multipers 2.3.3b5__cp312-cp312-win_amd64.whl → 2.3.3b7__cp312-cp312-win_amd64.whl

multipers/ml/signed_measures.py

@@ -9,12 +9,107 @@ from sklearn.base import BaseEstimator, TransformerMixin
 from tqdm import tqdm
 
 import multipers as mp
-from multipers.array_api import api_from_tensor
+from multipers.array_api import api_from_tensor, api_from_tensors
 from multipers.filtrations.density import available_kernels, convolution_signed_measures
-from multipers.grids import compute_grid
+from multipers.grids import compute_grid, todense
 from multipers.point_measure import rank_decomposition_by_rectangles, signed_betti
 
 
+def batch_signed_measure_convolutions(
+    signed_measures,  # array of shape (num_data,num_pts,D)
+    x,  # array of shape (num_x, D) or (num_data, num_x, D)
+    bandwidth,  # either float or matrix if multivariate kernel
+    kernel: available_kernels,
+    api=None,
+):
+    """
+    Input
+    -----
+     - signed_measures: unragged, of shape (num_data, num_pts, D+1)
+       where last coord is weights, (0 for dummy points)
+     - x : the points to convolve (num_x,D)
+     - bandwidth : the bandwidths or covariance matrix inverse or ... of the kernel
+     - kernel : "gaussian", "multivariate_gaussian", "exponential", or Callable (x_i, y_i, bandwidth)->float
+
+    Output
+    ------
+    Array of shape (num_convolutions, (num_axis), num_data,
+    Array of shape (num_convolutions, (num_axis), num_data, max_x_size)
+    """
+    from multipers.filtrations.density import _kernel
+
+    if api is None:
+        api = api_from_tensors(signed_measures, x)
+    if signed_measures.ndim == 2:
+        signed_measures = signed_measures[None, :, :]
+    sms = signed_measures[..., :-1]
+    weights = signed_measures[..., -1]
+    _sms = api.LazyTensor(api.ascontiguous(sms[..., None, :]))
+    _x = api.ascontiguous(x[..., None, :, :])
+
+    sms_kernel = _kernel(kernel)(_sms, _x, bandwidth)
+    out = (sms_kernel * api.ascontiguous(weights[..., None, None])).sum(
+        signed_measures.ndim - 2
+    )
+    assert out.shape[-1] == 1, "Pykeops bug fixed, TODO : refix this "
+    out = out[..., 0]  ## pykeops bug + ensures its a tensor
+    # assert out.shape == (x.shape[0], x.shape[1]), f"{x.shape=}, {out.shape=}"
+    return out
+
+
+def sm2deep(signed_measure, api=None):
+    if api is None:
+        api = api_from_tensor(signed_measure[0])
+    dirac_positions, dirac_signs = signed_measure
+    dtype = dirac_positions.dtype
+    new_shape = list(dirac_positions.shape)
+    new_shape[1] += 1
+    c = api.empty(new_shape, dtype=dtype)
+    c[:, :-1] = dirac_positions
+    c[:, -1] = api.astensor(dirac_signs)
+    return c
+
+
+def deep_unrag(sms, api=None):
+    if api is None:
+        api = api_from_tensor(sms[0][0])
+    num_sm = len(sms)
+    if num_sm == 0:
+        return api.tensor([])
+    first = sms[0][0]
+    num_parameters = first.shape[1]
+    dtype = first.dtype
+    deep_sms = tuple(sm2deep(sm, api=api) for sm in sms)
+    max_num_pts = np.max([sm[0].shape[0] for sm in sms])
+    unragged_sms = api.zeros((num_sm, max_num_pts, num_parameters + 1), dtype=dtype)
+
+    for data in range(num_sm):
+        sm = deep_sms[data]
+        a, b = sm.shape
+        unragged_sms[data, :a, :b] = sm
+    return unragged_sms
+
+
+def sm_convolution(
+    sms,
+    grid,
+    bandwidth,
+    kernel: available_kernels = "gaussian",
+    plot: bool = False,
+    **plt_kwargs,
+):
+    dense_grid = todense(grid)
+    api = api_from_tensors(sms[0][0], dense_grid)
+    sms = deep_unrag(sms, api=api)
+    convs = batch_signed_measure_convolutions(
+        sms, dense_grid, bandwidth, kernel, api=api
+    ).reshape(sms.shape[0], *(len(g) for g in grid))
+    if plot:
+        from multipers.plots import plot_surfaces
+        plot_surfaces((grid, convs), **plt_kwargs)
+    return convs
+
+
 class FilteredComplex2SignedMeasure(BaseEstimator, TransformerMixin):
     """
     Input
@@ -547,27 +642,6 @@ def rescale_sparse_signed_measure(
     return out
 
 
-def sm2deep(signed_measure):
-    dirac_positions, dirac_signs = signed_measure
-    dtype = dirac_positions.dtype
-    new_shape = list(dirac_positions.shape)
-    new_shape[1] += 1
-    if isinstance(dirac_positions, np.ndarray):
-        c = np.empty(new_shape, dtype=dtype)
-        c[:, :-1] = dirac_positions
-        c[:, -1] = dirac_signs
-
-    else:
-        import torch
-
-        c = torch.empty(new_shape, dtype=dtype)
-        c[:, :-1] = dirac_positions
-        if isinstance(dirac_signs, np.ndarray):
-            dirac_signs = torch.from_numpy(dirac_signs)
-        c[:, -1] = dirac_signs
-    return c
-
-
 class SignedMeasureFormatter(BaseEstimator, TransformerMixin):
     """
     Input
@@ -759,7 +833,9 @@ class SignedMeasureFormatter(BaseEstimator, TransformerMixin):
                 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)
+            self._normalization_factors = self._backend.astensor(
+                self._normalization_factors
+            )
             # else:
             #     (
             #         self._filtrations_bounds,
@@ -784,9 +860,11 @@ class SignedMeasureFormatter(BaseEstimator, TransformerMixin):
             ]
             # axis, filtration_values
             filtration_values = [
-                self._backend.astensor(compute_grid(
-                    f_ax.T, resolution=self.resolution, strategy=self.grid_strategy
-                ))
+                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

multipers/mma_structures.pyx

@@ -751,7 +751,7 @@ cdef class PyModule_f64:
               axs = [plt.gca()]
             for image, degree, i in zip(image_vector, degrees, range(num_degrees)):
                 ax = axs[i]
-                temp = multipers.plots.plot_surface(grid, image.T, ax=ax)
+                temp = multipers.plots.plot_surface(grid, image, ax=ax)
                 plt.colorbar(temp, ax = ax)
                 if degree < 0 :
                     ax.set_title(rf"$H_{i}$ $2$-persistence image")
@@ -1712,7 +1712,7 @@ cdef class PyModule_f32:
               axs = [plt.gca()]
             for image, degree, i in zip(image_vector, degrees, range(num_degrees)):
                 ax = axs[i]
-                temp = multipers.plots.plot_surface(grid, image.T, ax=ax)
+                temp = multipers.plots.plot_surface(grid, image, ax=ax)
                 plt.colorbar(temp, ax = ax)
                 if degree < 0 :
                     ax.set_title(rf"$H_{i}$ $2$-persistence image")

multipers/mma_structures.pyx.tp

@@ -773,7 +773,7 @@ cdef class PyModule_{{SHORT}}:
               axs = [plt.gca()]
             for image, degree, i in zip(image_vector, degrees, range(num_degrees)):
                 ax = axs[i]
-                temp = multipers.plots.plot_surface(grid, image.T, ax=ax)
+                temp = multipers.plots.plot_surface(grid, image, ax=ax)
                 plt.colorbar(temp, ax = ax)
                 if degree < 0 :
                     ax.set_title(rf"$H_{i}$ $2$-persistence image")

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", 50)
+        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/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
@@ -910,7 +912,7 @@ cdef class SimplexTreeMulti_KFi32:
 
         #TODO : multi-critical
         if filtration_grid is None:  
-            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, **filtration_grid_kwargs)
+            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, resolution=resolution, **filtration_grid_kwargs)
         else:
             filtration_grid = sanitize_grid(filtration_grid)
             if len(filtration_grid) != self.num_parameters:
@@ -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
@@ -2349,7 +2353,7 @@ cdef class SimplexTreeMulti_Fi32:
 
         #TODO : multi-critical
         if filtration_grid is None:  
-            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, **filtration_grid_kwargs)
+            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, resolution=resolution, **filtration_grid_kwargs)
         else:
             filtration_grid = sanitize_grid(filtration_grid)
             if len(filtration_grid) != self.num_parameters:
@@ -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
@@ -3498,7 +3504,7 @@ cdef class SimplexTreeMulti_KFi64:
 
         #TODO : multi-critical
         if filtration_grid is None:  
-            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, **filtration_grid_kwargs)
+            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, resolution=resolution, **filtration_grid_kwargs)
         else:
             filtration_grid = sanitize_grid(filtration_grid)
             if len(filtration_grid) != self.num_parameters:
@@ -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
@@ -4937,7 +4945,7 @@ cdef class SimplexTreeMulti_Fi64:
 
         #TODO : multi-critical
         if filtration_grid is None:  
-            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, **filtration_grid_kwargs)
+            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, resolution=resolution, **filtration_grid_kwargs)
         else:
             filtration_grid = sanitize_grid(filtration_grid)
             if len(filtration_grid) != self.num_parameters:
@@ -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
@@ -6086,7 +6096,7 @@ cdef class SimplexTreeMulti_KFf32:
 
         #TODO : multi-critical
         if filtration_grid is None:  
-            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, **filtration_grid_kwargs)
+            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, resolution=resolution, **filtration_grid_kwargs)
         else:
             filtration_grid = sanitize_grid(filtration_grid)
             if len(filtration_grid) != self.num_parameters:
@@ -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
@@ -7525,7 +7537,7 @@ cdef class SimplexTreeMulti_Ff32:
 
         #TODO : multi-critical
         if filtration_grid is None:  
-            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, **filtration_grid_kwargs)
+            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, resolution=resolution, **filtration_grid_kwargs)
         else:
             filtration_grid = sanitize_grid(filtration_grid)
             if len(filtration_grid) != self.num_parameters:
@@ -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
@@ -8674,7 +8688,7 @@ cdef class SimplexTreeMulti_KFf64:
 
         #TODO : multi-critical
         if filtration_grid is None:  
-            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, **filtration_grid_kwargs)
+            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, resolution=resolution, **filtration_grid_kwargs)
         else:
             filtration_grid = sanitize_grid(filtration_grid)
             if len(filtration_grid) != self.num_parameters:
@@ -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
@@ -10113,7 +10129,7 @@ cdef class SimplexTreeMulti_Ff64:
 
         #TODO : multi-critical
         if filtration_grid is None:  
-            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, **filtration_grid_kwargs)
+            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, resolution=resolution, **filtration_grid_kwargs)
         else:
             filtration_grid = sanitize_grid(filtration_grid)
             if len(filtration_grid) != self.num_parameters:

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
@@ -1357,7 +1359,7 @@ cdef class SimplexTreeMulti_{{FSHORT}}:
 
         #TODO : multi-critical
         if filtration_grid is None:  
-            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, **filtration_grid_kwargs)
+            filtration_grid = self.get_filtration_grid(grid_strategy=strategy, resolution=resolution, **filtration_grid_kwargs)
         else:
             filtration_grid = sanitize_grid(filtration_grid)
             if len(filtration_grid) != self.num_parameters: