multipers 2.3.2__tar.gz → 2.3.3b1__tar.gz

{multipers-2.3.2/multipers.egg-info → multipers-2.3.3b1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: multipers
-Version: 2.3.2
+Version: 2.3.3b1
 Summary: Multiparameter Topological Persistence for Machine Learning
 Author-email: David Loiseaux <david.lapous@proton.me>, Hannah Schreiber <hannah.schreiber@inria.fr>
 Maintainer-email: David Loiseaux <david.lapous@proton.me>

{multipers-2.3.2 → multipers-2.3.3b1}/multipers/plots.py

@@ -2,13 +2,16 @@ from typing import Optional
 
 import matplotlib.pyplot as plt
 import numpy as np
+from numpy.typing import ArrayLike
 
 try:
     import torch
+
     istensor = torch.is_tensor
 except ImportError:
     istensor = lambda x: False
 
+
 def _plot_rectangle(rectangle: np.ndarray, weight, **plt_kwargs):
     rectangle = np.asarray(rectangle)
     x_axis = rectangle[[0, 2]]
@@ -137,7 +140,9 @@ def plot_signed_measure(signed_measure, threshold=None, ax=None, **plt_kwargs):
             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)
+        threshold = np.max(
+            [threshold, [plt.gca().get_xlim()[1], plt.gca().get_ylim()[1]]], axis=0
+        )
     if isinstance(pts, np.ndarray):
         pass
     else:
@@ -255,7 +260,7 @@ def plot2d_PyModule(
     dimension=-1,
     separated=False,
     min_persistence=0,
-    alpha=.8,
+    alpha=0.8,
     verbose=False,
     save=False,
     dpi=200,
@@ -341,3 +346,84 @@ def plot2d_PyModule(
         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))
+    color_idx = lambda d: np.searchsorted(qs, d) / 100
+
+    from matplotlib.pyplot import get_cmap
+
+    color = lambda d: 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):
+    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 = 1 - function
+    qs = np.quantile(values, np.linspace(0, 1, 100))
+    color_idx = lambda d: np.searchsorted(qs, d) / 100
+    from matplotlib.pyplot import get_cmap
+    from matplotlib.collections import PatchCollection
+
+    color = lambda d: get_cmap("viridis")([0, color_idx(d), 1])[1]
+    ax = plt.gca()
+    idx = function <= y
+    circles = [plt.Circle(pt, x, color=color(c)) for pt, c in zip(pts[idx], function)]
+    pc = PatchCollection(circles, alpha=0.3)
+    ax.add_collection(pc)
+    plt.scatter(*pts.T, c=-function, s=20)
+    ax.set_aspect(1)

{multipers-2.3.2 → multipers-2.3.3b1/multipers.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: multipers
-Version: 2.3.2
+Version: 2.3.3b1
 Summary: Multiparameter Topological Persistence for Machine Learning
 Author-email: David Loiseaux <david.lapous@proton.me>, Hannah Schreiber <hannah.schreiber@inria.fr>
 Maintainer-email: David Loiseaux <david.lapous@proton.me>

{multipers-2.3.2 → multipers-2.3.3b1}/pyproject.toml

@@ -9,7 +9,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "multipers"
-version = "2.3.2"
+version = "2.3.3b1"
 description = "Multiparameter Topological Persistence for Machine Learning"
 readme = "README.md"
 authors = [

{multipers-2.3.2 → multipers-2.3.3b1}/setup.py

@@ -167,6 +167,8 @@ extensions = [
         language="c++",
         extra_compile_args=[
             "-O3",  # -Ofast disables infinity values for filtration values
+            "-fassociative-math",
+            "-funsafe-math-optimizations",
             # "-g",
             # "-march=native",
             "/std:c++20" if platform.system() == "Windows" else "-std=c++20",

{multipers-2.3.2 → multipers-2.3.3b1}/multipers/slicer.pyx

@@ -19914,7 +19914,7 @@ def _from_bitmapi64(image, **slicer_kwargs):
             #     print(f"F = {np.asarray(F[i])}")
     slicer = _Slicer(gen_maps, gen_dims, filtration_values)
     return slicer
-def _from_bitmapi32(image, **slicer_kwargs):
+def _from_bitmapf64(image, **slicer_kwargs):
     from multipers import Slicer
     dtype = slicer_kwargs.get("dtype", image.dtype)
     slicer_kwargs["dtype"] = dtype
@@ -19932,9 +19932,9 @@ def _from_bitmapi32(image, **slicer_kwargs):
     cdef cset[unsigned int] vertices
 
     cdef unsigned int num_gens = gen_dims.size()
-    filtration_values = np.zeros(shape=(num_gens, num_parameters), dtype = np.int32) - _Slicer._inf_value()
-    cdef int32_t[:,:] F = filtration_values
-    cdef int32_t[:,:] c_img = image.reshape(-1,num_parameters)
+    filtration_values = np.zeros(shape=(num_gens, num_parameters), dtype = np.float64) - _Slicer._inf_value()
+    cdef double[:,:] F = filtration_values
+    cdef double[:,:] c_img = image.reshape(-1,num_parameters)
     with nogil:
         for i in range(num_gens):
             # with gil:
@@ -19990,7 +19990,7 @@ def _from_bitmapf32(image, **slicer_kwargs):
             #     print(f"F = {np.asarray(F[i])}")
     slicer = _Slicer(gen_maps, gen_dims, filtration_values)
     return slicer
-def _from_bitmapf64(image, **slicer_kwargs):
+def _from_bitmapi32(image, **slicer_kwargs):
     from multipers import Slicer
     dtype = slicer_kwargs.get("dtype", image.dtype)
     slicer_kwargs["dtype"] = dtype
@@ -20008,9 +20008,9 @@ def _from_bitmapf64(image, **slicer_kwargs):
     cdef cset[unsigned int] vertices
 
     cdef unsigned int num_gens = gen_dims.size()
-    filtration_values = np.zeros(shape=(num_gens, num_parameters), dtype = np.float64) - _Slicer._inf_value()
-    cdef double[:,:] F = filtration_values
-    cdef double[:,:] c_img = image.reshape(-1,num_parameters)
+    filtration_values = np.zeros(shape=(num_gens, num_parameters), dtype = np.int32) - _Slicer._inf_value()
+    cdef int32_t[:,:] F = filtration_values
+    cdef int32_t[:,:] c_img = image.reshape(-1,num_parameters)
     with nogil:
         for i in range(num_gens):
             # with gil:
@@ -20033,12 +20033,12 @@ def from_bitmap(img, **kwargs):
     img = np.asarray(img)
     if img.dtype == np.int64:
         return _from_bitmapi64(img, **kwargs)
-    if img.dtype == np.int32:
-        return _from_bitmapi32(img, **kwargs)
-    if img.dtype == np.float32:
-        return _from_bitmapf32(img, **kwargs)
     if img.dtype == np.float64:
         return _from_bitmapf64(img, **kwargs)
+    if img.dtype == np.float32:
+        return _from_bitmapf32(img, **kwargs)
+    if img.dtype == np.int32:
+        return _from_bitmapi32(img, **kwargs)
     raise ValueError(f"Invalid dtype. Got {img.dtype=}, was expecting {available_dtype=}.")
 
 def from_function_delaunay(