multipers 2.3.3b5__tar.gz → 2.3.3b6__tar.gz

{multipers-2.3.3b5/multipers.egg-info → multipers-2.3.3b6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: multipers
-Version: 2.3.3b5
+Version: 2.3.3b6
 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-2.3.3b5 → multipers-2.3.3b6}/multipers/filtrations/filtrations.py

@@ -17,7 +17,6 @@ try:
 
     from multipers.filtrations.density import KDE
 except ImportError:
-
     from sklearn.neighbors import KernelDensity
 
     warn("pykeops not found. Falling back to sklearn.")
@@ -67,7 +66,9 @@ def RipsLowerstar(
         function = function[:, None]
     if function.ndim != 2:
         raise ValueError(
-            f"`function.ndim` should be 0 or 1 . Got {function.ndim=}.{function=}"
+            f"""
+            `function.ndim` should be 0 or 1 . Got {function.ndim=}.{function=}
+            """
         )
     num_parameters = function.shape[1] + 1
     st = SimplexTreeMulti(st, num_parameters=num_parameters)
@@ -154,6 +155,9 @@ def DelaunayLowerstar(
         verbose=verbose,
         clear=clear,
     )
+    if reduce_degree >= 0:
+        # Force resolution to avoid confusion with hilbert.
+        slicer = slicer.minpres(degree=reduce_degree, force=True)
     if flagify:
         from multipers.slicer import to_simplextree
 
@@ -192,7 +196,7 @@ def DelaunayCodensity(
     ), "Density estimation is either via kernels or dtm."
     if bandwidth is not None:
         kde = KDE(bandwidth=bandwidth, kernel=kernel, return_log=return_log)
-        f = kde.fit(points).score_samples(points)
+        f = -kde.fit(points).score_samples(points)
     elif dtm_mass is not None:
         f = DTM(masses=[dtm_mass]).fit(points).score_samples(points)[0]
     else:
@@ -287,11 +291,17 @@ def CoreDelaunay(
         "safe",
         "exact",
         "fast",
-    ], f"The parameter precision must be one of ['safe', 'exact', 'fast'], got {precision}."
+    ], f"""
+    The parameter precision must be one of ['safe', 'exact', 'fast'],
+    got {precision}.
+    """
 
     if verbose:
         print(
-            f"Computing the Delaunay Core Bifiltration of {len(points)} points in dimension {points.shape[1]} with parameters:"
+            f"""Computing the Delaunay Core Bifiltration
+            of {len(points)} points in dimension {points.shape[1]}
+            with parameters:
+            """
         )
         print(f"\tbeta = {beta}")
         print(f"\tks = {ks}")
@@ -333,7 +343,10 @@ def CoreDelaunay(
         num_simplices = len(vertex_array)
         if verbose:
             print(
-                f"Inserting {num_simplices} simplices of dimension {dim} ({num_simplices * len(ks)} birth values)..."
+                f"""
+                Inserting {num_simplices} simplices of dimension {dim}
+                ({num_simplices * len(ks)} birth values)...
+                """
             )
         max_knn_distances = np.max(knn_distances[vertex_array], axis=1)
         critical_radii = np.maximum(alphas[:, None], beta * max_knn_distances)

{multipers-2.3.3b5 → multipers-2.3.3b6}/multipers/plots.py

@@ -15,9 +15,9 @@ _custom_colors = [
     "#00b4d8",
     "#90e0ef",
 ]
-_cmap = ListedColormap(_custom_colors)
-_continuous_cmap = mcolors.LinearSegmentedColormap.from_list(
-    "continuous_cmap", _cmap.colors, N=256
+_cmap_ = ListedColormap(_custom_colors)
+_cmap = mcolors.LinearSegmentedColormap.from_list(
+    "continuous_cmap", _cmap_.colors, N=256
 )
 
 
@@ -180,8 +180,9 @@ def plot_surface(
     fig=None,
     ax=None,
     cmap: Optional[str] = None,
-    discrete_surface=False,
-    has_negative_values=False,
+    discrete_surface: bool = False,
+    has_negative_values: bool = False,
+    contour: bool = True,
     **plt_args,
 ):
     import matplotlib
@@ -213,7 +214,12 @@ def plot_surface(
         )
         cbar.set_ticks(ticks=bounds, labels=bounds)
         return im
-    im = ax.contourf(grid[0], grid[1], hf.T, cmap=cmap, **plt_args)
+
+    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
 
 

{multipers-2.3.3b5 → multipers-2.3.3b6}/multipers/simplex_tree_multi.pyx

@@ -883,6 +883,8 @@ cdef class SimplexTreeMulti_KFi32:
             bool coordinate_values=True,
             bool force=False,
             str strategy:_available_strategies = "exact",
+            resolution:Optional[int|list[int]] = None,
+            bool coordinates = False,
             grid_strategy=None,
             bool inplace=False,
             **filtration_grid_kwargs
@@ -2322,6 +2324,8 @@ cdef class SimplexTreeMulti_Fi32:
             bool coordinate_values=True,
             bool force=False,
             str strategy:_available_strategies = "exact",
+            resolution:Optional[int|list[int]] = None,
+            bool coordinates = False,
             grid_strategy=None,
             bool inplace=False,
             **filtration_grid_kwargs
@@ -3471,6 +3475,8 @@ cdef class SimplexTreeMulti_KFi64:
             bool coordinate_values=True,
             bool force=False,
             str strategy:_available_strategies = "exact",
+            resolution:Optional[int|list[int]] = None,
+            bool coordinates = False,
             grid_strategy=None,
             bool inplace=False,
             **filtration_grid_kwargs
@@ -4910,6 +4916,8 @@ cdef class SimplexTreeMulti_Fi64:
             bool coordinate_values=True,
             bool force=False,
             str strategy:_available_strategies = "exact",
+            resolution:Optional[int|list[int]] = None,
+            bool coordinates = False,
             grid_strategy=None,
             bool inplace=False,
             **filtration_grid_kwargs
@@ -6059,6 +6067,8 @@ cdef class SimplexTreeMulti_KFf32:
             bool coordinate_values=True,
             bool force=False,
             str strategy:_available_strategies = "exact",
+            resolution:Optional[int|list[int]] = None,
+            bool coordinates = False,
             grid_strategy=None,
             bool inplace=False,
             **filtration_grid_kwargs
@@ -7498,6 +7508,8 @@ cdef class SimplexTreeMulti_Ff32:
             bool coordinate_values=True,
             bool force=False,
             str strategy:_available_strategies = "exact",
+            resolution:Optional[int|list[int]] = None,
+            bool coordinates = False,
             grid_strategy=None,
             bool inplace=False,
             **filtration_grid_kwargs
@@ -8647,6 +8659,8 @@ cdef class SimplexTreeMulti_KFf64:
             bool coordinate_values=True,
             bool force=False,
             str strategy:_available_strategies = "exact",
+            resolution:Optional[int|list[int]] = None,
+            bool coordinates = False,
             grid_strategy=None,
             bool inplace=False,
             **filtration_grid_kwargs
@@ -10086,6 +10100,8 @@ cdef class SimplexTreeMulti_Ff64:
             bool coordinate_values=True,
             bool force=False,
             str strategy:_available_strategies = "exact",
+            resolution:Optional[int|list[int]] = None,
+            bool coordinates = False,
             grid_strategy=None,
             bool inplace=False,
             **filtration_grid_kwargs

{multipers-2.3.3b5 → multipers-2.3.3b6}/multipers/simplex_tree_multi.pyx.tp

@@ -1330,6 +1330,8 @@ cdef class SimplexTreeMulti_{{FSHORT}}:
             bool coordinate_values=True,
             bool force=False,
             str strategy:_available_strategies = "exact",
+            resolution:Optional[int|list[int]] = None,
+            bool coordinates = False,
             grid_strategy=None,
             bool inplace=False,
             **filtration_grid_kwargs