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

multipers/slicer.pyx.tp

@@ -28,8 +28,8 @@ from multipers.filtrations cimport *
 from multipers.filtration_conversions cimport *
 ## TODO: these two are not needed, remove that by updating rank code.
 from multipers.point_measure import sparsify, rank_decomposition_by_rectangles
-from multipers.grids import compute_grid, sanitize_grid, evaluate_in_grid, _push_pts_to_line 
-from multipers.array_api import api_from_tensor
+from multipers.grids import compute_grid, sanitize_grid, evaluate_in_grid, _push_pts_to_lines, _inf_value
+from multipers.array_api import api_from_tensor, api_from_tensors
 
 import numpy as np
 cimport cython
@@ -37,6 +37,7 @@ from libcpp.string cimport string
 # python_value_type = np.float32
 from typing import Union
 from cython.operator cimport dereference
+import time
 
 ## WARNING : This is repeated in the pxd file ...
 python_indices_type=np.int32
@@ -302,10 +303,8 @@ cdef class {{D['PYTHON_TYPE']}}:
     def persistence_on_line(self,basepoint,direction=None, bool keep_inf=True, bool full=False, bool ignore_infinite_filtration_values = True):
         """
         Computes the persistence on a line L defined by 
-         - a basepoint (num_parameters,) array
-         - an optional direction (num_parameters,) array
-        
-        Warning: This is not parallelizable. Use `persitence_on_lines`.
+         - a basepoint (num_parameters,) or (num_basepoints, num_parameters,) array
+         - an optional direction (num_parameters,) or (num_basepoints, num_parameters,) array
         """
         {{if D['IS_FLOAT']}}
         self.push_to_line(basepoint,direction)
@@ -320,21 +319,25 @@ cdef class {{D['PYTHON_TYPE']}}:
         return bcs
         {{else}}
         if not self.is_squeezed:
-            raise ValueError("Unsqueeze tensor, or provide a filtration grid. Cannot slice lines with integers...")
-        api = api_from_tensor(self.filtration_grid[0])
-        s = self.unsqueeze()
+            raise ValueError("Unsqueeze tensor, or provide a filtration grid. Cannot slice lines with integers.")
+        api = api_from_tensors(basepoint, *self.filtration_grid)
+        basepoint = api.astensor(basepoint)
         fil = evaluate_in_grid(np.asarray(self.get_filtrations()), self.filtration_grid)
-        projected_fil =_push_pts_to_line(fil, basepoint, direction)
-        s.compute_persistence(projected_fil)
-        bcs_idx = s.get_barcode_idx()
-        bcs = tuple(
-                api.stack([projected_fil[bc[:,0]], projected_fil[bc[:,1]]], axis=1) 
-                if bc.size>0 
-                else api.empty((0,2), dtype = self.filtration_grid[0].dtype)
-                for bc in bcs_idx
-            )
+        if basepoint.ndim == 0 or basepoint.ndim >2:
+            raise ValueError(f"Expected a basepoint shape of the form (num_parameters,). Got {basepoint.shape=}")
+        if basepoint.ndim == 1:
+            basepoint = basepoint[None]
+        if direction is not None:
+            direction = api.astensor(direction)
+            if direction.ndim == 0 or direction.ndim >2:
+                raise ValueError(f"Expected a direction shape of the form (num_parameters,). Got {direction.shape=}")
+            if direction.ndim == 1:
+                direction = direction[None]
+        projected_fil = _push_pts_to_lines(fil, basepoint, direction, api=api)
+        bcs = self.compute_persistence(projected_fil, ignore_infinite_filtration_values=ignore_infinite_filtration_values)
         if full:
-            bcs = self._bc_to_full(bcs, basepoint, direction)
+            _dirs = [None]*len(basepoint) if direction is None else direction
+            bcs = tuple({{D['PYTHON_TYPE']}}._bc_to_full(bcs, bp, dir) for bcs, bp, dir in zip(bcs,basepoint,_dirs))
         return bcs
         {{endif}}
 
@@ -412,18 +415,16 @@ cdef class {{D['PYTHON_TYPE']}}:
 
 
 
-    def compute_persistence(self,one_filtration=None, bool ignore_infinite_filtration_values = True)->tuple:
+    def compute_persistence(self,one_filtration=None, bool ignore_infinite_filtration_values = True, bool verbose=False)->tuple:
         """
         Computes the current persistence, or the persistence
-        given by the filtration one_filtration (num_generators,).
+        given by the filtration one_filtration (num_generators,) or (num_filtrations, num_generators,).
         """
         if one_filtration is not None:
+            if verbose:
+                print(f"Computing persistence on custom filtration: {one_filtration.shape=} {one_filtration.dtype=}")
             api = api_from_tensor(one_filtration)
             one_filtration=api.astensor(one_filtration)
-            # self.truc.set_one_filtration(one_filtration)
-            # s = self.unsqueeze()
-            # fil = evaluate_in_grid(np.asarray(self.get_filtrations()), self.filtration_grid)
-            # projected_fil =_push_pts_to_line(fil, basepoint, direction)
             if one_filtration.ndim > 2 or one_filtration.ndim == 0:
                 raise ValueError(f"Expected a filtration shape of the form ((num_1_param), num_generators). Got {one_filtration.shape=}")
             squeeze = False
@@ -431,16 +432,25 @@ cdef class {{D['PYTHON_TYPE']}}:
                 one_filtration = one_filtration[None]
                 squeeze = True
 
-            bcs = self._custom_persistences_idx(api.asnumpy(one_filtration),ignore_infinite_filtration_values)
-            
+            if self.is_squeezed:
+                if verbose:
+                    print(f"Input is squeezed. Unsqueezing it for the line projection.")
+                temp = self.unsqueeze() ## TODO : optimize
+                bcs = temp._custom_persistences_idx(api.asnumpy(one_filtration),ignore_infinite_filtration_values)
+            else:
+                bcs = self._custom_persistences_idx(api.asnumpy(one_filtration),ignore_infinite_filtration_values)
+
+            num_filtrations = one_filtration.shape[0]
             bcs = tuple(tuple(
-                    api.stack([F[bc[:,0]], F[bc[:,1]]], axis=1) 
-                    if bc.size>0 
-                    else api.empty((0,2), dtype = F.dtype)
-                    for bc in bcs_idx
-                )
-                for bcs_idx,F in zip(bcs,one_filtration)
+                    evaluate_in_grid(
+                        np.asarray(bcs[i][j]) if len(bcs[i][j]) else np.empty((0,2), dtype=np.int32),
+                        [one_filtration[i]]*2, # 2 bc of 1d barcode
+                        input_inf_value=-1,
+                    )
+                    for j in range(len(bcs[i])))
+                for i in range(num_filtrations)
             )
+
             return bcs[0] if squeeze else bcs
 
         # TODO: Later
@@ -449,7 +459,6 @@ cdef class {{D['PYTHON_TYPE']}}:
         # else:
         #     self.truc.compute_persistence()
         self.truc.compute_persistence(ignore_infinite_filtration_values)
-        # return self
         return self.get_barcode()
     def get_barcode(self):
         """
@@ -496,14 +505,21 @@ cdef class {{D['PYTHON_TYPE']}}:
                 strategy=grid_strategy,
                 **infer_grid_kwargs,
             )
-    def get_filtrations(self):
+    def get_filtrations(self, bool unsqueeze = False):
         """
         Returns a view of the filtration values, as a list of numpy arrays.
         """
         {{if D['IS_KCRITICAL']}}
+        if unsqueeze:
+            raise NotImplementedError("Unsqueezed version not implemented for multicritical filtrations.")
         return _vff2kcview_{{D['SHORT_VALUE_TYPE']}}(self.truc.get_filtrations(), copy=False, duplicate=self.num_parameters)
         {{else}}
-        return _vff21cview_{{D['SHORT_VALUE_TYPE']}}(self.truc.get_filtrations(), copy=False, duplicate=self.num_parameters)
+        out =  _vff21cview_{{D['SHORT_VALUE_TYPE']}}(self.truc.get_filtrations(), copy=False, duplicate=self.num_parameters)
+        if not unsqueeze:
+            return out
+        if not self.is_squeezed:
+            raise ValueError(f"Already unsqueezed. Got {unsqueeze=}")
+        return evaluate_in_grid(np.asarray(out), self.filtration_grid)
         {{endif}}
 
     def get_dimensions(self)-> np.ndarray:
@@ -523,6 +539,35 @@ cdef class {{D['PYTHON_TYPE']}}:
         """
         self.truc.prune_above_dimension(max_dimension)
         return self
+    {{if not D["IS_KCRITICAL"]}}
+    def make_filtration_non_decreasing(self, bool safe=True):
+        if self.is_squeezed and safe:
+            for i_ in range(self.num_parameters):
+                F = self.filtration_grid[i_]
+                if not (F[1:]>=F[:-1]).all():
+                    raise ValueError("Found non-sorted grid.")
+
+        cdef int i = 0
+        cdef int N = len(self)
+        cdef vector[int] dims = self.truc.get_dimensions()
+        cdef Py_ssize_t num_parameters = self.num_parameters
+        cdef vector[vector[unsigned int]] B = self.truc.get_boundaries() # const issues, I was lazy
+
+        with nogil:
+            for i in range(N):
+                for b in B[i]:
+                    for j in range(num_parameters):
+                        self.truc.get_filtrations()[b][j] = max(
+                                self.truc.get_filtrations()[b][j],
+                                self.truc.get_filtrations()[i][j]
+                         )
+        return self
+
+
+
+
+    {{endif}}
+
     def get_boundaries(self)->tuple[tuple]:
         """
         Returns the boundaries of the generators.
@@ -686,8 +731,6 @@ cdef class {{D['PYTHON_TYPE']}}:
         return self
 
     def unsqueeze(self, grid=None)->{{D['PYTHON_TYPE'][:-3]+"f64"}}:
-        from multipers.grids import evaluate_in_grid, sanitize_grid
-        from multipers import Slicer
         grid = self.filtration_grid if grid is None else grid
         grid = sanitize_grid(grid, numpyfy=True)
         new_filtrations = evaluate_in_grid(np.asarray(self.get_filtrations(), dtype=np.int32), grid)
@@ -1049,7 +1092,11 @@ def _rank_from_slicer(
     grid_shape_with_degree = np.asarray(np.concatenate([[len(degrees)], grid_shape, grid_shape]), dtype=python_indices_type)
     if verbose:
         print("Container shape: ", grid_shape_with_degree)
+        print("Mallocing...", end="", flush=True)
+        t0 = time.time()
     container_array = np.ascontiguousarray(np.zeros(grid_shape_with_degree, dtype=python_tensor_dtype).ravel())
+    if verbose:
+        print(f" Done. ({time.time()-t0:.3f}s).")
     assert len(container_array) < np.iinfo(python_indices_type).max, "Too large container. Raise an issue on github if you encounter this issue. (Due to tensor's operator[])"
     # if zero_pad:
     #     grid_shape_with_degree[1:] -= 1
@@ -1059,20 +1106,25 @@ def _rank_from_slicer(
 
     ## SLICERS
     if verbose:
-        print("Computing rank invariant...", end="")
+        print("Computing rank invariant...", end="", flush=True)
+        t0 = time.time()
     _compute_rank_invariant(slicer, container_ptr, c_grid_shape, degrees, n_jobs, ignore_inf)
     if verbose:
-        print("Done.")
+        print(f" Done. ({time.time()-t0:.3f}s).")
 
     if verbose:
-        print("Computing Möbius inversion...", end="")
+        print("Computing Möbius inversion...", end="", flush=True)
+        t0 = time.time()
     # if zero_pad:
     #     grid_shape_with_degree[1:] += 1
     rank = container_array.reshape(grid_shape_with_degree)
     rank = tuple(rank_decomposition_by_rectangles(rank_of_degree, threshold=zero_pad) for rank_of_degree in rank)
+    if verbose:
+        print(f" Done. ({time.time()-t0:.3f}s).")
+
     if return_raw:
         return rank
-    out = []
+
     def clean_rank(rank_decomposition):
         (coords, weights) = sparsify(np.ascontiguousarray(rank_decomposition))
         births = coords[:,:num_parameters]
@@ -1082,7 +1134,12 @@ def _rank_from_slicer(
         weights = weights[correct_indices]
         return coords, weights
 
+    if verbose:
+        print("Cleaning output...", end="", flush=True)
+        t0 = time.time()
     out = tuple(clean_rank(rank_decomposition) for rank_decomposition in rank)
     if verbose:
-        print("Done.")
+        print(f" Done. ({time.time()-t0:.3f}s).")
     return out
+# %%
+

{multipers-2.3.4.dist-info → multipers-2.3.5b2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: multipers
-Version: 2.3.4
+Version: 2.3.5b2
 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-2.3.4.dist-info → multipers-2.3.5b2.dist-info}/RECORD

@@ -1,45 +1,45 @@
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 multipers/_slicer_meta.py,sha256=mjIGR-B6HnQLSiMowEQ8EWQkD_IF3bBnDVzvwrZugZ4,7203
 multipers/distances.py,sha256=uAZj2GtUQp50OxN2qU7sl2JqsmJ74IG9j5tZapLO2Us,6220
 multipers/filtration_conversions.pxd,sha256=Je7a3F4zS1PQn6Ul1YCXgA6p39X2FouStru-XtN-aOw,10800
 multipers/filtration_conversions.pxd.tp,sha256=_9tUvZVUA7J_RUM3q7BxY48fYgDHCUA7Xhy4nBfLLs0,3309
 multipers/filtrations.pxd,sha256=08ONkZNCjs8Nme8lcD9myPz-K662sA-EDpSwzgC2_ts,9461
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 multipers/function_rips.pyx,sha256=j5NjbK3YrAv_2s8YHB1JB0k6m9NC7RQCSFlJe-w_kgE,5252
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 multipers/io.pyx,sha256=pQBH_rSqaCZqDSxTLnhlyECP3fLbX2tR_RKJHydHm_0,22210
-multipers/mma_structures.cp311-win_amd64.pyd,sha256=cuWqpQM9hS8vQraIXXAEqp_0fROGr1U-FgQy3R1HKDU,1325056
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 multipers/mma_structures.pxd,sha256=jh1QnQRidt_VK0CK7losQi6rAl_1qG5DNuR23J42pUA,6595
 multipers/mma_structures.pyx,sha256=1FQ_sqkpHHkCyCLLKkR9lUgZKDZFt-YgjnDd8NGmw6Q,109526
 multipers/mma_structures.pyx.tp,sha256=QLo4ZZDnFuWNot771jYkYHc9ZQq6CJIpkRkeRwGi7XA,42297
 multipers/multiparameter_edge_collapse.py,sha256=MFt0eKQQSv2354omeIqOmzASYTKIMsYdxZHFZauQr8g,1229
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 multipers/multiparameter_module_approximation.pyx,sha256=wp7la7Z9wBngnfw6WOVddf93mPyXf4HfNT6dKW2Z0r0,9030
 multipers/pickle.py,sha256=YYVt4iHiD16E1x5Yn_4mX6P5P8rKi56pNGjJo5IzPhc,2579
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 multipers/simplex_tree_multi.pxd,sha256=KBX_vcNgtBjNHThUUOXp0r4HWj3EX1DGa6cX9mDi6aI,6649
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 multipers/tensor.pxd,sha256=MSmaMU0sOP9CHLmg4dym7nOGaI1S4cOdM01TQ9flI54,417
 multipers/test.pyx,sha256=-g7WU-jKrZK8H0c-6eAPsfrApjvTKrUoswVYFu8LoV4,1798
 multipers/array_api/__init__.py,sha256=jyvi7Gzd7Si_imgaodz80fcA-68MikAGk8g79_vj6yo,1545
-multipers/array_api/numpy.py,sha256=5XfqM4_ykFtCsn0Rel0qPceEXyzhu-6ekkbsM_94kM8,2439
-multipers/array_api/torch.py,sha256=cTtwOhZXT-UWYnQJe3rVPcs0f0jm6saxdMmWEmr9I5Q,2553
+multipers/array_api/numpy.py,sha256=0Ln_jY891Jei_HQlWY9S_1-lLPYYOzXRyZknPO5ZYTc,2518
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 multipers/data/MOL2.py,sha256=nLZHy2OSFN9Z2uJKsbqWOEG2R7G-uH6dCLHG48UjvR4,15428
 multipers/data/UCR.py,sha256=PuT8l3i26y0goBzIESwdgJAe6YFCyDiWSoxECcP5rhs,798
 multipers/data/__init__.py,sha256=w7uUe4LOHbdbKU4R8MNs7em65wZJN0v5ukoG1otFanQ,24
@@ -51,7 +51,7 @@ multipers/data/shape3d.py,sha256=AE-vvjKrhKxOwMo-lurUsFqqLjIg5obo-RTbRZF_5Mk,389
 multipers/data/synthetic.py,sha256=RvLWIBE5j99kJSt-D7cnPGI3c7skD4p8_qofJbMIXM0,3078
 multipers/filtrations/__init__.py,sha256=Lg0EHe2cxT32UQAg0kr_Vpua-xPBZxGol8VIfz8UwWk,319
 multipers/filtrations/density.py,sha256=XNPHCwyC8FwAdSfNp1ofxcxfP5ZFGZ6K-DUeXsfM4eg,18155
-multipers/filtrations/filtrations.py,sha256=O2WK3KBmClYvQH4Hr-9rsq3RJqcPjP8Q3Sjsi7Un6jU,13378
+multipers/filtrations/filtrations.py,sha256=5d-i6JfxM5_WzteVkBHtTelZvD1lsL9hsHBYvbeY8FM,13454
 multipers/gudhi/Persistence_slices_interface.h,sha256=QnUeCCKi9K8CfqI3W5i3Ra1Jy2Z1IIivr3MIpnBsnYU,6562
 multipers/gudhi/Simplex_tree_interface.h,sha256=kkq8pE3jKGLY1dK7sYpb_uERHaWGurrRXfaw_ygs-mY,10217
 multipers/gudhi/Simplex_tree_multi_interface.h,sha256=7D9EqyO9dgi-VMTf-O8SR2UMQL95q_TL9ApmmN4ggFw,25484
@@ -151,11 +151,11 @@ multipers/ml/sliced_wasserstein.py,sha256=jgq4ND3EWwwJBopqRvfJLsoOptiMHjS3zEAENB
 multipers/ml/tools.py,sha256=DOPcqmvZP2bA7M08GrwccdebwDq1HEwYdhNRGT7eZMI,3453
 multipers/multi_parameter_rank_invariant/diff_helpers.h,sha256=wMCOhAewWd6-lulLND0y8M0MZoru6zn_8J3qfXDjLds,3477
 multipers/multi_parameter_rank_invariant/euler_characteristic.h,sha256=gLzz-VCY2xPW11Fmi1kG_On33h7EHFmW1TdsVWdzovA,3295
-multipers/multi_parameter_rank_invariant/function_rips.h,sha256=aUox99Y4X5kRgQ-nfpDApX2VC5iV0NJMyLBV-C7glo0,13505
+multipers/multi_parameter_rank_invariant/function_rips.h,sha256=Fl-CqyQ3PGKjHWZbFa_aBh6-vmR8RKOFliC--Ho_2yo,13507
 multipers/multi_parameter_rank_invariant/hilbert_function.h,sha256=S_LRkNSU_bjjcPRS1pWpVHWOLMFQIAYa9dbAhwz0W8c,36412
 multipers/multi_parameter_rank_invariant/persistence_slices.h,sha256=oVMsNkn_VB5lQ_2qsKw5ydPoHnMuGbtvrIN_ga7XnGQ,5986
 multipers/multi_parameter_rank_invariant/rank_invariant.h,sha256=-W_ai4I_wkAIodU3Ubgvuc5cD_VLJzB4479EsVSynsM,16371
-multipers/multiparameter_module_approximation/approximation.h,sha256=WoTIj3TsTikKtLb5WzrQ3hNBPdZBbtt0VQ1rwqVIi_c,96821
+multipers/multiparameter_module_approximation/approximation.h,sha256=VbVNRdxvNqrSJKfszPwbYK4Fyxfox8S-rstVRRDdz6s,96988
 multipers/multiparameter_module_approximation/combinatory.h,sha256=Ck-VKQ56wsXCgQvIbpfTnBOweSBRm4rnChLfHf6JWlc,3605
 multipers/multiparameter_module_approximation/debug.h,sha256=yy7miaqw-Lj8u1yMB9HmtJL02abf3K6JlqS6LbkUVfI,2692
 multipers/multiparameter_module_approximation/euler_curves.h,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -178,8 +178,8 @@ multipers/tests/__init__.py,sha256=-7Fj-zFAfBJv18trg0CPglQTmYu_ehySZGqtJzPlN8U,1
 multipers/torch/__init__.py,sha256=OLxIiZ389uCqehpUxBPUI_x1SYu531onc4tiTscAuIw,27
 multipers/torch/diff_grids.py,sha256=2YK-c351tBpj8sfzjf26fbE1l0xlWse7oVVfDHD3zwM,7492
 multipers/torch/rips_density.py,sha256=H-kmSzY8hXhmVn15Oltc71DHs1IUHg5oPRgNyWW8L4Q,11706
-multipers-2.3.4.dist-info/licenses/LICENSE,sha256=UsQRnvlo_9wpQS9DNt52GEraERHwK2GIRwuqr2Yv5JI,1071
-multipers-2.3.4.dist-info/METADATA,sha256=yKi_0X_lBr3ivsS1mxPrZzR-lpR3myBPemRiMBAadOg,9823
-multipers-2.3.4.dist-info/WHEEL,sha256=JLOMsP7F5qtkAkINx5UnzbFguf8CqZeraV8o04b0I8I,101
-multipers-2.3.4.dist-info/top_level.txt,sha256=L9e0AGmhRzrNw9FpuUx-zlqi5NcBOmrI9wYY8kYWr8A,10
-multipers-2.3.4.dist-info/RECORD,,
+multipers-2.3.5b2.dist-info/licenses/LICENSE,sha256=UsQRnvlo_9wpQS9DNt52GEraERHwK2GIRwuqr2Yv5JI,1071
+multipers-2.3.5b2.dist-info/METADATA,sha256=KHctITvlAapkwilssVT9VkgDMeuatKEzPNZOU62f5Ik,9825
+multipers-2.3.5b2.dist-info/WHEEL,sha256=JLOMsP7F5qtkAkINx5UnzbFguf8CqZeraV8o04b0I8I,101
+multipers-2.3.5b2.dist-info/top_level.txt,sha256=L9e0AGmhRzrNw9FpuUx-zlqi5NcBOmrI9wYY8kYWr8A,10
+multipers-2.3.5b2.dist-info/RECORD,,