multipers 2.3.3b6__cp311-cp311-macosx_11_0_arm64.whl

multipers/plots.py

@@ -0,0 +1,456 @@
+from typing import Optional
+from warnings import warn
+
+import matplotlib.colors as mcolors
+import matplotlib.pyplot as plt
+import numpy as np
+from matplotlib.colors import ListedColormap
+from numpy.typing import ArrayLike
+
+from multipers.array_api import to_numpy
+
+_custom_colors = [
+    "#03045e",
+    "#0077b6",
+    "#00b4d8",
+    "#90e0ef",
+]
+_cmap_ = ListedColormap(_custom_colors)
+_cmap = mcolors.LinearSegmentedColormap.from_list(
+    "continuous_cmap", _cmap_.colors, N=256
+)
+
+
+def _plot_rectangle(rectangle: np.ndarray, weight, **plt_kwargs):
+    rectangle = np.asarray(rectangle)
+    x_axis = rectangle[[0, 2]]
+    y_axis = rectangle[[1, 3]]
+    color = "blue" if weight > 0 else "red"
+    plt.plot(x_axis, y_axis, c=color, **plt_kwargs)
+
+
+def _plot_signed_measure_2(
+    pts, weights, temp_alpha=0.7, threshold=(np.inf, np.inf), **plt_kwargs
+):
+    import matplotlib.colors
+
+    pts = np.clip(pts, a_min=-np.inf, a_max=np.asarray(threshold)[None, :])
+    weights = np.asarray(weights)
+    color_weights = np.array(weights, dtype=float)
+    neg_idx = weights < 0
+    pos_idx = weights > 0
+    if np.any(neg_idx):
+        current_weights = -weights[neg_idx]
+        min_weight = np.max(current_weights)
+        color_weights[neg_idx] /= min_weight
+        color_weights[neg_idx] -= 1
+    else:
+        min_weight = 0
+
+    if np.any(pos_idx):
+        current_weights = weights[pos_idx]
+        max_weight = np.max(current_weights)
+        color_weights[pos_idx] /= max_weight
+        color_weights[pos_idx] += 1
+    else:
+        max_weight = 1
+
+    bordeaux = np.array([0.70567316, 0.01555616, 0.15023281, 1])
+    light_bordeaux = np.array([0.70567316, 0.01555616, 0.15023281, temp_alpha])
+    bleu = np.array([0.2298057, 0.29871797, 0.75368315, 1])
+    light_bleu = np.array([0.2298057, 0.29871797, 0.75368315, temp_alpha])
+    norm = plt.Normalize(-2, 2)
+    cmap = matplotlib.colors.LinearSegmentedColormap.from_list(
+        "", [bordeaux, light_bordeaux, "white", light_bleu, bleu]
+    )
+    plt.scatter(
+        pts[:, 0], pts[:, 1], c=color_weights, cmap=cmap, norm=norm, **plt_kwargs
+    )
+    plt.scatter([], [], color=bleu, label="positive mass", **plt_kwargs)
+    plt.scatter([], [], color=bordeaux, label="negative mass", **plt_kwargs)
+    plt.legend()
+
+
+def _plot_signed_measure_4(
+    pts,
+    weights,
+    x_smoothing: float = 1,
+    area_alpha: bool = True,
+    threshold=(np.inf, np.inf),
+    alpha=None,
+    **plt_kwargs,  # ignored ftm
+):
+    # compute the maximal rectangle area
+    pts = np.clip(pts, a_min=-np.inf, a_max=np.array((*threshold, *threshold))[None, :])
+    alpha_rescaling = 0
+    for rectangle, weight in zip(pts, weights):
+        if rectangle[2] >= x_smoothing * rectangle[0]:
+            alpha_rescaling = max(
+                alpha_rescaling,
+                (rectangle[2] / x_smoothing - rectangle[0])
+                * (rectangle[3] - rectangle[1]),
+            )
+    # draw the rectangles
+    for rectangle, weight in zip(pts, weights):
+        # draw only the rectangles that have not been reduced to the empty set
+        if rectangle[2] >= x_smoothing * rectangle[0]:
+            # make the alpha channel proportional to the rectangle's area
+            if area_alpha:
+                _plot_rectangle(
+                    rectangle=[
+                        rectangle[0],
+                        rectangle[1],
+                        rectangle[2] / x_smoothing,
+                        rectangle[3],
+                    ],
+                    weight=weight,
+                    alpha=(
+                        (rectangle[2] / x_smoothing - rectangle[0])
+                        * (rectangle[3] - rectangle[1])
+                        / alpha_rescaling
+                        if alpha is None
+                        else alpha
+                    ),
+                    **plt_kwargs,
+                )
+            else:
+                _plot_rectangle(
+                    rectangle=[
+                        rectangle[0],
+                        rectangle[1],
+                        rectangle[2] / x_smoothing,
+                        rectangle[3],
+                    ],
+                    weight=weight,
+                    alpha=1 if alpha is None else alpha,
+                    **plt_kwargs,
+                )
+
+
+def plot_signed_measure(signed_measure, threshold=None, ax=None, **plt_kwargs):
+    if ax is None:
+        ax = plt.gca()
+    else:
+        plt.sca(ax)
+    pts, weights = signed_measure
+    pts = to_numpy(pts)
+    weights = to_numpy(weights)
+    num_pts = pts.shape[0]
+    num_parameters = pts.shape[1]
+    if threshold is None:
+        if num_pts == 0:
+            threshold = (np.inf, np.inf)
+        else:
+            if num_parameters == 4:
+                pts_ = np.concatenate([pts[:, :2], pts[:, 2:]], axis=0)
+            else:
+                pts_ = pts
+            threshold = np.max(np.ma.masked_invalid(pts_), axis=0)
+        threshold = np.max(
+            [threshold, [plt.gca().get_xlim()[1], plt.gca().get_ylim()[1]]], axis=0
+        )
+
+    assert num_parameters in (2, 4)
+    if num_parameters == 2:
+        _plot_signed_measure_2(
+            pts=pts, weights=weights, threshold=threshold, **plt_kwargs
+        )
+    else:
+        _plot_signed_measure_4(
+            pts=pts, weights=weights, threshold=threshold, **plt_kwargs
+        )
+
+
+def plot_signed_measures(signed_measures, threshold=None, size=4):
+    num_degrees = len(signed_measures)
+    if num_degrees <= 1:
+        axes = [plt.gca()]
+    else:
+        fig, axes = plt.subplots(
+            nrows=1, ncols=num_degrees, figsize=(num_degrees * size, size)
+        )
+    for ax, signed_measure in zip(axes, signed_measures):
+        plot_signed_measure(signed_measure=signed_measure, ax=ax, threshold=threshold)
+    plt.tight_layout()
+
+
+def plot_surface(
+    grid,
+    hf,
+    fig=None,
+    ax=None,
+    cmap: Optional[str] = None,
+    discrete_surface: bool = False,
+    has_negative_values: bool = False,
+    contour: bool = True,
+    **plt_args,
+):
+    import matplotlib
+
+    if ax is None:
+        ax = plt.gca()
+    else:
+        plt.sca(ax)
+    if hf.ndim == 3 and hf.shape[0] == 1:
+        hf = hf[0]
+    assert hf.ndim == 2, "Can only plot a 2d surface"
+    fig = plt.gcf() if fig is None else fig
+    if cmap is None:
+        if discrete_surface:
+            cmap = matplotlib.colormaps["gray_r"]
+        else:
+            cmap = _cmap
+    if discrete_surface:
+        if has_negative_values:
+            bounds = np.arange(-5, 6, 1, dtype=int)
+        else:
+            bounds = np.arange(0, 11, 1, dtype=int)
+        norm = matplotlib.colors.BoundaryNorm(bounds, cmap.N, extend="max")
+        im = ax.pcolormesh(grid[0], grid[1], hf.T, cmap=cmap, norm=norm, **plt_args)
+        cbar = fig.colorbar(
+            matplotlib.cm.ScalarMappable(cmap=cmap, norm=norm),
+            spacing="proportional",
+            ax=ax,
+        )
+        cbar.set_ticks(ticks=bounds, labels=bounds)
+        return im
+
+    if contour:
+        levels = plt_args.pop("levels", 20)
+        im = ax.contourf(grid[0], grid[1], hf.T, cmap=cmap, levels=levels, **plt_args)
+    else:
+        im = ax.pcolormesh(grid[0], grid[1], hf.T, cmap=cmap, **plt_args)
+    return im
+
+
+def plot_surfaces(HF, size=4, **plt_args):
+    grid, hf = HF
+    assert (
+        hf.ndim == 3
+    ), f"Found hf.shape = {hf.shape}, expected ndim = 3 : degree, 2-parameter surface."
+    num_degrees = hf.shape[0]
+    fig, axes = plt.subplots(
+        nrows=1, ncols=num_degrees, figsize=(num_degrees * size, size)
+    )
+    if num_degrees == 1:
+        axes = [axes]
+    for ax, hf_of_degree in zip(axes, hf):
+        plot_surface(grid=grid, hf=hf_of_degree, fig=fig, ax=ax, **plt_args)
+    plt.tight_layout()
+
+
+def _rectangle(x, y, color, alpha):
+    """
+    Defines a rectangle patch in the format {z | x  ≤ z ≤ y} with color and alpha
+    """
+    from matplotlib.patches import Rectangle as RectanglePatch
+
+    return RectanglePatch(
+        x, max(y[0] - x[0], 0), max(y[1] - x[1], 0), color=color, alpha=alpha
+    )
+
+
+def _d_inf(a, b):
+    a = np.asarray(a)
+    b = np.asarray(b)
+    return np.min(np.abs(b - a))
+
+
+def plot2d_PyModule(
+    corners,
+    box,
+    *,
+    dimension=-1,
+    separated=False,
+    min_persistence=0,
+    alpha=None,
+    verbose=False,
+    save=False,
+    dpi=200,
+    shapely=True,
+    xlabel=None,
+    ylabel=None,
+    cmap=None,
+):
+    import matplotlib
+
+    try:
+        from shapely import union_all
+        from shapely.geometry import Polygon as _Polygon
+        from shapely.geometry import box as _rectangle_box
+
+        shapely = True and shapely
+    except ImportError:
+        shapely = False
+        warn(
+            "Shapely not installed. Fallbacking to matplotlib. The plots may be inacurate."
+        )
+    if alpha is None:
+        alpha = 0.8 if shapely else 1
+    if not shapely and alpha != 1:
+        warn("Opacity without shapely will lead to incorect plots.")
+    cmap = (
+        matplotlib.colormaps["Spectral"] if cmap is None else matplotlib.colormaps[cmap]
+    )
+    box = list(box)
+    if not (separated):
+        # fig, ax = plt.subplots()
+        ax = plt.gca()
+        ax.set(xlim=[box[0][0], box[1][0]], ylim=[box[0][1], box[1][1]])
+    n_summands = len(corners)
+    for i in range(n_summands):
+        trivial_summand = True
+        list_of_rect = []
+        for birth in corners[i][0]:
+            if len(birth) == 1:
+                birth = np.asarray([birth[0]] * 2)
+            birth = np.asarray(birth).clip(min=box[0])
+            for death in corners[i][1]:
+                if len(death) == 1:
+                    death = np.asarray([death[0]] * 2)
+                death = np.asarray(death).clip(max=box[1])
+                if death[1] > birth[1] and death[0] > birth[0]:
+                    if trivial_summand and _d_inf(birth, death) > min_persistence:
+                        trivial_summand = False
+                    if shapely:
+                        list_of_rect.append(
+                            _rectangle_box(birth[0], birth[1], death[0], death[1])
+                        )
+                    else:
+                        list_of_rect.append(
+                            _rectangle(birth, death, cmap(i / n_summands), alpha)
+                        )
+        if not (trivial_summand):
+            if separated:
+                fig, ax = plt.subplots()
+                ax.set(xlim=[box[0][0], box[1][0]], ylim=[box[0][1], box[1][1]])
+            if shapely:
+                summand_shape = union_all(list_of_rect)
+                if type(summand_shape) is _Polygon:
+                    xs, ys = summand_shape.exterior.xy
+                    ax.fill(xs, ys, alpha=alpha, fc=cmap(i / n_summands), ec="None")
+                else:
+                    for polygon in summand_shape.geoms:
+                        xs, ys = polygon.exterior.xy
+                        ax.fill(xs, ys, alpha=alpha, fc=cmap(i / n_summands), ec="None")
+            else:
+                for rectangle in list_of_rect:
+                    ax.add_patch(rectangle)
+            if separated:
+                if xlabel:
+                    plt.xlabel(xlabel)
+                if ylabel:
+                    plt.ylabel(ylabel)
+                if dimension >= 0:
+                    plt.title(rf"$H_{dimension}$ $2$-persistence")
+    if not (separated):
+        if xlabel is not None:
+            plt.xlabel(xlabel)
+        if ylabel is not None:
+            plt.ylabel(ylabel)
+        if dimension >= 0:
+            plt.title(rf"$H_{dimension}$ $2$-persistence")
+    return
+
+
+def plot_simplicial_complex(
+    st, pts: ArrayLike, x: float, y: float, mma=None, degree=None
+):
+    """
+    Scatters the points, with the simplices in the filtration at coordinates (x,y).
+    if an mma module is given, plots it in a second axis
+    """
+    if mma is not None:
+        fig, (a, b) = plt.subplots(ncols=2, figsize=(15, 5))
+        plt.sca(a)
+        plot_simplicial_complex(st, pts, x, y)
+        plt.sca(b)
+        mma.plot(degree=degree)
+        box = mma.get_box()
+        a, b, c, d = box.ravel()
+        mma.plot(degree=1, min_persistence=0.01)
+        plt.vlines(x, b, d, color="k", linestyle="--")
+        plt.hlines(y, a, c, color="k", linestyle="--")
+        plt.scatter([x], [y], c="r", zorder=10)
+        plt.text(x + 0.01 * (b - a), y + 0.01 * (d - c), f"({x},{y})")
+        return
+
+    pts = np.asarray(pts)
+    values = np.array([-f[1] for s, f in st.get_skeleton(0)])
+    qs = np.quantile(values, np.linspace(0, 1, 100))
+
+    def color_idx(d):
+        return np.searchsorted(qs, d) / 100
+
+    from matplotlib.pyplot import get_cmap
+
+    def color(d):
+        return get_cmap("viridis")([0, color_idx(d), 1])[1]
+
+    cols_pc = np.asarray([color(v) for v in values])
+    ax = plt.gca()
+    for s, f in st:  # simplexe, filtration
+        density = -f[1]
+        if len(s) <= 1 or f[0] > x or density < -y:  # simplexe  = point
+            continue
+        if len(s) == 2:  # simplexe = segment
+            xx = np.array([pts[a, 0] for a in s])
+            yy = np.array([pts[a, 1] for a in s])
+            plt.plot(xx, yy, c=color(density), alpha=1, zorder=10 * density, lw=1.5)
+        if len(s) == 3:  # simplexe = triangle
+            xx = np.array([pts[a, 0] for a in s])
+            yy = np.array([pts[a, 1] for a in s])
+            _c = color(density)
+            ax.fill(xx, yy, c=_c, alpha=0.3, zorder=0)
+    out = plt.scatter(pts[:, 0], pts[:, 1], c=cols_pc, zorder=10, s=10)
+    ax.set_aspect(1)
+    return out
+
+
+def plot_point_cloud(
+    pts,
+    function,
+    x,
+    y,
+    mma=None,
+    degree=None,
+    ball_alpha=0.3,
+    point_cmap="viridis",
+    color_bias=1,
+    ball_color=None,
+    point_size=20,
+):
+    if mma is not None:
+        fig, (a, b) = plt.subplots(ncols=2, figsize=(15, 5))
+        plt.sca(a)
+        plot_point_cloud(pts, function, x, y)
+        plt.sca(b)
+        mma.plot(degree=degree)
+        box = mma.get_box()
+        a, b, c, d = box.ravel()
+        mma.plot(degree=1, min_persistence=0.01)
+        plt.vlines(x, b, d, color="k", linestyle="--")
+        plt.hlines(y, a, c, color="k", linestyle="--")
+        plt.scatter([x], [y], c="r", zorder=10)
+        plt.text(x + 0.01 * (b - a), y + 0.01 * (d - c), f"({x},{y})")
+        return
+    values = -function
+    qs = np.quantile(values, np.linspace(0, 1, 100))
+
+    def color_idx(d):
+        return np.searchsorted(qs, d * color_bias) / 100
+
+    from matplotlib.collections import PatchCollection
+    from matplotlib.pyplot import get_cmap
+
+    def color(d):
+        return get_cmap(point_cmap)([0, color_idx(d), 1])[1]
+
+    _colors = np.array([color(v) for v in values])
+    ax = plt.gca()
+    idx = function <= y
+    circles = [plt.Circle(pt, x) for pt, c in zip(pts[idx], function)]
+    pc = PatchCollection(circles, alpha=ball_alpha, color=ball_color)
+    ax.add_collection(pc)
+    plt.scatter(*pts.T, c=_colors, s=point_size)
+    ax.set_aspect(1)