multipers 2.3.4__cp311-cp311-win_amd64.whl → 2.3.5b2__cp311-cp311-win_amd64.whl

multipers/_signed_measure_meta.py

@@ -2,6 +2,7 @@ from collections.abc import Iterable, Sequence
 from typing import Optional, Union
 
 import numpy as np
+import time
 
 from multipers.grids import compute_grid, sms_in_grid
 from multipers.plots import plot_signed_measures
@@ -176,10 +177,12 @@ def signed_measure(
 
     if not filtered_complex.is_squeezed:
         if verbose:
-            print("Coarsening complex...", end="")
+            print("Coarsening complex...", end="",flush=True)
+            t0 = time.time()
         filtered_complex_ = filtered_complex.grid_squeeze(grid)
+
         if verbose:
-            print("Done.")
+            print(f"Done. ({time.time() - t0:.3f}s)")
     else:
         filtered_complex_ = filtered_complex.copy()
 
@@ -190,26 +193,18 @@ def signed_measure(
         else:
             max_degree = np.max(degrees) + 1
             if verbose:
-                print(f"Pruning simplicies up to {max_degree}...", end="")
+                print(f"Pruning simplicies up to {max_degree}...", end="", flush=True)
+                t0 = time.time()
             if filtered_complex_.dimension > max_degree:
                 filtered_complex_.prune_above_dimension(max_degree)
             if verbose:
-                print("Done.")
+                print(f"Done. ({time.time() - t0:.3f}s)")
 
     num_parameters = filtered_complex.num_parameters
     assert num_parameters == len(
         grid
     ), f"Number of parameter do not coincide. Got (grid) {len(grid)} and (filtered complex) {num_parameters}."
 
-    # if is_simplextree_multi(filtered_complex_):
-    #     # if num_collapses != 0:
-    #     #     if verbose:
-    #     #         print("Collapsing edges...", end="")
-    #     #     filtered_complex_.collapse_edges(num_collapses)
-    #     #     if verbose:
-    #     #         print("Done.")
-    #     # if backend is not None:
-    #     #     filtered_complex_ = mp.Slicer(filtered_complex_, vineyard=vineyard)
 
     fix_mass_default = mass_default is not None
     if is_slicer(filtered_complex_):
@@ -217,59 +212,14 @@ def signed_measure(
             print("Input is a slicer.")
         if backend is not None and not filtered_complex_.is_minpres:
             raise ValueError("giving a backend to this function is deprecated")
-        #     from multipers.slicer import minimal_presentation
-        #
-        #     assert (
-        #         invariant != "euler"
-        #     ), "Euler Characteristic cannot be speed up by a backend"
-        #     # This returns a list of reduced complexes
-        #     if verbose:
-        #         print("Reducing complex...", end="")
-        #     reduced_complex = minimal_presentation(
-        #         filtered_complex_,
-        #         degrees=degrees,
-        #         backend=backend,
-        #         vineyard=vineyard,
-        #         verbose=verbose,
-        #     )
-        #     if verbose:
-        #         print("Done.")
-        #     if invariant is not None and "rank" in invariant:
-        #         if verbose:
-        #             print("Computing rank...", end="")
-        #         sms = [
-        #             _rank_from_slicer(
-        #                 s,
-        #                 degrees=[d],
-        #                 n_jobs=n_jobs,
-        #                 # grid_shape=tuple(len(g) for g in grid),
-        #                 zero_pad=fix_mass_default,
-        #                 ignore_inf=ignore_infinite_filtration_values,
-        #             )[0]
-        #             for s, d in zip(reduced_complex, degrees)
-        #         ]
-        #         fix_mass_default = False
-        #         if verbose:
-        #             print("Done.")
-        #     else:
-        #         if verbose:
-        #             print("Reduced slicer. Retrieving measure from it...", end="")
-        #         sms = [
-        #             _signed_measure_from_slicer(
-        #                 s,
-        #                 shift=(
-        #                     reduced_complex.minpres_degree & 1 if d is None else d & 1
-        #                 ),
-        #             )[0]
-        #             for s, d in zip(reduced_complex, degrees)
-        #         ]
-        #         if verbose:
-        #             print("Done.")
         else:  # No backend
-            if invariant is not None and ("rank" in invariant or "hook" in invariant or "rectangle" 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="")
+                    print("Computing rank...", end="", flush=True)
+                    t0 = time.time()
                 sms = _rank_from_slicer(
                     filtered_complex_,
                     degrees=degrees,
@@ -280,10 +230,11 @@ def signed_measure(
                 )
                 fix_mass_default = False
                 if verbose:
-                    print("Done.")
+                    print(f"Done. ({time.time() - t0:.3f}s)")
             elif filtered_complex_.is_minpres:
                 if verbose:
-                    print("Reduced slicer. Retrieving measure from it...", end="")
+                    print("Reduced slicer. Retrieving measure from it...", end="",flush=True)
+                    t0 = time.time()
                 sms = [
                     _signed_measure_from_slicer(
                         filtered_complex_,
@@ -294,21 +245,23 @@ def signed_measure(
                     for d in degrees
                 ]
                 if verbose:
-                    print("Done.")
+                    print(f"Done. ({time.time() - t0:.3f}s)")
             elif (invariant is None or "euler" in invariant) and (
                 len(degrees) == 1 and degrees[0] is None
             ):
                 if verbose:
-                    print("Retrieving measure from slicer...", end="")
+                    print("Retrieving measure from slicer...", end="",flush=True)
+                    t0 = time.time()
                 sms = _signed_measure_from_slicer(
                     filtered_complex_,
                     shift=0,  # no minpres
                 )
                 if verbose:
-                    print("Done.")
+                    print(f"Done. ({time.time() - t0:.3f}s)")
             else:
                 if verbose:
-                    print("Computing Hilbert function...", end="")
+                    print("Computing Hilbert function...", end="", flush=True)
+                    t0 = time.time()
                 sms = _hilbert_signed_measure(
                     filtered_complex_,
                     degrees=degrees,
@@ -319,7 +272,7 @@ def signed_measure(
                 )
                 fix_mass_default = False
                 if verbose:
-                    print("Done.")
+                    print(f"Done. ({time.time() - t0:.3f}s)")
 
     elif is_simplextree_multi(filtered_complex_):
         if verbose:
@@ -327,7 +280,9 @@ def signed_measure(
         ## we still have a simplextree here
         if invariant in ["rank_invariant", "rank", "hook", "rectangle"]:
             if verbose:
-                print("Computing rank invariant...", end="")
+                print("Computing rank invariant...", end="", flush=True)
+                t0 = time.time()
+
             assert (
                 num_parameters == 2
             ), "Rank invariant only implemented for 2-parameter modules."
@@ -342,10 +297,11 @@ def signed_measure(
             )
             fix_mass_default = False
             if verbose:
-                print("Done.")
+                print(f"Done. ({time.time() - t0:.3f}s)")
         elif len(degrees) == 1 and degrees[0] is None:
             if verbose:
-                print("Computing Euler Characteristic...", end="")
+                print("Computing Euler Characteristic...", end="", flush=True)
+                t0 = time.time()
             assert invariant is None or invariant in [
                 "euler",
                 "euler_characteristic",
@@ -362,10 +318,11 @@ def signed_measure(
             ]
             fix_mass_default = False
             if verbose:
-                print("Done.")
+                print(f"Done. ({time.time() - t0:.3f}s)")
         else:
             if verbose:
-                print("Computing Hilbert Function...", end="")
+                print("Computing Hilbert Function...", end="", flush=True)
+                t0 = time.time()
             assert invariant is None or invariant in [
                 "hilbert",
                 "hilbert_function",
@@ -384,19 +341,21 @@ def signed_measure(
             )
             fix_mass_default = False
             if verbose:
-                print("Done.")
+                print(f"Done. ({time.time() - t0:.3f}s)")
     else:
         raise ValueError("Filtered complex has to be a SimplexTree or a Slicer.")
 
     if clean:
         if verbose:
-            print("Cleaning measure...", end="")
+            print("Cleaning measure...", end="",flush=True)
+            t0 = time.time()
         sms = clean_sms(sms)
         if verbose:
-            print("Done.")
+            print(f"Done. ({time.time() - t0:.3f}s)")
     if grid is not None and not coordinate_measure:
         if verbose:
-            print("Pushing back the measure to the grid...", end="")
+            print("Pushing back the measure to the grid...", end="", flush=True)
+            t0 = time.time()
         sms = sms_in_grid(
             sms,
             grid=grid,
@@ -404,21 +363,28 @@ def signed_measure(
             # num_parameters=num_parameters,
         )
         if verbose:
-            print("Done.")
+            print(f"Done. ({time.time() - t0:.3f}s)")
 
     if fix_mass_default:
         # TODO : some methods need to use this, this could be optimized
         if verbose:
-            print("Seems that fixing mass default is necessary...", end="")
+            print("Seems that fixing mass default is necessary...", end="", flush=True)
+            t0 = time.time()
         sms = zero_out_sms(sms, mass_default=mass_default)
         if verbose:
-            print("Done.")
+            print(f"Done. ({time.time() - t0:.3f}s)")
 
     if invariant == "hook":
+        if verbose:
+            print("Converting rank decomposition to hook decomposition...", end="",flush=True)
+            t0 = time.time()
         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]
+
+        sms = [rectangle_to_hook_minimal_signed_barcode(pts, w) for pts, w in sms]
+        if verbose:
+            print(f"Done. ({time.time() - t0:.3f}s)")
     if plot:
-        plot_signed_measures(sms)
+        plot_signed_measures(sms, alpha=1 if invariant == "hook" else None)
     return sms
 
 

multipers/array_api/numpy.py

@@ -22,6 +22,13 @@ unique = _np.unique
 inf = _np.inf
 searchsorted = _np.searchsorted
 LazyTensor = None
+abs = _np.abs
+exp = _np.exp
+
+
+def relu(x):
+    return _np.where(x >= 0, x, 0)
+
 
 # Test keops
 _is_keops_available = None

multipers/array_api/torch.py

@@ -20,6 +20,9 @@ cartesian_product = _t.cartesian_prod
 inf = _t.inf
 searchsorted = _t.searchsorted
 LazyTensor = None
+relu = _t.relu
+abs = _t.abs
+exp = _t.exp
 
 
 _is_keops_available = None
@@ -53,6 +56,8 @@ def check_keops():
         _is_keops_available = False
 
     return _is_keops_available
+
+
 check_keops()
 
 
@@ -101,8 +106,8 @@ def maxvalues(x: _t.Tensor, **kwargs):
     return _t.max(x, **kwargs).values
 
 
-def asnumpy(x):
-    return x.detach().numpy()
+def asnumpy(x: _t.Tensor):
+    return x.cpu().detach().numpy()
 
 
 def is_tensor(x):

multipers/filtrations/filtrations.py

@@ -79,6 +79,7 @@ def RipsLowerstar(
         filtration_values = [D.ravel(), *[f for f in function.T]]
         grid = compute_grid(filtration_values)
         st = st.grid_squeeze(grid)
+        st._clean_filtration_grid()
     return st
 
 
@@ -239,6 +240,7 @@ def Cubical(image: ArrayLike, **slicer_kwargs):
             ).reshape(slice_shape)
         slicer = from_bitmap(coord_img, **slicer_kwargs)
         slicer.filtration_grid = grid
+        slicer._clean_filtration_grid()
         return slicer
 
     return from_bitmap(image, **slicer_kwargs)

multipers/grids.pyx

@@ -369,7 +369,7 @@ def _inf_value(array):
         return torch.iinfo(dtype).max
     raise ValueError(f"Dtype must be integer or floating like (got {dtype})")
 
-def evaluate_in_grid(pts, grid, mass_default=None):
+def evaluate_in_grid(pts, grid, mass_default=None, input_inf_value=None, output_inf_value=None):
     """    
     Input
     -----
@@ -379,28 +379,21 @@ def evaluate_in_grid(pts, grid, mass_default=None):
     assert pts.ndim == 2
     first_filtration = grid[0]
     dtype = first_filtration.dtype
-    if isinstance(first_filtration, np.ndarray):
-        if mass_default is not None:
-            grid = tuple(np.concatenate([g, [m]]) for g,m in zip(grid, mass_default))
-        def empty_like(x):
-            return np.empty_like(x, dtype=dtype)
-    else: 
-        import torch
-        # assert isinstance(first_filtration, torch.Tensor), f"Invalid grid type. Got {type(grid[0])}, expected numpy or torch array."
-        if mass_default is not None:
-            grid = tuple(torch.cat([g, torch.tensor(m)[None]]) for g,m in zip(grid, mass_default))
-        def empty_like(x):
-            return torch.empty(x.shape,dtype=dtype)
+    api = api_from_tensors(*grid)
+    if mass_default is not None:
+        grid = tuple(api.cat([g, api.astensor(m)[None]]) for g,m in zip(grid, mass_default))
+    def empty_like(x):
+        return api.empty(x.shape, dtype=dtype)
 
     coords=empty_like(pts)
     cdef int dim = coords.shape[1]
-    pts_inf = _inf_value(pts)
-    coords_inf = _inf_value(coords)
+    pts_inf = _inf_value(pts) if input_inf_value is None else input_inf_value
+    coords_inf = _inf_value(coords) if output_inf_value is None else output_inf_value
     idx = np.argwhere(pts == pts_inf)
-    pts[idx] == 0
+    pts[idx[:,0],idx[:,1]] = 0
     for i in range(dim):
         coords[:,i] = grid[i][pts[:,i]]
-    coords[idx] = coords_inf
+    coords[idx[:,0],idx[:,1]] = coords_inf
     return coords
 
 def sm_in_grid(pts, weights, grid, mass_default=None):
@@ -452,8 +445,9 @@ def sms_in_grid(sms, grid, mass_default=None):
     return sms
 
 
-def _push_pts_to_line(pts, basepoint, direction=None):
-    api = api_from_tensors(pts, basepoint)
+def _push_pts_to_line(pts, basepoint, direction=None, api=None):
+    if api is None:
+        api = api_from_tensors(pts, basepoint)
     pts = api.astensor(pts)
     basepoint = api.astensor(basepoint)
     num_parameters = basepoint.shape[0]
@@ -479,3 +473,47 @@ def _push_pts_to_line(pts, basepoint, direction=None):
     else:
         xs = xa
     return xs.squeeze()
+
+def _push_pts_to_lines(pts, basepoints, directions=None, api=None):
+    if api is None:
+        api = api_from_tensors(pts,basepoints)
+    cdef int num_lines = len(basepoints)
+    cdef int num_pts = len(pts)
+
+    pts = api.astensor(pts)
+    basepoints = api.astensor(basepoints)
+    if directions is None:
+        directions = [None]*num_lines
+    else:
+        directions = api.astensor(directions)
+
+    out = api.empty((num_lines, num_pts), dtype=pts.dtype)
+    for i in range(num_lines):
+        out[i] = _push_pts_to_line(pts, basepoints[i], directions[i], api=api)[None]
+    return out
+
+
+def evaluate_mod_in_grid(mod, grid, box=None):
+    """Given an MMA module, pushes it into the specified grid.
+    Useful for e.g., make it differentiable.
+
+    Input
+    -----
+     - mod: PyModule
+     - grid: Iterable of 1d array, for num_parameters
+    Ouput
+    -----
+    torch-compatible module in the format:
+    (num_degrees) x (num_interval of degree) x ((num_birth, num_parameter), (num_death, num_parameters))
+
+    """
+    (birth_sizes, death_sizes), births, deaths = mod.to_flat_idx(grid)
+    births = evaluate_in_grid(births, grid)
+    deaths = evaluate_in_grid(deaths, grid)
+    diff_mod = tuple(
+        zip(
+            births.split_with_sizes(birth_sizes.tolist()),
+            deaths.split_with_sizes(death_sizes.tolist()),
+        )
+    )
+    return diff_mod

multipers/multi_parameter_rank_invariant/function_rips.h

@@ -61,7 +61,7 @@ inline get_degree_filtrations( // also return max_degree,filtration_values
   // preprocess
   filtration_lists edge_filtration_of_nodes(st.num_vertices());
   for (auto sh : st.complex_simplex_range()) {
-    if (st.dimension() == 0)
+    if (st.dimension(sh) == 0)
       continue;
     value_type filtration = st.filtration(sh);
     for (auto node : st.simplex_vertex_range(sh)) {

multipers/multiparameter_module_approximation/approximation.h

@@ -1477,8 +1477,14 @@ std::vector<int> inline to_grid_coord(const Gudhi::multi_filtration::One_critica
       out[i] = grid[i].size() - 1;
     else if (pt[i] <= grid[i][0]) [[unlikely]] {
       out[i] = 0;
-    } else
-      out[i] = std::distance(grid[i].begin(), std::lower_bound(grid[i].begin(), grid[i].end(), pt[i]));
+    } else {
+      auto temp = std::distance(grid[i].begin(), std::lower_bound(grid[i].begin(), grid[i].end(), pt[i]));
+      if (std::abs(grid[i][temp] - pt[i]) < std::abs(grid[i][temp - 1] - pt[i])) {
+        out[i] = temp;
+      } else {
+        out[i] = temp - 1;
+      }
+    }
   }
   return out;
 }

multipers/plots.py

@@ -162,7 +162,7 @@ def plot_signed_measure(signed_measure, threshold=None, ax=None, **plt_kwargs):
         )
 
 
-def plot_signed_measures(signed_measures, threshold=None, size=4):
+def plot_signed_measures(signed_measures, threshold=None, size=4, alpha=None):
     num_degrees = len(signed_measures)
     if num_degrees <= 1:
         axes = [plt.gca()]
@@ -172,7 +172,8 @@ def plot_signed_measures(signed_measures, threshold=None, size=4):
         )
     for ax, signed_measure in zip(axes, signed_measures):
         plot_signed_measure(signed_measure=signed_measure,
-                            ax=ax, threshold=threshold)
+                            ax=ax, threshold=threshold,
+                            alpha=alpha)
     plt.tight_layout()
 
 

multipers/point_measure.pyx

@@ -366,7 +366,7 @@ def rectangle_to_hook_minimal_signed_barcode(pts,w,):
     # print("horizontal:", pts_H)
     
     
-    new_w = api.cat([-w, w, w,  w_proj,w_V,w_H])
+    new_w = np.concatenate([-w, w, w,  w_proj,w_V,w_H])
     
     pts_b0a1 = api.tensor(pts)
     pts_b0a1[:,3] = pts[:,1]