multipers 2.3.2__cp313-cp313-win_amd64.whl → 2.3.3b1__cp313-cp313-win_amd64.whl

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/slicer.pyx

@@ -19876,7 +19876,7 @@ cdef extern from "gudhi/cubical_to_boundary.h" namespace "":
   void _to_boundary(const vector[unsigned int]&, vector[vector[unsigned int]]&, vector[int]&) except + nogil
   void get_vertices(unsigned int, cset[unsigned int]&, const vector[vector[unsigned int]]&) nogil
 
-def _from_bitmapi64(image, **slicer_kwargs):
+def _from_bitmapf32(image, **slicer_kwargs):
     from multipers import Slicer
     dtype = slicer_kwargs.get("dtype", image.dtype)
     slicer_kwargs["dtype"] = dtype
@@ -19894,9 +19894,9 @@ def _from_bitmapi64(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.int64) - _Slicer._inf_value()
-    cdef int64_t[:,:] F = filtration_values
-    cdef int64_t[:,:] c_img = image.reshape(-1,num_parameters)
+    filtration_values = np.zeros(shape=(num_gens, num_parameters), dtype = np.float32) - _Slicer._inf_value()
+    cdef float[:,:] F = filtration_values
+    cdef float[:,:] c_img = image.reshape(-1,num_parameters)
     with nogil:
         for i in range(num_gens):
             # with gil:
@@ -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_bitmapf32(image, **slicer_kwargs):
+def _from_bitmapi32(image, **slicer_kwargs):
     from multipers import Slicer
     dtype = slicer_kwargs.get("dtype", image.dtype)
     slicer_kwargs["dtype"] = dtype
@@ -19932,9 +19932,9 @@ def _from_bitmapf32(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.float32) - _Slicer._inf_value()
-    cdef float[:,:] F = filtration_values
-    cdef float[:,:] 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:
@@ -19952,7 +19952,7 @@ 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_bitmapi32(image, **slicer_kwargs):
+def _from_bitmapi64(image, **slicer_kwargs):
     from multipers import Slicer
     dtype = slicer_kwargs.get("dtype", image.dtype)
     slicer_kwargs["dtype"] = dtype
@@ -19970,9 +19970,9 @@ 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.int64) - _Slicer._inf_value()
+    cdef int64_t[:,:] F = filtration_values
+    cdef int64_t[:,:] c_img = image.reshape(-1,num_parameters)
     with nogil:
         for i in range(num_gens):
             # with gil:
@@ -20031,12 +20031,12 @@ def _from_bitmapf64(image, **slicer_kwargs):
 
 def from_bitmap(img, **kwargs):
     img = np.asarray(img)
-    if img.dtype == np.int64:
-        return _from_bitmapi64(img, **kwargs)
     if img.dtype == np.float32:
         return _from_bitmapf32(img, **kwargs)
     if img.dtype == np.int32:
         return _from_bitmapi32(img, **kwargs)
+    if img.dtype == np.int64:
+        return _from_bitmapi64(img, **kwargs)
     if img.dtype == np.float64:
         return _from_bitmapf64(img, **kwargs)
     raise ValueError(f"Invalid dtype. Got {img.dtype=}, was expecting {available_dtype=}.")

{multipers-2.3.2.dist-info → multipers-2.3.3b1.dist-info}/METADATA

@@ -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.dist-info → multipers-2.3.3b1.dist-info}/RECORD

@@ -5,31 +5,31 @@ multipers/distances.py,sha256=uAZj2GtUQp50OxN2qU7sl2JqsmJ74IG9j5tZapLO2Us,6220
 multipers/filtration_conversions.pxd,sha256=Je7a3F4zS1PQn6Ul1YCXgA6p39X2FouStru-XtN-aOw,10800
 multipers/filtration_conversions.pxd.tp,sha256=_9tUvZVUA7J_RUM3q7BxY48fYgDHCUA7Xhy4nBfLLs0,3309
 multipers/filtrations.pxd,sha256=08ONkZNCjs8Nme8lcD9myPz-K662sA-EDpSwzgC2_ts,9461
-multipers/function_rips.cp313-win_amd64.pyd,sha256=7TmvRfkzxQS9e7goaNUFEKou8R0oFBGzxCloHO0wuTA,332800
+multipers/function_rips.cp313-win_amd64.pyd,sha256=4CygDQQN_t5nsfXNsozoqR1ArtbxQaQ6OS_HWh9fX2w,332800
 multipers/function_rips.pyx,sha256=j5NjbK3YrAv_2s8YHB1JB0k6m9NC7RQCSFlJe-w_kgE,5252
-multipers/grids.cp313-win_amd64.pyd,sha256=XNpPv2IKqcHLhyKxsRH-lf8NF7VyORAJbW2HBVSJB0M,480768
+multipers/grids.cp313-win_amd64.pyd,sha256=n4UM7QfQY-yuI9ZvoOnQzzjHqlGiOp6WLVJofxQFSA4,480768
 multipers/grids.pyx,sha256=ONN_RKkuxqwb9IaS9gd42FUGaiBLc8QWcd3L-ubZjKE,16575
-multipers/io.cp313-win_amd64.pyd,sha256=ehj-ef2cQX5eI6PqvQeIt-MNgNQWxRoUttU3k1pMZ_g,221696
+multipers/io.cp313-win_amd64.pyd,sha256=LErGBShjAZieqNU4chR2ZprMVkI9rijWAeJlVwkgiFY,221696
 multipers/io.pyx,sha256=pQBH_rSqaCZqDSxTLnhlyECP3fLbX2tR_RKJHydHm_0,22210
-multipers/mma_structures.cp313-win_amd64.pyd,sha256=9Lxo9hbKD8g7yBYkZqR5d123gBKgVlWlKtmtpTL44ZY,1302528
+multipers/mma_structures.cp313-win_amd64.pyd,sha256=zGcv95AD29KrQs7JS2SdODt0QsB_LzhsNyqfKgWyhrM,1302528
 multipers/mma_structures.pxd,sha256=jh1QnQRidt_VK0CK7losQi6rAl_1qG5DNuR23J42pUA,6595
 multipers/mma_structures.pyx,sha256=4zNC6ePfFKMvx0MrH-FqJVouyTMciRc49oevKDnsJhI,109530
 multipers/mma_structures.pyx.tp,sha256=hWuuk9USDFa8CbQVRHNjWSAdGgpkWKvSCNjTtVuSzwM,42299
 multipers/multiparameter_edge_collapse.py,sha256=MFt0eKQQSv2354omeIqOmzASYTKIMsYdxZHFZauQr8g,1229
-multipers/multiparameter_module_approximation.cp313-win_amd64.pyd,sha256=UzhLl4T5PSgcrLDYm5V4Ud8grp_f2PhwQqIIhdg3afI,456704
+multipers/multiparameter_module_approximation.cp313-win_amd64.pyd,sha256=9AKU9VkCOyioTEmau3HlGpnEphSm5DtjA3jsF9JXQIg,456704
 multipers/multiparameter_module_approximation.pyx,sha256=wp7la7Z9wBngnfw6WOVddf93mPyXf4HfNT6dKW2Z0r0,9030
 multipers/pickle.py,sha256=YYVt4iHiD16E1x5Yn_4mX6P5P8rKi56pNGjJo5IzPhc,2579
-multipers/plots.py,sha256=qE08IhzCIDBUsqbxbuxDsMf2T1SBRCSeeys2dpn7I9U,11236
-multipers/point_measure.cp313-win_amd64.pyd,sha256=BGh8sXbtw7_EdMNQZprglVRkKERmBUIpev6swYXs5Yk,587264
+multipers/plots.py,sha256=9yLuNLJ3XefALKTbdtGu6cJfOt0faXyE0bMGDyFRL4g,14417
+multipers/point_measure.cp313-win_amd64.pyd,sha256=x_2NRlgF0Pqx3MAcnt31qycDxCg6ea7WKp2nkj_71F4,587264
 multipers/point_measure.pyx,sha256=DVhal6HgCCuALSJMcHHKOW16CwDQCVTc2PpK8cGCqx8,12109
-multipers/simplex_tree_multi.cp313-win_amd64.pyd,sha256=PBHWDATyqDMjfiHmaeBupK5PBCsSlRnrohhWgA4GlnE,3599872
+multipers/simplex_tree_multi.cp313-win_amd64.pyd,sha256=CkgyuH5p0ffN8yRjjhCnpOzxZz5B15h5fSUIsX2BZ54,3599872
 multipers/simplex_tree_multi.pxd,sha256=KpyDEQNPoMC2sOU9-d4LtrGXx_UVCJGxMJ1kk1AzHgU,6631
 multipers/simplex_tree_multi.pyx,sha256=reHyva5AR1lOQyiCs2_jQ2XfwHtktcQ1nmY_BNmyxhk,498156
 multipers/simplex_tree_multi.pyx.tp,sha256=fUTuIscfDlNjsImWU1YALVZ1Mf9OEkdl-IFKcRQqalI,89202
-multipers/slicer.cp313-win_amd64.pyd,sha256=fs6jwesHH5qq2eKe8MTn-ADJP6VPw1-4UV8dfzXU6wQ,11776000
+multipers/slicer.cp313-win_amd64.pyd,sha256=vp1-NXjDx0vDl9zMFcP6kvnHQ1s3vMvCUJrNP0M2ABA,11775488
 multipers/slicer.pxd,sha256=bHcV5COzDcjhaVcL3bWSHivUYtdkSx4bdj24fVOe_DU,185230
 multipers/slicer.pxd.tp,sha256=fLOUPtPGqiY9o1fPDyc_whBrgKLh_6HVfvl7OtE-34Y,10243
-multipers/slicer.pyx,sha256=l9GfAqFy9YYpQhM-sbmMvfWMjsTVZFkUKCUYumOCe0I,894068
+multipers/slicer.pyx,sha256=lR1XDmAGA10rwuZKNX6BoMPQeMmCapoEqZtQ5izLJ7Y,894068
 multipers/slicer.pyx.tp,sha256=0oSaqT6-traFiDW9R3IFRQ-u0kYle9Hum8xVzkVsa3c,44550
 multipers/tbb12.dll,sha256=6AsPR4GauU53hj2xqJNM0SfLkCKCDskjy-uKeS01tCk,338944
 multipers/tbbbind_2_5.dll,sha256=8TtH7JJZlCEKF0UwfyJoiyrFt9utOI_x5AFOxpP-pGw,23040
@@ -178,8 +178,8 @@ multipers/tests/__init__.py,sha256=-7Fj-zFAfBJv18trg0CPglQTmYu_ehySZGqtJzPlN8U,1
 multipers/torch/__init__.py,sha256=OLxIiZ389uCqehpUxBPUI_x1SYu531onc4tiTscAuIw,27
 multipers/torch/diff_grids.py,sha256=2YK-c351tBpj8sfzjf26fbE1l0xlWse7oVVfDHD3zwM,7492
 multipers/torch/rips_density.py,sha256=H-kmSzY8hXhmVn15Oltc71DHs1IUHg5oPRgNyWW8L4Q,11706
-multipers-2.3.2.dist-info/licenses/LICENSE,sha256=UsQRnvlo_9wpQS9DNt52GEraERHwK2GIRwuqr2Yv5JI,1071
-multipers-2.3.2.dist-info/METADATA,sha256=mnYnepTC_P_J1PoIYU7rSkfEnylYH1O02xdXlOrz0QM,9670
-multipers-2.3.2.dist-info/WHEEL,sha256=bs-xhrmTp6GOYHnarwiqzzaLhy3P3WRx2sA2M-7RxtA,101
-multipers-2.3.2.dist-info/top_level.txt,sha256=L9e0AGmhRzrNw9FpuUx-zlqi5NcBOmrI9wYY8kYWr8A,10
-multipers-2.3.2.dist-info/RECORD,,
+multipers-2.3.3b1.dist-info/licenses/LICENSE,sha256=UsQRnvlo_9wpQS9DNt52GEraERHwK2GIRwuqr2Yv5JI,1071
+multipers-2.3.3b1.dist-info/METADATA,sha256=MU-U7yqOEIFamD8-E2ctFsjHx2xpWJXSpbV6JEiSPXQ,9672
+multipers-2.3.3b1.dist-info/WHEEL,sha256=qV0EIPljj1XC_vuSatRWjn02nZIz3N1t8jsZz7HBr2U,101
+multipers-2.3.3b1.dist-info/top_level.txt,sha256=L9e0AGmhRzrNw9FpuUx-zlqi5NcBOmrI9wYY8kYWr8A,10
+multipers-2.3.3b1.dist-info/RECORD,,

{multipers-2.3.2.dist-info → multipers-2.3.3b1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.8.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: false
 Tag: cp313-cp313-win_amd64