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import networkx as nx
import numpy as np
from numpy.lib.stride_tricks import as_strided
from scipy import ndimage as ndi
from scipy import sparse
import math
from ... import measure, segmentation, util, color
def _edge_generator_from_csr(csr_matrix):
"""Yield weighted edge triples for use by NetworkX from a CSR matrix.
This function is a straight rewrite of
`networkx.convert_matrix._csr_gen_triples`. Since that is a private
function, it is safer to include our own here.
csr_matrix : scipy.sparse.csr_matrix
The input matrix. An edge (i, j, w) will be yielded if there is a
data value for coordinates (i, j) in the matrix, even if that value
is 0.
i, j, w : (int, int, float) tuples
Each value `w` in the matrix along with its coordinates (i, j).
>>> dense = np.eye(2, dtype=np.float)
>>> csr = sparse.csr_matrix(dense)
>>> edges = _edge_generator_from_csr(csr)
>>> list(edges)
[(0, 0, 1.0), (1, 1, 1.0)]
nrows = csr_matrix.shape[0]
values =
indptr = csr_matrix.indptr
col_indices = csr_matrix.indices
for i in range(nrows):
for j in range(indptr[i], indptr[i + 1]):
yield i, col_indices[j], values[j]
def min_weight(graph, src, dst, n):
"""Callback to handle merging nodes by choosing minimum weight.
Returns a dictionary with `"weight"` set as either the weight between
(`src`, `n`) or (`dst`, `n`) in `graph` or the minimum of the two when
both exist.
graph : RAG
The graph under consideration.
src, dst : int
The verices in `graph` to be merged.
n : int
A neighbor of `src` or `dst` or both.
data : dict
A dict with the `"weight"` attribute set the weight between
(`src`, `n`) or (`dst`, `n`) in `graph` or the minimum of the two when
both exist.
# cover the cases where n only has edge to either `src` or `dst`
default = {'weight': np.inf}
w1 = graph[n].get(src, default)['weight']
w2 = graph[n].get(dst, default)['weight']
return {'weight': min(w1, w2)}
def _add_edge_filter(values, graph):
"""Create edge in `graph` between central element of `values` and the rest.
Add an edge between the middle element in `values` and
all other elements of `values` into `graph`. ``values[len(values) // 2]``
is expected to be the central value of the footprint used.
values : array
The array to process.
graph : RAG
The graph to add edges in.
0 : float
Always returns 0. The return value is required so that `generic_filter`
can put it in the output array, but it is ignored by this filter.
values = values.astype(int)
center = values[len(values) // 2]
for value in values:
if value != center and not graph.has_edge(center, value):
graph.add_edge(center, value)
return 0.
class RAG(nx.Graph):
The Region Adjacency Graph (RAG) of an image, subclasses
`networx.Graph <>`_
label_image : array of int
An initial segmentation, with each region labeled as a different
integer. Every unique value in ``label_image`` will correspond to
a node in the graph.
connectivity : int in {1, ..., ``label_image.ndim``}, optional
The connectivity between pixels in ``label_image``. For a 2D image,
a connectivity of 1 corresponds to immediate neighbors up, down,
left, and right, while a connectivity of 2 also includes diagonal
neighbors. See `scipy.ndimage.generate_binary_structure`.
data : networkx Graph specification, optional
Initial or additional edges to pass to the NetworkX Graph
constructor. See `networkx.Graph`. Valid edge specifications
include edge list (list of tuples), NumPy arrays, and SciPy
sparse matrices.
**attr : keyword arguments, optional
Additional attributes to add to the graph.
def __init__(self, label_image=None, connectivity=1, data=None, **attr):
super(RAG, self).__init__(data, **attr)
if self.number_of_nodes() == 0:
self.max_id = 0
self.max_id = max(self.nodes())
if label_image is not None:
fp = ndi.generate_binary_structure(label_image.ndim, connectivity)
# In the next ``ndi.generic_filter`` function, the kwarg
# ``output`` is used to provide a strided array with a single
# 64-bit floating point number, to which the function repeatedly
# writes. This is done because even if we don't care about the
# output, without this, a float array of the same shape as the
# input image will be created and that could be expensive in
# memory consumption.
output=as_strided(np.empty((1,), dtype=np.float_),
strides=((0,) * label_image.ndim)),
def merge_nodes(self, src, dst, weight_func=min_weight, in_place=True,
extra_arguments=[], extra_keywords={}):
"""Merge node `src` and `dst`.
The new combined node is adjacent to all the neighbors of `src`
and `dst`. `weight_func` is called to decide the weight of edges
incident on the new node.
src, dst : int
Nodes to be merged.
weight_func : callable, optional
Function to decide the attributes of edges incident on the new
node. For each neighbor `n` for `src and `dst`, `weight_func` will
be called as follows: `weight_func(src, dst, n, *extra_arguments,
**extra_keywords)`. `src`, `dst` and `n` are IDs of vertices in the
RAG object which is in turn a subclass of `networkx.Graph`. It is
expected to return a dict of attributes of the resulting edge.
in_place : bool, optional
If set to `True`, the merged node has the id `dst`, else merged
node has a new id which is returned.
extra_arguments : sequence, optional
The sequence of extra positional arguments passed to
extra_keywords : dictionary, optional
The dict of keyword arguments passed to the `weight_func`.
id : int
The id of the new node.
If `in_place` is `False` the resulting node has a new id, rather than
src_nbrs = set(self.neighbors(src))
dst_nbrs = set(self.neighbors(dst))
neighbors = (src_nbrs | dst_nbrs) - {src, dst}
if in_place:
new = dst
new = self.next_id()
for neighbor in neighbors:
data = weight_func(self, src, new, neighbor, *extra_arguments,
self.add_edge(neighbor, new, attr_dict=data)
self.node[new]['labels'] = (self.node[src]['labels'] +
if not in_place:
return new
def add_node(self, n, attr_dict=None, **attr):
"""Add node `n` while updating the maximum node id.
.. seealso:: :func:`networkx.Graph.add_node`."""
if attr_dict is None: # compatibility with old networkx
attr_dict = attr
super(RAG, self).add_node(n, **attr_dict)
self.max_id = max(n, self.max_id)
def add_edge(self, u, v, attr_dict=None, **attr):
"""Add an edge between `u` and `v` while updating max node id.
.. seealso:: :func:`networkx.Graph.add_edge`."""
if attr_dict is None: # compatibility with old networkx
attr_dict = attr
super(RAG, self).add_edge(u, v, **attr_dict)
self.max_id = max(u, v, self.max_id)
def copy(self):
"""Copy the graph with its max node id.
.. seealso:: :func:`networkx.Graph.copy`."""
g = super(RAG, self).copy()
g.max_id = self.max_id
return g
def fresh_copy(self):
"""Return a fresh copy graph with the same data structure.
A fresh copy has no nodes, edges or graph attributes. It is
the same data structure as the current graph. This method is
typically used to create an empty version of the graph.
This is required when subclassing Graph with networkx v2 and
does not cause problems for v1. Here is more detail from
the network migrating from 1.x to 2.x document::
With the new GraphViews (SubGraph, ReversedGraph, etc)
you can't assume that ``G.__class__()`` will create a new
instance of the same graph type as ``G``. In fact, the
call signature for ``__class__`` differs depending on
whether ``G`` is a view or a base class. For v2.x you
should use ``G.fresh_copy()`` to create a null graph of
the correct type---ready to fill with nodes and edges.
return RAG()
def next_id(self):
"""Returns the `id` for the new node to be inserted.
The current implementation returns one more than the maximum `id`.
id : int
The `id` of the new node to be inserted.
return self.max_id + 1
def _add_node_silent(self, n):
"""Add node `n` without updating the maximum node id.
This is a convenience method used internally.
.. seealso:: :func:`networkx.Graph.add_node`."""
super(RAG, self).add_node(n)
def rag_mean_color(image, labels, connectivity=2, mode='distance',
"""Compute the Region Adjacency Graph using mean colors.
Given an image and its initial segmentation, this method constructs the
corresponding Region Adjacency Graph (RAG). Each node in the RAG
represents a set of pixels within `image` with the same label in `labels`.
The weight between two adjacent regions represents how similar or
dissimilar two regions are depending on the `mode` parameter.
image : ndarray, shape(M, N, [..., P,] 3)
Input image.
labels : ndarray, shape(M, N, [..., P])
The labelled image. This should have one dimension less than
`image`. If `image` has dimensions `(M, N, 3)` `labels` should have
dimensions `(M, N)`.
connectivity : int, optional
Pixels with a squared distance less than `connectivity` from each other
are considered adjacent. It can range from 1 to `labels.ndim`. Its
behavior is the same as `connectivity` parameter in
mode : {'distance', 'similarity'}, optional
The strategy to assign edge weights.
'distance' : The weight between two adjacent regions is the
:math:`|c_1 - c_2|`, where :math:`c_1` and :math:`c_2` are the mean
colors of the two regions. It represents the Euclidean distance in
their average color.
'similarity' : The weight between two adjacent is
:math:`e^{-d^2/sigma}` where :math:`d=|c_1 - c_2|`, where
:math:`c_1` and :math:`c_2` are the mean colors of the two regions.
It represents how similar two regions are.
sigma : float, optional
Used for computation when `mode` is "similarity". It governs how
close to each other two colors should be, for their corresponding edge
weight to be significant. A very large value of `sigma` could make
any two colors behave as though they were similar.
out : RAG
The region adjacency graph.
>>> from skimage import data, segmentation
>>> from skimage.future import graph
>>> img = data.astronaut()
>>> labels = segmentation.slic(img)
>>> rag = graph.rag_mean_color(img, labels)
.. [1] Alain Tremeau and Philippe Colantoni
"Regions Adjacency Graph Applied To Color Image Segmentation"
graph = RAG(labels, connectivity=connectivity)
for n in graph:
graph.node[n].update({'labels': [n],
'pixel count': 0,
'total color': np.array([0, 0, 0],
for index in np.ndindex(labels.shape):
current = labels[index]
graph.node[current]['pixel count'] += 1
graph.node[current]['total color'] += image[index]
for n in graph:
graph.node[n]['mean color'] = (graph.node[n]['total color'] /
graph.node[n]['pixel count'])
for x, y, d in graph.edges(data=True):
diff = graph.node[x]['mean color'] - graph.node[y]['mean color']
diff = np.linalg.norm(diff)
if mode == 'similarity':
d['weight'] = math.e ** (-(diff ** 2) / sigma)
elif mode == 'distance':
d['weight'] = diff
raise ValueError("The mode '%s' is not recognised" % mode)
return graph
def rag_boundary(labels, edge_map, connectivity=2):
""" Comouter RAG based on region boundaries
Given an image's initial segmentation and its edge map this method
constructs the corresponding Region Adjacency Graph (RAG). Each node in the
RAG represents a set of pixels within the image with the same label in
`labels`. The weight between two adjacent regions is the average value
in `edge_map` along their boundary.
labels : ndarray
The labelled image.
edge_map : ndarray
This should have the same shape as that of `labels`. For all pixels
along the boundary between 2 adjacent regions, the average value of the
corresponding pixels in `edge_map` is the edge weight between them.
connectivity : int, optional
Pixels with a squared distance less than `connectivity` from each other
are considered adjacent. It can range from 1 to `labels.ndim`. Its
behavior is the same as `connectivity` parameter in
>>> from skimage import data, segmentation, filters, color
>>> from skimage.future import graph
>>> img = data.chelsea()
>>> labels = segmentation.slic(img)
>>> edge_map = filters.sobel(color.rgb2gray(img))
>>> rag = graph.rag_boundary(labels, edge_map)
conn = ndi.generate_binary_structure(labels.ndim, connectivity)
eroded = ndi.grey_erosion(labels, footprint=conn)
dilated = ndi.grey_dilation(labels, footprint=conn)
boundaries0 = (eroded != labels)
boundaries1 = (dilated != labels)
labels_small = np.concatenate((eroded[boundaries0], labels[boundaries1]))
labels_large = np.concatenate((labels[boundaries0], dilated[boundaries1]))
n = np.max(labels_large) + 1
# use a dummy broadcast array as data for RAG
ones = as_strided(np.ones((1,), dtype=np.float), shape=labels_small.shape,
count_matrix = sparse.coo_matrix((ones, (labels_small, labels_large)),
dtype=np.int_, shape=(n, n)).tocsr()
data = np.concatenate((edge_map[boundaries0], edge_map[boundaries1]))
data_coo = sparse.coo_matrix((data, (labels_small, labels_large)))
graph_matrix = data_coo.tocsr() /=
rag = RAG()
for n in rag.nodes():
rag.node[n].update({'labels': [n]})
return rag
def show_rag(labels, rag, image, border_color='black', edge_width=1.5,
edge_cmap='magma', img_cmap='bone', in_place=True, ax=None):
"""Show a Region Adjacency Graph on an image.
Given a labelled image and its corresponding RAG, show the nodes and edges
of the RAG on the image with the specified colors. Edges are displayed between
the centroid of the 2 adjacent regions in the image.
labels : ndarray, shape (M, N)
The labelled image.
rag : RAG
The Region Adjacency Graph.
image : ndarray, shape (M, N[, 3])
Input image. If `colormap` is `None`, the image should be in RGB
border_color : color spec, optional
Color with which the borders between regions are drawn.
edge_width : float, optional
The thickness with which the RAG edges are drawn.
edge_cmap : :py:class:`matplotlib.colors.Colormap`, optional
Any matplotlib colormap with which the edges are drawn.
img_cmap : :py:class:`matplotlib.colors.Colormap`, optional
Any matplotlib colormap with which the image is draw. If set to `None`
the image is drawn as it is.
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']``.
ax : :py:class:`matplotlib.axes.Axes`, optional
The axes to draw on. If not specified, new axes are created and drawn
lc : :py:class:`matplotlib.collections.LineCollection`
A colection of lines that represent the edges of the graph. It can be
passed to the :meth:`matplotlib.figure.Figure.colorbar` function.
>>> from skimage import data, segmentation
>>> from skimage.future import graph
>>> import matplotlib.pyplot as plt
>>> img =
>>> labels = segmentation.slic(img)
>>> g = graph.rag_mean_color(img, labels)
>>> lc = graph.show_rag(labels, g, img)
>>> cbar = plt.colorbar(lc)
from matplotlib import colors, cm
from matplotlib import pyplot as plt
from matplotlib.collections import LineCollection
if not in_place:
rag = rag.copy()
if ax is None:
fig, ax = plt.subplots()
out = util.img_as_float(image, force_copy=True)
if img_cmap is None:
if image.ndim < 3 or image.shape[2] not in [3, 4]:
msg = 'If colormap is `None`, an RGB or RGBA image should be given'
raise ValueError(msg)
# Ignore the alpha channel
out = image[:, :, :3]
img_cmap = cm.get_cmap(img_cmap)
out = color.rgb2gray(image)
# Ignore the alpha channel
out = img_cmap(out)[:, :, :3]
edge_cmap = cm.get_cmap(edge_cmap)
# 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(data=True):
for label in d['labels']:
map_array[label] = offset
offset += 1
rag_labels = map_array[labels]
regions = measure.regionprops(rag_labels)
for (n, data), region in zip(rag.nodes(data=True), regions):
data['centroid'] = tuple(map(int, region['centroid']))
cc = colors.ColorConverter()
if border_color is not None:
border_color = cc.to_rgb(border_color)
out = segmentation.mark_boundaries(out, rag_labels, color=border_color)
# Defining the end points of the edges
# The tuple[::-1] syntax reverses a tuple as matplotlib uses (x,y)
# convention while skimage uses (row, column)
lines = [[rag.node[n1]['centroid'][::-1], rag.node[n2]['centroid'][::-1]]
for (n1, n2) in rag.edges()]
lc = LineCollection(lines, linewidths=edge_width, cmap=edge_cmap)
edge_weights = [d['weight'] for x, y, d in rag.edges(data=True)]
return lc
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