iplotx 0.0.1__py3-none-any.whl

iplotx/edge/undirected.py

@@ -0,0 +1,447 @@
+from math import atan2, tan, cos, pi, sin
+from collections import defaultdict
+import numpy as np
+import matplotlib as mpl
+
+from .common import _compute_loops_per_angle
+from .label import LabelCollection
+from ..utils.matplotlib import (
+    _compute_mid_coord,
+    _stale_wrapper,
+)
+
+
+class UndirectedEdgeCollection(mpl.collections.PatchCollection):
+    def __init__(self, *args, **kwargs):
+        kwargs["match_original"] = True
+        self._vertex_ids = kwargs.pop("vertex_ids", None)
+        self._vertex_centers = kwargs.pop("vertex_centers", None)
+        self._vertex_paths = kwargs.pop("vertex_paths", None)
+        self._style = kwargs.pop("style", None)
+        self._labels = kwargs.pop("labels", None)
+        super().__init__(*args, **kwargs)
+
+    @staticmethod
+    def _get_edge_vertex_sizes(edge_vertices):
+        sizes = []
+        for visual_vertex in edge_vertices:
+            if visual_vertex.size is not None:
+                sizes.append(visual_vertex.size)
+            else:
+                sizes.append(max(visual_vertex.width, visual_vertex.height))
+        return sizes
+
+    @staticmethod
+    def _compute_edge_angles(path, trans):
+        """Compute edge angles for both starting and ending vertices.
+
+        NOTE: The domain of atan2 is (-pi, pi].
+        """
+        positions = trans(path.vertices)
+
+        # first angle
+        x1, y1 = positions[0]
+        x2, y2 = positions[1]
+        angle1 = atan2(y2 - y1, x2 - x1)
+
+        # second angle
+        x1, y1 = positions[-1]
+        x2, y2 = positions[-2]
+        angle2 = atan2(y2 - y1, x2 - x1)
+        return (angle1, angle2)
+
+    def _compute_paths(self, transform=None):
+        """Compute paths for the edges.
+
+        Loops split the largest wedge left open by other
+        edges of that vertex. The algo is:
+        (i) Find what vertices each loop belongs to
+        (ii) While going through the edges, record the angles
+             for vertices with loops
+        (iii) Plot each loop based on the recorded angles
+        """
+        vids = self._vertex_ids
+        vpaths = self._vertex_paths
+        vcenters = self._vertex_centers
+        if transform is None:
+            transform = self.get_transform()
+        trans = transform.transform
+        trans_inv = transform.inverted().transform
+
+        # 1. Make a list of vertices with loops, and store them for later
+        loop_vertex_dict = {}
+        for i, (v1, v2) in enumerate(vids):
+            if v1 != v2:
+                continue
+            if v1 not in loop_vertex_dict:
+                loop_vertex_dict[v1] = {
+                    "indices": [],
+                    "edge_angles": [],
+                }
+            loop_vertex_dict[v1]["indices"].append(i)
+
+        # 2. Make paths for non-loop edges
+        # NOTE: keep track of parallel edges to offset them
+        parallel_edges = defaultdict(list)
+
+        # Get actual coordinates of the vertex border
+        paths = []
+        for i, (v1, v2) in enumerate(vids):
+            # Postpone loops (step 3)
+            if v1 == v2:
+                paths.append(None)
+                continue
+
+            # Coordinates of the adjacent vertices, in data coords
+            vcoord_data = vcenters[i]
+
+            # Coordinates in figure (default) coords
+            vcoord_fig = trans(vcoord_data)
+
+            # Vertex paths in figure (default) coords
+            vpath_fig = vpaths[i]
+
+            # Shorten edge
+            if not self._style.get("curved", False):
+                path = self._shorten_path_undirected_straight(
+                    vcoord_fig,
+                    vpath_fig,
+                    trans_inv,
+                )
+            else:
+                path = self._shorten_path_undirected_curved(
+                    vcoord_fig,
+                    vpath_fig,
+                    trans_inv,
+                    tension=self._style.get("tension", 1.5),
+                )
+
+            # Collect angles for this vertex, to be used for loops plotting below
+            if (v1 in loop_vertex_dict) or (v2 in loop_vertex_dict):
+                angles = self._compute_edge_angles(
+                    path,
+                    trans,
+                )
+                if v1 in loop_vertex_dict:
+                    loop_vertex_dict[v1]["edge_angles"].append(angles[0])
+                if v2 in loop_vertex_dict:
+                    loop_vertex_dict[v2]["edge_angles"].append(angles[1])
+
+            # Add the path for this non-loop edge
+            paths.append(path)
+            # FIXME: curved parallel edges depend on the direction of curvature...!
+            parallel_edges[(v1, v2)].append(i)
+
+        # Fix parallel edges
+        # If none found, empty the dictionary already
+        if max(parallel_edges.values(), key=len) == 1:
+            parallel_edges = {}
+        if not self._style.get("curved", False):
+            while len(parallel_edges) > 0:
+                (v1, v2), indices = parallel_edges.popitem()
+                indices_inv = parallel_edges.pop((v2, v1), [])
+                nparallel = len(indices)
+                nparallel_inv = len(indices_inv)
+                ntot = len(indices) + len(indices_inv)
+                if ntot > 1:
+                    self._fix_parallel_edges_straight(
+                        paths,
+                        indices,
+                        indices_inv,
+                        trans,
+                        trans_inv,
+                        offset=self._style.get("offset", 3),
+                    )
+
+        # 3. Deal with loops at the end
+        for vid, ldict in loop_vertex_dict.items():
+            vpath = vpaths[ldict["indices"][0]][0]
+            vcoord_fig = trans(vcenters[ldict["indices"][0]][0])
+            nloops = len(ldict["indices"])
+            edge_angles = ldict["edge_angles"]
+
+            # The space between the existing angles is where we can fit the loops
+            # One loop we can fit in the largest wedge, multiple loops we need
+            nloops_per_angle = _compute_loops_per_angle(nloops, edge_angles)
+
+            idx = 0
+            for theta1, theta2, nloops in nloops_per_angle:
+                # Angular size of each loop in this wedge
+                delta = (theta2 - theta1) / nloops
+
+                # Iterate over individual loops
+                for j in range(nloops):
+                    thetaj1 = theta1 + j * delta
+                    # Use 60 degrees as the largest possible loop wedge
+                    thetaj2 = thetaj1 + min(delta, pi / 3)
+
+                    # Get the path for this loop
+                    path = self._compute_loop_path(
+                        vcoord_fig,
+                        vpath,
+                        thetaj1,
+                        thetaj2,
+                        trans_inv,
+                    )
+                    paths[ldict["indices"][idx]] = path
+                    idx += 1
+
+        return paths
+
+    def _fix_parallel_edges_straight(
+        self,
+        paths,
+        indices,
+        indices_inv,
+        trans,
+        trans_inv,
+        offset=3,
+    ):
+        """Offset parallel edges along the same path."""
+        ntot = len(indices) + len(indices_inv)
+
+        # This is straight so two vertices anyway
+        # NOTE: all paths will be the same, which is why we need to offset them
+        vs, ve = trans(paths[indices[0]].vertices)
+
+        # Move orthogonal to the line
+        fracs = (
+            (vs - ve) / np.sqrt(((vs - ve) ** 2).sum()) @ np.array([[0, 1], [-1, 0]])
+        )
+
+        # NOTE: for now treat both direction the same
+        for i, idx in enumerate(indices + indices_inv):
+            # Offset the path
+            paths[idx].vertices = trans_inv(
+                trans(paths[idx].vertices) + fracs * offset * (i - ntot / 2)
+            )
+
+    def _compute_loop_path(
+        self,
+        vcoord_fig,
+        vpath,
+        angle1,
+        angle2,
+        trans_inv,
+    ):
+        # Shorten at starting angle
+        start = _get_shorter_edge_coords(vpath, angle1) + vcoord_fig
+        # Shorten at end angle
+        end = _get_shorter_edge_coords(vpath, angle2) + vcoord_fig
+
+        aux1 = (start - vcoord_fig) * 2.5 + vcoord_fig
+        aux2 = (end - vcoord_fig) * 2.5 + vcoord_fig
+
+        vertices = np.vstack(
+            [
+                start,
+                aux1,
+                aux2,
+                end,
+            ]
+        )
+        codes = ["MOVETO"] + ["CURVE4"] * 3
+
+        # Offset to place and transform to data coordinates
+        vertices = trans_inv(vertices)
+        codes = [getattr(mpl.path.Path, x) for x in codes]
+        path = mpl.path.Path(
+            vertices,
+            codes=codes,
+        )
+        return path
+
+    def _shorten_path_undirected_straight(
+        self,
+        vcoord_fig,
+        vpath_fig,
+        trans_inv,
+    ):
+        # Straight SVG instructions
+        path = {
+            "vertices": [],
+            "codes": ["MOVETO", "LINETO"],
+        }
+
+        # Angle of the straight line
+        theta = atan2(*((vcoord_fig[1] - vcoord_fig[0])[::-1]))
+
+        # Shorten at starting vertex
+        vs = _get_shorter_edge_coords(vpath_fig[0], theta) + vcoord_fig[0]
+        path["vertices"].append(vs)
+
+        # Shorten at end vertex
+        ve = _get_shorter_edge_coords(vpath_fig[1], theta + pi) + vcoord_fig[1]
+        path["vertices"].append(ve)
+
+        path = mpl.path.Path(
+            path["vertices"],
+            codes=[getattr(mpl.path.Path, x) for x in path["codes"]],
+        )
+        path.vertices = trans_inv(path.vertices)
+        return path
+
+    def _shorten_path_undirected_curved(
+        self,
+        vcoord_fig,
+        vpath_fig,
+        trans_inv,
+        tension=+1.5,
+    ):
+        # Angle of the straight line
+        theta = atan2(*((vcoord_fig[1] - vcoord_fig[0])[::-1]))
+
+        # Shorten at starting vertex
+        vs = _get_shorter_edge_coords(vpath_fig[0], theta) + vcoord_fig[0]
+
+        # Shorten at end vertex
+        ve = _get_shorter_edge_coords(vpath_fig[1], theta + pi) + vcoord_fig[1]
+
+        edge_straight_length = np.sqrt(((ve - vs) ** 2).sum())
+
+        aux1 = vs + 0.33 * (ve - vs)
+        aux2 = vs + 0.67 * (ve - vs)
+
+        # Move Bezier points orthogonal to the line
+        fracs = (
+            (vs - ve) / np.sqrt(((vs - ve) ** 2).sum()) @ np.array([[0, 1], [-1, 0]])
+        )
+        aux1 += 0.1 * fracs * tension * edge_straight_length
+        aux2 += 0.1 * fracs * tension * edge_straight_length
+
+        path = {
+            "vertices": [
+                vs,
+                aux1,
+                aux2,
+                ve,
+            ],
+            "codes": ["MOVETO"] + ["CURVE4"] * 3,
+        }
+
+        path = mpl.path.Path(
+            path["vertices"],
+            codes=[getattr(mpl.path.Path, x) for x in path["codes"]],
+        )
+        path.vertices = trans_inv(path.vertices)
+        return path
+
+    def _compute_labels(self):
+        style = self._style.get("label", None) if self._style is not None else None
+        offsets = []
+        for path in self._paths:
+            offset = _compute_mid_coord(path)
+            offsets.append(offset)
+
+        if not hasattr(self, "_label_collection"):
+            self._label_collection = LabelCollection(
+                self._labels,
+                style=style,
+            )
+
+            # Forward a bunch of mpl settings that are needed
+            self._label_collection.set_figure(self.figure)
+            self._label_collection.axes = self.axes
+            # forward the clippath/box to the children need this logic
+            # because mpl exposes some fast-path logic
+            clip_path = self.get_clip_path()
+            if clip_path is None:
+                clip_box = self.get_clip_box()
+                self._label_collection.set_clip_box(clip_box)
+            else:
+                self._label_collection.set_clip_path(clip_path)
+
+            # Finally make the patches
+            self._label_collection._create_labels()
+        self._label_collection.set_offsets(offsets)
+
+    def get_children(self):
+        children = []
+        if hasattr(self, "_label_collection"):
+            children.append(self._label_collection)
+        return children
+
+    @_stale_wrapper
+    def draw(self, renderer, *args, **kwds):
+        if self._vertex_paths is not None:
+            self._paths = self._compute_paths()
+            if self._labels is not None:
+                self._compute_labels()
+        super().draw(renderer)
+
+        for child in self.get_children():
+            child.draw(renderer, *args, **kwds)
+
+    @property
+    def stale(self):
+        return super().stale
+
+    @stale.setter
+    def stale(self, val):
+        mpl.collections.PatchCollection.stale.fset(self, val)
+        if val and hasattr(self, "stale_callback_post"):
+            self.stale_callback_post(self)
+
+
+def make_stub_patch(**kwargs):
+    """Make a stub undirected edge patch, without actual path information."""
+    kwargs["clip_on"] = kwargs.get("clip_on", True)
+    if ("color" in kwargs) and ("edgecolor" not in kwargs):
+        kwargs["edgecolor"] = kwargs.pop("color")
+    # Edges are always hollow, because they are not closed paths
+    kwargs["facecolor"] = "none"
+
+    # Forget specific properties that are not supported here
+    forbidden_props = [
+        "curved",
+        "tension",
+        "offset",
+        "label",
+    ]
+    for prop in forbidden_props:
+        if prop in kwargs:
+            kwargs.pop(prop)
+
+    # NOTE: the path is overwritten later anyway, so no reason to spend any time here
+    art = mpl.patches.PathPatch(
+        mpl.path.Path([[0, 0]]),
+        **kwargs,
+    )
+    return art
+
+
+def _get_shorter_edge_coords(vpath, theta):
+    # Bound theta from -pi to pi (why is that not guaranteed?)
+    theta = (theta + pi) % (2 * pi) - pi
+
+    for i in range(len(vpath)):
+        v1 = vpath.vertices[i]
+        v2 = vpath.vertices[(i + 1) % len(vpath)]
+        theta1 = atan2(*((v1)[::-1]))
+        theta2 = atan2(*((v2)[::-1]))
+
+        # atan2 ranges ]-3.14, 3.14]
+        # so it can be that theta1 is -3 and theta2 is +3
+        # therefore we need two separate cases, one that cuts at pi and one at 0
+        cond1 = theta1 <= theta <= theta2
+        cond2 = (
+            (theta1 + 2 * pi) % (2 * pi)
+            <= (theta + 2 * pi) % (2 * pi)
+            <= (theta2 + 2 * pi) % (2 * pi)
+        )
+        if cond1 or cond2:
+            break
+    else:
+        raise ValueError("Angle for patch not found")
+
+    # The edge meets the patch of the vertex on the v1-v2 size,
+    # at angle theta from the center
+    mtheta = tan(theta)
+    if v2[0] == v1[0]:
+        xe = v1[0]
+    else:
+        m12 = (v2[1] - v1[1]) / (v2[0] - v1[0])
+        xe = (v1[1] - m12 * v1[0]) / (mtheta - m12)
+    ye = mtheta * xe
+    ve = np.array([xe, ye])
+    return ve

iplotx/groups.py

@@ -0,0 +1,141 @@
+from typing import Union, Sequence
+from copy import deepcopy
+from collections import defaultdict
+import numpy as np
+import pandas as pd
+import matplotlib as mpl
+from matplotlib.collections import PatchCollection
+
+
+from .importing import igraph
+from .typing import (
+    GroupingType,
+    LayoutType,
+)
+from .heuristics import normalise_layout, normalise_grouping
+from .styles import get_style, rotate_style
+from .utils.geometry import (
+    convex_hull,
+    _compute_group_path_with_vertex_padding,
+)
+
+
+class GroupingArtist(PatchCollection):
+    def __init__(
+        self,
+        grouping: GroupingType,
+        layout: LayoutType,
+        vertexpadding: Union[None, int] = None,
+        *args,
+        **kwargs,
+    ):
+        """Container artist for vertex groupings, e.g. covers or clusterings.
+
+        Parameters:
+            grouping: This can be a sequence of sets (a la networkx), an igraph Clustering
+                or Cover instance (including VertexClustering/VertexCover), or a sequence
+                of integers/strings indicating memberships for each vertex.
+            layout: The layout of the vertices. If this object has no keys/index, the
+                vertices are assumed to have IDs corresponding to integers starting from
+                zero.
+        """
+        if vertexpadding is not None:
+            self._vertexpadding = vertexpadding
+        else:
+            style = get_style(".grouping")
+            self._vertexpadding = style.get("vertexpadding", 10)
+        patches, grouping, layout = self._create_patches(grouping, layout, **kwargs)
+        self._grouping = grouping
+        self._layout = layout
+        kwargs["match_original"] = True
+
+        super().__init__(patches, *args, **kwargs)
+
+    def _create_patches(self, grouping, layout, **kwargs):
+        layout = normalise_layout(layout)
+        grouping = normalise_grouping(grouping, layout)
+        style = get_style(".grouping")
+        style.pop("vertexpadding", None)
+
+        style.update(kwargs)
+
+        patches = []
+        for i, (name, vids) in enumerate(grouping.items()):
+            if len(vids) == 0:
+                continue
+            vids = np.array(list(vids))
+            coords = layout.loc[vids].values
+            idx_hull = convex_hull(coords)
+            coords_hull = coords[idx_hull]
+
+            stylei = rotate_style(style, i)
+
+            # NOTE: the transform is set later on
+            patch = _compute_group_patch_stub(
+                coords_hull,
+                self._vertexpadding,
+                label=name,
+                **stylei,
+            )
+
+            patches.append(patch)
+        return patches, grouping, layout
+
+    def _compute_paths(self):
+        if self._vertexpadding > 0:
+            for i, path in enumerate(self._paths):
+                self._paths[i].vertices = _compute_group_path_with_vertex_padding(
+                    path.vertices,
+                    self.get_transform(),
+                    vertexpadding=self._vertexpadding,
+                )
+
+    def _process(self):
+        self.set_transform(self.axes.transData)
+        self._compute_paths()
+
+    def draw(self, renderer):
+        self._compute_paths()
+        super().draw(renderer)
+
+
+def _compute_group_patch_stub(
+    points,
+    vertexpadding,
+    **kwargs,
+):
+    if vertexpadding == 0:
+        return mpl.patches.Polygon(
+            points,
+            **kwargs,
+        )
+
+    # NOTE: Closing point: mpl is a bit quirky here
+    vertices = []
+    codes = []
+    if len(points) == 0:
+        vertices = np.zeros((0, 2))
+    elif len(points) == 1:
+        vertices = [points[0]] * 9
+        codes = ["MOVETO"] + ["CURVE3"] * 8
+    elif len(points) == 2:
+        vertices = [points[0]] * 5 + [points[1]] * 5 + [points[0]]
+        codes = ["MOVETO"] + ["CURVE3"] * 4 + ["LINETO"] + ["CURVE3"] * 4 + ["LINETO"]
+    else:
+        for point in points:
+            vertices.extend([point] * 3)
+            codes.extend(["LINETO", "CURVE3", "CURVE3"])
+        vertices.append(vertices[0])
+        codes.append("LINETO")
+        codes[0] = "MOVETO"
+
+    codes = [getattr(mpl.path.Path, x) for x in codes]
+    patch = mpl.patches.PathPatch(
+        mpl.path.Path(
+            vertices,
+            codes=codes,
+        ),
+        **kwargs,
+    )
+
+    return patch

iplotx/heuristics.py

@@ -0,0 +1,114 @@
+from collections import defaultdict
+import numpy as np
+import pandas as pd
+
+from .importing import igraph, networkx
+from .typing import GraphType, GroupingType, LayoutType
+
+
+def network_library(
+    network: GraphType,
+) -> str:
+    if igraph is not None and isinstance(network, igraph.Graph):
+        return "igraph"
+    if networkx is not None:
+        if isinstance(network, networkx.Graph):
+            return "networkx"
+        if isinstance(network, networkx.DiGraph):
+            return "networkx"
+        if isinstance(network, networkx.MultiGraph):
+            return "networkx"
+        if isinstance(network, networkx.MultiDiGraph):
+            return "networkx"
+    raise TypeError("Unsupported graph type. Supported types are igraph and networkx.")
+
+
+def detect_directedness(
+    network: GraphType,
+) -> np.ndarray:
+    """Detect if the network is directed or not."""
+    if network_library(network) == "igraph":
+        return network.is_directed()
+    if isinstance(network, (networkx.DiGraph, networkx.MultiDiGraph)):
+        return True
+    return False
+
+
+def normalise_layout(layout):
+    """Normalise the layout to a pandas.DataFrame."""
+    if layout is None:
+        return None
+    if isinstance(layout, dict):
+        layout = pd.DataFrame(layout).T
+    if isinstance(layout, str):
+        raise NotImplementedError("Layout as a string is not supported yet.")
+    if isinstance(layout, (list, tuple)):
+        return pd.DataFrame(np.array(layout))
+    if isinstance(layout, pd.DataFrame):
+        return layout
+    if isinstance(layout, np.ndarray):
+        return pd.DataFrame(layout)
+    raise TypeError(
+        "Layout must be a string, list, tuple, numpy array or pandas DataFrame."
+    )
+
+
+def normalise_grouping(
+    grouping: GroupingType,
+    layout: LayoutType,
+) -> dict[set]:
+
+    if len(grouping) == 0:
+        return {}
+
+    if isinstance(grouping, dict):
+        val0 = next(iter(grouping.values()))
+        # If already the right data type or compatible, leave as is
+        if isinstance(val0, (set, frozenset)):
+            return grouping
+
+        # If a dict of integers or strings, assume each key is a vertex id and each value is a
+        # group, convert (i.e. invert the dict)
+        if isinstance(val0, (int, str)):
+            group_dic = defaultdict(set)
+            for key, val in grouping.items():
+                group_dic[val].add(key)
+            return group_dic
+
+    # If an igraph object, convert to a dict of sets
+    if igraph is not None:
+        if isinstance(grouping, igraph.clustering.Clustering):
+            layout = normalise_layout(layout)
+            group_dic = defaultdict(set)
+            for i, member in enumerate(grouping.membership):
+                group_dic[member].add(i)
+            return group_dic
+
+        if isinstance(grouping, igraph.clustering.Cover):
+            layout = normalise_layout(layout)
+            group_dic = defaultdict(set)
+            for i, members in enumerate(grouping.membership):
+                for member in members:
+                    group_dic[member].add(i)
+            return group_dic
+
+    # Assume it's a sequence, so convert to list
+    grouping = list(grouping)
+
+    # If the values are already sets, assume group indices are integers
+    # and values are as is
+    if isinstance(grouping[0], set):
+        group_dic = {i: val for i, val in enumerate(grouping)}
+        return group_dic
+
+    # If the values are integers or strings, assume each key is a vertex id and each value is a
+    # group, convert to dict of sets
+    if isinstance(grouping[0], (int, str)):
+        group_dic = defaultdict(set)
+        for i, val in enumerate(grouping):
+            group_dic[val].add(i)
+        return group_dic
+
+    raise TypeError(
+        "Could not standardise grouping from object.",
+    )