multipers 2.3.2b1__tar.gz → 2.3.3b2__tar.gz

{multipers-2.3.2b1/multipers.egg-info → multipers-2.3.3b2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: multipers
-Version: 2.3.2b1
+Version: 2.3.3b2
 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-2.3.2b1 → multipers-2.3.3b2}/multipers/array_api/__init__.py

@@ -37,3 +37,7 @@ def api_from_tensors(*args):
     if is_torch:
         return torchapi
     raise ValueError(f"Incompatible types got {[type(x) for x in args]=}.")
+
+def to_numpy(x):
+    api = api_from_tensor(x)
+    return api.asnumpy(x)

{multipers-2.3.2b1 → multipers-2.3.3b2}/multipers/ml/mma.py

@@ -478,7 +478,7 @@ class MMAFormatter(BaseEstimator, TransformerMixin):
                 if self.weights is None
                 else np.asarray(self.weights)
             )
-            standard_box = PyBox_f64([0] * self._num_parameters, w)
+            standard_box = np.array([[0] * self._num_parameters, w])
 
             X_copy = [
                 [

{multipers-2.3.2b1 → multipers-2.3.3b2}/multipers/multiparameter_module_approximation.pyx

@@ -168,7 +168,8 @@ def module_approximation(
                 delayed(module_approximation)(slicer, box, max_error, nlines, slicer_backend, minpres, degree, complete, threshold, verbose, ignore_warnings, id, direction, swap_box_coords)
                 for slicer in input
             ))
-        mod = PyModule_f64().set_box(PyBox_f64(*modules[0].get_box()))
+        box = modules[0].get_box()
+        mod = PyModule_f64().set_box(box)
         for i,m in enumerate(modules):
             mod.merge(m, input[i].minpres_degree)
         return mod

{multipers-2.3.2b1 → multipers-2.3.3b2}/multipers/plots.py

@@ -2,12 +2,11 @@ from typing import Optional
 
 import matplotlib.pyplot as plt
 import numpy as np
+from numpy.typing import ArrayLike
+from warnings import warn
+from multipers.array_api import to_numpy
+
 
-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)
@@ -121,11 +120,8 @@ def plot_signed_measure(signed_measure, threshold=None, ax=None, **plt_kwargs):
     else:
         plt.sca(ax)
     pts, weights = signed_measure
-    if istensor(pts):
-        pts = pts.detach().numpy()
-    if istensor(weights):
-        weights = weights.detach().numpy()
-    pts = np.asarray(pts)
+    pts = to_numpy(pts)
+    weights = to_numpy(weights)
     num_pts = pts.shape[0]
     num_parameters = pts.shape[1]
     if threshold is None:
@@ -137,16 +133,9 @@ 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)
-    if isinstance(pts, np.ndarray):
-        pass
-    else:
-        import torch
-
-        if isinstance(pts, torch.Tensor):
-            pts = pts.detach().numpy()
-        else:
-            raise Exception("Invalid measure type.")
+        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:
@@ -217,9 +206,9 @@ def plot_surface(
 
 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)
@@ -255,7 +244,7 @@ def plot2d_PyModule(
     dimension=-1,
     separated=False,
     min_persistence=0,
-    alpha=.8,
+    alpha=None,
     verbose=False,
     save=False,
     dpi=200,
@@ -273,12 +262,14 @@ def plot2d_PyModule(
 
         shapely = True and shapely
     except ImportError:
-        from warnings import warn
-
         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]
     )
@@ -341,3 +332,93 @@ 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))
+
+    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):
+    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))
+
+    def color_idx(d):
+        return np.searchsorted(qs, d) / 100
+
+    from matplotlib.pyplot import get_cmap
+    from matplotlib.collections import PatchCollection
+
+    def color(d):
+        return 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-2.3.2b1 → multipers-2.3.3b2}/multipers/simplex_tree_multi.pyx

@@ -881,10 +881,10 @@ cdef class SimplexTreeMulti_KFi32:
             self,
             filtration_grid:np.ndarray|list|None=None,
             bool coordinate_values=True,
-            force=False,
-            strategy:_available_strategies = "exact",
+            bool force=False,
+            str strategy:_available_strategies = "exact",
             grid_strategy=None,
-            inplace=False,
+            bool inplace=False,
             **filtration_grid_kwargs
         )->SimplexTreeMulti_KFi32 | SimplexTreeMulti_KFi32:
         """
@@ -1982,7 +1982,16 @@ cdef class SimplexTreeMulti_Fi32:
             out = self.get_ptr().get_edge_list()
         return out
 
-    def collapse_edges(self, int num=1, int max_dimension = 0, bool progress=False, bool strong=True, bool full=False, bool ignore_warning=False)->SimplexTreeMulti_Fi32:
+    def collapse_edges(
+            self,
+            int num=1,
+            int max_dimension = 0,
+            bool progress=False,
+            bool strong=True,
+            bool full=False,
+            bool ignore_warning=False,
+            bool auto_clean=True,
+        )->SimplexTreeMulti_Fi32:
         """Edge collapse for 1-critical 2-parameter clique complex (see https://arxiv.org/abs/2211.05574).
         It uses the code from the github repository https://github.com/aj-alonso/filtration_domination .
 
@@ -2032,6 +2041,8 @@ cdef class SimplexTreeMulti_Fi32:
         edges = _collapse_edge_list(edges, num=num, full=full, strong=strong, progress=progress)
         # Retrieves the collapsed simplicial complex
         self._reconstruct_from_edge_list(edges, swap=True, expand_dimension=max_dimension)
+        if self.is_squeezed and auto_clean:
+            self._clean_filtration_grid()
         return self
 
     @cython.inline
@@ -2309,10 +2320,10 @@ cdef class SimplexTreeMulti_Fi32:
             self,
             filtration_grid:np.ndarray|list|None=None,
             bool coordinate_values=True,
-            force=False,
-            strategy:_available_strategies = "exact",
+            bool force=False,
+            str strategy:_available_strategies = "exact",
             grid_strategy=None,
-            inplace=False,
+            bool inplace=False,
             **filtration_grid_kwargs
         )->SimplexTreeMulti_Fi32 | SimplexTreeMulti_Fi32:
         """
@@ -3458,10 +3469,10 @@ cdef class SimplexTreeMulti_KFi64:
             self,
             filtration_grid:np.ndarray|list|None=None,
             bool coordinate_values=True,
-            force=False,
-            strategy:_available_strategies = "exact",
+            bool force=False,
+            str strategy:_available_strategies = "exact",
             grid_strategy=None,
-            inplace=False,
+            bool inplace=False,
             **filtration_grid_kwargs
         )->SimplexTreeMulti_KFi32 | SimplexTreeMulti_KFi64:
         """
@@ -4559,7 +4570,16 @@ cdef class SimplexTreeMulti_Fi64:
             out = self.get_ptr().get_edge_list()
         return out
 
-    def collapse_edges(self, int num=1, int max_dimension = 0, bool progress=False, bool strong=True, bool full=False, bool ignore_warning=False)->SimplexTreeMulti_Fi64:
+    def collapse_edges(
+            self,
+            int num=1,
+            int max_dimension = 0,
+            bool progress=False,
+            bool strong=True,
+            bool full=False,
+            bool ignore_warning=False,
+            bool auto_clean=True,
+        )->SimplexTreeMulti_Fi64:
         """Edge collapse for 1-critical 2-parameter clique complex (see https://arxiv.org/abs/2211.05574).
         It uses the code from the github repository https://github.com/aj-alonso/filtration_domination .
 
@@ -4609,6 +4629,8 @@ cdef class SimplexTreeMulti_Fi64:
         edges = _collapse_edge_list(edges, num=num, full=full, strong=strong, progress=progress)
         # Retrieves the collapsed simplicial complex
         self._reconstruct_from_edge_list(edges, swap=True, expand_dimension=max_dimension)
+        if self.is_squeezed and auto_clean:
+            self._clean_filtration_grid()
         return self
 
     @cython.inline
@@ -4886,10 +4908,10 @@ cdef class SimplexTreeMulti_Fi64:
             self,
             filtration_grid:np.ndarray|list|None=None,
             bool coordinate_values=True,
-            force=False,
-            strategy:_available_strategies = "exact",
+            bool force=False,
+            str strategy:_available_strategies = "exact",
             grid_strategy=None,
-            inplace=False,
+            bool inplace=False,
             **filtration_grid_kwargs
         )->SimplexTreeMulti_Fi32 | SimplexTreeMulti_Fi64:
         """
@@ -6035,10 +6057,10 @@ cdef class SimplexTreeMulti_KFf32:
             self,
             filtration_grid:np.ndarray|list|None=None,
             bool coordinate_values=True,
-            force=False,
-            strategy:_available_strategies = "exact",
+            bool force=False,
+            str strategy:_available_strategies = "exact",
             grid_strategy=None,
-            inplace=False,
+            bool inplace=False,
             **filtration_grid_kwargs
         )->SimplexTreeMulti_KFi32 | SimplexTreeMulti_KFf32:
         """
@@ -7136,7 +7158,16 @@ cdef class SimplexTreeMulti_Ff32:
             out = self.get_ptr().get_edge_list()
         return out
 
-    def collapse_edges(self, int num=1, int max_dimension = 0, bool progress=False, bool strong=True, bool full=False, bool ignore_warning=False)->SimplexTreeMulti_Ff32:
+    def collapse_edges(
+            self,
+            int num=1,
+            int max_dimension = 0,
+            bool progress=False,
+            bool strong=True,
+            bool full=False,
+            bool ignore_warning=False,
+            bool auto_clean=True,
+        )->SimplexTreeMulti_Ff32:
         """Edge collapse for 1-critical 2-parameter clique complex (see https://arxiv.org/abs/2211.05574).
         It uses the code from the github repository https://github.com/aj-alonso/filtration_domination .
 
@@ -7186,6 +7217,8 @@ cdef class SimplexTreeMulti_Ff32:
         edges = _collapse_edge_list(edges, num=num, full=full, strong=strong, progress=progress)
         # Retrieves the collapsed simplicial complex
         self._reconstruct_from_edge_list(edges, swap=True, expand_dimension=max_dimension)
+        if self.is_squeezed and auto_clean:
+            self._clean_filtration_grid()
         return self
 
     @cython.inline
@@ -7463,10 +7496,10 @@ cdef class SimplexTreeMulti_Ff32:
             self,
             filtration_grid:np.ndarray|list|None=None,
             bool coordinate_values=True,
-            force=False,
-            strategy:_available_strategies = "exact",
+            bool force=False,
+            str strategy:_available_strategies = "exact",
             grid_strategy=None,
-            inplace=False,
+            bool inplace=False,
             **filtration_grid_kwargs
         )->SimplexTreeMulti_Fi32 | SimplexTreeMulti_Ff32:
         """
@@ -8612,10 +8645,10 @@ cdef class SimplexTreeMulti_KFf64:
             self,
             filtration_grid:np.ndarray|list|None=None,
             bool coordinate_values=True,
-            force=False,
-            strategy:_available_strategies = "exact",
+            bool force=False,
+            str strategy:_available_strategies = "exact",
             grid_strategy=None,
-            inplace=False,
+            bool inplace=False,
             **filtration_grid_kwargs
         )->SimplexTreeMulti_KFi32 | SimplexTreeMulti_KFf64:
         """
@@ -9713,7 +9746,16 @@ cdef class SimplexTreeMulti_Ff64:
             out = self.get_ptr().get_edge_list()
         return out
 
-    def collapse_edges(self, int num=1, int max_dimension = 0, bool progress=False, bool strong=True, bool full=False, bool ignore_warning=False)->SimplexTreeMulti_Ff64:
+    def collapse_edges(
+            self,
+            int num=1,
+            int max_dimension = 0,
+            bool progress=False,
+            bool strong=True,
+            bool full=False,
+            bool ignore_warning=False,
+            bool auto_clean=True,
+        )->SimplexTreeMulti_Ff64:
         """Edge collapse for 1-critical 2-parameter clique complex (see https://arxiv.org/abs/2211.05574).
         It uses the code from the github repository https://github.com/aj-alonso/filtration_domination .
 
@@ -9763,6 +9805,8 @@ cdef class SimplexTreeMulti_Ff64:
         edges = _collapse_edge_list(edges, num=num, full=full, strong=strong, progress=progress)
         # Retrieves the collapsed simplicial complex
         self._reconstruct_from_edge_list(edges, swap=True, expand_dimension=max_dimension)
+        if self.is_squeezed and auto_clean:
+            self._clean_filtration_grid()
         return self
 
     @cython.inline
@@ -10040,10 +10084,10 @@ cdef class SimplexTreeMulti_Ff64:
             self,
             filtration_grid:np.ndarray|list|None=None,
             bool coordinate_values=True,
-            force=False,
-            strategy:_available_strategies = "exact",
+            bool force=False,
+            str strategy:_available_strategies = "exact",
             grid_strategy=None,
-            inplace=False,
+            bool inplace=False,
             **filtration_grid_kwargs
         )->SimplexTreeMulti_Fi32 | SimplexTreeMulti_Ff64:
         """

{multipers-2.3.2b1 → multipers-2.3.3b2}/multipers/simplex_tree_multi.pyx.tp

@@ -972,7 +972,16 @@ cdef class SimplexTreeMulti_{{FSHORT}}:
             out = self.get_ptr().get_edge_list()
         return out
 
-    def collapse_edges(self, int num=1, int max_dimension = 0, bool progress=False, bool strong=True, bool full=False, bool ignore_warning=False)->SimplexTreeMulti_{{FSHORT}}:
+    def collapse_edges(
+            self,
+            int num=1,
+            int max_dimension = 0,
+            bool progress=False,
+            bool strong=True,
+            bool full=False,
+            bool ignore_warning=False,
+            bool auto_clean=True,
+        )->SimplexTreeMulti_{{FSHORT}}:
         """Edge collapse for 1-critical 2-parameter clique complex (see https://arxiv.org/abs/2211.05574).
         It uses the code from the github repository https://github.com/aj-alonso/filtration_domination .
 
@@ -1022,6 +1031,8 @@ cdef class SimplexTreeMulti_{{FSHORT}}:
         edges = _collapse_edge_list(edges, num=num, full=full, strong=strong, progress=progress)
         # Retrieves the collapsed simplicial complex
         self._reconstruct_from_edge_list(edges, swap=True, expand_dimension=max_dimension)
+        if self.is_squeezed and auto_clean:
+            self._clean_filtration_grid()
         return self
 
     @cython.inline
@@ -1317,10 +1328,10 @@ cdef class SimplexTreeMulti_{{FSHORT}}:
             self,
             filtration_grid:np.ndarray|list|None=None,
             bool coordinate_values=True,
-            force=False,
-            strategy:_available_strategies = "exact",
+            bool force=False,
+            str strategy:_available_strategies = "exact",
             grid_strategy=None,
-            inplace=False,
+            bool inplace=False,
             **filtration_grid_kwargs
         )->SimplexTreeMulti_{{FSHORT[:-3] + "i32"}} | SimplexTreeMulti_{{FSHORT}}:
         """

{multipers-2.3.2b1 → multipers-2.3.3b2}/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_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
@@ -19894,9 +19894,9 @@ 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:
@@ -19914,7 +19914,7 @@ def _from_bitmapi32(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_bitmapf32(image, **slicer_kwargs):
     from multipers import Slicer
     dtype = slicer_kwargs.get("dtype", image.dtype)
     slicer_kwargs["dtype"] = dtype
@@ -19932,9 +19932,9 @@ 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.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:
@@ -19952,7 +19952,7 @@ 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_bitmapi64(image, **slicer_kwargs):
+def _from_bitmapf64(image, **slicer_kwargs):
     from multipers import Slicer
     dtype = slicer_kwargs.get("dtype", image.dtype)
     slicer_kwargs["dtype"] = dtype
@@ -19970,9 +19970,9 @@ 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.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_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
@@ -20008,9 +20008,9 @@ 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:
@@ -20031,14 +20031,14 @@ def _from_bitmapf32(image, **slicer_kwargs):
 
 def from_bitmap(img, **kwargs):
     img = np.asarray(img)
-    if img.dtype == np.int32:
-        return _from_bitmapi32(img, **kwargs)
-    if img.dtype == np.float64:
-        return _from_bitmapf64(img, **kwargs)
     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)
     raise ValueError(f"Invalid dtype. Got {img.dtype=}, was expecting {available_dtype=}.")
 
 def from_function_delaunay(
@@ -20046,7 +20046,7 @@ def from_function_delaunay(
     grades,
     int degree=-1,
     backend:Optional[_valid_pers_backend]=None,
-    vineyard=None, # TODO : Optional[bool] when cython fixes it
+    vineyard=None, # Optionmal[bool], wait for cython
     dtype=np.float64,
     bool verbose = False,
     bool clear = True,
@@ -20061,9 +20061,9 @@ def from_function_delaunay(
     backend : slicer backend, e.g. "matrix", "clement"
     vineyard : bool, use a vineyard-compatible backend
     """
-    from multipers.io import _check_available, function_delaunay_presentation_to_slicer
+    from multipers.io import function_delaunay_presentation_to_slicer, _init_external_softwares
     s = multipers.Slicer(None, backend=backend, vineyard=vineyard, dtype=dtype)
-    assert _check_available("function_delaunay"), f"Could not find function_delaunay"
+    _init_external_softwares(requires=["function_delaunay"])
     function_delaunay_presentation_to_slicer(s, points, grades, degree=degree, verbose=verbose,clear=clear)
     if degree >= 0:
         s.minpres_degree = degree
@@ -20100,6 +20100,7 @@ def minimal_presentation(
         dtype:type|_valid_dtypes=None,
         int n_jobs = -1,
         bool force=False,
+        bool auto_clean = True,
         **minpres_kwargs
         ):
     """
@@ -20138,6 +20139,8 @@ def minimal_presentation(
 
     new_slicer.minpres_degree = degree
     new_slicer.filtration_grid = slicer.filtration_grid if slicer.is_squeezed else None
+    if new_slicer.is_squeezed and auto_clean:
+        new_slicer = new_slicer._clean_filtration_grid()
     return new_slicer
 
 

{multipers-2.3.2b1 → multipers-2.3.3b2}/multipers/slicer.pyx.tp

@@ -764,7 +764,7 @@ def from_function_delaunay(
     grades,
     int degree=-1,
     backend:Optional[_valid_pers_backend]=None,
-    vineyard=None, # TODO : Optional[bool] when cython fixes it
+    vineyard=None, # Optionmal[bool], wait for cython
     dtype=np.float64,
     bool verbose = False,
     bool clear = True,
@@ -779,9 +779,9 @@ def from_function_delaunay(
     backend : slicer backend, e.g. "matrix", "clement"
     vineyard : bool, use a vineyard-compatible backend
     """
-    from multipers.io import _check_available, function_delaunay_presentation_to_slicer
+    from multipers.io import function_delaunay_presentation_to_slicer, _init_external_softwares
     s = multipers.Slicer(None, backend=backend, vineyard=vineyard, dtype=dtype)
-    assert _check_available("function_delaunay"), f"Could not find function_delaunay"
+    _init_external_softwares(requires=["function_delaunay"])
     function_delaunay_presentation_to_slicer(s, points, grades, degree=degree, verbose=verbose,clear=clear)
     if degree >= 0:
         s.minpres_degree = degree
@@ -818,6 +818,7 @@ def minimal_presentation(
         dtype:type|_valid_dtypes=None,
         int n_jobs = -1,
         bool force=False,
+        bool auto_clean = True,
         **minpres_kwargs
         ):
     """
@@ -856,6 +857,8 @@ def minimal_presentation(
 
     new_slicer.minpres_degree = degree
     new_slicer.filtration_grid = slicer.filtration_grid if slicer.is_squeezed else None
+    if new_slicer.is_squeezed and auto_clean:
+        new_slicer = new_slicer._clean_filtration_grid()
     return new_slicer
 
 

{multipers-2.3.2b1 → multipers-2.3.3b2/multipers.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: multipers
-Version: 2.3.2b1
+Version: 2.3.3b2
 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-2.3.2b1 → multipers-2.3.3b2}/pyproject.toml

@@ -9,7 +9,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "multipers"
-version = "2.3.2b1"
+version = "2.3.3b2"
 description = "Multiparameter Topological Persistence for Machine Learning"
 readme = "README.md"
 authors = [