コード例 #1
0
def check_relationships(branches):

    ancestors = {b: set() for b in branches}
    length = len(branches) * (len(branches) - 1)
    for b1, b2 in ub.ProgIter(it.combinations(branches, 2), length=length):
        ret = ub.cmd('git merge-base --is-ancestor {} {}'.format(b1, b2))['ret']
        if ret == 0:
            ancestors[b1].add(b2)
        ret = ub.cmd('git merge-base --is-ancestor {} {}'.format(b2, b1))['ret']
        if ret == 0:
            ancestors[b2].add(b1)
    print('<key> is an ancestor of <value>')
    print(ub.repr2(ancestors))

    descendants = {b: set() for b in branches}
    for key, others in ancestors.items():
        for o in others:
            descendants[o].add(key)
    print('<key> descends from <value>')
    print(ub.repr2(descendants))

    import plottool as pt
    import networkx as nx
    G = nx.DiGraph()
    G.add_nodes_from(branches)
    for key, others in ancestors.items():
        for o in others:
            # G.add_edge(key, o)
            G.add_edge(o, key)

    from networkx.algorithms.connectivity.edge_augmentation import collapse
    flag = True
    G2 = G
    while flag:
        flag = False
        for u, v in list(G2.edges()):
            if G2.has_edge(v, u):
                G2 = collapse(G2, [[u, v]])

                node_relabel = ub.ddict(list)
                for old, new in G2.graph['mapping'].items():
                    node_relabel[new].append(old)
                G2 = nx.relabel_nodes(G2, {k: '\n'.join(v) for k, v in node_relabel.items()})
                flag = True
                break

    G3 = nx.transitive_reduction(G2)
    pt.show_nx(G3, arrow_width=1.5, prog='dot', layoutkw=dict(prog='dot'))
    pt.zoom_factory()
    pt.pan_factory()
    pt.plt.show()
コード例 #2
0
ファイル: pgm_viz.py プロジェクト: whaozl/ibeis
def draw_bayesian_model(model,
                        evidence={},
                        soft_evidence={},
                        fnum=None,
                        pnum=None,
                        **kwargs):

    from pgmpy.models import BayesianModel
    if not isinstance(model, BayesianModel):
        model = model.to_bayesian_model()

    import plottool as pt
    import networkx as nx
    kwargs = kwargs.copy()
    factor_list = kwargs.pop('factor_list', [])

    ttype_colors, ttype_scalars = make_colorcodes(model)

    textprops = {
        'horizontalalignment': 'left',
        'family': 'monospace',
        'size': 8,
    }

    # build graph attrs
    tup = get_node_viz_attrs(model, evidence, soft_evidence, factor_list,
                             ttype_colors, **kwargs)
    node_color, pos_list, pos_dict, takws = tup

    # draw graph
    has_infered = evidence or 'factor_list' in kwargs

    if False:
        fig = pt.figure(fnum=fnum, pnum=pnum, doclf=True)  # NOQA
        ax = pt.gca()
        drawkw = dict(pos=pos_dict,
                      ax=ax,
                      with_labels=True,
                      node_size=1100,
                      node_color=node_color)
        nx.draw(model, **drawkw)
    else:
        # BE VERY CAREFUL
        if 1:
            graph = model.copy()
            graph.__class__ = nx.DiGraph
            graph.graph['groupattrs'] = ut.ddict(dict)
            #graph = model.
            if getattr(graph, 'ttype2_cpds', None) is not None:
                # Add invis edges and ttype groups
                for ttype in model.ttype2_cpds.keys():
                    ttype_cpds = model.ttype2_cpds[ttype]
                    # use defined ordering
                    ttype_nodes = ut.list_getattr(ttype_cpds, 'variable')
                    # ttype_nodes = sorted(ttype_nodes)
                    invis_edges = list(ut.itertwo(ttype_nodes))
                    graph.add_edges_from(invis_edges)
                    nx.set_edge_attributes(
                        graph, 'style',
                        {edge: 'invis'
                         for edge in invis_edges})
                    nx.set_node_attributes(
                        graph, 'groupid',
                        {node: ttype
                         for node in ttype_nodes})
                    graph.graph['groupattrs'][ttype]['rank'] = 'same'
                    graph.graph['groupattrs'][ttype]['cluster'] = False
        else:
            graph = model
        pt.show_nx(graph,
                   layout_kw={'prog': 'dot'},
                   fnum=fnum,
                   pnum=pnum,
                   verbose=0)
        pt.zoom_factory()
        fig = pt.gcf()
        ax = pt.gca()
        pass
    hacks = [
        pt.draw_text_annotations(textprops=textprops, **takw) for takw in takws
        if takw
    ]

    xmin, ymin = np.array(pos_list).min(axis=0)
    xmax, ymax = np.array(pos_list).max(axis=0)
    if 'name' in model.ttype2_template:
        num_names = len(model.ttype2_template['name'].basis)
        num_annots = len(model.ttype2_cpds['name'])
        if num_annots > 4:
            ax.set_xlim((xmin - 40, xmax + 40))
            ax.set_ylim((ymin - 50, ymax + 50))
            fig.set_size_inches(30, 7)
        else:
            ax.set_xlim((xmin - 42, xmax + 42))
            ax.set_ylim((ymin - 50, ymax + 50))
            fig.set_size_inches(23, 7)
        title = 'num_names=%r, num_annots=%r' % (
            num_names,
            num_annots,
        )
    else:
        title = ''
    map_assign = kwargs.get('map_assign', None)

    def word_insert(text):
        return '' if len(text) == 0 else text + ' '

    top_assignments = kwargs.get('top_assignments', None)
    if top_assignments is not None:
        map_assign, map_prob = top_assignments[0]
        if map_assign is not None:
            title += '\n%sMAP: ' % (word_insert(kwargs.get('method', '')))
            title += map_assign + ' @' + '%.2f%%' % (100 * map_prob, )
    if kwargs.get('show_title', True):
        pt.set_figtitle(title, size=14)

    for hack in hacks:
        hack()

    if has_infered:
        # Hack in colorbars
        # if ut.list_type(basis) is int:
        #     pt.colorbar(scalars, colors, lbl='score', ticklabels=np.array(basis) + 1)
        # else:
        #     pt.colorbar(scalars, colors, lbl='score', ticklabels=basis)
        keys = ['name', 'score']
        locs = ['left', 'right']
        for key, loc in zip(keys, locs):
            if key in ttype_colors:
                basis = model.ttype2_template[key].basis
                # scalars =
                colors = ttype_colors[key]
                scalars = ttype_scalars[key]
                pt.colorbar(scalars,
                            colors,
                            lbl=key,
                            ticklabels=basis,
                            ticklocation=loc)
コード例 #3
0
ファイル: specialdraw.py プロジェクト: whaozl/ibeis
def intraoccurrence_connected():
    r"""
    CommandLine:
        python -m ibeis.scripts.specialdraw intraoccurrence_connected --show
        python -m ibeis.scripts.specialdraw intraoccurrence_connected --show --postcut
        python -m ibeis.scripts.specialdraw intraoccurrence_connected --show --smaller

    Example:
        >>> # DISABLE_DOCTEST
        >>> from ibeis.scripts.specialdraw import *  # NOQA
        >>> result = intraoccurrence_connected()
        >>> print(result)
        >>> ut.quit_if_noshow()
        >>> import plottool as pt
        >>> ut.show_if_requested()
    """
    import ibeis
    import plottool as pt
    from ibeis.viz import viz_graph
    import networkx as nx
    pt.ensure_pylab_qt4()
    ibs = ibeis.opendb(defaultdb='PZ_Master1')
    nid2_aid = {
        #4880: [3690, 3696, 3703, 3706, 3712, 3721],
        4880: [3690, 3696, 3703],
        6537: [3739],
        6653: [7671],
        6610: [7566, 7408],
        #6612: [7664, 7462, 7522],
        #6624: [7465, 7360],
        #6625: [7746, 7383, 7390, 7477, 7376, 7579],
        6630: [7586, 7377, 7464, 7478],
        #6677: [7500]
    }
    nid2_dbaids = {4880: [33, 6120, 7164], 6537: [7017, 7206], 6653: [7660]}
    if ut.get_argflag('--small') or ut.get_argflag('--smaller'):
        del nid2_aid[6630]
        del nid2_aid[6537]
        del nid2_dbaids[6537]
        if ut.get_argflag('--smaller'):
            nid2_dbaids[4880].remove(33)
            nid2_aid[4880].remove(3690)
            nid2_aid[6610].remove(7408)
        #del nid2_aid[4880]
        #del nid2_dbaids[4880]

    aids = ut.flatten(nid2_aid.values())

    temp_nids = [1] * len(aids)
    postcut = ut.get_argflag('--postcut')
    aids_list = ibs.group_annots_by_name(aids)[0]
    ensure_edges = 'all' if True or not postcut else None
    unlabeled_graph = viz_graph.make_netx_graph_from_aid_groups(
        ibs,
        aids_list,
        #invis_edges=invis_edges,
        ensure_edges=ensure_edges,
        temp_nids=temp_nids)
    viz_graph.color_by_nids(unlabeled_graph,
                            unique_nids=[1] *
                            len(list(unlabeled_graph.nodes())))
    viz_graph.ensure_node_images(ibs, unlabeled_graph)
    nx.set_node_attributes(unlabeled_graph, 'shape', 'rect')
    #unlabeled_graph = unlabeled_graph.to_undirected()

    # Find the "database exemplars for these annots"
    if False:
        gt_aids = ibs.get_annot_groundtruth(aids)
        gt_aids = [ut.setdiff(s, aids) for s in gt_aids]
        dbaids = ut.unique(ut.flatten(gt_aids))
        dbaids = ibs.filter_annots_general(dbaids, minqual='good')
        ibs.get_annot_quality_texts(dbaids)
    else:
        dbaids = ut.flatten(nid2_dbaids.values())
    exemplars = nx.DiGraph()
    #graph = exemplars  # NOQA
    exemplars.add_nodes_from(dbaids)

    def add_clique(graph, nodes, edgeattrs={}, nodeattrs={}):
        edge_list = ut.upper_diag_self_prodx(nodes)
        graph.add_edges_from(edge_list, **edgeattrs)
        return edge_list

    for aids_, nid in zip(*ibs.group_annots_by_name(dbaids)):
        add_clique(exemplars, aids_)
    viz_graph.ensure_node_images(ibs, exemplars)
    viz_graph.color_by_nids(exemplars, ibs=ibs)

    nx.set_node_attributes(unlabeled_graph, 'framewidth', False)
    nx.set_node_attributes(exemplars, 'framewidth', 4.0)

    nx.set_node_attributes(unlabeled_graph, 'group', 'unlab')
    nx.set_node_attributes(exemplars, 'group', 'exemp')

    #big_graph = nx.compose_all([unlabeled_graph])
    big_graph = nx.compose_all([exemplars, unlabeled_graph])

    # add sparse connections from unlabeled to exemplars
    import numpy as np
    rng = np.random.RandomState(0)
    if True or not postcut:
        for aid_ in unlabeled_graph.nodes():
            flags = rng.rand(len(exemplars)) > .5
            nid_ = ibs.get_annot_nids(aid_)
            exnids = np.array(ibs.get_annot_nids(list(exemplars.nodes())))
            flags = np.logical_or(exnids == nid_, flags)
            exmatches = ut.compress(list(exemplars.nodes()), flags)
            big_graph.add_edges_from(list(ut.product([aid_], exmatches)),
                                     color=pt.ORANGE,
                                     implicit=True)
    else:
        for aid_ in unlabeled_graph.nodes():
            flags = rng.rand(len(exemplars)) > .5
            exmatches = ut.compress(list(exemplars.nodes()), flags)
            nid_ = ibs.get_annot_nids(aid_)
            exnids = np.array(ibs.get_annot_nids(exmatches))
            exmatches = ut.compress(exmatches, exnids == nid_)
            big_graph.add_edges_from(list(ut.product([aid_], exmatches)))
        pass

    nx.set_node_attributes(big_graph, 'shape', 'rect')
    #if False and postcut:
    #    ut.nx_delete_node_attr(big_graph, 'nid')
    #    ut.nx_delete_edge_attr(big_graph, 'color')
    #    viz_graph.ensure_graph_nid_labels(big_graph, ibs=ibs)
    #    viz_graph.color_by_nids(big_graph, ibs=ibs)
    #    big_graph = big_graph.to_undirected()

    layoutkw = {
        'sep': 1 / 5,
        'prog': 'neato',
        'overlap': 'false',
        #'splines': 'ortho',
        'splines': 'spline',
    }

    as_directed = False
    #as_directed = True
    #hacknode = True
    hacknode = 0

    graph = big_graph
    ut.nx_ensure_agraph_color(graph)
    if hacknode:
        nx.set_edge_attributes(graph, 'taillabel',
                               {e: str(e[0])
                                for e in graph.edges()})
        nx.set_edge_attributes(graph, 'headlabel',
                               {e: str(e[1])
                                for e in graph.edges()})

    explicit_graph = pt.get_explicit_graph(graph)
    _, layout_info = pt.nx_agraph_layout(explicit_graph,
                                         orig_graph=graph,
                                         inplace=True,
                                         **layoutkw)

    if ut.get_argflag('--smaller'):
        graph.node[7660]['pos'] = np.array([550, 350])
        graph.node[6120]['pos'] = np.array([200, 600]) + np.array([350, -400])
        graph.node[7164]['pos'] = np.array([200, 480]) + np.array([350, -400])
        nx.set_node_attributes(graph, 'pin', 'true')
        _, layout_info = pt.nx_agraph_layout(graph, inplace=True, **layoutkw)
    elif ut.get_argflag('--small'):
        graph.node[7660]['pos'] = np.array([750, 350])
        graph.node[33]['pos'] = np.array([300, 600]) + np.array([350, -400])
        graph.node[6120]['pos'] = np.array([500, 600]) + np.array([350, -400])
        graph.node[7164]['pos'] = np.array([410, 480]) + np.array([350, -400])
        nx.set_node_attributes(graph, 'pin', 'true')
        _, layout_info = pt.nx_agraph_layout(graph, inplace=True, **layoutkw)

    if not postcut:
        #pt.show_nx(graph.to_undirected(), layout='agraph', layoutkw=layoutkw,
        #           as_directed=False)
        #pt.show_nx(graph, layout='agraph', layoutkw=layoutkw,
        #           as_directed=as_directed, hacknode=hacknode)

        pt.show_nx(graph,
                   layout='custom',
                   layoutkw=layoutkw,
                   as_directed=as_directed,
                   hacknode=hacknode)
    else:
        #explicit_graph = pt.get_explicit_graph(graph)
        #_, layout_info = pt.nx_agraph_layout(explicit_graph, orig_graph=graph,
        #                                     **layoutkw)

        #layout_info['edge']['alpha'] = .8
        #pt.apply_graph_layout_attrs(graph, layout_info)

        #graph_layout_attrs = layout_info['graph']
        ##edge_layout_attrs  = layout_info['edge']
        ##node_layout_attrs  = layout_info['node']

        #for key, vals in layout_info['node'].items():
        #    #print('[special] key = %r' % (key,))
        #    nx.set_node_attributes(graph, key, vals)

        #for key, vals in layout_info['edge'].items():
        #    #print('[special] key = %r' % (key,))
        #    nx.set_edge_attributes(graph, key, vals)

        #nx.set_edge_attributes(graph, 'alpha', .8)
        #graph.graph['splines'] = graph_layout_attrs.get('splines', 'line')
        #graph.graph['splines'] = 'polyline'   # graph_layout_attrs.get('splines', 'line')
        #graph.graph['splines'] = 'line'

        cut_graph = graph.copy()
        edge_list = list(cut_graph.edges())
        edge_nids = np.array(ibs.unflat_map(ibs.get_annot_nids, edge_list))
        cut_flags = edge_nids.T[0] != edge_nids.T[1]
        cut_edges = ut.compress(edge_list, cut_flags)
        cut_graph.remove_edges_from(cut_edges)
        ut.nx_delete_node_attr(cut_graph, 'nid')
        viz_graph.ensure_graph_nid_labels(cut_graph, ibs=ibs)

        #ut.nx_get_default_node_attributes(exemplars, 'color', None)
        ut.nx_delete_node_attr(cut_graph,
                               'color',
                               nodes=unlabeled_graph.nodes())
        aid2_color = ut.nx_get_default_node_attributes(cut_graph, 'color',
                                                       None)
        nid2_colors = ut.group_items(aid2_color.values(),
                                     ibs.get_annot_nids(aid2_color.keys()))
        nid2_colors = ut.map_dict_vals(ut.filter_Nones, nid2_colors)
        nid2_colors = ut.map_dict_vals(ut.unique, nid2_colors)
        #for val in nid2_colors.values():
        #    assert len(val) <= 1
        # Get initial colors
        nid2_color_ = {
            nid: colors_[0]
            for nid, colors_ in nid2_colors.items() if len(colors_) == 1
        }

        graph = cut_graph
        viz_graph.color_by_nids(cut_graph, ibs=ibs, nid2_color_=nid2_color_)
        nx.set_node_attributes(cut_graph, 'framewidth', 4)

        pt.show_nx(cut_graph,
                   layout='custom',
                   layoutkw=layoutkw,
                   as_directed=as_directed,
                   hacknode=hacknode)

    pt.zoom_factory()
コード例 #4
0
ファイル: specialdraw.py プロジェクト: whaozl/ibeis
def setcover_example():
    """
    CommandLine:
        python -m ibeis.scripts.specialdraw setcover_example --show

    Example:
        >>> # DISABLE_DOCTEST
        >>> from ibeis.scripts.specialdraw import *  # NOQA
        >>> result = setcover_example()
        >>> print(result)
        >>> ut.quit_if_noshow()
        >>> import plottool as pt
        >>> ut.show_if_requested()
    """
    import ibeis
    import plottool as pt
    from ibeis.viz import viz_graph
    import networkx as nx
    pt.ensure_pylab_qt4()
    ibs = ibeis.opendb(defaultdb='testdb2')

    if False:
        # Select a good set
        aids = ibs.get_name_aids(ibs.get_valid_nids())
        # ibeis.testdata_aids('testdb2', a='default:mingt=2')
        aids = [a for a in aids if len(a) > 1]
        for a in aids:
            print(ut.repr3(ibs.get_annot_stats_dict(a)))
        print(aids[-2])
    #aids = [78, 79, 80, 81, 88, 91]
    aids = [78, 79, 81, 88, 91]
    qreq_ = ibs.depc.new_request('vsone', aids, aids, cfgdict={})
    cm_list = qreq_.execute()
    from ibeis.algo.hots import graph_iden
    infr = graph_iden.AnnotInference(cm_list)
    unique_aids, prob_annots = infr.make_prob_annots()
    import numpy as np
    print(
        ut.hz_str(
            'prob_annots = ',
            ut.array2string2(prob_annots,
                             precision=2,
                             max_line_width=140,
                             suppress_small=True)))
    # ut.setcover_greedy(candidate_sets_dict)
    max_weight = 3
    prob_annots[np.diag_indices(len(prob_annots))] = np.inf
    prob_annots = prob_annots
    thresh_points = np.sort(prob_annots[np.isfinite(prob_annots)])

    # probably not the best way to go about searching for these thresholds
    # but when you have a hammer...
    if False:
        quant = sorted(np.diff(thresh_points))[(len(thresh_points) - 1) // 2]
        candset = {
            point: thresh_points[np.abs(thresh_points - point) < quant]
            for point in thresh_points
        }
        check_thresholds = len(aids) * 2
        thresh_points2 = np.array(
            ut.setcover_greedy(candset, max_weight=check_thresholds).keys())
        thresh_points = thresh_points2

    # pt.plot(sorted(thresh_points), 'rx')
    # pt.plot(sorted(thresh_points2), 'o')

    # prob_annots = prob_annots.T

    # thresh_start = np.mean(thresh_points)
    current_idxs = []
    current_covers = []
    current_val = np.inf
    for thresh in thresh_points:
        covering_sets = [np.where(row >= thresh)[0] for row in (prob_annots)]
        candidate_sets_dict = {
            ax: others
            for ax, others in enumerate(covering_sets)
        }
        soln_cover = ut.setcover_ilp(candidate_sets_dict,
                                     max_weight=max_weight)
        exemplar_idxs = list(soln_cover.keys())
        soln_weight = len(exemplar_idxs)
        val = max_weight - soln_weight
        # print('val = %r' % (val,))
        # print('soln_weight = %r' % (soln_weight,))
        if val < current_val:
            current_val = val
            current_covers = covering_sets
            current_idxs = exemplar_idxs
    exemplars = ut.take(aids, current_idxs)
    ensure_edges = [(aids[ax], aids[ax2])
                    for ax, other_xs in enumerate(current_covers)
                    for ax2 in other_xs]
    graph = viz_graph.make_netx_graph_from_aid_groups(
        ibs, [aids],
        allow_directed=True,
        ensure_edges=ensure_edges,
        temp_nids=[1] * len(aids))
    viz_graph.ensure_node_images(ibs, graph)

    nx.set_node_attributes(graph, 'framewidth', False)
    nx.set_node_attributes(graph, 'framewidth',
                           {aid: 4.0
                            for aid in exemplars})
    nx.set_edge_attributes(graph, 'color', pt.ORANGE)
    nx.set_node_attributes(graph, 'color', pt.LIGHT_BLUE)
    nx.set_node_attributes(graph, 'shape', 'rect')

    layoutkw = {
        'sep': 1 / 10,
        'prog': 'neato',
        'overlap': 'false',
        #'splines': 'ortho',
        'splines': 'spline',
    }
    pt.show_nx(graph, layout='agraph', layoutkw=layoutkw)
    pt.zoom_factory()
コード例 #5
0
ファイル: specialdraw.py プロジェクト: whaozl/ibeis
def double_depcache_graph():
    r"""
    CommandLine:
        python -m ibeis.scripts.specialdraw double_depcache_graph --show --testmode

        python -m ibeis.scripts.specialdraw double_depcache_graph --save=figures5/doubledepc.png --dpath ~/latex/cand/  --diskshow  --figsize=8,20 --dpi=220 --testmode --show --clipwhite
        python -m ibeis.scripts.specialdraw double_depcache_graph --save=figures5/doubledepc.png --dpath ~/latex/cand/  --diskshow  --figsize=8,20 --dpi=220 --testmode --show --clipwhite --arrow-width=.5

        python -m ibeis.scripts.specialdraw double_depcache_graph --save=figures5/doubledepc.png --dpath ~/latex/cand/  --diskshow  --figsize=8,20 --dpi=220 --testmode --show --clipwhite --arrow-width=5

    Example:
        >>> # DISABLE_DOCTEST
        >>> from ibeis.scripts.specialdraw import *  # NOQA
        >>> result = double_depcache_graph()
        >>> print(result)
        >>> ut.quit_if_noshow()
        >>> import plottool as pt
        >>> ut.show_if_requested()
    """
    import ibeis
    import networkx as nx
    import plottool as pt
    pt.ensure_pylab_qt4()
    # pt.plt.xkcd()
    ibs = ibeis.opendb('testdb1')
    reduced = True
    implicit = True
    annot_graph = ibs.depc_annot.make_graph(reduced=reduced, implicit=implicit)
    image_graph = ibs.depc_image.make_graph(reduced=reduced, implicit=implicit)
    to_rename = ut.isect(image_graph.nodes(), annot_graph.nodes())
    nx.relabel_nodes(annot_graph, {x: 'annot_' + x
                                   for x in to_rename},
                     copy=False)
    nx.relabel_nodes(image_graph, {x: 'image_' + x
                                   for x in to_rename},
                     copy=False)
    graph = nx.compose_all([image_graph, annot_graph])
    #graph = nx.union_all([image_graph, annot_graph], rename=('image', 'annot'))
    # userdecision = ut.nx_makenode(graph, 'user decision', shape='rect', color=pt.DARK_YELLOW, style='diagonals')
    # userdecision = ut.nx_makenode(graph, 'user decision', shape='circle', color=pt.DARK_YELLOW)
    userdecision = ut.nx_makenode(
        graph,
        'User decision',
        shape='rect',
        #width=100, height=100,
        color=pt.YELLOW,
        style='diagonals')
    #longcat = True
    longcat = False

    #edge = ('feat', 'neighbor_index')
    #data = graph.get_edge_data(*edge)[0]
    #print('data = %r' % (data,))
    #graph.remove_edge(*edge)
    ## hack
    #graph.add_edge('featweight', 'neighbor_index', **data)

    graph.add_edge('detections',
                   userdecision,
                   constraint=longcat,
                   color=pt.PINK)
    graph.add_edge(userdecision,
                   'annotations',
                   constraint=longcat,
                   color=pt.PINK)
    # graph.add_edge(userdecision, 'annotations', implicit=True, color=[0, 0, 0])
    if not longcat:
        pass
        #graph.add_edge('images', 'annotations', style='invis')
        #graph.add_edge('thumbnails', 'annotations', style='invis')
        #graph.add_edge('thumbnails', userdecision, style='invis')
    graph.remove_node('Has_Notch')
    graph.remove_node('annotmask')
    layoutkw = {
        'ranksep': 5,
        'nodesep': 5,
        'dpi': 96,
        # 'nodesep': 1,
    }
    ns = 1000

    ut.nx_set_default_node_attributes(graph, 'fontsize', 72)
    ut.nx_set_default_node_attributes(graph, 'fontname', 'Ubuntu')
    ut.nx_set_default_node_attributes(graph, 'style', 'filled')

    ut.nx_set_default_node_attributes(graph, 'width', ns * ut.PHI)
    ut.nx_set_default_node_attributes(graph, 'height', ns * (1 / ut.PHI))

    #for u, v, d in graph.edge(data=True):
    for u, vkd in graph.edge.items():
        for v, dk in vkd.items():
            for k, d in dk.items():
                localid = d.get('local_input_id')
                if localid:
                    # d['headlabel'] = localid
                    if localid not in ['1']:
                        d['taillabel'] = localid
                    #d['label'] = localid
                if d.get('taillabel') in {'1'}:
                    del d['taillabel']

    node_alias = {
        'chips': 'Chip',
        'images': 'Image',
        'feat': 'Feat',
        'featweight': 'Feat Weights',
        'thumbnails': 'Thumbnail',
        'detections': 'Detections',
        'annotations': 'Annotation',
        'Notch_Tips': 'Notch Tips',
        'probchip': 'Prob Chip',
        'Cropped_Chips': 'Croped Chip',
        'Trailing_Edge': 'Trailing\nEdge',
        'Block_Curvature': 'Block\nCurvature',
        # 'BC_DTW': 'block curvature /\n dynamic time warp',
        'BC_DTW': 'DTW Distance',
        'vsone': 'Hots vsone',
        'feat_neighbs': 'Nearest\nNeighbors',
        'neighbor_index': 'Neighbor\nIndex',
        'vsmany': 'Hots vsmany',
        'annot_labeler': 'Annot Labeler',
        'labeler': 'Labeler',
        'localizations': 'Localizations',
        'classifier': 'Classifier',
        'sver': 'Spatial\nVerification',
        'Classifier': 'Existence',
        'image_labeler': 'Image Labeler',
    }
    node_alias = {
        'Classifier': 'existence',
        'feat_neighbs': 'neighbors',
        'sver': 'spatial_verification',
        'Cropped_Chips': 'cropped_chip',
        'BC_DTW': 'dtw_distance',
        'Block_Curvature': 'curvature',
        'Trailing_Edge': 'trailing_edge',
        'Notch_Tips': 'notch_tips',
        'thumbnails': 'thumbnail',
        'images': 'image',
        'annotations': 'annotation',
        'chips': 'chip',
        #userdecision: 'User de'
    }
    node_alias = ut.delete_dict_keys(
        node_alias, ut.setdiff(node_alias.keys(), graph.nodes()))
    nx.relabel_nodes(graph, node_alias, copy=False)

    fontkw = dict(fontname='Ubuntu', fontweight='normal', fontsize=12)
    #pt.gca().set_aspect('equal')
    #pt.figure()
    pt.show_nx(graph, layoutkw=layoutkw, fontkw=fontkw)
    pt.zoom_factory()
コード例 #6
0
ファイル: specialdraw.py プロジェクト: whaozl/ibeis
def graphcut_flow():
    r"""
    Returns:
        ?: name

    CommandLine:
        python -m ibeis.scripts.specialdraw graphcut_flow --show --save cutflow.png --diskshow --clipwhite
        python -m ibeis.scripts.specialdraw graphcut_flow --save figures4/cutiden.png --diskshow --clipwhite --dpath ~/latex/crall-candidacy-2015/ --figsize=24,10 --arrow-width=2.0

    Example:
        >>> # DISABLE_DOCTEST
        >>> from ibeis.scripts.specialdraw import *  # NOQA
        >>> graphcut_flow()
        >>> ut.quit_if_noshow()
        >>> import plottool as pt
        >>> ut.show_if_requested()
    """
    import plottool as pt
    pt.ensure_pylab_qt4()
    import networkx as nx
    # pt.plt.xkcd()

    graph = nx.DiGraph()

    def makecluster(name, num, **attrkw):
        return [
            ut.nx_makenode(graph, name + str(n), **attrkw) for n in range(num)
        ]

    def add_edge2(u, v, *args, **kwargs):
        v = ut.ensure_iterable(v)
        u = ut.ensure_iterable(u)
        for _u, _v in ut.product(u, v):
            graph.add_edge(_u, _v, *args, **kwargs)

    ns = 512

    # *** Primary color:
    p_shade2 = '#41629A'
    # *** Secondary color
    s1_shade2 = '#E88B53'
    # *** Secondary color
    s2_shade2 = '#36977F'
    # *** Complement color
    c_shade2 = '#E8B353'

    annot1 = ut.nx_makenode(graph,
                            'Unlabeled\nannotations\n(query)',
                            width=ns,
                            height=ns,
                            groupid='annot',
                            color=p_shade2)
    annot2 = ut.nx_makenode(graph,
                            'Labeled\nannotations\n(database)',
                            width=ns,
                            height=ns,
                            groupid='annot',
                            color=s1_shade2)
    occurprob = ut.nx_makenode(graph,
                               'Dense \nprobabilities',
                               color=lighten_hex(p_shade2, .1))
    cacheprob = ut.nx_makenode(graph,
                               'Cached \nprobabilities',
                               color=lighten_hex(s1_shade2, .1))
    sparseprob = ut.nx_makenode(graph,
                                'Sparse\nprobabilities',
                                color=lighten_hex(c_shade2, .1))

    graph.add_edge(annot1, occurprob)

    graph.add_edge(annot1, sparseprob)
    graph.add_edge(annot2, sparseprob)
    graph.add_edge(annot2, cacheprob)

    matchgraph = ut.nx_makenode(graph,
                                'Graph of\npotential matches',
                                color=lighten_hex(s2_shade2, .1))
    cutalgo = ut.nx_makenode(graph,
                             'Graph cut algorithm',
                             color=lighten_hex(s2_shade2, .2),
                             shape='ellipse')
    cc_names = ut.nx_makenode(
        graph,
        'Identifications,\n splits, and merges are\nconnected compoments',
        color=lighten_hex(s2_shade2, .3))

    graph.add_edge(occurprob, matchgraph)
    graph.add_edge(sparseprob, matchgraph)
    graph.add_edge(cacheprob, matchgraph)

    graph.add_edge(matchgraph, cutalgo)
    graph.add_edge(cutalgo, cc_names)

    ut.nx_set_default_node_attributes(graph, 'shape', 'rect')
    ut.nx_set_default_node_attributes(graph, 'style', 'filled,rounded')
    ut.nx_set_default_node_attributes(graph, 'fixedsize', 'true')
    ut.nx_set_default_node_attributes(graph, 'width', ns * ut.PHI)
    ut.nx_set_default_node_attributes(graph, 'height', ns * (1 / ut.PHI))
    ut.nx_set_default_node_attributes(graph, 'regular', False)

    layoutkw = {
        'prog': 'dot',
        'rankdir': 'LR',
        'splines': 'line',
        'sep': 100 / 72,
        'nodesep': 300 / 72,
        'ranksep': 300 / 72,
    }

    fontkw = dict(fontname='Ubuntu', fontweight='light', fontsize=14)
    pt.show_nx(graph, layout='agraph', layoutkw=layoutkw, **fontkw)
    pt.zoom_factory()
コード例 #7
0
ファイル: specialdraw.py プロジェクト: whaozl/ibeis
def general_identify_flow():
    r"""
    CommandLine:
        python -m ibeis.scripts.specialdraw general_identify_flow --show --save pairsim.png --dpi=100 --diskshow --clipwhite

        python -m ibeis.scripts.specialdraw general_identify_flow --dpi=200 --diskshow --clipwhite --dpath ~/latex/cand/ --figsize=20,10  --save figures4/pairprob.png --arrow-width=2.0


    Example:
        >>> # SCRIPT
        >>> from ibeis.scripts.specialdraw import *  # NOQA
        >>> general_identify_flow()
        >>> ut.quit_if_noshow()
        >>> ut.show_if_requested()
    """
    import networkx as nx
    import plottool as pt
    pt.ensure_pylab_qt4()
    # pt.plt.xkcd()

    graph = nx.DiGraph()

    def makecluster(name, num, **attrkw):
        return [ut.nx_makenode(name + str(n), **attrkw) for n in range(num)]

    def add_edge2(u, v, *args, **kwargs):
        v = ut.ensure_iterable(v)
        u = ut.ensure_iterable(u)
        for _u, _v in ut.product(u, v):
            graph.add_edge(_u, _v, *args, **kwargs)

    # *** Primary color:
    p_shade2 = '#41629A'
    # *** Secondary color
    s1_shade2 = '#E88B53'
    # *** Secondary color
    s2_shade2 = '#36977F'
    # *** Complement color
    c_shade2 = '#E8B353'

    ns = 512

    ut.inject_func_as_method(graph, ut.nx_makenode)

    annot1_color = p_shade2
    annot2_color = s1_shade2
    #annot1_color2 = pt.color_funcs.lighten_rgb(colors.hex2color(annot1_color), .01)

    annot1 = graph.nx_makenode('Annotation X',
                               width=ns,
                               height=ns,
                               groupid='annot',
                               color=annot1_color)
    annot2 = graph.nx_makenode('Annotation Y',
                               width=ns,
                               height=ns,
                               groupid='annot',
                               color=annot2_color)

    featX = graph.nx_makenode('Features X',
                              size=(ns / 1.2, ns / 2),
                              groupid='feats',
                              color=lighten_hex(annot1_color, .1))
    featY = graph.nx_makenode('Features Y',
                              size=(ns / 1.2, ns / 2),
                              groupid='feats',
                              color=lighten_hex(annot2_color, .1))
    #'#4771B3')

    global_pairvec = graph.nx_makenode(
        'Global similarity\n(viewpoint, quality, ...)',
        width=ns * ut.PHI * 1.2,
        color=s2_shade2)
    findnn = graph.nx_makenode('Find correspondences\n(nearest neighbors)',
                               shape='ellipse',
                               color=c_shade2)
    local_pairvec = graph.nx_makenode(
        'Local similarities\n(LNBNN, spatial error, ...)',
        size=(ns * 2.2, ns),
        color=lighten_hex(c_shade2, .1))
    agglocal = graph.nx_makenode('Aggregate',
                                 size=(ns / 1.1, ns / 2),
                                 shape='ellipse',
                                 color=lighten_hex(c_shade2, .2))
    catvecs = graph.nx_makenode('Concatenate',
                                size=(ns / 1.1, ns / 2),
                                shape='ellipse',
                                color=lighten_hex(s2_shade2, .1))
    pairvec = graph.nx_makenode('Vector of\npairwise similarities',
                                color=lighten_hex(s2_shade2, .2))
    classifier = graph.nx_makenode('Classifier\n(SVM/RF/DNN)',
                                   color=lighten_hex(s2_shade2, .3))
    prob = graph.nx_makenode(
        'Matching Probability\n(same individual given\nsimilar viewpoint)',
        color=lighten_hex(s2_shade2, .4))

    graph.add_edge(annot1, global_pairvec)
    graph.add_edge(annot2, global_pairvec)

    add_edge2(annot1, featX)
    add_edge2(annot2, featY)

    add_edge2(featX, findnn)
    add_edge2(featY, findnn)

    add_edge2(findnn, local_pairvec)

    graph.add_edge(local_pairvec, agglocal, constraint=True)
    graph.add_edge(agglocal, catvecs, constraint=False)
    graph.add_edge(global_pairvec, catvecs)

    graph.add_edge(catvecs, pairvec)

    # graph.add_edge(annot1, classifier, style='invis')
    # graph.add_edge(pairvec, classifier , constraint=False)
    graph.add_edge(pairvec, classifier)
    graph.add_edge(classifier, prob)

    ut.nx_set_default_node_attributes(graph, 'shape', 'rect')
    #ut.nx_set_default_node_attributes(graph, 'fillcolor', nx.get_node_attributes(graph, 'color'))
    #ut.nx_set_default_node_attributes(graph, 'style',  'rounded')
    ut.nx_set_default_node_attributes(graph, 'style', 'filled,rounded')
    ut.nx_set_default_node_attributes(graph, 'fixedsize', 'true')
    ut.nx_set_default_node_attributes(graph, 'xlabel',
                                      nx.get_node_attributes(graph, 'label'))
    ut.nx_set_default_node_attributes(graph, 'width', ns * ut.PHI)
    ut.nx_set_default_node_attributes(graph, 'height', ns)
    ut.nx_set_default_node_attributes(graph, 'regular', False)

    #font = 'MonoDyslexic'
    #font = 'Mono_Dyslexic'
    font = 'Ubuntu'
    ut.nx_set_default_node_attributes(graph, 'fontsize', 72)
    ut.nx_set_default_node_attributes(graph, 'fontname', font)

    #ut.nx_delete_node_attr(graph, 'width')
    #ut.nx_delete_node_attr(graph, 'height')
    #ut.nx_delete_node_attr(graph, 'fixedsize')
    #ut.nx_delete_node_attr(graph, 'style')
    #ut.nx_delete_node_attr(graph, 'regular')
    #ut.nx_delete_node_attr(graph, 'shape')

    #graph.node[annot1]['label'] = "<f0> left|<f1> mid&#92; dle|<f2> right"
    #graph.node[annot2]['label'] = ut.codeblock(
    #    '''
    #    <<TABLE BORDER="0" CELLBORDER="1" CELLSPACING="0">
    #      <TR><TD>left</TD><TD PORT="f1">mid dle</TD><TD PORT="f2">right</TD></TR>
    #    </TABLE>>
    #    ''')
    #graph.node[annot1]['label'] = ut.codeblock(
    #    '''
    #    <<TABLE BORDER="0" CELLBORDER="1" CELLSPACING="0">
    #      <TR><TD>left</TD><TD PORT="f1">mid dle</TD><TD PORT="f2">right</TD></TR>
    #    </TABLE>>
    #    ''')

    #graph.node[annot1]['shape'] = 'none'
    #graph.node[annot1]['margin'] = '0'

    layoutkw = {
        'forcelabels': True,
        'prog': 'dot',
        'rankdir': 'LR',
        # 'splines': 'curved',
        'splines': 'line',
        'samplepoints': 20,
        'showboxes': 1,
        # 'splines': 'polyline',
        #'splines': 'spline',
        'sep': 100 / 72,
        'nodesep': 300 / 72,
        'ranksep': 300 / 72,
        #'inputscale': 72,
        # 'inputscale': 1,
        # 'dpi': 72,
        # 'concentrate': 'true', # merges edge lines
        # 'splines': 'ortho',
        # 'aspect': 1,
        # 'ratio': 'compress',
        # 'size': '5,4000',
        # 'rank': 'max',
    }

    #fontkw = dict(fontfamilty='sans-serif', fontweight='normal', fontsize=12)
    #fontkw = dict(fontname='Ubuntu', fontweight='normal', fontsize=12)
    #fontkw = dict(fontname='Ubuntu', fontweight='light', fontsize=20)
    fontkw = dict(fontname=font, fontweight='light', fontsize=12)
    #prop = fm.FontProperties(fname='/usr/share/fonts/truetype/groovygh.ttf')

    pt.show_nx(graph, layout='agraph', layoutkw=layoutkw, **fontkw)
    pt.zoom_factory()
コード例 #8
0
ファイル: pgm_viz.py プロジェクト: Erotemic/ibeis
def draw_bayesian_model(model, evidence={}, soft_evidence={}, fnum=None,
                        pnum=None, **kwargs):

    from pgmpy.models import BayesianModel
    if not isinstance(model, BayesianModel):
        model = model.to_bayesian_model()

    import plottool as pt
    import networkx as nx
    kwargs = kwargs.copy()
    factor_list = kwargs.pop('factor_list', [])

    ttype_colors, ttype_scalars = make_colorcodes(model)

    textprops = {
        'horizontalalignment': 'left', 'family': 'monospace', 'size': 8, }

    # build graph attrs
    tup = get_node_viz_attrs(
        model, evidence, soft_evidence, factor_list, ttype_colors, **kwargs)
    node_color, pos_list, pos_dict, takws = tup

    # draw graph
    has_infered = evidence or 'factor_list' in kwargs

    if False:
        fig = pt.figure(fnum=fnum, pnum=pnum, doclf=True)  # NOQA
        ax = pt.gca()
        drawkw = dict(pos=pos_dict, ax=ax, with_labels=True, node_size=1100,
                      node_color=node_color)
        nx.draw(model, **drawkw)
    else:
        # BE VERY CAREFUL
        if 1:
            graph = model.copy()
            graph.__class__ = nx.DiGraph
            graph.graph['groupattrs'] = ut.ddict(dict)
            #graph = model.
            if getattr(graph, 'ttype2_cpds', None) is not None:
                # Add invis edges and ttype groups
                for ttype in model.ttype2_cpds.keys():
                    ttype_cpds = model.ttype2_cpds[ttype]
                    # use defined ordering
                    ttype_nodes = ut.list_getattr(ttype_cpds, 'variable')
                    # ttype_nodes = sorted(ttype_nodes)
                    invis_edges = list(ut.itertwo(ttype_nodes))
                    graph.add_edges_from(invis_edges)
                    nx.set_edge_attributes(graph, 'style', {edge: 'invis' for edge in invis_edges})
                    nx.set_node_attributes(graph, 'groupid', {node: ttype for node in ttype_nodes})
                    graph.graph['groupattrs'][ttype]['rank'] = 'same'
                    graph.graph['groupattrs'][ttype]['cluster'] = False
        else:
            graph = model
        pt.show_nx(graph, layout_kw={'prog': 'dot'}, fnum=fnum, pnum=pnum, verbose=0)
        pt.zoom_factory()
        fig = pt.gcf()
        ax = pt.gca()
        pass
    hacks = [pt.draw_text_annotations(textprops=textprops, **takw)
             for takw in takws if takw]

    xmin, ymin = np.array(pos_list).min(axis=0)
    xmax, ymax = np.array(pos_list).max(axis=0)
    if 'name' in model.ttype2_template:
        num_names = len(model.ttype2_template['name'].basis)
        num_annots = len(model.ttype2_cpds['name'])
        if num_annots > 4:
            ax.set_xlim((xmin - 40, xmax + 40))
            ax.set_ylim((ymin - 50, ymax + 50))
            fig.set_size_inches(30, 7)
        else:
            ax.set_xlim((xmin - 42, xmax + 42))
            ax.set_ylim((ymin - 50, ymax + 50))
            fig.set_size_inches(23, 7)
        title = 'num_names=%r, num_annots=%r' % (num_names, num_annots,)
    else:
        title = ''
    map_assign = kwargs.get('map_assign', None)

    def word_insert(text):
        return '' if len(text) == 0 else text + ' '

    top_assignments = kwargs.get('top_assignments', None)
    if top_assignments is not None:
        map_assign, map_prob = top_assignments[0]
        if map_assign is not None:
            title += '\n%sMAP: ' % (word_insert(kwargs.get('method', '')))
            title += map_assign + ' @' + '%.2f%%' % (100 * map_prob,)
    if kwargs.get('show_title', True):
        pt.set_figtitle(title, size=14)

    for hack in hacks:
        hack()

    if has_infered:
        # Hack in colorbars
        # if ut.list_type(basis) is int:
        #     pt.colorbar(scalars, colors, lbl='score', ticklabels=np.array(basis) + 1)
        # else:
        #     pt.colorbar(scalars, colors, lbl='score', ticklabels=basis)
        keys = ['name', 'score']
        locs = ['left', 'right']
        for key, loc in zip(keys, locs):
            if key in ttype_colors:
                basis = model.ttype2_template[key].basis
                # scalars =
                colors = ttype_colors[key]
                scalars = ttype_scalars[key]
                pt.colorbar(scalars, colors, lbl=key, ticklabels=basis,
                            ticklocation=loc)
コード例 #9
0
ファイル: iface_caffe.py プロジェクト: lclibardi/clab
def _model_data_flow_to_networkx(model_info):
    layers = model_info['layer']
    import networkx as nx
    G = nx.DiGraph()

    prev = None
    # Stores last node with the data for this layer in it
    prev_map = {}

    SHOW_LOOPS = False

    for layer in layers:
        name = layer.get('name')
        print('name = {!r}'.format(name))
        G.add_node(name)
        bottom = set(layer.get('bottom', []))
        top = set(layer.get('top', []))

        both = top.intersection(bottom)
        if both:
            if prev is None:
                prev = both
            for b in both:
                prev_map[b] = name
            for b in prev:
                print('  * b = {!r}'.format(b))
                G.add_edge(b, name, constraint=False)
            for b in both:
                print('  * b = {!r}'.format(b))
                kw = {}
                if not G.has_edge(b, name):
                    kw['color'] = 'red'
                G.add_edge(b, name, constraint=True, **kw)
            prev = [name]
        else:
            prev = None

        # for b in (bottom - both):
        for b in bottom:
            print('  * b = {!r}'.format(b))
            constraint = True
            G.add_edge(prev_map.get(b, b), name, constraint=constraint)
            if SHOW_LOOPS:
                G.add_edge(b, name)
        # for t in (bottom - top):
        for t in top:
            print('  * t = {!r}'.format(t))
            constraint = True
            G.add_edge(name, prev_map.get(t, t), constraint=constraint)
            if SHOW_LOOPS:
                G.add_edge(name, t)

    G.remove_edges_from(list(G.selfloop_edges()))

    import plottool as pt
    pt.qtensure()
    pt.show_nx(G, arrow_width=1)
    pt.adjust_subplots(left=0, right=1, top=1, bottom=0)
    pt.pan_factory()
    pt.zoom_factory()

    list(nx.topological_sort(G))
コード例 #10
0
ファイル: mixin_viz.py プロジェクト: simplesoftMX/ibeis
    def show_graph(infr,
                   graph=None,
                   use_image=False,
                   update_attrs=True,
                   with_colorbar=False,
                   pnum=(1, 1, 1),
                   zoomable=True,
                   pickable=False,
                   **kwargs):
        r"""
        Args:
            infr (?):
            graph (None): (default = None)
            use_image (bool): (default = False)
            update_attrs (bool): (default = True)
            with_colorbar (bool): (default = False)
            pnum (tuple):  plot number(default = (1, 1, 1))
            zoomable (bool): (default = True)
            pickable (bool): (de = False)
            **kwargs: verbose, with_labels, fnum, layout, ax, pos, img_dict,
                      title, layoutkw, framewidth, modify_ax, as_directed,
                      hacknoedge, hacknode, node_labels, arrow_width, fontsize,
                      fontweight, fontname, fontfamilty, fontproperties

        CommandLine:
            python -m ibeis.algo.graph.mixin_viz GraphVisualization.show_graph --show

        Example:
            >>> # ENABLE_DOCTEST
            >>> from ibeis.algo.graph.mixin_viz import *  # NOQA
            >>> from ibeis.algo.graph import demo
            >>> import plottool as pt
            >>> infr = demo.demodata_infr(ccs=ut.estarmap(
            >>>    range, [(1, 6), (6, 10), (10, 13), (13, 15), (15, 16),
            >>>            (17, 20)]))
            >>> pnum_ = pt.make_pnum_nextgen(nRows=1, nCols=3)
            >>> infr.show_graph(show_cand=True, simple_labels=True, pickable=True, fnum=1, pnum=pnum_())
            >>> infr.add_feedback((1, 5), INCMP)
            >>> infr.add_feedback((14, 18), INCMP)
            >>> infr.refresh_candidate_edges()
            >>> infr.show_graph(show_cand=True, simple_labels=True, pickable=True, fnum=1, pnum=pnum_())
            >>> infr.add_feedback((17, 18), NEGTV)  # add inconsistency
            >>> infr.apply_nondynamic_update()
            >>> infr.show_graph(show_cand=True, simple_labels=True, pickable=True, fnum=1, pnum=pnum_())
            >>> ut.show_if_requested()
        """
        import plottool as pt
        if graph is None:
            graph = infr.graph
        # kwargs['fontsize'] = kwargs.get('fontsize', 8)
        with warnings.catch_warnings():
            warnings.simplefilter("ignore")
            # default_update_kw = ut.get_func_kwargs(infr.update_visual_attrs)
            # update_kw = ut.update_existing(default_update_kw, kwargs)
            # infr.update_visual_attrs(**update_kw)
            if update_attrs:
                infr.update_visual_attrs(graph=graph, **kwargs)
            verbose = kwargs.pop('verbose', infr.verbose)
            pt.show_nx(graph,
                       layout='custom',
                       as_directed=False,
                       modify_ax=False,
                       use_image=use_image,
                       pnum=pnum,
                       verbose=verbose,
                       **kwargs)
            if zoomable:
                pt.zoom_factory()
                pt.pan_factory(pt.gca())

        # if with_colorbar:
        #     # Draw a colorbar
        #     _normal_ticks = np.linspace(0, 1, num=11)
        #     _normal_scores = np.linspace(0, 1, num=500)
        #     _normal_colors = infr.get_colored_weights(_normal_scores)
        #     cb = pt.colorbar(_normal_scores, _normal_colors, lbl='weights',
        #                      ticklabels=_normal_ticks)

        #     # point to threshold location
        #     thresh = None
        #     if thresh is not None:
        #         xy = (1, thresh)
        #         xytext = (2.5, .3 if thresh < .5 else .7)
        #         cb.ax.annotate('threshold', xy=xy, xytext=xytext,
        #                        arrowprops=dict(
        #                            alpha=.5, fc="0.6",
        #                            connectionstyle="angle3,angleA=90,angleB=0"),)

        # infr.graph
        if graph.graph.get('dark_background', None):
            pt.dark_background(force=True)

        if pickable:
            fig = pt.gcf()
            fig.canvas.mpl_connect('pick_event', ut.partial(on_pick,
                                                            infr=infr))
コード例 #11
0
ファイル: specialdraw.py プロジェクト: Erotemic/ibeis
def intraoccurrence_connected():
    r"""
    CommandLine:
        python -m ibeis.scripts.specialdraw intraoccurrence_connected --show
        python -m ibeis.scripts.specialdraw intraoccurrence_connected --show --postcut
        python -m ibeis.scripts.specialdraw intraoccurrence_connected --show --smaller

    Example:
        >>> # DISABLE_DOCTEST
        >>> from ibeis.scripts.specialdraw import *  # NOQA
        >>> result = intraoccurrence_connected()
        >>> print(result)
        >>> ut.quit_if_noshow()
        >>> import plottool as pt
        >>> ut.show_if_requested()
    """
    import ibeis
    import plottool as pt
    from ibeis.viz import viz_graph
    import networkx as nx
    pt.ensure_pylab_qt4()
    ibs = ibeis.opendb(defaultdb='PZ_Master1')
    nid2_aid = {
        #4880: [3690, 3696, 3703, 3706, 3712, 3721],
        4880: [3690, 3696, 3703],
        6537: [3739],
        6653: [7671],
        6610: [7566, 7408],
        #6612: [7664, 7462, 7522],
        #6624: [7465, 7360],
        #6625: [7746, 7383, 7390, 7477, 7376, 7579],
        6630: [7586, 7377, 7464, 7478],
        #6677: [7500]
    }
    nid2_dbaids = {
        4880: [33, 6120, 7164],
        6537: [7017, 7206],
        6653: [7660]
    }
    if ut.get_argflag('--small') or ut.get_argflag('--smaller'):
        del nid2_aid[6630]
        del nid2_aid[6537]
        del nid2_dbaids[6537]
        if ut.get_argflag('--smaller'):
            nid2_dbaids[4880].remove(33)
            nid2_aid[4880].remove(3690)
            nid2_aid[6610].remove(7408)
        #del nid2_aid[4880]
        #del nid2_dbaids[4880]

    aids = ut.flatten(nid2_aid.values())

    temp_nids = [1] * len(aids)
    postcut = ut.get_argflag('--postcut')
    aids_list = ibs.group_annots_by_name(aids)[0]
    ensure_edges = 'all' if True or not postcut else None
    unlabeled_graph = viz_graph.make_netx_graph_from_aid_groups(
        ibs, aids_list,
        #invis_edges=invis_edges,
        ensure_edges=ensure_edges, temp_nids=temp_nids)
    viz_graph.color_by_nids(unlabeled_graph, unique_nids=[1] *
                            len(list(unlabeled_graph.nodes())))
    viz_graph.ensure_node_images(ibs, unlabeled_graph)
    nx.set_node_attributes(unlabeled_graph, 'shape', 'rect')
    #unlabeled_graph = unlabeled_graph.to_undirected()

    # Find the "database exemplars for these annots"
    if False:
        gt_aids = ibs.get_annot_groundtruth(aids)
        gt_aids = [ut.setdiff(s, aids) for s in gt_aids]
        dbaids = ut.unique(ut.flatten(gt_aids))
        dbaids = ibs.filter_annots_general(dbaids, minqual='good')
        ibs.get_annot_quality_texts(dbaids)
    else:
        dbaids = ut.flatten(nid2_dbaids.values())
    exemplars = nx.DiGraph()
    #graph = exemplars  # NOQA
    exemplars.add_nodes_from(dbaids)

    def add_clique(graph, nodes, edgeattrs={}, nodeattrs={}):
        edge_list = ut.upper_diag_self_prodx(nodes)
        graph.add_edges_from(edge_list, **edgeattrs)
        return edge_list

    for aids_, nid in zip(*ibs.group_annots_by_name(dbaids)):
        add_clique(exemplars, aids_)
    viz_graph.ensure_node_images(ibs, exemplars)
    viz_graph.color_by_nids(exemplars, ibs=ibs)

    nx.set_node_attributes(unlabeled_graph, 'framewidth', False)
    nx.set_node_attributes(exemplars,  'framewidth', 4.0)

    nx.set_node_attributes(unlabeled_graph, 'group', 'unlab')
    nx.set_node_attributes(exemplars,  'group', 'exemp')

    #big_graph = nx.compose_all([unlabeled_graph])
    big_graph = nx.compose_all([exemplars, unlabeled_graph])

    # add sparse connections from unlabeled to exemplars
    import numpy as np
    rng = np.random.RandomState(0)
    if True or not postcut:
        for aid_ in unlabeled_graph.nodes():
            flags = rng.rand(len(exemplars)) > .5
            nid_ = ibs.get_annot_nids(aid_)
            exnids = np.array(ibs.get_annot_nids(list(exemplars.nodes())))
            flags = np.logical_or(exnids == nid_, flags)
            exmatches = ut.compress(list(exemplars.nodes()), flags)
            big_graph.add_edges_from(list(ut.product([aid_], exmatches)),
                                     color=pt.ORANGE, implicit=True)
    else:
        for aid_ in unlabeled_graph.nodes():
            flags = rng.rand(len(exemplars)) > .5
            exmatches = ut.compress(list(exemplars.nodes()), flags)
            nid_ = ibs.get_annot_nids(aid_)
            exnids = np.array(ibs.get_annot_nids(exmatches))
            exmatches = ut.compress(exmatches, exnids == nid_)
            big_graph.add_edges_from(list(ut.product([aid_], exmatches)))
        pass

    nx.set_node_attributes(big_graph, 'shape', 'rect')
    #if False and postcut:
    #    ut.nx_delete_node_attr(big_graph, 'nid')
    #    ut.nx_delete_edge_attr(big_graph, 'color')
    #    viz_graph.ensure_graph_nid_labels(big_graph, ibs=ibs)
    #    viz_graph.color_by_nids(big_graph, ibs=ibs)
    #    big_graph = big_graph.to_undirected()

    layoutkw = {
        'sep' : 1 / 5,
        'prog': 'neato',
        'overlap': 'false',
        #'splines': 'ortho',
        'splines': 'spline',
    }

    as_directed = False
    #as_directed = True
    #hacknode = True
    hacknode = 0

    graph = big_graph
    ut.nx_ensure_agraph_color(graph)
    if hacknode:
        nx.set_edge_attributes(graph, 'taillabel', {e: str(e[0]) for e in graph.edges()})
        nx.set_edge_attributes(graph, 'headlabel', {e: str(e[1]) for e in graph.edges()})

    explicit_graph = pt.get_explicit_graph(graph)
    _, layout_info = pt.nx_agraph_layout(explicit_graph, orig_graph=graph,
                                         inplace=True, **layoutkw)

    if ut.get_argflag('--smaller'):
        graph.node[7660]['pos'] = np.array([550, 350])
        graph.node[6120]['pos'] = np.array([200, 600]) + np.array([350, -400])
        graph.node[7164]['pos'] = np.array([200, 480]) + np.array([350, -400])
        nx.set_node_attributes(graph, 'pin', 'true')
        _, layout_info = pt.nx_agraph_layout(graph,
                                             inplace=True, **layoutkw)
    elif ut.get_argflag('--small'):
        graph.node[7660]['pos'] = np.array([750, 350])
        graph.node[33]['pos'] = np.array([300, 600]) + np.array([350, -400])
        graph.node[6120]['pos'] = np.array([500, 600]) + np.array([350, -400])
        graph.node[7164]['pos'] = np.array([410, 480]) + np.array([350, -400])
        nx.set_node_attributes(graph, 'pin', 'true')
        _, layout_info = pt.nx_agraph_layout(graph,
                                             inplace=True, **layoutkw)

    if not postcut:
        #pt.show_nx(graph.to_undirected(), layout='agraph', layoutkw=layoutkw,
        #           as_directed=False)
        #pt.show_nx(graph, layout='agraph', layoutkw=layoutkw,
        #           as_directed=as_directed, hacknode=hacknode)

        pt.show_nx(graph, layout='custom', layoutkw=layoutkw,
                   as_directed=as_directed, hacknode=hacknode)
    else:
        #explicit_graph = pt.get_explicit_graph(graph)
        #_, layout_info = pt.nx_agraph_layout(explicit_graph, orig_graph=graph,
        #                                     **layoutkw)

        #layout_info['edge']['alpha'] = .8
        #pt.apply_graph_layout_attrs(graph, layout_info)

        #graph_layout_attrs = layout_info['graph']
        ##edge_layout_attrs  = layout_info['edge']
        ##node_layout_attrs  = layout_info['node']

        #for key, vals in layout_info['node'].items():
        #    #print('[special] key = %r' % (key,))
        #    nx.set_node_attributes(graph, key, vals)

        #for key, vals in layout_info['edge'].items():
        #    #print('[special] key = %r' % (key,))
        #    nx.set_edge_attributes(graph, key, vals)

        #nx.set_edge_attributes(graph, 'alpha', .8)
        #graph.graph['splines'] = graph_layout_attrs.get('splines', 'line')
        #graph.graph['splines'] = 'polyline'   # graph_layout_attrs.get('splines', 'line')
        #graph.graph['splines'] = 'line'

        cut_graph = graph.copy()
        edge_list = list(cut_graph.edges())
        edge_nids = np.array(ibs.unflat_map(ibs.get_annot_nids, edge_list))
        cut_flags = edge_nids.T[0] != edge_nids.T[1]
        cut_edges = ut.compress(edge_list, cut_flags)
        cut_graph.remove_edges_from(cut_edges)
        ut.nx_delete_node_attr(cut_graph, 'nid')
        viz_graph.ensure_graph_nid_labels(cut_graph, ibs=ibs)

        #ut.nx_get_default_node_attributes(exemplars, 'color', None)
        ut.nx_delete_node_attr(cut_graph, 'color', nodes=unlabeled_graph.nodes())
        aid2_color = ut.nx_get_default_node_attributes(cut_graph, 'color', None)
        nid2_colors = ut.group_items(aid2_color.values(), ibs.get_annot_nids(aid2_color.keys()))
        nid2_colors = ut.map_dict_vals(ut.filter_Nones, nid2_colors)
        nid2_colors = ut.map_dict_vals(ut.unique, nid2_colors)
        #for val in nid2_colors.values():
        #    assert len(val) <= 1
        # Get initial colors
        nid2_color_ = {nid: colors_[0] for nid, colors_ in nid2_colors.items()
                       if len(colors_) == 1}

        graph = cut_graph
        viz_graph.color_by_nids(cut_graph, ibs=ibs, nid2_color_=nid2_color_)
        nx.set_node_attributes(cut_graph, 'framewidth', 4)

        pt.show_nx(cut_graph, layout='custom', layoutkw=layoutkw,
                   as_directed=as_directed, hacknode=hacknode)

    pt.zoom_factory()
コード例 #12
0
ファイル: specialdraw.py プロジェクト: Erotemic/ibeis
def double_depcache_graph():
    r"""
    CommandLine:
        python -m ibeis.scripts.specialdraw double_depcache_graph --show --testmode

        python -m ibeis.scripts.specialdraw double_depcache_graph --save=figures5/doubledepc.png --dpath ~/latex/cand/  --diskshow  --figsize=8,20 --dpi=220 --testmode --show --clipwhite
        python -m ibeis.scripts.specialdraw double_depcache_graph --save=figures5/doubledepc.png --dpath ~/latex/cand/  --diskshow  --figsize=8,20 --dpi=220 --testmode --show --clipwhite --arrow-width=.5

        python -m ibeis.scripts.specialdraw double_depcache_graph --save=figures5/doubledepc.png --dpath ~/latex/cand/  --diskshow  --figsize=8,20 --dpi=220 --testmode --show --clipwhite --arrow-width=5

    Example:
        >>> # DISABLE_DOCTEST
        >>> from ibeis.scripts.specialdraw import *  # NOQA
        >>> result = double_depcache_graph()
        >>> print(result)
        >>> ut.quit_if_noshow()
        >>> import plottool as pt
        >>> ut.show_if_requested()
    """
    import ibeis
    import networkx as nx
    import plottool as pt
    pt.ensure_pylab_qt4()
    # pt.plt.xkcd()
    ibs = ibeis.opendb('testdb1')
    reduced = True
    implicit = True
    annot_graph = ibs.depc_annot.make_graph(reduced=reduced, implicit=implicit)
    image_graph = ibs.depc_image.make_graph(reduced=reduced, implicit=implicit)
    to_rename = ut.isect(image_graph.nodes(), annot_graph.nodes())
    nx.relabel_nodes(annot_graph, {x: 'annot_' + x for x in to_rename}, copy=False)
    nx.relabel_nodes(image_graph, {x: 'image_' + x for x in to_rename}, copy=False)
    graph = nx.compose_all([image_graph, annot_graph])
    #graph = nx.union_all([image_graph, annot_graph], rename=('image', 'annot'))
    # userdecision = ut.nx_makenode(graph, 'user decision', shape='rect', color=pt.DARK_YELLOW, style='diagonals')
    # userdecision = ut.nx_makenode(graph, 'user decision', shape='circle', color=pt.DARK_YELLOW)
    userdecision = ut.nx_makenode(graph, 'User decision', shape='rect',
                                  #width=100, height=100,
                                  color=pt.YELLOW, style='diagonals')
    #longcat = True
    longcat = False

    #edge = ('feat', 'neighbor_index')
    #data = graph.get_edge_data(*edge)[0]
    #print('data = %r' % (data,))
    #graph.remove_edge(*edge)
    ## hack
    #graph.add_edge('featweight', 'neighbor_index', **data)

    graph.add_edge('detections', userdecision, constraint=longcat, color=pt.PINK)
    graph.add_edge(userdecision, 'annotations', constraint=longcat, color=pt.PINK)
    # graph.add_edge(userdecision, 'annotations', implicit=True, color=[0, 0, 0])
    if not longcat:
        pass
        #graph.add_edge('images', 'annotations', style='invis')
        #graph.add_edge('thumbnails', 'annotations', style='invis')
        #graph.add_edge('thumbnails', userdecision, style='invis')
    graph.remove_node('Has_Notch')
    graph.remove_node('annotmask')
    layoutkw = {
        'ranksep': 5,
        'nodesep': 5,
        'dpi': 96,
        # 'nodesep': 1,
    }
    ns = 1000

    ut.nx_set_default_node_attributes(graph, 'fontsize', 72)
    ut.nx_set_default_node_attributes(graph, 'fontname', 'Ubuntu')
    ut.nx_set_default_node_attributes(graph, 'style',  'filled')

    ut.nx_set_default_node_attributes(graph, 'width', ns * ut.PHI)
    ut.nx_set_default_node_attributes(graph, 'height', ns * (1 / ut.PHI))

    #for u, v, d in graph.edge(data=True):
    for u, vkd in graph.edge.items():
        for v, dk in vkd.items():
            for k, d in dk.items():
                localid = d.get('local_input_id')
                if localid:
                    # d['headlabel'] = localid
                    if localid not in ['1']:
                        d['taillabel'] = localid
                    #d['label'] = localid
                if d.get('taillabel') in {'1'}:
                    del d['taillabel']

    node_alias = {
        'chips': 'Chip',
        'images': 'Image',
        'feat': 'Feat',
        'featweight': 'Feat Weights',
        'thumbnails': 'Thumbnail',
        'detections': 'Detections',
        'annotations': 'Annotation',
        'Notch_Tips': 'Notch Tips',
        'probchip': 'Prob Chip',
        'Cropped_Chips': 'Croped Chip',
        'Trailing_Edge': 'Trailing\nEdge',
        'Block_Curvature': 'Block\nCurvature',
        # 'BC_DTW': 'block curvature /\n dynamic time warp',
        'BC_DTW': 'DTW Distance',
        'vsone': 'Hots vsone',
        'feat_neighbs': 'Nearest\nNeighbors',
        'neighbor_index': 'Neighbor\nIndex',
        'vsmany': 'Hots vsmany',
        'annot_labeler': 'Annot Labeler',
        'labeler': 'Labeler',
        'localizations': 'Localizations',
        'classifier': 'Classifier',
        'sver': 'Spatial\nVerification',
        'Classifier': 'Existence',
        'image_labeler': 'Image Labeler',
    }
    node_alias = {
        'Classifier': 'existence',
        'feat_neighbs': 'neighbors',
        'sver': 'spatial_verification',
        'Cropped_Chips': 'cropped_chip',
        'BC_DTW': 'dtw_distance',
        'Block_Curvature': 'curvature',
        'Trailing_Edge': 'trailing_edge',
        'Notch_Tips': 'notch_tips',
        'thumbnails': 'thumbnail',
        'images': 'image',
        'annotations': 'annotation',
        'chips': 'chip',
        #userdecision: 'User de'
    }
    node_alias = ut.delete_dict_keys(node_alias, ut.setdiff(node_alias.keys(),
                                                            graph.nodes()))
    nx.relabel_nodes(graph, node_alias, copy=False)

    fontkw = dict(fontname='Ubuntu', fontweight='normal', fontsize=12)
    #pt.gca().set_aspect('equal')
    #pt.figure()
    pt.show_nx(graph, layoutkw=layoutkw, fontkw=fontkw)
    pt.zoom_factory()
コード例 #13
0
ファイル: specialdraw.py プロジェクト: Erotemic/ibeis
def setcover_example():
    """
    CommandLine:
        python -m ibeis.scripts.specialdraw setcover_example --show

    Example:
        >>> # DISABLE_DOCTEST
        >>> from ibeis.scripts.specialdraw import *  # NOQA
        >>> result = setcover_example()
        >>> print(result)
        >>> ut.quit_if_noshow()
        >>> import plottool as pt
        >>> ut.show_if_requested()
    """
    import ibeis
    import plottool as pt
    from ibeis.viz import viz_graph
    import networkx as nx
    pt.ensure_pylab_qt4()
    ibs = ibeis.opendb(defaultdb='testdb2')

    if False:
        # Select a good set
        aids = ibs.get_name_aids(ibs.get_valid_nids())
        # ibeis.testdata_aids('testdb2', a='default:mingt=2')
        aids = [a for a in aids if len(a) > 1]
        for a in aids:
            print(ut.repr3(ibs.get_annot_stats_dict(a)))
        print(aids[-2])
    #aids = [78, 79, 80, 81, 88, 91]
    aids = [78, 79, 81, 88, 91]
    qreq_ = ibs.depc.new_request('vsone', aids, aids, cfgdict={})
    cm_list = qreq_.execute()
    from ibeis.algo.hots import graph_iden
    infr = graph_iden.AnnotInference(cm_list)
    unique_aids, prob_annots = infr.make_prob_annots()
    import numpy as np
    print(ut.hz_str('prob_annots = ', ut.array2string2(prob_annots, precision=2, max_line_width=140, suppress_small=True)))
    # ut.setcover_greedy(candidate_sets_dict)
    max_weight = 3
    prob_annots[np.diag_indices(len(prob_annots))] = np.inf
    prob_annots = prob_annots
    thresh_points = np.sort(prob_annots[np.isfinite(prob_annots)])

    # probably not the best way to go about searching for these thresholds
    # but when you have a hammer...
    if False:
        quant = sorted(np.diff(thresh_points))[(len(thresh_points) - 1) // 2 ]
        candset = {point: thresh_points[np.abs(thresh_points - point) < quant] for point in thresh_points}
        check_thresholds = len(aids) * 2
        thresh_points2 = np.array(ut.setcover_greedy(candset, max_weight=check_thresholds).keys())
        thresh_points = thresh_points2

    # pt.plot(sorted(thresh_points), 'rx')
    # pt.plot(sorted(thresh_points2), 'o')

    # prob_annots = prob_annots.T

    # thresh_start = np.mean(thresh_points)
    current_idxs = []
    current_covers = []
    current_val = np.inf
    for thresh in thresh_points:
        covering_sets = [np.where(row >= thresh)[0] for row in (prob_annots)]
        candidate_sets_dict = {ax: others for ax, others in enumerate(covering_sets)}
        soln_cover = ut.setcover_ilp(candidate_sets_dict, max_weight=max_weight)
        exemplar_idxs = list(soln_cover.keys())
        soln_weight = len(exemplar_idxs)
        val = max_weight - soln_weight
        # print('val = %r' % (val,))
        # print('soln_weight = %r' % (soln_weight,))
        if val < current_val:
            current_val = val
            current_covers = covering_sets
            current_idxs = exemplar_idxs
    exemplars = ut.take(aids, current_idxs)
    ensure_edges = [(aids[ax], aids[ax2]) for ax, other_xs in enumerate(current_covers) for ax2 in other_xs]
    graph = viz_graph.make_netx_graph_from_aid_groups(
        ibs, [aids], allow_directed=True, ensure_edges=ensure_edges,
        temp_nids=[1] * len(aids))
    viz_graph.ensure_node_images(ibs, graph)

    nx.set_node_attributes(graph, 'framewidth', False)
    nx.set_node_attributes(graph, 'framewidth', {aid: 4.0 for aid in exemplars})
    nx.set_edge_attributes(graph, 'color', pt.ORANGE)
    nx.set_node_attributes(graph, 'color', pt.LIGHT_BLUE)
    nx.set_node_attributes(graph, 'shape', 'rect')

    layoutkw = {
        'sep' : 1 / 10,
        'prog': 'neato',
        'overlap': 'false',
        #'splines': 'ortho',
        'splines': 'spline',
    }
    pt.show_nx(graph, layout='agraph', layoutkw=layoutkw)
    pt.zoom_factory()
コード例 #14
0
ファイル: specialdraw.py プロジェクト: Erotemic/ibeis
def graphcut_flow():
    r"""
    Returns:
        ?: name

    CommandLine:
        python -m ibeis.scripts.specialdraw graphcut_flow --show --save cutflow.png --diskshow --clipwhite
        python -m ibeis.scripts.specialdraw graphcut_flow --save figures4/cutiden.png --diskshow --clipwhite --dpath ~/latex/crall-candidacy-2015/ --figsize=24,10 --arrow-width=2.0

    Example:
        >>> # DISABLE_DOCTEST
        >>> from ibeis.scripts.specialdraw import *  # NOQA
        >>> graphcut_flow()
        >>> ut.quit_if_noshow()
        >>> import plottool as pt
        >>> ut.show_if_requested()
    """
    import plottool as pt
    pt.ensure_pylab_qt4()
    import networkx as nx
    # pt.plt.xkcd()

    graph = nx.DiGraph()

    def makecluster(name, num, **attrkw):
        return [ut.nx_makenode(graph, name + str(n), **attrkw) for n in range(num)]

    def add_edge2(u, v, *args, **kwargs):
        v = ut.ensure_iterable(v)
        u = ut.ensure_iterable(u)
        for _u, _v in ut.product(u, v):
            graph.add_edge(_u, _v, *args, **kwargs)

    ns = 512

    # *** Primary color:
    p_shade2 = '#41629A'
    # *** Secondary color
    s1_shade2 = '#E88B53'
    # *** Secondary color
    s2_shade2 = '#36977F'
    # *** Complement color
    c_shade2 = '#E8B353'

    annot1 = ut.nx_makenode(graph, 'Unlabeled\nannotations\n(query)', width=ns, height=ns,
                            groupid='annot', color=p_shade2)
    annot2 = ut.nx_makenode(graph, 'Labeled\nannotations\n(database)', width=ns, height=ns,
                            groupid='annot', color=s1_shade2)
    occurprob = ut.nx_makenode(graph, 'Dense \nprobabilities', color=lighten_hex(p_shade2, .1))
    cacheprob = ut.nx_makenode(graph, 'Cached \nprobabilities', color=lighten_hex(s1_shade2, .1))
    sparseprob = ut.nx_makenode(graph, 'Sparse\nprobabilities', color=lighten_hex(c_shade2, .1))

    graph.add_edge(annot1, occurprob)

    graph.add_edge(annot1, sparseprob)
    graph.add_edge(annot2, sparseprob)
    graph.add_edge(annot2, cacheprob)

    matchgraph = ut.nx_makenode(graph, 'Graph of\npotential matches', color=lighten_hex(s2_shade2, .1))
    cutalgo = ut.nx_makenode(graph, 'Graph cut algorithm', color=lighten_hex(s2_shade2, .2), shape='ellipse')
    cc_names = ut.nx_makenode(graph, 'Identifications,\n splits, and merges are\nconnected compoments', color=lighten_hex(s2_shade2, .3))

    graph.add_edge(occurprob, matchgraph)
    graph.add_edge(sparseprob, matchgraph)
    graph.add_edge(cacheprob, matchgraph)

    graph.add_edge(matchgraph, cutalgo)
    graph.add_edge(cutalgo, cc_names)

    ut.nx_set_default_node_attributes(graph, 'shape',  'rect')
    ut.nx_set_default_node_attributes(graph, 'style',  'filled,rounded')
    ut.nx_set_default_node_attributes(graph, 'fixedsize', 'true')
    ut.nx_set_default_node_attributes(graph, 'width', ns * ut.PHI)
    ut.nx_set_default_node_attributes(graph, 'height', ns * (1 / ut.PHI))
    ut.nx_set_default_node_attributes(graph, 'regular', False)

    layoutkw = {
        'prog': 'dot',
        'rankdir': 'LR',
        'splines': 'line',
        'sep': 100 / 72,
        'nodesep': 300 / 72,
        'ranksep': 300 / 72,
    }

    fontkw = dict(fontname='Ubuntu', fontweight='light', fontsize=14)
    pt.show_nx(graph, layout='agraph', layoutkw=layoutkw, **fontkw)
    pt.zoom_factory()
コード例 #15
0
ファイル: specialdraw.py プロジェクト: Erotemic/ibeis
def general_identify_flow():
    r"""
    CommandLine:
        python -m ibeis.scripts.specialdraw general_identify_flow --show --save pairsim.png --dpi=100 --diskshow --clipwhite

        python -m ibeis.scripts.specialdraw general_identify_flow --dpi=200 --diskshow --clipwhite --dpath ~/latex/cand/ --figsize=20,10  --save figures4/pairprob.png --arrow-width=2.0


    Example:
        >>> # SCRIPT
        >>> from ibeis.scripts.specialdraw import *  # NOQA
        >>> general_identify_flow()
        >>> ut.quit_if_noshow()
        >>> ut.show_if_requested()
    """
    import networkx as nx
    import plottool as pt
    pt.ensure_pylab_qt4()
    # pt.plt.xkcd()

    graph = nx.DiGraph()

    def makecluster(name, num, **attrkw):
        return [ut.nx_makenode(name + str(n), **attrkw) for n in range(num)]

    def add_edge2(u, v, *args, **kwargs):
        v = ut.ensure_iterable(v)
        u = ut.ensure_iterable(u)
        for _u, _v in ut.product(u, v):
            graph.add_edge(_u, _v, *args, **kwargs)

    # *** Primary color:
    p_shade2 = '#41629A'
    # *** Secondary color
    s1_shade2 = '#E88B53'
    # *** Secondary color
    s2_shade2 = '#36977F'
    # *** Complement color
    c_shade2 = '#E8B353'

    ns = 512

    ut.inject_func_as_method(graph, ut.nx_makenode)

    annot1_color = p_shade2
    annot2_color = s1_shade2
    #annot1_color2 = pt.color_funcs.lighten_rgb(colors.hex2color(annot1_color), .01)

    annot1 = graph.nx_makenode('Annotation X', width=ns, height=ns, groupid='annot', color=annot1_color)
    annot2 = graph.nx_makenode('Annotation Y', width=ns, height=ns, groupid='annot', color=annot2_color)

    featX = graph.nx_makenode('Features X', size=(ns / 1.2, ns / 2), groupid='feats', color=lighten_hex(annot1_color, .1))
    featY = graph.nx_makenode('Features Y', size=(ns / 1.2, ns / 2), groupid='feats', color=lighten_hex(annot2_color, .1))
    #'#4771B3')

    global_pairvec = graph.nx_makenode('Global similarity\n(viewpoint, quality, ...)', width=ns * ut.PHI * 1.2, color=s2_shade2)
    findnn = graph.nx_makenode('Find correspondences\n(nearest neighbors)', shape='ellipse', color=c_shade2)
    local_pairvec = graph.nx_makenode('Local similarities\n(LNBNN, spatial error, ...)',
                                      size=(ns * 2.2, ns), color=lighten_hex(c_shade2, .1))
    agglocal = graph.nx_makenode('Aggregate', size=(ns / 1.1, ns / 2), shape='ellipse', color=lighten_hex(c_shade2, .2))
    catvecs = graph.nx_makenode('Concatenate', size=(ns / 1.1, ns / 2), shape='ellipse', color=lighten_hex(s2_shade2, .1))
    pairvec = graph.nx_makenode('Vector of\npairwise similarities', color=lighten_hex(s2_shade2, .2))
    classifier = graph.nx_makenode('Classifier\n(SVM/RF/DNN)', color=lighten_hex(s2_shade2, .3))
    prob = graph.nx_makenode('Matching Probability\n(same individual given\nsimilar viewpoint)', color=lighten_hex(s2_shade2, .4))

    graph.add_edge(annot1, global_pairvec)
    graph.add_edge(annot2, global_pairvec)

    add_edge2(annot1, featX)
    add_edge2(annot2, featY)

    add_edge2(featX, findnn)
    add_edge2(featY, findnn)

    add_edge2(findnn, local_pairvec)

    graph.add_edge(local_pairvec, agglocal, constraint=True)
    graph.add_edge(agglocal, catvecs, constraint=False)
    graph.add_edge(global_pairvec, catvecs)

    graph.add_edge(catvecs, pairvec)

    # graph.add_edge(annot1, classifier, style='invis')
    # graph.add_edge(pairvec, classifier , constraint=False)
    graph.add_edge(pairvec, classifier)
    graph.add_edge(classifier, prob)

    ut.nx_set_default_node_attributes(graph, 'shape',  'rect')
    #ut.nx_set_default_node_attributes(graph, 'fillcolor', nx.get_node_attributes(graph, 'color'))
    #ut.nx_set_default_node_attributes(graph, 'style',  'rounded')
    ut.nx_set_default_node_attributes(graph, 'style',  'filled,rounded')
    ut.nx_set_default_node_attributes(graph, 'fixedsize', 'true')
    ut.nx_set_default_node_attributes(graph, 'xlabel', nx.get_node_attributes(graph, 'label'))
    ut.nx_set_default_node_attributes(graph, 'width', ns * ut.PHI)
    ut.nx_set_default_node_attributes(graph, 'height', ns)
    ut.nx_set_default_node_attributes(graph, 'regular', False)

    #font = 'MonoDyslexic'
    #font = 'Mono_Dyslexic'
    font = 'Ubuntu'
    ut.nx_set_default_node_attributes(graph, 'fontsize', 72)
    ut.nx_set_default_node_attributes(graph, 'fontname', font)

    #ut.nx_delete_node_attr(graph, 'width')
    #ut.nx_delete_node_attr(graph, 'height')
    #ut.nx_delete_node_attr(graph, 'fixedsize')
    #ut.nx_delete_node_attr(graph, 'style')
    #ut.nx_delete_node_attr(graph, 'regular')
    #ut.nx_delete_node_attr(graph, 'shape')

    #graph.node[annot1]['label'] = "<f0> left|<f1> mid&#92; dle|<f2> right"
    #graph.node[annot2]['label'] = ut.codeblock(
    #    '''
    #    <<TABLE BORDER="0" CELLBORDER="1" CELLSPACING="0">
    #      <TR><TD>left</TD><TD PORT="f1">mid dle</TD><TD PORT="f2">right</TD></TR>
    #    </TABLE>>
    #    ''')
    #graph.node[annot1]['label'] = ut.codeblock(
    #    '''
    #    <<TABLE BORDER="0" CELLBORDER="1" CELLSPACING="0">
    #      <TR><TD>left</TD><TD PORT="f1">mid dle</TD><TD PORT="f2">right</TD></TR>
    #    </TABLE>>
    #    ''')

    #graph.node[annot1]['shape'] = 'none'
    #graph.node[annot1]['margin'] = '0'

    layoutkw = {
        'forcelabels': True,
        'prog': 'dot',
        'rankdir': 'LR',
        # 'splines': 'curved',
        'splines': 'line',
        'samplepoints': 20,
        'showboxes': 1,
        # 'splines': 'polyline',
        #'splines': 'spline',
        'sep': 100 / 72,
        'nodesep': 300 / 72,
        'ranksep': 300 / 72,
        #'inputscale': 72,
        # 'inputscale': 1,
        # 'dpi': 72,
        # 'concentrate': 'true', # merges edge lines
        # 'splines': 'ortho',
        # 'aspect': 1,
        # 'ratio': 'compress',
        # 'size': '5,4000',
        # 'rank': 'max',
    }

    #fontkw = dict(fontfamilty='sans-serif', fontweight='normal', fontsize=12)
    #fontkw = dict(fontname='Ubuntu', fontweight='normal', fontsize=12)
    #fontkw = dict(fontname='Ubuntu', fontweight='light', fontsize=20)
    fontkw = dict(fontname=font, fontweight='light', fontsize=12)
    #prop = fm.FontProperties(fname='/usr/share/fonts/truetype/groovygh.ttf')

    pt.show_nx(graph, layout='agraph', layoutkw=layoutkw, **fontkw)
    pt.zoom_factory()