multipers 2.3.3b2__tar.gz → 2.3.3b4__tar.gz

{multipers-2.3.3b2/multipers.egg-info → multipers-2.3.3b4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: multipers
-Version: 2.3.3b2
+Version: 2.3.3b4
 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>
@@ -62,6 +62,11 @@ or
 ```sh
 conda install multipers -c conda-forge
 ```
+Pre-releases are available via
+```sh
+pip install --pre multipers
+```
+These release usually contain small bugfixes or unstable new features.
 
 Windows support is experimental, and some core dependencies are not available on Windows.
 We hence recommend Windows user to use [WSL](https://learn.microsoft.com/en-us/windows/wsl/).

{multipers-2.3.3b2 → multipers-2.3.3b4}/README.md

@@ -26,6 +26,11 @@ or
 ```sh
 conda install multipers -c conda-forge
 ```
+Pre-releases are available via
+```sh
+pip install --pre multipers
+```
+These release usually contain small bugfixes or unstable new features.
 
 Windows support is experimental, and some core dependencies are not available on Windows.
 We hence recommend Windows user to use [WSL](https://learn.microsoft.com/en-us/windows/wsl/).

{multipers-2.3.3b2 → multipers-2.3.3b4}/multipers/ml/signed_measures.py

@@ -758,6 +758,8 @@ class SignedMeasureFormatter(BaseEstimator, TransformerMixin):
                 ) = self._get_filtration_bounds(X, axis=ax)
                 self._filtrations_bounds.append(filtration_bounds)
                 self._normalization_factors.append(normalization_factors)
+            self._filtrations_bounds = self._backend.astensor(self._filtrations_bounds)
+            self._normalization_factors = self._backend.astensor(self._normalization_factors)
             # else:
             #     (
             #         self._filtrations_bounds,
@@ -782,9 +784,9 @@ class SignedMeasureFormatter(BaseEstimator, TransformerMixin):
             ]
             # axis, filtration_values
             filtration_values = [
-                compute_grid(
+                self._backend.astensor(compute_grid(
                     f_ax.T, resolution=self.resolution, strategy=self.grid_strategy
-                )
+                ))
                 for f_ax in filtration_values
             ]
             self._infered_grids = filtration_values
@@ -848,7 +850,7 @@ class SignedMeasureFormatter(BaseEstimator, TransformerMixin):
 
         if self.flatten:
             out = np.concatenate(out).flatten()
-        if self.axis == -1:
+        elif self.axis == -1:
             return np.asarray(out)
         else:
             return np.asarray(out)[0]

{multipers-2.3.3b2 → multipers-2.3.3b4}/multipers/plots.py

@@ -1,11 +1,24 @@
 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 warnings import warn
+
 from multipers.array_api import to_numpy
 
+_custom_colors = [
+    "#03045e",
+    "#0077b6",
+    "#00b4d8",
+    "#90e0ef",
+]
+_cmap = ListedColormap(_custom_colors)
+_continuous_cmap = mcolors.LinearSegmentedColormap.from_list(
+    "continuous_cmap", _cmap.colors, N=256
+)
 
 
 def _plot_rectangle(rectangle: np.ndarray, weight, **plt_kwargs):
@@ -185,7 +198,7 @@ def plot_surface(
         if discrete_surface:
             cmap = matplotlib.colormaps["gray_r"]
         else:
-            cmap = matplotlib.colormaps["plasma"]
+            cmap = _cmap
     if discrete_surface:
         if has_negative_values:
             bounds = np.arange(-5, 6, 1, dtype=int)
@@ -200,15 +213,15 @@ def plot_surface(
         )
         cbar.set_ticks(ticks=bounds, labels=bounds)
         return im
-    im = ax.pcolormesh(grid[0], grid[1], hf.T, cmap=cmap, **plt_args)
+    im = ax.contourf(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."
-    )
+    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)
@@ -388,7 +401,19 @@ def plot_simplicial_complex(
     return out
 
 
-def plot_point_cloud(pts, function, x, y, mma=None, degree=None):
+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)
@@ -403,22 +428,23 @@ def plot_point_cloud(pts, function, x, y, mma=None, degree=None):
         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
+    values = -function
     qs = np.quantile(values, np.linspace(0, 1, 100))
 
     def color_idx(d):
-        return np.searchsorted(qs, d) / 100
+        return np.searchsorted(qs, d * color_bias) / 100
 
-    from matplotlib.pyplot import get_cmap
     from matplotlib.collections import PatchCollection
+    from matplotlib.pyplot import get_cmap
 
     def color(d):
-        return get_cmap("viridis")([0, color_idx(d), 1])[1]
+        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, color=color(c)) for pt, c in zip(pts[idx], function)]
-    pc = PatchCollection(circles, alpha=0.3)
+    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=-function, s=20)
+    plt.scatter(*pts.T, c=_colors, s=point_size)
     ax.set_aspect(1)

{multipers-2.3.3b2 → multipers-2.3.3b4/multipers.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: multipers
-Version: 2.3.3b2
+Version: 2.3.3b4
 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>
@@ -62,6 +62,11 @@ or
 ```sh
 conda install multipers -c conda-forge
 ```
+Pre-releases are available via
+```sh
+pip install --pre multipers
+```
+These release usually contain small bugfixes or unstable new features.
 
 Windows support is experimental, and some core dependencies are not available on Windows.
 We hence recommend Windows user to use [WSL](https://learn.microsoft.com/en-us/windows/wsl/).

{multipers-2.3.3b2 → multipers-2.3.3b4}/pyproject.toml

@@ -9,7 +9,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "multipers"
-version = "2.3.3b2"
+version = "2.3.3b4"
 description = "Multiparameter Topological Persistence for Machine Learning"
 readme = "README.md"
 authors = [

{multipers-2.3.3b2 → multipers-2.3.3b4}/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_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_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.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:
@@ -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_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
@@ -19970,9 +19970,9 @@ 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:
@@ -19990,7 +19990,7 @@ def _from_bitmapf64(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
@@ -20008,9 +20008,9 @@ 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:
@@ -20031,14 +20031,14 @@ def _from_bitmapi32(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.float64:
         return _from_bitmapf64(img, **kwargs)
     if img.dtype == np.int32:
         return _from_bitmapi32(img, **kwargs)
+    if img.dtype == np.int64:
+        return _from_bitmapi64(img, **kwargs)
     raise ValueError(f"Invalid dtype. Got {img.dtype=}, was expecting {available_dtype=}.")
 
 def from_function_delaunay(