multipers 2.3.3b4__tar.gz → 2.3.3b6__tar.gz

{multipers-2.3.3b4/multipers.egg-info → multipers-2.3.3b6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: multipers
-Version: 2.3.3b4
+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-2.3.3b4 → multipers-2.3.3b6}/multipers/_signed_measure_meta.py

@@ -3,7 +3,6 @@ from typing import Optional, Union
 
 import numpy as np
 
-import multipers as mp
 from multipers.grids import compute_grid, sms_in_grid
 from multipers.plots import plot_signed_measures
 from multipers.point_measure import clean_sms, zero_out_sms
@@ -31,7 +30,7 @@ def signed_measure(
     verbose: bool = False,
     n_jobs: int = -1,
     expand_collapse: bool = False,
-    backend: Optional[str] = None, # deprecated
+    backend: Optional[str] = None,  # deprecated
     grid: Optional[Iterable] = None,
     coordinate_measure: bool = False,
     num_collapses: int = 0,  # TODO : deprecate
@@ -99,12 +98,21 @@ def signed_measure(
      - Rank: Same as Hilbert.
     """
     if backend is not None:
-        raise ValueError("backend is deprecated. reduce the complex before this function.")
-    if num_collapses >0:
-        raise ValueError("num_collapses is deprecated. reduce the complex before this function.")
+        raise ValueError(
+            "backend is deprecated. reduce the complex before this function."
+        )
+    if num_collapses > 0:
+        raise ValueError(
+            "num_collapses is deprecated. reduce the complex before this function."
+        )
     ## TODO : add timings in verbose
     if len(filtered_complex) == 0:
-        return [(np.empty((0,2), dtype=filtered_complex.dtype), np.empty(shape=(0,), dtype=int))]
+        return [
+            (
+                np.empty((0, 2), dtype=filtered_complex.dtype),
+                np.empty(shape=(0,), dtype=int),
+            )
+        ]
     if grid_conversion is not None:
         grid = tuple(f for f in grid_conversion)
         raise DeprecationWarning(
@@ -134,6 +142,8 @@ def signed_measure(
         "rank",
         "euler_characteristic",
         "hilbert_function",
+        "rectangle",
+        "hook",
     ]
 
     assert (
@@ -256,7 +266,7 @@ def signed_measure(
         #         if verbose:
         #             print("Done.")
         else:  # No backend
-            if invariant is not None and "rank" in invariant:
+            if invariant is not None and ("rank" in invariant or "hook" in invariant or "rectangle" in invariant):
                 degrees = np.asarray(degrees, dtype=int)
                 if verbose:
                     print("Computing rank...", end="")
@@ -269,6 +279,10 @@ def signed_measure(
                     ignore_inf=ignore_infinite_filtration_values,
                 )
                 fix_mass_default = False
+
+                if "hook" in invariant:
+                    from multipers.point_measure import rectangle_to_hook_minimal_signed_barcode
+                    sms = [rectangle_to_hook_minimal_signed_barcode(pts,w) for pts,w in sms]
                 if verbose:
                     print("Done.")
             elif filtered_complex_.is_minpres:
@@ -315,7 +329,7 @@ def signed_measure(
         if verbose:
             print("Input is a simplextree.")
         ## we still have a simplextree here
-        if invariant in ["rank_invariant", "rank"]:
+        if invariant in ["rank_invariant", "rank", "hook", "rectangle"]:
             if verbose:
                 print("Computing rank invariant...", end="")
             assert (
@@ -331,6 +345,9 @@ def signed_measure(
                 expand_collapse=expand_collapse,
             )
             fix_mass_default = False
+            if "hook" in invariant:
+                from multipers.point_measure import rectangle_to_hook_minimal_signed_barcode
+                sms = [rectangle_to_hook_minimal_signed_barcode(pts,w) for pts,w in sms]
             if verbose:
                 print("Done.")
         elif len(degrees) == 1 and degrees[0] is None:

{multipers-2.3.3b4 → multipers-2.3.3b6}/multipers/array_api/__init__.py

@@ -1,6 +1,7 @@
-def api_from_tensor(x, *, verbose: bool = False):
-    import multipers.array_api.numpy as npapi
+import multipers.array_api.numpy as npapi
+
 
+def api_from_tensor(x, *, verbose: bool = False):
     if npapi.is_promotable(x):
         if verbose:
             print("using numpy backend")
@@ -38,6 +39,7 @@ def api_from_tensors(*args):
         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-2.3.3b4 → multipers-2.3.3b6}/multipers/array_api/numpy.py

@@ -16,6 +16,8 @@ no_grad = nullcontext
 zeros = _np.zeros
 min = _np.min
 max = _np.max
+repeat_interleave = _np.repeat
+cdist = cdist  # type: ignore[no-redef]
 
 
 def minvalues(x: _np.ndarray, **kwargs):

{multipers-2.3.3b4 → multipers-2.3.3b6}/multipers/array_api/torch.py

@@ -13,6 +13,7 @@ cdist = _t.cdist
 zeros = _t.zeros
 min = _t.min
 max = _t.max
+repeat_interleave = _t.repeat_interleave
 
 
 def minvalues(x: _t.Tensor, **kwargs):

{multipers-2.3.3b4 → 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-2.3.3b4 → 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
 )
 
 
@@ -84,7 +84,7 @@ def _plot_signed_measure_4(
     pts = np.clip(pts, a_min=-np.inf, a_max=np.array((*threshold, *threshold))[None, :])
     alpha_rescaling = 0
     for rectangle, weight in zip(pts, weights):
-        if rectangle[2] > x_smoothing * rectangle[0]:
+        if rectangle[2] >= x_smoothing * rectangle[0]:
             alpha_rescaling = max(
                 alpha_rescaling,
                 (rectangle[2] / x_smoothing - rectangle[0])
@@ -93,7 +93,7 @@ def _plot_signed_measure_4(
     # draw the rectangles
     for rectangle, weight in zip(pts, weights):
         # draw only the rectangles that have not been reduced to the empty set
-        if rectangle[2] > x_smoothing * rectangle[0]:
+        if rectangle[2] >= x_smoothing * rectangle[0]:
             # make the alpha channel proportional to the rectangle's area
             if area_alpha:
                 _plot_rectangle(
@@ -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-2.3.3b4 → multipers-2.3.3b6}/multipers/point_measure.pyx

@@ -11,6 +11,7 @@ from collections import defaultdict
 cnp.import_array()
 from scipy import sparse
 
+from multipers.array_api import api_from_tensor
 
 import multipers.grids as mpg
 
@@ -31,7 +32,6 @@ import cython
 cimport cython
 
 
-
 # from scipy.sparse import coo_array
 # from scipy.ndimage import convolve1d
 
@@ -169,7 +169,7 @@ def sparsify(x):
 
 @cython.boundscheck(False)
 @cython.wraparound(False)
-def clean_signed_measure(some_float[:,:] pts, some_int[:] weights, dtype = np.float32):
+def clean_signed_measure_old(some_float[:,:] pts, some_int[:] weights, dtype = np.float32):
     """
     Sum the diracs at the same locations. i.e.,
     returns the minimal sized measure to represent the input.
@@ -190,6 +190,14 @@ def clean_signed_measure(some_float[:,:] pts, some_int[:] weights, dtype = np.fl
     new_weights = new_weights[idx]
     return (new_pts, new_weights)
 
+def clean_signed_measure(pts, w, dtype=np.int32):
+    api = api_from_tensor(pts)
+    _, idx, inv = np.unique(api.asnumpy(pts), return_index=True, return_inverse=True, axis=0)
+    new_w = np.bincount(inv, weights=w).astype(w.dtype)
+    pts, w = pts[idx], new_w
+    idx = w!=0
+    return pts[idx],w[idx]
+
 def clean_sms(sms):
     """
     Sum the diracs at the same locations. i.e.,
@@ -324,3 +332,64 @@ def estimate_rank_from_rank_sm(sm:tuple, a, b)->np.int64:
     return w[idx].sum()
 
 
+def rectangle_to_hook_minimal_signed_barcode(pts,w,):
+    if pts.shape[1] != 4:
+        raise NotImplementedError(
+            "Only works for 2-parameter persistence modules for the moment."
+        )
+    api = api_from_tensor(pts)
+    pts = api.astensor(pts)
+    w = np.asarray(w)
+    ## [a,b], [a, a0b1], [a,b0a1], proj, V,H 
+
+    projectives_idx = (pts[:,3] == np.inf) * (pts[:,2] == np.inf)
+    pts_proj = pts[projectives_idx]
+    w_proj = w[projectives_idx]
+    pts = pts[~projectives_idx]
+    w = w[~projectives_idx]
+    # print("projectives:", pts_proj)
+    
+    vert_blocks_idx = pts[:,3] == np.inf
+    pts_V = pts[vert_blocks_idx]
+    w_V = w[vert_blocks_idx]
+    pts_V[:,3] = pts_V[:,1]
+    pts = pts[~vert_blocks_idx]
+    w = w[~vert_blocks_idx]
+    # print("vertical:", pts_V)
+
+    h_idx = pts[:,2] == np.inf
+    pts_H = pts[h_idx]
+    w_H = w[h_idx]
+    pts_H[:,2] = pts_H[:,0]
+    pts = pts[~h_idx]
+    w = w[~h_idx]
+    # print("horizontal:", pts_H)
+    
+    
+    new_w = api.cat([-w, w, w,  w_proj,w_V,w_H])
+    
+    pts_b0a1 = api.tensor(pts)
+    pts_b0a1[:,3] = pts[:,1]
+    pts_a0b1 = api.tensor(pts)
+    pts_a0b1[:,2] = pts[:,0]
+    
+    new_pts = api.cat([
+        pts,
+        pts_b0a1,
+        pts_a0b1,
+        pts_proj, 
+        pts_V,
+        pts_H
+    ], axis=0)
+    # pts,w = new_pts,new_w
+    pts,w = clean_signed_measure(new_pts,new_w)
+
+    # Everything infinite is handled separately anyway
+    # inf0 = pts[:,2] == np.inf
+    # inf1 = pts[:,3] == np.inf
+    # pts[inf0,3] = pts[inf0,1]
+    # pts[inf1,2] = pts[inf1,0]
+    # pts,w = clean_signed_measure(pts,w)  
+
+    return pts,w
+

{multipers-2.3.3b4 → 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-2.3.3b4 → 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