# Copyright 2019 NeuroData (http://neurodata.io)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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#     http://www.apache.org/licenses/LICENSE-2.0
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# distributed under the License is distributed on an "AS IS" BASIS,
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import warnings
from collections import Iterable
from functools import reduce
from pathlib import Path

import networkx as nx
import numpy as np
from sklearn.utils import check_array


def import_graph(graph):
    """
    A function for reading a graph and returning a shared data type. 

    Parameters
    ----------
    graph: object
        Either array-like, shape (n_vertices, n_vertices) numpy array,
        or an object of type networkx.Graph.

    Returns
    -------
    out: array-like, shape (n_vertices, n_vertices)
        A graph.
        
    See Also
    --------
    networkx.Graph, numpy.array
	"""
    if isinstance(graph, (nx.Graph, nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph)):
        out = nx.to_numpy_array(graph, nodelist=sorted(graph.nodes), dtype=np.float)
    elif isinstance(graph, (np.ndarray, np.memmap)):
        maximum = np.max(graph.shape)
        out = check_array(
            graph,
            dtype=[np.float64, np.float32],
            ensure_2d=True,
            allow_nd=True,  # For omni tensor input
            ensure_min_features=maximum,
            ensure_min_samples=maximum,
            copy=True,
        )
    else:
        msg = "Input must be networkx.Graph or np.array, not {}.".format(type(graph))
        raise TypeError(msg)
    return out


def import_edgelist(
    path, extension="edgelist", delimiter=None, nodetype=int, return_vertices=False
):
    """
    Function for reading a single or multiple edgelists. When importing multiple 
    edgelists, the union of vertices from all graphs is computed so that each output
    graph have matched vertex set. The order of nodes are sorted by node values.

    Parameters
    ----------
    path : str, Path object, or iterable
        If ``path`` is a directory, then the importing order will be sorted in 
        alphabetical order.

    extension : str, optional
        If ``path`` is a directory, then the function will convert all files
        with matching extension. 

    delimiter : str or None, default=None, optional
        Delimiter of edgelist. If None, the delimiter is whitespace.

    nodetype : int (default), float, str, Python type, optional
       Convert node data from strings to specified type.

    return_vertices : bool, default=False, optional
        Returns the union of all ind

    Returns
    -------
    out : list of array-like, or array-like, shape (n_vertices, n_vertices)
        If ``path`` is a directory, a list of arrays is returned. If ``path`` is a file,
        an array is returned.

    vertices : array-like, shape (n_vertices, )
        If ``return_vertices`` == True, then returns an array of all vertices that were 
        included in the output graphs. 
    """
    # p = Path(path)
    if not isinstance(path, (str, Path, Iterable)):
        msg = "path must be a string or Iterable, not {}".format(type(path))
        raise TypeError(msg)

    # get a list of files to import
    if isinstance(path, (str, Path)):
        p = Path(path)
        if p.is_dir():
            files = sorted(p.glob("*" + extension))
        elif p.is_file():
            files = [p]
        else:
            raise ValueError("No graphs founds to import.")
    else:  # path is an iterable
        files = [Path(f) for f in path]

    if len(files) == 0:
        msg = "No files found with '{}' extension found.".format(extension)
        raise ValueError(msg)

    graphs = [
        nx.read_weighted_edgelist(f, nodetype=nodetype, delimiter=delimiter)
        for f in files
    ]

    if all(len(G.nodes) == 0 for G in graphs):
        msg = (
            "All graphs have 0 vertices. Please double check if proper "
            + "'delimiter' is given."
        )
        warnings.warn(msg, UserWarning)

    # Compute union of all vertices
    vertices = np.sort(reduce(np.union1d, [G.nodes for G in graphs]))
    out = [nx.to_numpy_array(G, nodelist=vertices, dtype=np.float) for G in graphs]

    # only return adjacency matrix if input is only 1 graph
    if len(out) == 1:
        out = out[0]

    if return_vertices:
        return out, vertices
    else:
        return out


def is_symmetric(X):
    return np.array_equal(X, X.T)


def is_loopless(X):
    return not np.any(np.diag(X) != 0)


def is_unweighted(X):
    return ((X == 0) | (X == 1)).all()


def is_almost_symmetric(X, atol=1e-15):
    return np.allclose(X, X.T, atol=atol)


def symmetrize(graph, method="triu"):
    """
    A function for forcing symmetry upon a graph.

    Parameters
    ----------
    graph: object
        Either array-like, (n_vertices, n_vertices) numpy matrix,
        or an object of type networkx.Graph.

    method: {'triu' (default), 'tril', 'avg'}, optional
        An option indicating which half of the edges to
        retain when symmetrizing. 

            - 'triu'
                Retain the upper right triangle.
            - 'tril'
                Retain the lower left triangle.
            - 'avg'
                Retain the average weight between the upper and lower 
                right triangle, of the adjacency matrix.

    Returns
    -------
    graph: array-like, shape (n_vertices, n_vertices)
        the graph with asymmetries removed.
    """
    # graph = import_graph(graph)
    if method is "triu":
        graph = np.triu(graph)
    elif method is "tril":
        graph = np.tril(graph)
    elif method is "avg":
        graph = (np.triu(graph) + np.tril(graph)) / 2
    else:
        msg = "You have not passed a valid parameter for the method."
        raise ValueError(msg)
    # A = A + A' - diag(A)
    graph = graph + graph.T - np.diag(np.diag(graph))
    return graph


def remove_loops(graph):
    """
    A function to remove loops from a graph.

    Parameters
    ----------
    graph: object
        Either array-like, (n_vertices, n_vertices) numpy matrix,
        or an object of type networkx.Graph.

    Returns
    -------
    graph: array-like, shape(n_vertices, n_vertices)
        the graph with self-loops (edges between the same node) removed.
    """
    graph = import_graph(graph)
    graph = graph - np.diag(np.diag(graph))

    return graph


def to_laplace(graph, form="DAD", regularizer=None):
    r"""
    A function to convert graph adjacency matrix to graph laplacian. 

    Currently supports I-DAD, DAD, and R-DAD laplacians, where D is the diagonal
    matrix of degrees of each node raised to the -1/2 power, I is the 
    identity matrix, and A is the adjacency matrix.
    
    R-DAD is regularized laplacian: where :math:`D_t = D + regularizer*I`.

    Parameters
    ----------
    graph: object
        Either array-like, (n_vertices, n_vertices) numpy array,
        or an object of type networkx.Graph.

    form: {'I-DAD' (default), 'DAD', 'R-DAD'}, string, optional
        
        - 'I-DAD'
            Computes :math:`L = I - D*A*D`
        - 'DAD'
            Computes :math:`L = D*A*D`
        - 'R-DAD'
            Computes :math:`L = D_t*A*D_t` where :math:`D_t = D + regularizer*I`

    regularizer: int, float or None, optional (default=None)
        Constant to be added to the diagonal of degree matrix. If None, average 
        node degree is added. If int or float, must be >= 0. Only used when 
        ``form`` == 'R-DAD'.

    Returns
    -------
    L: numpy.ndarray
        2D (n_vertices, n_vertices) array representing graph 
        laplacian of specified form
	
    References
    ----------
    .. [1] Qin, Tai, and Karl Rohe. "Regularized spectral clustering
           under the degree-corrected stochastic blockmodel." In Advances
           in Neural Information Processing Systems, pp. 3120-3128. 2013
    """
    valid_inputs = ["I-DAD", "DAD", "R-DAD"]
    if form not in valid_inputs:
        raise TypeError("Unsuported Laplacian normalization")

    A = import_graph(graph)

    if not is_almost_symmetric(A):
        raise ValueError("Laplacian not implemented/defined for directed graphs")

    D_vec = np.sum(A, axis=0)
    # regularize laplacian with parameter
    # set to average degree
    if form == "R-DAD":
        if regularizer == None:
            regularizer = np.mean(D_vec)
        elif not isinstance(regularizer, (int, float)):
            raise TypeError(
                "Regularizer must be a int or float, not {}".format(type(regularizer))
            )
        elif regularizer < 0:
            raise ValueError("Regularizer must be greater than or equal to 0")
        D_vec += regularizer

    with np.errstate(divide="ignore"):
        D_root = 1 / np.sqrt(D_vec)  # this is 10x faster than ** -0.5
    D_root[np.isinf(D_root)] = 0
    D_root = np.diag(D_root)  # just change to sparse diag for sparse support

    if form == "I-DAD":
        L = np.diag(D_vec) - A
        L = D_root @ L @ D_root
    elif form == "DAD" or form == "R-DAD":
        L = D_root @ A @ D_root
    return symmetrize(L, method="avg")  # sometimes machine prec. makes this necessary


def is_fully_connected(graph):
    r"""
    Checks whether the input graph is fully connected in the undirected case
    or weakly connected in the directed case. 

    Connected means one can get from any vertex u to vertex v by traversing
    the graph. For a directed graph, weakly connected means that the graph 
    is connected after it is converted to an unweighted graph (ignore the 
    direction of each edge)

    Parameters
    ----------
    graph: nx.Graph, nx.DiGraph, nx.MultiDiGraph, nx.MultiGraph, np.ndarray
        Input graph in any of the above specified formats. If np.ndarray, 
        interpreted as an :math:`n \times n` adjacency matrix

    Returns
    -------
        boolean: True if the entire input graph is connected

    References
    ----------
        http://mathworld.wolfram.com/ConnectedGraph.html
        http://mathworld.wolfram.com/WeaklyConnectedDigraph.html

    """
    if type(graph) is np.ndarray:
        if is_symmetric(graph):
            g_object = nx.Graph()
        else:
            g_object = nx.DiGraph()
        graph = nx.from_numpy_array(graph, create_using=g_object)
    if type(graph) in [nx.Graph, nx.MultiGraph]:
        return nx.is_connected(graph)
    elif type(graph) in [nx.DiGraph, nx.MultiDiGraph]:
        return nx.is_weakly_connected(graph)


def get_lcc(graph, return_inds=False):
    r"""
    Finds the largest connected component for the input graph. 

    The largest connected component is the fully connected subgraph
    which has the most nodes. 

    Parameters
    ----------
    graph: nx.Graph, nx.DiGraph, nx.MultiDiGraph, nx.MultiGraph, np.ndarray
        Input graph in any of the above specified formats. If np.ndarray, 
        interpreted as an :math:`n \times n` adjacency matrix
    
    return_inds: boolean, default: False
        Whether to return a np.ndarray containing the indices in the original
        adjacency matrix that were kept and are now in the returned graph.
        Ignored when input is networkx object

    Returns
    -------
    graph: nx.Graph, nx.DiGraph, nx.MultiDiGraph, nx.MultiGraph, np.ndarray
        New graph of the largest connected component of the input parameter. 

    inds: (optional)
        Indices from the original adjacency matrix that were kept after taking
        the largest connected component 
    """

    input_ndarray = False
    if type(graph) is np.ndarray:
        input_ndarray = True
        if is_symmetric(graph):
            g_object = nx.Graph()
        else:
            g_object = nx.DiGraph()
        graph = nx.from_numpy_array(graph, create_using=g_object)
    if type(graph) in [nx.Graph, nx.MultiGraph]:
        lcc_nodes = max(nx.connected_components(graph), key=len)
    elif type(graph) in [nx.DiGraph, nx.MultiDiGraph]:
        lcc_nodes = max(nx.weakly_connected_components(graph), key=len)
    lcc = graph.subgraph(lcc_nodes).copy()
    lcc.remove_nodes_from([n for n in lcc if n not in lcc_nodes])
    if return_inds:
        nodelist = np.array(list(lcc_nodes))
    if input_ndarray:
        lcc = nx.to_numpy_array(lcc)
    if return_inds:
        return lcc, nodelist
    return lcc


def get_multigraph_union_lcc(graphs, return_inds=False):
    r"""
    Finds the union of all multiple graphs, then compute the largest connected
    component.

    Parameters
    ----------
    graphs: list or np.ndarray
        List of array-like, (n_vertices, n_vertices), or list of np.ndarray
        nx.Graph, nx.DiGraph, nx.MultiDiGraph, nx.MultiGraph.
        
    return_inds: boolean, default: False
        Whether to return a np.ndarray containing the indices in the original
        adjacency matrix that were kept and are now in the returned graph.
        Ignored when input is networkx object
    
    Returns
    -------
    out : list or np.ndarray
        If input was a list
    """
    if isinstance(graphs, list):
        if not isinstance(graphs[0], np.ndarray):
            raise NotImplementedError

        out = [import_graph(g) for g in graphs]
        if len(set(map(np.shape, out))) != 1:
            msg = "All input graphs must have the same size"
            raise ValueError(msg)
        bar = np.stack(out).mean(axis=0)
    elif isinstance(graphs, np.ndarray):
        shape = graphs.shape
        if shape[1] != shape[2]:
            msg = "Input graphs must be square"
            raise ValueError(msg)
        bar = graphs.mean(axis=0)
    else:
        msg = "Expected list or np.ndarray, but got {} instead.".format(type(graphs))
        raise ValueError(msg)

    _, idx = get_lcc(bar, return_inds=True)
    idx = np.array(idx)

    if isinstance(graphs, np.ndarray):
        graphs[:, idx[:, None], idx]
    elif isinstance(graphs, list):
        if isinstance(graphs[0], np.ndarray):
            graphs = [g[idx[:, None], idx] for g in graphs]
    if return_inds:
        return graphs, idx
    return graphs


def get_multigraph_intersect_lcc(graphs, return_inds=False):
    r"""
    Finds the intersection of multiple graphs's largest connected components. 

    Computes the largest connected component for each graph that was input, and 
    takes the intersection over all of these resulting graphs. Note that this 
    does not guarantee finding the largest graph where every node is shared among
    all of the input graphs.

    Parameters
    ----------
    graphs: list or np.ndarray
        if list, each element must be an :math:`n \times n` np.ndarray adjacency matrix
        
    return_inds: boolean, default: False
        Whether to return a np.ndarray containing the indices in the original
        adjacency matrix that were kept and are now in the returned graph.
        Ignored when input is networkx object
    
    Returns
    -------
    graph: nx.Graph, nx.DiGraph, nx.MultiDiGraph, nx.MultiGraph, np.ndarray
        New graph of the largest connected component of the input parameter. 

    inds: (optional)
        Indices from the original adjacency matrix that were kept after taking
        the largest connected component 
    """
    lcc_by_graph = []
    inds_by_graph = []
    for graph in graphs:
        lcc, inds = get_lcc(graph, return_inds=True)
        lcc_by_graph.append(lcc)
        inds_by_graph.append(inds)
    inds_intersection = reduce(np.intersect1d, inds_by_graph)
    new_graphs = []
    for graph in graphs:
        if type(graph) is np.ndarray:
            lcc = graph[inds_intersection, :][:, inds_intersection]
        else:
            lcc = graph.subgraph(inds_intersection).copy()
            lcc.remove_nodes_from([n for n in lcc if n not in inds_intersection])
        new_graphs.append(lcc)
    # this is not guaranteed be connected after one iteration because taking the
    # intersection of nodes among graphs can cause some components to become
    # disconnected, so, we check for this and run again if necessary
    recurse = False
    for new_graph in new_graphs:
        if not is_fully_connected(new_graph):
            recurse = True
            break
    if recurse:
        new_graphs, new_inds_intersection = get_multigraph_intersect_lcc(
            new_graphs, return_inds=True
        )
        # new inds intersection are the indices of new_graph that were kept on recurse
        # need to do this because indices could have shifted during recursion
        if type(graphs[0]) is np.ndarray:
            inds_intersection = inds_intersection[new_inds_intersection]
        else:
            inds_intersection = new_inds_intersection
    if type(graphs) != list:
        new_graphs = np.stack(new_graphs)
    if return_inds:
        return new_graphs, inds_intersection
    else:
        return new_graphs


def augment_diagonal(graph, weight=1):
    r"""
    Replaces the diagonal of adjacency matrix with 
    :math:`\frac{degree}{nverts - 1}` for the degree associated
    with each node. 

    For directed graphs, the degree used is the out degree (number) of 
    edges leaving the vertex. Ignores self-loops when calculating degree

    Parameters
    ----------
    graph: nx.Graph, nx.DiGraph, nx.MultiDiGraph, nx.MultiGraph, np.ndarray
        Input graph in any of the above specified formats. If np.ndarray, 
        interpreted as an :math:`n \times n` adjacency matrix 
    """
    graph = import_graph(graph)
    graph = remove_loops(graph)
    divisor = graph.shape[0] - 1
    # use out degree for directed graph
    # ignore self loops in either case
    degrees = np.count_nonzero(graph, axis=1)
    diag = weight * degrees / divisor
    graph += np.diag(diag)
    return graph
