MCP_Geometric, MCP_Connect, MCP_Flexible, route_through_ar
 from .rag import rag_mean_color, RAG
 from .graph_cut import cut_threshold, cut_normalized
 from .rag import rag_mean_color, RAG, rag_draw
+from .rag import rag_mean_color, RAG, draw_rag
 from .graph_cut import cut_threshold
 ncut = cut_normalized
 
@@ -18,4 +19,5 @@ __all__ = ['shortest_path',
            'cut_normalized',
            'ncut',
            'rag_draw',
+           'draw_rag',
            'RAG']
diff --git a/skimage/graph/rag.py b/skimage/graph/rag.py
index 9368f558..4447c4e3 100644
--- a/skimage/graph/rag.py
+++ b/skimage/graph/rag.py
@@ -9,11 +9,21 @@ except ImportError:
                 raise ImportError(msg)
     import warnings
     warnings.warn(msg)
+
 import numpy as np
 from scipy.ndimage import filters
 from scipy import ndimage as nd
+<<<<<<< HEAD
 import math
 from .. import draw, measure, segmentation
+=======
+from .. import draw
+from .. import measure
+from .. import segmentation
+from matplotlib import colors
+from matplotlib import cm
+from .. import util
+>>>>>>> rebase and change API to support mpl colorspec
 
 
 def min_weight(graph, src, dst, n):
@@ -239,8 +249,8 @@ def rag_mean_color(image, labels, connectivity=2, mode='distance',
     return graph
 
 
-def rag_draw(labels, rag, img, border_color=(0, 0, 0), node_color = (1, 1, 0),
-             low_color = (0, 1, 0), high_color=None, thresh=np.inf):
+def draw_rag(labels, rag, img, border_color=None, node_color='yellow',
+             edge_color='green', colormap=None, thresh=np.inf):
     """Draw a Region Adjacency Graph on an image.
 
     Given a labelled image and its corresponding RAG, draw the nodes and edges
@@ -249,30 +259,24 @@ def rag_draw(labels, rag, img, border_color=(0, 0, 0), node_color = (1, 1, 0),
 
     Parameters
     ----------
-    labels : ndarray, shape(M, N, [..., P,])
-        The labelled image. This should have one dimension less than
-        `img`. If `img` has dimensions `(M, N, 3)` `labels` should have
-         dimensions `(M, N)`.
+    labels : ndarray, shape(M, N)
+        The labelled image.
     rag : RAG
         The Region Adjacency Graph.
-    img : ndarray, shape(M, N, [..., P,] 3)
+    img : ndarray, shape(M, N, 3)
         Input image.
-    border_color : length-3 sequence, optional
-        RGB color of the border of regions. Specifying `None` won't draw
-        the border. Black by default.
-    node_color : length-3 sequeunce, optional
-        RGB color of the centroid of nodes. Yellow by default.
-    low_color : length-3 sequeunce, optional
-        RGB color of the edges. If `high_color` is not specified, all edges
-        are draw with `low_color`. Green by default.
-    high_color : length-3 sequeunce, optional
-        RGB color of the edges with high weight. If specified, the edges are
-        color mapped between `low_color` and `high_color` depending on their
-        weight. Edges with low weights are more like `low_color` whereas edges
-        with high weights are more like `high_color`.
-    thresh : float, optiona;
+    border_color : colorspec, optional
+        Any matplotlib colorspec.
+    node_color : colorspec, optional
+        Any matplotlib colorspec. Yellow by default.
+    edge_color : colorspec, optional
+        Any matplotlib colorspec. Green by default.
+    colormap : colormap, optional
+        Any matplotlib colormap. If specified the edges are colormapped with
+        the specified color map.
+    thresh : float, optional
         Edges with weight below `thresh` are not drawn, or considered for color
-        mapping in case `high_color` is specified.
+        mapping.
 
     Returns
     -------
@@ -282,41 +286,44 @@ def rag_draw(labels, rag, img, border_color=(0, 0, 0), node_color = (1, 1, 0),
     Examples
     --------
     >>> from skimage import data, graph, segmentation
-    >>> img = data.lena()
+    >>> img = data.coffee()
     >>> labels = segmentation.slic(img)
     >>> g =  graph.rag_mean_color(img, labels)
     >>> out = graph.rag_draw(labels, g, img)
     """
     rag = rag.copy()
-    rag_labels = labels.copy()
-    out = img.copy()
+    out = util.img_as_float(img)
+    cc = colors.ColorConverter()
 
-    low_color = np.array(low_color)
-
-    if not high_color is None:
-        high_color = np.array(high_color)
+    edge_color = cc.to_rgb(edge_color)
+    node_color = cc.to_rgb(node_color)
 
     # Handling the case where one node has multiple labels
     # offset is 1 so that regionprops does not ignore 0
     offset = 1
+    map_array = np.arange(labels.max() + 1)
     for n, d in rag.nodes_iter(data=True):
-        for l in d['labels']:
-            rag_labels[labels == l] = offset
+        for label in d['labels']:
+            map_array[label] = offset
         offset += 1
 
+    rag_labels = map_array[labels]
+
     regions = measure.regionprops(rag_labels)
     for region in regions:
         # Because we kept the offset as 1
         rag.node[region['label'] - 1]['centroid'] = region['centroid']
 
     if not border_color is None:
+        border_color = cc.to_rgb(border_color)
         out = segmentation.mark_boundaries(out, rag_labels, color=border_color)
 
-    if not high_color is None:
-        max_weight = max([d['weight'] for x, y, d in rag.edges_iter(data=True)
-                          if d['weight'] < thresh])
-        min_weight = min([d['weight'] for x, y, d in rag.edges_iter(data=True)
-                          if d['weight'] < thresh])
+    if colormap is not None:
+        edge_weight_list = [d['weight'] for x, y, d in
+                            rag.edges_iter(data=True) if d['weight'] < thresh]
+        norm = colors.Normalize()
+        norm.autoscale(edge_weight_list)
+        smap = cm.ScalarMappable(norm, colormap)
 
     for n1, n2, data in rag.edges_iter(data=True):
 
@@ -327,13 +334,11 @@ def rag_draw(labels, rag, img, border_color=(0, 0, 0), node_color = (1, 1, 0),
 
         line = draw.line(r1, c1, r2, c2)
 
-        if not high_color is None:
-            norm_weight = ((rag[n1][n2]['weight'] - min_weight) /
-                           (max_weight - min_weight))
-            out[line] = (norm_weight * high_color +
-                         (1 - norm_weight) * low_color)
+        if colormap is not None:
+            current_color = smap.to_rgba([data['weight']])[0][:-1]
+            out[line] = current_color
         else:
-            out[line] = low_color
+            out[line] = edge_color
 
         circle = draw.circle(r1, c1, 2)
         out[circle] = node_color

From 95b20adee7ab33880163ffa81d51bd7f836a33e0 Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Tue, 5 Aug 2014 23:07:39 +0530
Subject: [PATCH 07/21] None comparison

---
 skimage/graph/rag.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skimage/graph/rag.py b/skimage/graph/rag.py
index 4447c4e3..f3c22f83 100644
--- a/skimage/graph/rag.py
+++ b/skimage/graph/rag.py
@@ -314,7 +314,7 @@ def draw_rag(labels, rag, img, border_color=None, node_color='yellow',
         # Because we kept the offset as 1
         rag.node[region['label'] - 1]['centroid'] = region['centroid']
 
-    if not border_color is None:
+    if border_color is not None:
         border_color = cc.to_rgb(border_color)
         out = segmentation.mark_boundaries(out, rag_labels, color=border_color)
 

From adeb8689afaeea1852cb3d0dd9ccf76c0ccb509a Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Tue, 5 Aug 2014 23:43:07 +0530
Subject: [PATCH 08/21] Fixed doctest

---
 skimage/graph/rag.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skimage/graph/rag.py b/skimage/graph/rag.py
index f3c22f83..7e87a784 100644
--- a/skimage/graph/rag.py
+++ b/skimage/graph/rag.py
@@ -289,7 +289,7 @@ def draw_rag(labels, rag, img, border_color=None, node_color='yellow',
     >>> img = data.coffee()
     >>> labels = segmentation.slic(img)
     >>> g =  graph.rag_mean_color(img, labels)
-    >>> out = graph.rag_draw(labels, g, img)
+    >>> out = graph.draw_rag(labels, g, img)
     """
     rag = rag.copy()
     out = util.img_as_float(img)

From 5bd55071bc28a9ff402e966b976ef7d379c4e89d Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Wed, 6 Aug 2014 00:32:47 +0530
Subject: [PATCH 09/21] handled matplotlib not present case

---
 skimage/graph/rag.py | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/skimage/graph/rag.py b/skimage/graph/rag.py
index 7e87a784..e3849184 100644
--- a/skimage/graph/rag.py
+++ b/skimage/graph/rag.py
@@ -13,17 +13,14 @@ except ImportError:
 import numpy as np
 from scipy.ndimage import filters
 from scipy import ndimage as nd
-<<<<<<< HEAD
 import math
-from .. import draw, measure, segmentation
-=======
-from .. import draw
-from .. import measure
-from .. import segmentation
-from matplotlib import colors
-from matplotlib import cm
-from .. import util
->>>>>>> rebase and change API to support mpl colorspec
+from .. import draw, measure, segmentation, util
+try:
+    from matplotlib import colors
+    from matplotlib import cm
+except ImportError:
+    pass
+
 
 
 def min_weight(graph, src, dst, n):

From bcbfdb28f59170c2c96aea9444c093e9556f6df2 Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Thu, 14 Aug 2014 01:20:55 +0530
Subject: [PATCH 10/21] add desaturate option

---
 doc/examples/plot_rag_draw.py |  4 ++--
 skimage/graph/rag.py          | 38 ++++++++++++++++++++++-------------
 2 files changed, 26 insertions(+), 16 deletions(-)

diff --git a/doc/examples/plot_rag_draw.py b/doc/examples/plot_rag_draw.py
index 21dbbc28..61d7e134 100644
--- a/doc/examples/plot_rag_draw.py
+++ b/doc/examples/plot_rag_draw.py
@@ -19,8 +19,8 @@ plt.figure()
 plt.title("RAG with all edges shown in green.")
 plt.imshow(out)
 
-cmap = colors.ListedColormap(['cyan', 'red'])
-out = graph.draw_rag(labels, g, img, colormap=cmap, thresh=30)
+cmap = colors.ListedColormap(['#00ff00', '#ff0000'])
+out = graph.draw_rag(labels, g, img,colormap=cmap, thresh=30, desaturate=True)
 plt.figure()
 plt.title("RAG with edge weights less than 30, color "
           "mapped between green and red.")
diff --git a/skimage/graph/rag.py b/skimage/graph/rag.py
index e3849184..e1ab79ca 100644
--- a/skimage/graph/rag.py
+++ b/skimage/graph/rag.py
@@ -14,7 +14,7 @@ import numpy as np
 from scipy.ndimage import filters
 from scipy import ndimage as nd
 import math
-from .. import draw, measure, segmentation, util
+from .. import draw, measure, segmentation, util, color
 try:
     from matplotlib import colors
     from matplotlib import cm
@@ -246,8 +246,9 @@ def rag_mean_color(image, labels, connectivity=2, mode='distance',
     return graph
 
 
-def draw_rag(labels, rag, img, border_color=None, node_color='yellow',
-             edge_color='green', colormap=None, thresh=np.inf):
+def draw_rag(labels, rag, img, border_color=None, node_color='#ffff00',
+             edge_color='#00ff00', colormap=None, thresh=np.inf,
+             desaturate=False, in_place=True):
     """Draw a Region Adjacency Graph on an image.
 
     Given a labelled image and its corresponding RAG, draw the nodes and edges
@@ -256,11 +257,11 @@ def draw_rag(labels, rag, img, border_color=None, node_color='yellow',
 
     Parameters
     ----------
-    labels : ndarray, shape(M, N)
+    labels : ndarray, shape (M, N)
         The labelled image.
     rag : RAG
         The Region Adjacency Graph.
-    img : ndarray, shape(M, N, 3)
+    img : ndarray, shape (M, N, 3)
         Input image.
     border_color : colorspec, optional
         Any matplotlib colorspec.
@@ -274,10 +275,16 @@ def draw_rag(labels, rag, img, border_color=None, node_color='yellow',
     thresh : float, optional
         Edges with weight below `thresh` are not drawn, or considered for color
         mapping.
+    desaturate : bool, optional
+        Convert the image to grayscale before displaying. Particularly helps
+        visualiztion when using the `colormap` option.
+    in_place : bool, optional
+        If set, the RAG is modified in place. For each node `n` the function
+        will set a new attribute ``rag.node[n]['centroid']``.
 
     Returns
     -------
-    out : ndarray, shape(M, N, [..., P,] 3)
+    out : ndarray, shape (M, N, 3)
         The image with the RAG drawn.
 
     Examples
@@ -288,7 +295,13 @@ def draw_rag(labels, rag, img, border_color=None, node_color='yellow',
     >>> g =  graph.rag_mean_color(img, labels)
     >>> out = graph.draw_rag(labels, g, img)
     """
-    rag = rag.copy()
+    if not in_place:
+        rag = rag.copy()
+
+    if desaturate:
+        img = color.rgb2gray(img)
+        img = color.gray2rgb(img)
+
     out = util.img_as_float(img)
     cc = colors.ColorConverter()
 
@@ -305,11 +318,10 @@ def draw_rag(labels, rag, img, border_color=None, node_color='yellow',
         offset += 1
 
     rag_labels = map_array[labels]
-
     regions = measure.regionprops(rag_labels)
-    for region in regions:
-        # Because we kept the offset as 1
-        rag.node[region['label'] - 1]['centroid'] = region['centroid']
+
+    for (n, data), region in zip(rag.nodes_iter(data=True), regions):
+        data['centroid'] = region['centroid']
 
     if border_color is not None:
         border_color = cc.to_rgb(border_color)
@@ -328,12 +340,10 @@ def draw_rag(labels, rag, img, border_color=None, node_color='yellow',
             continue
         r1, c1 = map(int, rag.node[n1]['centroid'])
         r2, c2 = map(int, rag.node[n2]['centroid'])
-
         line = draw.line(r1, c1, r2, c2)
 
         if colormap is not None:
-            current_color = smap.to_rgba([data['weight']])[0][:-1]
-            out[line] = current_color
+            out[line] = smap.to_rgba([data['weight']])[0][:-1]
         else:
             out[line] = edge_color
 

From 3553809c55cb9042f197cfee1fdd89b8fafc5da3 Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Thu, 14 Aug 2014 01:24:02 +0530
Subject: [PATCH 11/21] pep8

---
 doc/examples/plot_rag_draw.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/examples/plot_rag_draw.py b/doc/examples/plot_rag_draw.py
index 61d7e134..9c9d68b0 100644
--- a/doc/examples/plot_rag_draw.py
+++ b/doc/examples/plot_rag_draw.py
@@ -20,7 +20,7 @@ plt.title("RAG with all edges shown in green.")
 plt.imshow(out)
 
 cmap = colors.ListedColormap(['#00ff00', '#ff0000'])
-out = graph.draw_rag(labels, g, img,colormap=cmap, thresh=30, desaturate=True)
+out = graph.draw_rag(labels, g, img, colormap=cmap, thresh=30, desaturate=True)
 plt.figure()
 plt.title("RAG with edge weights less than 30, color "
           "mapped between green and red.")

From 5c5b60df4cde95d1115c8c303ca9f48fe708f169 Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Fri, 15 Aug 2014 02:32:23 +0530
Subject: [PATCH 12/21] Chnaged palette in example

---
 doc/examples/plot_rag_draw.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/doc/examples/plot_rag_draw.py b/doc/examples/plot_rag_draw.py
index 9c9d68b0..bb8042d8 100644
--- a/doc/examples/plot_rag_draw.py
+++ b/doc/examples/plot_rag_draw.py
@@ -19,8 +19,11 @@ plt.figure()
 plt.title("RAG with all edges shown in green.")
 plt.imshow(out)
 
-cmap = colors.ListedColormap(['#00ff00', '#ff0000'])
-out = graph.draw_rag(labels, g, img, colormap=cmap, thresh=30, desaturate=True)
+# The color palette used was taken from
+# http://www.colorcombos.com/color-schemes/2/ColorCombo2.html
+cmap = colors.ListedColormap(['#6599FF', '#ff9900'])
+out = graph.draw_rag(labels, g, img, node_color="#ffde00", colormap=cmap,
+                     thresh=30, desaturate=True)
 plt.figure()
 plt.title("RAG with edge weights less than 30, color "
           "mapped between green and red.")

From cfaa83cf26f3d12f0454b1a62e41fabc0e76a63b Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Fri, 15 Aug 2014 02:33:09 +0530
Subject: [PATCH 13/21] Chnaged palette in example

---
 doc/examples/plot_rag_draw.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/examples/plot_rag_draw.py b/doc/examples/plot_rag_draw.py
index bb8042d8..49bdf42c 100644
--- a/doc/examples/plot_rag_draw.py
+++ b/doc/examples/plot_rag_draw.py
@@ -18,6 +18,7 @@ out = graph.draw_rag(labels, g, img)
 plt.figure()
 plt.title("RAG with all edges shown in green.")
 plt.imshow(out)
+io.imsave("/home/vighnesh/Desktop/1.png")
 
 # The color palette used was taken from
 # http://www.colorcombos.com/color-schemes/2/ColorCombo2.html
@@ -28,5 +29,6 @@ plt.figure()
 plt.title("RAG with edge weights less than 30, color "
           "mapped between green and red.")
 
+io.imsave("/home/vighnesh/Desktop/2.png")
 plt.imshow(out)
 plt.show()

From 82f158482e38e519cdb9af776e7937c23dbbe67f Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Fri, 15 Aug 2014 02:35:28 +0530
Subject: [PATCH 14/21] removed file save

---
 doc/examples/plot_rag_draw.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/doc/examples/plot_rag_draw.py b/doc/examples/plot_rag_draw.py
index 49bdf42c..bb8042d8 100644
--- a/doc/examples/plot_rag_draw.py
+++ b/doc/examples/plot_rag_draw.py
@@ -18,7 +18,6 @@ out = graph.draw_rag(labels, g, img)
 plt.figure()
 plt.title("RAG with all edges shown in green.")
 plt.imshow(out)
-io.imsave("/home/vighnesh/Desktop/1.png")
 
 # The color palette used was taken from
 # http://www.colorcombos.com/color-schemes/2/ColorCombo2.html
@@ -29,6 +28,5 @@ plt.figure()
 plt.title("RAG with edge weights less than 30, color "
           "mapped between green and red.")
 
-io.imsave("/home/vighnesh/Desktop/2.png")
 plt.imshow(out)
 plt.show()

From e42c0652434535459d3f4c903d7dd324091c8090 Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Fri, 15 Aug 2014 02:37:59 +0530
Subject: [PATCH 15/21] corrected title

---
 doc/examples/plot_rag_draw.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/examples/plot_rag_draw.py b/doc/examples/plot_rag_draw.py
index bb8042d8..2572a3fb 100644
--- a/doc/examples/plot_rag_draw.py
+++ b/doc/examples/plot_rag_draw.py
@@ -26,7 +26,7 @@ out = graph.draw_rag(labels, g, img, node_color="#ffde00", colormap=cmap,
                      thresh=30, desaturate=True)
 plt.figure()
 plt.title("RAG with edge weights less than 30, color "
-          "mapped between green and red.")
+          "mapped between blue and orange.")
 
 plt.imshow(out)
 plt.show()

From 7730eb004e68ffe382cf3a57ae0ca26f4ec618ef Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Fri, 15 Aug 2014 14:13:36 +0530
Subject: [PATCH 16/21] fixed init

---
 skimage/graph/__init__.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/skimage/graph/__init__.py b/skimage/graph/__init__.py
index 2cd422ba..29bcb031 100644
--- a/skimage/graph/__init__.py
+++ b/skimage/graph/__init__.py
@@ -2,7 +2,6 @@ from .spath import shortest_path
 from .mcp import MCP, MCP_Geometric, MCP_Connect, MCP_Flexible, route_through_array
 from .rag import rag_mean_color, RAG
 from .graph_cut import cut_threshold, cut_normalized
-from .rag import rag_mean_color, RAG, rag_draw
 from .rag import rag_mean_color, RAG, draw_rag
 from .graph_cut import cut_threshold
 ncut = cut_normalized
@@ -18,6 +17,5 @@ __all__ = ['shortest_path',
            'cut_threshold',
            'cut_normalized',
            'ncut',
-           'rag_draw',
            'draw_rag',
            'RAG']

From 4bb4076959b0c6e9f6986dbc7ef4381eb7bc21de Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Fri, 15 Aug 2014 14:15:02 +0530
Subject: [PATCH 17/21] fixed imports

---
 skimage/graph/__init__.py | 2 --
 skimage/graph/rag.py      | 1 -
 2 files changed, 3 deletions(-)

diff --git a/skimage/graph/__init__.py b/skimage/graph/__init__.py
index 29bcb031..6da4fcc8 100644
--- a/skimage/graph/__init__.py
+++ b/skimage/graph/__init__.py
@@ -1,9 +1,7 @@
 from .spath import shortest_path
 from .mcp import MCP, MCP_Geometric, MCP_Connect, MCP_Flexible, route_through_array
-from .rag import rag_mean_color, RAG
 from .graph_cut import cut_threshold, cut_normalized
 from .rag import rag_mean_color, RAG, draw_rag
-from .graph_cut import cut_threshold
 ncut = cut_normalized
 
 
diff --git a/skimage/graph/rag.py b/skimage/graph/rag.py
index e1ab79ca..74e4ab07 100644
--- a/skimage/graph/rag.py
+++ b/skimage/graph/rag.py
@@ -22,7 +22,6 @@ except ImportError:
     pass
 
 
-
 def min_weight(graph, src, dst, n):
     """Callback to handle merging nodes by choosing minimum weight.
 

From 6e09628fb909110bf1b79f333a411b4a02a5b57f Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Fri, 15 Aug 2014 14:37:14 +0530
Subject: [PATCH 18/21] update relase doc

---
 doc/release/release_dev.txt | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/doc/release/release_dev.txt b/doc/release/release_dev.txt
index 1123eb77..cbeded27 100644
--- a/doc/release/release_dev.txt
+++ b/doc/release/release_dev.txt
@@ -14,9 +14,12 @@ http://scikit-image.org
 
 New Features
 ------------
-
-
-
+Region Adjacency Graphs
+ - Color distance RAGs (#1031)
+ - Threshold Cut on RAGs (#1031)
+ - Similarity RAGs (#1080)
+ - Normalized Cut on RAGs (#1080)
+ - RAG Drawing (#1087)
 
 Improvements
 ------------

From c43180fa27b0add7a0ad71d9e159efdd156fac06 Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Fri, 15 Aug 2014 17:02:35 +0530
Subject: [PATCH 19/21] force copy

---
 skimage/graph/rag.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skimage/graph/rag.py b/skimage/graph/rag.py
index 74e4ab07..edd9ecde 100644
--- a/skimage/graph/rag.py
+++ b/skimage/graph/rag.py
@@ -301,7 +301,7 @@ def draw_rag(labels, rag, img, border_color=None, node_color='#ffff00',
         img = color.rgb2gray(img)
         img = color.gray2rgb(img)
 
-    out = util.img_as_float(img)
+    out = util.img_as_float(img, force_copy=True)
     cc = colors.ColorConverter()
 
     edge_color = cc.to_rgb(edge_color)

From 344e2a51c0cd4ec79843805393514402f1a18df9 Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Fri, 15 Aug 2014 17:52:25 +0530
Subject: [PATCH 20/21] cast labels in ncut

---
 skimage/graph/graph_cut.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skimage/graph/graph_cut.py b/skimage/graph/graph_cut.py
index 3f973e22..10ea77c4 100644
--- a/skimage/graph/graph_cut.py
+++ b/skimage/graph/graph_cut.py
@@ -120,7 +120,7 @@ def cut_normalized(labels, rag, thresh=0.001, num_cuts=10, in_place=True):
 
     _ncut_relabel(rag, thresh, num_cuts)
 
-    map_array = np.zeros(labels.max() + 1)
+    map_array = np.zeros(labels.max() + 1, dtype=labels.dtype)
     # Mapping from old labels to new
     for n, d in rag.nodes_iter(data=True):
         map_array[d['labels']] = d['ncut label']

From 3f7ce2e670b1be9c9f79ed8c7b51172c682c46b1 Mon Sep 17 00:00:00 2001
From: Vighnesh Birodkar <vighneshbirodkar@gmail.com>
Date: Fri, 15 Aug 2014 21:28:47 +0530
Subject: [PATCH 21/21] Added example with cubehelix

---
 doc/examples/plot_rag_draw.py | 7 +++++++
 skimage/graph/rag.py          | 6 +++---
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/doc/examples/plot_rag_draw.py b/doc/examples/plot_rag_draw.py
index 2572a3fb..abf2ba08 100644
--- a/doc/examples/plot_rag_draw.py
+++ b/doc/examples/plot_rag_draw.py
@@ -27,6 +27,13 @@ out = graph.draw_rag(labels, g, img, node_color="#ffde00", colormap=cmap,
 plt.figure()
 plt.title("RAG with edge weights less than 30, color "
           "mapped between blue and orange.")
+plt.imshow(out)
+
+plt.figure()
+plt.title("All edges drawn with cubehelix colormap")
+cmap = plt.get_cmap('cubehelix')
+out = graph.draw_rag(labels, g, img, colormap=cmap,
+                     desaturate=True)
 
 plt.imshow(out)
 plt.show()
diff --git a/skimage/graph/rag.py b/skimage/graph/rag.py
index edd9ecde..edaec4b3 100644
--- a/skimage/graph/rag.py
+++ b/skimage/graph/rag.py
@@ -251,8 +251,8 @@ def draw_rag(labels, rag, img, border_color=None, node_color='#ffff00',
     """Draw a Region Adjacency Graph on an image.
 
     Given a labelled image and its corresponding RAG, draw the nodes and edges
-    of the RAG on the image with the specified colors. Nodes are markes by
-    the centroids of the corresposning regions.
+    of the RAG on the image with the specified colors. Nodes are marked by
+    the centroids of the corresponding regions.
 
     Parameters
     ----------
@@ -276,7 +276,7 @@ def draw_rag(labels, rag, img, border_color=None, node_color='#ffff00',
         mapping.
     desaturate : bool, optional
         Convert the image to grayscale before displaying. Particularly helps
-        visualiztion when using the `colormap` option.
+        visualization when using the `colormap` option.
     in_place : bool, optional
         If set, the RAG is modified in place. For each node `n` the function
         will set a new attribute ``rag.node[n]['centroid']``.