Fixed database typo and removed unnecessary class identifier.

venv/Lib/site-packages/skimage/future/__init__.py

@@ -0,0 +1,15 @@
+"""Functionality with an experimental API. Although you can count on the
+functions in this package being around in the future, the API may change with
+any version update **and will not follow the skimage two-version deprecation
+path**. Therefore, use the functions herein with care, and do not use them in
+production code that will depend on updated skimage versions.
+"""
+
+from . import graph
+from .manual_segmentation import manual_polygon_segmentation
+from .manual_segmentation import manual_lasso_segmentation
+
+
+__all__ = ['graph',
+           'manual_lasso_segmentation',
+           'manual_polygon_segmentation']

venv/Lib/site-packages/skimage/future/graph/__init__.py

@@ -0,0 +1,13 @@
+from .graph_cut import cut_threshold, cut_normalized
+from .rag import rag_mean_color, RAG, show_rag, rag_boundary
+from .graph_merge import merge_hierarchical
+ncut = cut_normalized
+
+__all__ = ['rag_mean_color',
+           'cut_threshold',
+           'cut_normalized',
+           'ncut',
+           'show_rag',
+           'merge_hierarchical',
+           'rag_boundary',
+           'RAG']

venv/Lib/site-packages/skimage/future/graph/_ncut.py

@@ -0,0 +1,68 @@
+try:
+    import networkx as nx
+except ImportError:
+    from ..._shared.utils import warn
+    warn('RAGs require networkx')
+import numpy as np
+from scipy import sparse
+from . import _ncut_cy
+
+
+def DW_matrices(graph):
+    """Returns the diagonal and weight matrices of a graph.
+
+    Parameters
+    ----------
+    graph : RAG
+        A Region Adjacency Graph.
+
+    Returns
+    -------
+    D : csc_matrix
+        The diagonal matrix of the graph. ``D[i, i]`` is the sum of weights of
+        all edges incident on `i`. All other entries are `0`.
+    W : csc_matrix
+        The weight matrix of the graph. ``W[i, j]`` is the weight of the edge
+        joining `i` to `j`.
+    """
+    # sparse.eighsh is most efficient with CSC-formatted input
+    W = nx.to_scipy_sparse_matrix(graph, format='csc')
+    entries = W.sum(axis=0)
+    D = sparse.dia_matrix((entries, 0), shape=W.shape).tocsc()
+
+    return D, W
+
+
+def ncut_cost(cut, D, W):
+    """Returns the N-cut cost of a bi-partition of a graph.
+
+    Parameters
+    ----------
+    cut : ndarray
+        The mask for the nodes in the graph. Nodes corresponding to a `True`
+        value are in one set.
+    D : csc_matrix
+        The diagonal matrix of the graph.
+    W : csc_matrix
+        The weight matrix of the graph.
+
+    Returns
+    -------
+    cost : float
+        The cost of performing the N-cut.
+
+    References
+    ----------
+    .. [1] Normalized Cuts and Image Segmentation, Jianbo Shi and
+           Jitendra Malik, IEEE Transactions on Pattern Analysis and Machine
+           Intelligence, Page 889, Equation 2.
+    """
+    cut = np.array(cut)
+    cut_cost = _ncut_cy.cut_cost(cut, W)
+
+    # D has elements only along the diagonal, one per node, so we can directly
+    # index the data attribute with cut.
+    assoc_a = D.data[cut].sum()
+    assoc_b = D.data[~cut].sum()
+
+    return (cut_cost / assoc_a) + (cut_cost / assoc_b)

venv/Lib/site-packages/skimage/future/graph/graph_cut.py

@@ -0,0 +1,305 @@
+try:
+    import networkx as nx
+except ImportError:
+    from ..._shared.utils import warn
+    warn('RAGs require networkx')
+import numpy as np
+from . import _ncut
+from . import _ncut_cy
+from ..._shared.utils import check_random_state
+from scipy.sparse import linalg
+
+
+def cut_threshold(labels, rag, thresh, in_place=True):
+    """Combine regions separated by weight less than threshold.
+
+    Given an image's labels and its RAG, output new labels by
+    combining regions whose nodes are separated by a weight less
+    than the given threshold.
+
+    Parameters
+    ----------
+    labels : ndarray
+        The array of labels.
+    rag : RAG
+        The region adjacency graph.
+    thresh : float
+        The threshold. Regions connected by edges with smaller weights are
+        combined.
+    in_place : bool
+        If set, modifies `rag` in place. The function will remove the edges
+        with weights less that `thresh`. If set to `False` the function
+        makes a copy of `rag` before proceeding.
+
+    Returns
+    -------
+    out : ndarray
+        The new labelled array.
+
+    Examples
+    --------
+    >>> from skimage import data, segmentation
+    >>> from skimage.future import graph
+    >>> img = data.astronaut()
+    >>> labels = segmentation.slic(img)
+    >>> rag = graph.rag_mean_color(img, labels)
+    >>> new_labels = graph.cut_threshold(labels, rag, 10)
+
+    References
+    ----------
+    .. [1] Alain Tremeau and Philippe Colantoni
+           "Regions Adjacency Graph Applied To Color Image Segmentation"
+           :DOI:`10.1109/83.841950`
+
+    """
+    if not in_place:
+        rag = rag.copy()
+
+    # Because deleting edges while iterating through them produces an error.
+    to_remove = [(x, y) for x, y, d in rag.edges(data=True)
+                 if d['weight'] >= thresh]
+    rag.remove_edges_from(to_remove)
+
+    comps = nx.connected_components(rag)
+
+    # We construct an array which can map old labels to the new ones.
+    # All the labels within a connected component are assigned to a single
+    # label in the output.
+    map_array = np.arange(labels.max() + 1, dtype=labels.dtype)
+    for i, nodes in enumerate(comps):
+        for node in nodes:
+            for label in rag.nodes[node]['labels']:
+                map_array[label] = i
+
+    return map_array[labels]
+
+
+def cut_normalized(labels, rag, thresh=0.001, num_cuts=10, in_place=True,
+                   max_edge=1.0,
+                   *,
+                   random_state=None,
+                   ):
+    """Perform Normalized Graph cut on the Region Adjacency Graph.
+
+    Given an image's labels and its similarity RAG, recursively perform
+    a 2-way normalized cut on it. All nodes belonging to a subgraph
+    that cannot be cut further are assigned a unique label in the
+    output.
+
+    Parameters
+    ----------
+    labels : ndarray
+        The array of labels.
+    rag : RAG
+        The region adjacency graph.
+    thresh : float
+        The threshold. A subgraph won't be further subdivided if the
+        value of the N-cut exceeds `thresh`.
+    num_cuts : int
+        The number or N-cuts to perform before determining the optimal one.
+    in_place : bool
+        If set, modifies `rag` in place. For each node `n` the function will
+        set a new attribute ``rag.nodes[n]['ncut label']``.
+    max_edge : float, optional
+        The maximum possible value of an edge in the RAG. This corresponds to
+        an edge between identical regions. This is used to put self
+        edges in the RAG.
+    random_state : int, RandomState instance or None, optional
+        If int, random_state is the seed used by the random number generator;
+        If RandomState instance, random_state is the random number generator;
+        If None, the random number generator is the RandomState instance used
+        by `np.random`. The random state is used for the starting point
+        of `scipy.sparse.linalg.eigsh`.
+
+    Returns
+    -------
+    out : ndarray
+        The new labeled array.
+
+    Examples
+    --------
+    >>> from skimage import data, segmentation
+    >>> from skimage.future import graph
+    >>> img = data.astronaut()
+    >>> labels = segmentation.slic(img)
+    >>> rag = graph.rag_mean_color(img, labels, mode='similarity')
+    >>> new_labels = graph.cut_normalized(labels, rag)
+
+    References
+    ----------
+    .. [1] Shi, J.; Malik, J., "Normalized cuts and image segmentation",
+           Pattern Analysis and Machine Intelligence,
+           IEEE Transactions on, vol. 22, no. 8, pp. 888-905, August 2000.
+
+    """
+    random_state = check_random_state(random_state)
+    if not in_place:
+        rag = rag.copy()
+
+    for node in rag.nodes():
+        rag.add_edge(node, node, weight=max_edge)
+
+    _ncut_relabel(rag, thresh, num_cuts, random_state)
+
+    map_array = np.zeros(labels.max() + 1, dtype=labels.dtype)
+    # Mapping from old labels to new
+    for n, d in rag.nodes(data=True):
+        map_array[d['labels']] = d['ncut label']
+
+    return map_array[labels]
+
+
+def partition_by_cut(cut, rag):
+    """Compute resulting subgraphs from given bi-partition.
+
+    Parameters
+    ----------
+    cut : array
+        A array of booleans. Elements set to `True` belong to one
+        set.
+    rag : RAG
+        The Region Adjacency Graph.
+
+    Returns
+    -------
+    sub1, sub2 : RAG
+        The two resulting subgraphs from the bi-partition.
+    """
+    # `cut` is derived from `D` and `W` matrices, which also follow the
+    # ordering returned by `rag.nodes()` because we use
+    # nx.to_scipy_sparse_matrix.
+
+    # Example
+    # rag.nodes() = [3, 7, 9, 13]
+    # cut = [True, False, True, False]
+    # nodes1 = [3, 9]
+    # nodes2 = [7, 10]
+
+    nodes1 = [n for i, n in enumerate(rag.nodes()) if cut[i]]
+    nodes2 = [n for i, n in enumerate(rag.nodes()) if not cut[i]]
+
+    sub1 = rag.subgraph(nodes1)
+    sub2 = rag.subgraph(nodes2)
+
+    return sub1, sub2
+
+
+def get_min_ncut(ev, d, w, num_cuts):
+    """Threshold an eigenvector evenly, to determine minimum ncut.
+
+    Parameters
+    ----------
+    ev : array
+        The eigenvector to threshold.
+    d : ndarray
+        The diagonal matrix of the graph.
+    w : ndarray
+        The weight matrix of the graph.
+    num_cuts : int
+        The number of evenly spaced thresholds to check for.
+
+    Returns
+    -------
+    mask : array
+        The array of booleans which denotes the bi-partition.
+    mcut : float
+        The value of the minimum ncut.
+    """
+    mcut = np.inf
+    mn = ev.min()
+    mx = ev.max()
+
+    # If all values in `ev` are equal, it implies that the graph can't be
+    # further sub-divided. In this case the bi-partition is the the graph
+    # itself and an empty set.
+    min_mask = np.zeros_like(ev, dtype=np.bool)
+    if np.allclose(mn, mx):
+        return min_mask, mcut
+
+    # Refer Shi & Malik 2001, Section 3.1.3, Page 892
+    # Perform evenly spaced n-cuts and determine the optimal one.
+    for t in np.linspace(mn, mx, num_cuts, endpoint=False):
+        mask = ev > t
+        cost = _ncut.ncut_cost(mask, d, w)
+        if cost < mcut:
+            min_mask = mask
+            mcut = cost
+
+    return min_mask, mcut
+
+
+def _label_all(rag, attr_name):
+    """Assign a unique integer to the given attribute in the RAG.
+
+    This function assumes that all labels in `rag` are unique. It
+    picks up a random label from them and assigns it to the `attr_name`
+    attribute of all the nodes.
+
+    rag : RAG
+        The Region Adjacency Graph.
+    attr_name : string
+        The attribute to which a unique integer is assigned.
+    """
+    node = min(rag.nodes())
+    new_label = rag.nodes[node]['labels'][0]
+    for n, d in rag.nodes(data=True):
+        d[attr_name] = new_label
+
+
+def _ncut_relabel(rag, thresh, num_cuts, random_state):
+    """Perform Normalized Graph cut on the Region Adjacency Graph.
+
+    Recursively partition the graph into 2, until further subdivision
+    yields a cut greater than `thresh` or such a cut cannot be computed.
+    For such a subgraph, indices to labels of all its nodes map to a single
+    unique value.
+
+    Parameters
+    ----------
+    rag : RAG
+        The region adjacency graph.
+    thresh : float
+        The threshold. A subgraph won't be further subdivided if the
+        value of the N-cut exceeds `thresh`.
+    num_cuts : int
+        The number or N-cuts to perform before determining the optimal one.
+    random_state: RandomState instance
+        Provides initial values for eigenvalue solver.
+    """
+    d, w = _ncut.DW_matrices(rag)
+    m = w.shape[0]
+
+    if m > 2:
+        d2 = d.copy()
+        # Since d is diagonal, we can directly operate on its data
+        # the inverse of the square root
+        d2.data = np.reciprocal(np.sqrt(d2.data, out=d2.data), out=d2.data)
+
+        # Refer Shi & Malik 2001, Equation 7, Page 891
+        A = d2 * (d - w) * d2
+        # Initialize the vector to ensure reproducibility.
+        v0 = random_state.rand(A.shape[0])
+        vals, vectors = linalg.eigsh(A, which='SM', v0=v0,
+                                     k=min(100, m - 2))
+
+        # Pick second smallest eigenvector.
+        # Refer Shi & Malik 2001, Section 3.2.3, Page 893
+        vals, vectors = np.real(vals), np.real(vectors)
+        index2 = _ncut_cy.argmin2(vals)
+        ev = vectors[:, index2]
+
+        cut_mask, mcut = get_min_ncut(ev, d, w, num_cuts)
+        if (mcut < thresh):
+            # Sub divide and perform N-cut again
+            # Refer Shi & Malik 2001, Section 3.2.5, Page 893
+            sub1, sub2 = partition_by_cut(cut_mask, rag)
+
+            _ncut_relabel(sub1, thresh, num_cuts, random_state)
+            _ncut_relabel(sub2, thresh, num_cuts, random_state)
+            return
+
+    # The N-cut wasn't small enough, or could not be computed.
+    # The remaining graph is a region.
+    # Assign `ncut label` by picking any label from the existing nodes, since
+    # `labels` are unique, `new_label` is also unique.
+    _label_all(rag, 'ncut label')

venv/Lib/site-packages/skimage/future/graph/graph_merge.py

@@ -0,0 +1,137 @@
+import numpy as np
+import heapq
+
+
+def _revalidate_node_edges(rag, node, heap_list):
+    """Handles validation and invalidation of edges incident to a node.
+
+    This function invalidates all existing edges incident on `node` and inserts
+    new items in `heap_list` updated with the valid weights.
+
+    rag : RAG
+        The Region Adjacency Graph.
+    node : int
+        The id of the node whose incident edges are to be validated/invalidated
+        .
+    heap_list : list
+        The list containing the existing heap of edges.
+    """
+    # networkx updates data dictionary if edge exists
+    # this would mean we have to reposition these edges in
+    # heap if their weight is updated.
+    # instead we invalidate them
+
+    for nbr in rag.neighbors(node):
+        data = rag[node][nbr]
+        try:
+            # invalidate edges incident on `dst`, they have new weights
+            data['heap item'][3] = False
+            _invalidate_edge(rag, node, nbr)
+        except KeyError:
+            # will handle the case where the edge did not exist in the existing
+            # graph
+            pass
+
+        wt = data['weight']
+        heap_item = [wt, node, nbr, True]
+        data['heap item'] = heap_item
+        heapq.heappush(heap_list, heap_item)
+
+
+def _rename_node(graph, node_id, copy_id):
+    """ Rename `node_id` in `graph` to `copy_id`. """
+
+    graph._add_node_silent(copy_id)
+    graph.nodes[copy_id].update(graph.nodes[node_id])
+
+    for nbr in graph.neighbors(node_id):
+        wt = graph[node_id][nbr]['weight']
+        graph.add_edge(nbr, copy_id, {'weight': wt})
+
+    graph.remove_node(node_id)
+
+
+def _invalidate_edge(graph, n1, n2):
+    """ Invalidates the edge (n1, n2) in the heap. """
+    graph[n1][n2]['heap item'][3] = False
+
+
+def merge_hierarchical(labels, rag, thresh, rag_copy, in_place_merge,
+                       merge_func, weight_func):
+    """Perform hierarchical merging of a RAG.
+
+    Greedily merges the most similar pair of nodes until no edges lower than
+    `thresh` remain.
+
+    Parameters
+    ----------
+    labels : ndarray
+        The array of labels.
+    rag : RAG
+        The Region Adjacency Graph.
+    thresh : float
+        Regions connected by an edge with weight smaller than `thresh` are
+        merged.
+    rag_copy : bool
+        If set, the RAG copied before modifying.
+    in_place_merge : bool
+        If set, the nodes are merged in place. Otherwise, a new node is
+        created for each merge..
+    merge_func : callable
+        This function is called before merging two nodes. For the RAG `graph`
+        while merging `src` and `dst`, it is called as follows
+        ``merge_func(graph, src, dst)``.
+    weight_func : callable
+        The function to compute the new weights of the nodes adjacent to the
+        merged node. This is directly supplied as the argument `weight_func`
+        to `merge_nodes`.
+
+    Returns
+    -------
+    out : ndarray
+        The new labeled array.
+
+    """
+    if rag_copy:
+        rag = rag.copy()
+
+    edge_heap = []
+    for n1, n2, data in rag.edges(data=True):
+        # Push a valid edge in the heap
+        wt = data['weight']
+        heap_item = [wt, n1, n2, True]
+        heapq.heappush(edge_heap, heap_item)
+
+        # Reference to the heap item in the graph
+        data['heap item'] = heap_item
+
+    while len(edge_heap) > 0 and edge_heap[0][0] < thresh:
+        _, n1, n2, valid = heapq.heappop(edge_heap)
+
+        # Ensure popped edge is valid, if not, the edge is discarded
+        if valid:
+            # Invalidate all neigbors of `src` before its deleted
+
+            for nbr in rag.neighbors(n1):
+                _invalidate_edge(rag, n1, nbr)
+
+            for nbr in rag.neighbors(n2):
+                _invalidate_edge(rag, n2, nbr)
+
+            if not in_place_merge:
+                next_id = rag.next_id()
+                _rename_node(rag, n2, next_id)
+                src, dst = n1, next_id
+            else:
+                src, dst = n1, n2
+
+            merge_func(rag, src, dst)
+            new_id = rag.merge_nodes(src, dst, weight_func)
+            _revalidate_node_edges(rag, new_id, edge_heap)
+
+    label_map = np.arange(labels.max() + 1)
+    for ix, (n, d) in enumerate(rag.nodes(data=True)):
+        for label in d['labels']:
+            label_map[label] = ix
+
+    return label_map[labels]

venv/Lib/site-packages/skimage/future/graph/rag.py

@@ -0,0 +1,558 @@
+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.
+
+    Parameters
+    ----------
+    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.
+
+    Yields
+    ------
+    i, j, w : (int, int, float) tuples
+        Each value `w` in the matrix along with its coordinates (i, j).
+
+    Examples
+    --------
+
+    >>> 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 = csr_matrix.data
+    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.
+
+    Parameters
+    ----------
+    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.
+
+    Returns
+    -------
+    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.
+
+    Parameters
+    ----------
+    values : array
+        The array to process.
+    graph : RAG
+        The graph to add edges in.
+
+    Returns
+    -------
+    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 <http://networkx.github.io/documentation/latest/reference/classes/graph.html>`_
+
+    Parameters
+    ----------
+    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
+        else:
+            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.
+            ndi.generic_filter(
+                label_image,
+                function=_add_edge_filter,
+                footprint=fp,
+                mode='nearest',
+                output=as_strided(np.empty((1,), dtype=np.float_),
+                                  shape=label_image.shape,
+                                  strides=((0,) * label_image.ndim)),
+                extra_arguments=(self,))
+
+    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.
+
+        Parameters
+        ----------
+        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
+            `weight_func`.
+        extra_keywords : dictionary, optional
+            The dict of keyword arguments passed to the `weight_func`.
+
+        Returns
+        -------
+        id : int
+            The id of the new node.
+
+        Notes
+        -----
+        If `in_place` is `False` the resulting node has a new id, rather than
+        `dst`.
+        """
+        src_nbrs = set(self.neighbors(src))
+        dst_nbrs = set(self.neighbors(dst))
+        neighbors = (src_nbrs | dst_nbrs) - {src, dst}
+
+        if in_place:
+            new = dst
+        else:
+            new = self.next_id()
+            self.add_node(new)
+
+        for neighbor in neighbors:
+            data = weight_func(self, src, new, neighbor, *extra_arguments,
+                               **extra_keywords)
+            self.add_edge(neighbor, new, attr_dict=data)
+
+        self.nodes[new]['labels'] = (self.nodes[src]['labels'] +
+                                     self.nodes[dst]['labels'])
+        self.remove_node(src)
+
+        if not in_place:
+            self.remove_node(dst)
+
+        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
+        else:
+            attr_dict.update(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
+        else:
+            attr_dict.update(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`.
+
+        Returns
+        -------
+        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',
+                   sigma=255.0):
+    """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.
+
+    Parameters
+    ----------
+    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
+        ``scipy.ndimage.generate_binary_structure``.
+    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.
+
+    Returns
+    -------
+    out : RAG
+        The region adjacency graph.
+
+    Examples
+    --------
+    >>> from skimage import data, segmentation
+    >>> from skimage.future import graph
+    >>> img = data.astronaut()
+    >>> labels = segmentation.slic(img)
+    >>> rag = graph.rag_mean_color(img, labels)
+
+    References
+    ----------
+    .. [1] Alain Tremeau and Philippe Colantoni
+           "Regions Adjacency Graph Applied To Color Image Segmentation"
+           :DOI:`10.1109/83.841950`
+    """
+    graph = RAG(labels, connectivity=connectivity)
+
+    for n in graph:
+        graph.nodes[n].update({'labels': [n],
+                               'pixel count': 0,
+                               'total color': np.array([0, 0, 0],
+                                                      dtype=np.double)})
+
+    for index in np.ndindex(labels.shape):
+        current = labels[index]
+        graph.nodes[current]['pixel count'] += 1
+        graph.nodes[current]['total color'] += image[index]
+
+    for n in graph:
+        graph.nodes[n]['mean color'] = (graph.nodes[n]['total color'] /
+                                        graph.nodes[n]['pixel count'])
+
+    for x, y, d in graph.edges(data=True):
+        diff = graph.nodes[x]['mean color'] - graph.nodes[y]['mean color']
+        diff = np.linalg.norm(diff)
+        if mode == 'similarity':
+            d['weight'] = math.e ** (-(diff ** 2) / sigma)
+        elif mode == 'distance':
+            d['weight'] = diff
+        else:
+            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
+        `scipy.ndimage.filters.generate_binary_structure`.
+
+    Examples
+    --------
+    >>> 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,
+                      strides=(0,))
+    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()
+    graph_matrix.data /= count_matrix.data
+
+    rag = RAG()
+    rag.add_weighted_edges_from(_edge_generator_from_csr(graph_matrix),
+                                weight='weight')
+    rag.add_weighted_edges_from(_edge_generator_from_csr(count_matrix),
+                                weight='count')
+
+    for n in rag.nodes():
+        rag.nodes[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.
+
+    Parameters
+    ----------
+    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
+        format.
+    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.nodes[n]['centroid']``.
+    ax : :py:class:`matplotlib.axes.Axes`, optional
+        The axes to draw on. If not specified, new axes are created and drawn
+        on.
+
+    Returns
+    -------
+    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.
+
+    Examples
+    --------
+    >>> from skimage import data, segmentation
+    >>> from skimage.future import graph
+    >>> import matplotlib.pyplot as plt
+    >>>
+    >>> img = data.coffee()
+    >>> 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]
+    else:
+        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)
+
+    ax.imshow(out)
+
+    # 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.nodes[n1]['centroid'][::-1], rag.nodes[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)]
+    lc.set_array(np.array(edge_weights))
+    ax.add_collection(lc)
+
+    return lc

venv/Lib/site-packages/skimage/future/graph/setup.py

@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+
+from skimage._build import cython
+import os.path
+
+base_path = os.path.abspath(os.path.dirname(__file__))
+
+
+def configuration(parent_package='', top_path=None):
+    from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
+
+    config = Configuration('graph', parent_package, top_path)
+
+    # This function tries to create C files from the given .pyx files.  If
+    # it fails, try to build with pre-generated .c files.
+    cython(['_ncut_cy.pyx'], working_path=base_path)
+    config.add_extension('_ncut_cy', sources=['_ncut_cy.c'],
+                         include_dirs=[get_numpy_include_dirs()])
+    return config
+
+if __name__ == '__main__':
+    from numpy.distutils.core import setup
+    setup(maintainer='scikit-image Developers',
+          maintainer_email='scikit-image@python.org',
+          description='Graph-based Image-processing Algorithms',
+          url='https://github.com/scikit-image/scikit-image',
+          license='Modified BSD',
+          **(configuration(top_path='').todict())
+          )

venv/Lib/site-packages/skimage/future/manual_segmentation.py

@@ -0,0 +1,227 @@
+from functools import reduce
+import numpy as np
+from ..draw import polygon
+
+
+LEFT_CLICK = 1
+RIGHT_CLICK = 3
+
+
+def _mask_from_vertices(vertices, shape, label):
+    mask = np.zeros(shape, dtype=int)
+    pr = [y for x, y in vertices]
+    pc = [x for x, y in vertices]
+    rr, cc = polygon(pr, pc, shape)
+    mask[rr, cc] = label
+    return mask
+
+
+def _draw_polygon(ax, vertices, alpha=0.4):
+    from matplotlib.patches import Polygon
+    from matplotlib.collections import PatchCollection
+    import matplotlib.pyplot as plt
+
+    polygon = Polygon(vertices, closed=True)
+    p = PatchCollection([polygon], match_original=True, alpha=alpha)
+    polygon_object = ax.add_collection(p)
+    plt.draw()
+    return polygon_object
+
+
+def manual_polygon_segmentation(image, alpha=0.4, return_all=False):
+    """Return a label image based on polygon selections made with the mouse.
+
+    Parameters
+    ----------
+    image : (M, N[, 3]) array
+        Grayscale or RGB image.
+
+    alpha : float, optional
+        Transparency value for polygons drawn over the image.
+
+    return_all : bool, optional
+        If True, an array containing each separate polygon drawn is returned.
+        (The polygons may overlap.) If False (default), latter polygons
+        "overwrite" earlier ones where they overlap.
+
+    Returns
+    -------
+    labels : array of int, shape ([Q, ]M, N)
+        The segmented regions. If mode is `'separate'`, the leading dimension
+        of the array corresponds to the number of regions that the user drew.
+
+    Notes
+    -----
+    Use left click to select the vertices of the polygon
+    and right click to confirm the selection once all vertices are selected.
+
+    Examples
+    --------
+    >>> from skimage import data, future, io
+    >>> camera = data.camera()
+    >>> mask = future.manual_polygon_segmentation(camera)  # doctest: +SKIP
+    >>> io.imshow(mask)  # doctest: +SKIP
+    >>> io.show()  # doctest: +SKIP
+    """
+    import matplotlib
+    from matplotlib.patches import Polygon
+    from matplotlib.collections import PatchCollection
+    import matplotlib.pyplot as plt
+
+    list_of_vertex_lists = []
+    polygons_drawn = []
+
+    temp_list = []
+    preview_polygon_drawn = []
+
+    if image.ndim not in (2, 3):
+        raise ValueError('Only 2D grayscale or RGB images are supported.')
+
+    fig, ax = plt.subplots()
+    fig.subplots_adjust(bottom=0.2)
+    ax.imshow(image, cmap="gray")
+    ax.set_axis_off()
+
+    def _undo(*args, **kwargs):
+        if list_of_vertex_lists:
+            list_of_vertex_lists.pop()
+            # Remove last polygon from list of polygons...
+            last_poly = polygons_drawn.pop()
+            # ... then from the plot
+            last_poly.remove()
+            fig.canvas.draw_idle()
+
+    undo_pos = fig.add_axes([0.85, 0.05, 0.075, 0.075])
+    undo_button = matplotlib.widgets.Button(undo_pos, u'\u27F2')
+    undo_button.on_clicked(_undo)
+
+    def _extend_polygon(event):
+        # Do not record click events outside axis or in undo button
+        if event.inaxes is None or event.inaxes is undo_pos:
+            return
+        # Do not record click events when toolbar is active
+        if fig.canvas.manager.toolbar._active is not None:
+            return
+
+        if event.button == LEFT_CLICK:  # Select vertex
+            temp_list.append([event.xdata, event.ydata])
+            # Remove previously drawn preview polygon if any.
+            if preview_polygon_drawn:
+                poly = preview_polygon_drawn.pop()
+                poly.remove()
+
+            # Preview polygon with selected vertices.
+            polygon = _draw_polygon(ax, temp_list, alpha=(alpha / 1.4))
+            preview_polygon_drawn.append(polygon)
+
+        elif event.button == RIGHT_CLICK:  # Confirm the selection
+            if not temp_list:
+                return
+
+            # Store the vertices of the polygon as shown in preview.
+            # Redraw polygon and store it in polygons_drawn so that
+            # `_undo` works correctly.
+            list_of_vertex_lists.append(temp_list[:])
+            polygon_object = _draw_polygon(ax, temp_list, alpha=alpha)
+            polygons_drawn.append(polygon_object)
+
+            # Empty the temporary variables.
+            preview_poly = preview_polygon_drawn.pop()
+            preview_poly.remove()
+            del temp_list[:]
+
+            plt.draw()
+
+    fig.canvas.mpl_connect('button_press_event', _extend_polygon)
+
+    plt.show(block=True)
+
+    labels = (_mask_from_vertices(vertices, image.shape[:2], i)
+              for i, vertices in enumerate(list_of_vertex_lists, start=1))
+    if return_all:
+        return np.stack(labels)
+    else:
+        return reduce(np.maximum, labels, np.broadcast_to(0, image.shape[:2]))
+
+
+def manual_lasso_segmentation(image, alpha=0.4, return_all=False):
+    """Return a label image based on freeform selections made with the mouse.
+
+    Parameters
+    ----------
+    image : (M, N[, 3]) array
+        Grayscale or RGB image.
+
+    alpha : float, optional
+        Transparency value for polygons drawn over the image.
+
+    return_all : bool, optional
+        If True, an array containing each separate polygon drawn is returned.
+        (The polygons may overlap.) If False (default), latter polygons
+        "overwrite" earlier ones where they overlap.
+
+    Returns
+    -------
+    labels : array of int, shape ([Q, ]M, N)
+        The segmented regions. If mode is `'separate'`, the leading dimension
+        of the array corresponds to the number of regions that the user drew.
+
+    Notes
+    -----
+    Press and hold the left mouse button to draw around each object.
+
+    Examples
+    --------
+    >>> from skimage import data, future, io
+    >>> camera = data.camera()
+    >>> mask = future.manual_lasso_segmentation(camera)  # doctest: +SKIP
+    >>> io.imshow(mask)  # doctest: +SKIP
+    >>> io.show()  # doctest: +SKIP
+    """
+    import matplotlib
+    from matplotlib.patches import Polygon
+    from matplotlib.collections import PatchCollection
+    import matplotlib.pyplot as plt
+
+    list_of_vertex_lists = []
+    polygons_drawn = []
+
+    if image.ndim not in (2, 3):
+        raise ValueError('Only 2D grayscale or RGB images are supported.')
+
+    fig, ax = plt.subplots()
+    fig.subplots_adjust(bottom=0.2)
+    ax.imshow(image, cmap="gray")
+    ax.set_axis_off()
+
+    def _undo(*args, **kwargs):
+        if list_of_vertex_lists:
+            list_of_vertex_lists.pop()
+            # Remove last polygon from list of polygons...
+            last_poly = polygons_drawn.pop()
+            # ... then from the plot
+            last_poly.remove()
+            fig.canvas.draw_idle()
+
+    undo_pos = fig.add_axes([0.85, 0.05, 0.075, 0.075])
+    undo_button = matplotlib.widgets.Button(undo_pos, u'\u27F2')
+    undo_button.on_clicked(_undo)
+
+    def _on_lasso_selection(vertices):
+        if len(vertices) < 3:
+            return
+        list_of_vertex_lists.append(vertices)
+        polygon_object = _draw_polygon(ax, vertices, alpha=alpha)
+        polygons_drawn.append(polygon_object)
+        plt.draw()
+
+    lasso = matplotlib.widgets.LassoSelector(ax, _on_lasso_selection)
+
+    plt.show(block=True)
+
+    labels = (_mask_from_vertices(vertices, image.shape[:2], i)
+              for i, vertices in enumerate(list_of_vertex_lists, start=1))
+    if return_all:
+        return np.stack(labels)
+    else:
+        return reduce(np.maximum, labels, np.broadcast_to(0, image.shape[:2]))

venv/Lib/site-packages/skimage/future/setup.py

@@ -0,0 +1,12 @@
+
+def configuration(parent_package='skimage', top_path=None):
+    from numpy.distutils.misc_util import Configuration
+    config = Configuration('future', parent_package, top_path)
+    config.add_subpackage('graph')
+    return config
+
+if __name__ == "__main__":
+    from numpy.distutils.core import setup
+
+    config = configuration(top_path='').todict()
+    setup(**config)