multipers 2.3.5b4__tar.gz → 2.4.0__tar.gz

{multipers-2.3.5b4 → multipers-2.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: multipers
-Version: 2.3.5b4
+Version: 2.4.0
 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>
@@ -9,11 +9,13 @@ Project-URL: source, https://github.com/DavidLapous/multipers
 Project-URL: download, https://pypi.org/project/multipers/#files
 Project-URL: tracker, https://github.com/DavidLapous/multipers/issues
 Project-URL: release notes, https://github.com/DavidLapous/multipers/releases
-Keywords: TDA,Persistence,Multiparameter,sklearn
+Keywords: TDA,Persistence,Multiparameter,sklearn,autodiff
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
 Classifier: Topic :: Scientific/Engineering :: Mathematics
@@ -84,9 +86,9 @@ This library features a bunch of different functions and helpers. See below for
  - [x] [[Differentiability and Optimization of Multiparameter Persistent Homology, ICML2024]](https://proceedings.mlr.press/v235/scoccola24a.html) An approach to compute a (clarke) gradient for any reasonable multiparameter persistent invariant. Currently, any `multipers` computation is auto-differentiable using this strategy, provided that the input are pytorch gradient capable tensor.
  - [x] [[Multiparameter Persistence Landscapes, JMLR]](https://jmlr.org/papers/v21/19-054.html) A vectorization technic for multiparameter persistence modules.
  - [x] [[Filtration-Domination in Bifiltered Graphs, ALENEX2023]](https://doi.org/10.1137/1.9781611977561.ch3) Allows for 2-parameter edge collapses for 1-critical clique complexes. Very useful to speed up, e.g., Rips-Codensity bifiltrations.
- - [x] [[Chunk Reduction for Multi-Parameter Persistent Homology, SOCG2019]](https://doi.org/10.4230/LIPIcs.SoCG.2019.37) Multi-filtration preprocessing algorithm for homology computations.
+ - [x] [[Chunk Reduction for Multi-Parameter Persistent Homology, SoCG2019]](https://doi.org/10.4230/LIPIcs.SoCG.2019.37) Multi-filtration preprocessing algorithm for homology computations.
  - [x] [[Computing Minimal Presentations and Bigraded Betti Numbers of 2-Parameter Persistent Homology, JAAG]](https://doi.org/10.1137/20M1388425) Minimal presentation of multiparameter persistence modules, using [mpfree](https://bitbucket.org/mkerber/mpfree/src/master/). Hilbert, Rank Decomposition Signed Measures, and MMA decompositions can be computed using the mpfree backend.
- - [ ] [WIP] [[Decomposing Multiparameter Persistence Modules]](https://doi.org/10.4230/LIPIcs.SoCG.2025.41) Using the [AIDA](https://github.com/JanJend/AIDA) and [Persistence-Algebra](https://github.com/JanJend/Persistence-Algebra/) libraries.
+ - [ ] [WIP] [[Decomposing Multiparameter Persistence Modules, SoCG2025]](https://doi.org/10.4230/LIPIcs.SoCG.2025.41) Using the [AIDA](https://github.com/JanJend/AIDA) and [Persistence-Algebra](https://github.com/JanJend/Persistence-Algebra/) libraries.
  - [x] [[Delaunay Bifiltrations of Functions on Point Clouds, SODA2024]](https://epubs.siam.org/doi/10.1137/1.9781611977912.173) Provides an alternative to function rips bifiltrations, using Delaunay complexes. Very good alternative to Rips-Density like bifiltrations.
  - [x] [[Delaunay Core Bifiltration]](https://arxiv.org/abs/2405.01214) Bifiltration for point clouds, taking into account the density. Similar to Rips-Density. 
  - [x] [[Rivet]](https://github.com/rivetTDA/rivet) Interactive two parameter persistence
@@ -127,4 +129,3 @@ you can use the following journal bibtex entry
 ## Contributions
 Feel free to contribute, report a bug on a pipeline, or ask for documentation by opening an issue.<br>
 In particular, if you have a nice example or application that is not taken care in the documentation (see the `./docs/notebooks/` folder), please contact me to add it there.
-

{multipers-2.3.5b4 → multipers-2.4.0}/README.md

@@ -48,9 +48,9 @@ This library features a bunch of different functions and helpers. See below for
  - [x] [[Differentiability and Optimization of Multiparameter Persistent Homology, ICML2024]](https://proceedings.mlr.press/v235/scoccola24a.html) An approach to compute a (clarke) gradient for any reasonable multiparameter persistent invariant. Currently, any `multipers` computation is auto-differentiable using this strategy, provided that the input are pytorch gradient capable tensor.
  - [x] [[Multiparameter Persistence Landscapes, JMLR]](https://jmlr.org/papers/v21/19-054.html) A vectorization technic for multiparameter persistence modules.
  - [x] [[Filtration-Domination in Bifiltered Graphs, ALENEX2023]](https://doi.org/10.1137/1.9781611977561.ch3) Allows for 2-parameter edge collapses for 1-critical clique complexes. Very useful to speed up, e.g., Rips-Codensity bifiltrations.
- - [x] [[Chunk Reduction for Multi-Parameter Persistent Homology, SOCG2019]](https://doi.org/10.4230/LIPIcs.SoCG.2019.37) Multi-filtration preprocessing algorithm for homology computations.
+ - [x] [[Chunk Reduction for Multi-Parameter Persistent Homology, SoCG2019]](https://doi.org/10.4230/LIPIcs.SoCG.2019.37) Multi-filtration preprocessing algorithm for homology computations.
  - [x] [[Computing Minimal Presentations and Bigraded Betti Numbers of 2-Parameter Persistent Homology, JAAG]](https://doi.org/10.1137/20M1388425) Minimal presentation of multiparameter persistence modules, using [mpfree](https://bitbucket.org/mkerber/mpfree/src/master/). Hilbert, Rank Decomposition Signed Measures, and MMA decompositions can be computed using the mpfree backend.
- - [ ] [WIP] [[Decomposing Multiparameter Persistence Modules]](https://doi.org/10.4230/LIPIcs.SoCG.2025.41) Using the [AIDA](https://github.com/JanJend/AIDA) and [Persistence-Algebra](https://github.com/JanJend/Persistence-Algebra/) libraries.
+ - [ ] [WIP] [[Decomposing Multiparameter Persistence Modules, SoCG2025]](https://doi.org/10.4230/LIPIcs.SoCG.2025.41) Using the [AIDA](https://github.com/JanJend/AIDA) and [Persistence-Algebra](https://github.com/JanJend/Persistence-Algebra/) libraries.
  - [x] [[Delaunay Bifiltrations of Functions on Point Clouds, SODA2024]](https://epubs.siam.org/doi/10.1137/1.9781611977912.173) Provides an alternative to function rips bifiltrations, using Delaunay complexes. Very good alternative to Rips-Density like bifiltrations.
  - [x] [[Delaunay Core Bifiltration]](https://arxiv.org/abs/2405.01214) Bifiltration for point clouds, taking into account the density. Similar to Rips-Density. 
  - [x] [[Rivet]](https://github.com/rivetTDA/rivet) Interactive two parameter persistence
@@ -91,4 +91,3 @@ you can use the following journal bibtex entry
 ## Contributions
 Feel free to contribute, report a bug on a pipeline, or ask for documentation by opening an issue.<br>
 In particular, if you have a nice example or application that is not taken care in the documentation (see the `./docs/notebooks/` folder), please contact me to add it there.
-

{multipers-2.3.5b4 → multipers-2.4.0}/_tempita_grid_gen.py

@@ -14,7 +14,7 @@ columns_name = [  # only one column is necessary
         # "HEAP",
         # "UNORDERED_SET",
         # "NAIVE_VECTOR",
-        # "VECTOR",
+        "VECTOR",
         # "INTRUSIVE_LIST",
         # "LIST",
         # "SMALL_VECTOR",
@@ -24,8 +24,8 @@ columns_name = [  # only one column is necessary
 ## Value types : CTYPE, PYTHON_TYPE, short
 value_types = [
     ("int32_t", "np.int32", "i32"),  # necessary
-    # ("int64_t", "np.int64",   "i64"),
-    # ("float",   "np.float32", "f32"),
+    ("int64_t", "np.int64",   "i64"),
+    ("float",   "np.float32", "f32"),
     ("double", "np.float64", "f64"),  # necessary
 ]
 COARSENNED_VALUE_TYPE = ("int32_t", "np.int32", "i32")
@@ -52,7 +52,7 @@ matrix_types = [
     "Matrix",  # necessary
     # "Graph",
     # "Clement",
-    # "GudhiCohomology",
+    "GudhiCohomology",
 ]
 
 filtration_containers = [

{multipers-2.3.5b4 → multipers-2.4.0}/multipers/__init__.py

@@ -1,4 +1,5 @@
 from importlib.metadata import version as _version
+import sys
 
 __version__ = _version("multipers")
 # Doc
@@ -11,12 +12,16 @@ from multipers import (
     simplex_tree_multi,
     slicer,
 )
-from multipers._signed_measure_meta import signed_measure
+
+if sys.platform != "win32":
+    from multipers import ops
+
 
 # Shortcuts
 from multipers._slicer_meta import Slicer
 from multipers.multiparameter_module_approximation import module_approximation
 from multipers.simplex_tree_multi import SimplexTreeMulti
+from multipers._signed_measure_meta import signed_measure
 
 __all__ = [
     "data",
@@ -31,3 +36,6 @@ __all__ = [
     "module_approximation",
     "SimplexTreeMulti",
 ]
+
+if sys.platform != "win32":
+    __all__.append("ops")

{multipers-2.3.5b4 → multipers-2.4.0}/multipers/_slicer_meta.py

@@ -120,6 +120,7 @@ def Slicer(
     filtration_container: Optional[str] = None,
     max_dim: Optional[int] = None,
     return_type_only: bool = False,
+    _shift_dimension: int = 0,
 ) -> mps.Slicer_type:
     """
     Given a simplextree or blocks (a.k.a scc for python),
@@ -144,6 +145,13 @@ def Slicer(
     ------
     The corresponding slicer.
     """
+    if reduce:
+        from warnings import warn
+
+        warn(
+            "Deprecated argument `reduce`. just reduce it afterwards.",
+            DeprecationWarning,
+        )
     if max_dim is not None:
         raise DeprecationWarning("deprecated parameter.")
     if is_slicer(st, allow_minpres=False) or is_simplextree_multi(st):
@@ -180,22 +188,22 @@ def Slicer(
     )
     if return_type_only:
         return _Slicer
+
     if st is None:
         return _Slicer()
     elif mps.is_slicer(st):
-        # max_dim_idx = (
-        #     None
-        #     if max_dim is None
-        #     else np.searchsorted(st.get_dimensions(), max_dim + 1)
-        # )
         slicer = _Slicer(st)
-        # if st.is_squeezed:
-        #     slicer.filtration_grid = st.filtration_grid
-        # slicer.minpres_degree = st.minpres_degree
     elif is_simplextree_multi(st) and backend == "Graph":
         slicer = _slicer_from_simplextree(st, backend, vineyard)
         if st.is_squeezed:
             slicer.filtration_grid = st.filtration_grid
+
+    elif isinstance(st, str):
+        slicer = _Slicer()._build_from_scc_file(st, shift_dimension=_shift_dimension)
+    elif is_simplextree_multi(st):
+        slicer = _Slicer().build_from_simplex_tree(st)
+        if st.is_squeezed:
+            slicer.filtration_grid = st.filtration_grid
     elif backend == "Graph":
         raise ValueError(
             """
@@ -203,29 +211,16 @@ Graph is simplicial, incompatible with minpres.
 You can try using `multipers.slicer.to_simplextree`."""
         )
     else:
-        filtration_grid = None
-        # if max_dim is not None:  # no test for simplex tree?
-        #     st.prune_above_dimension(max_dim)
-        if isinstance(st, str):  # is_kcritical should be false
-            slicer = _Slicer()._build_from_scc_file(st)
-        else:
-            if is_simplextree_multi(st):
-                slicer = _Slicer().build_from_simplex_tree(st)
-                if st.is_squeezed:
-                    filtration_grid = st.filtration_grid
-            else:
-                blocks = st
-                slicer = _slicer_from_blocks(
-                    blocks,
-                    backend,
-                    vineyard,
-                    is_kcritical,
-                    dtype,
-                    column_type,
-                    filtration_container,
-                )
-        if filtration_grid is not None:
-            slicer.filtration_grid = filtration_grid
+        blocks = st
+        slicer = _slicer_from_blocks(
+            blocks,
+            backend,
+            vineyard,
+            is_kcritical,
+            dtype,
+            column_type,
+            filtration_container,
+        )
     if reduce:
         slicer = mps.minimal_presentation(
             slicer,

{multipers-2.3.5b4 → multipers-2.4.0}/multipers/filtration_conversions.pxd

@@ -516,6 +516,158 @@ cdef inline vector[Flat_i32] python_2_vect_Flat_i32(int32_t[:,:] filtrations) no
           f[j] = filtrations[i,j]
         out.emplace_back(f)
     return out
+cdef inline KFlat_i64_2_python(KFlat_i64* x, bool copy=False, bool raw=False):
+  cdef Py_ssize_t k = dereference(x).num_generators()
+
+
+  cdef int num_parameters = 2
+
+  cdef int64_t[:] data_view = <int64_t[:k]>(&(dereference(x)(0,0)))
+  numpy_view = np.asarray(data_view, dtype=np.int64)
+  if raw:
+    return numpy_view
+  return np.concatenate([numpy_view[:,None], np.arange(k, dtype=np.int64)[:,None]], axis=1)
+
+
+cdef inline  vect_KFlat_i64_2_python(vector[KFlat_i64]& x, bool copy = False, bool raw=False):
+  cdef Py_ssize_t num_stuff = x.size()
+  return [KFlat_i64_2_python(&(x[i]), copy=copy, raw=raw) for i in range(num_stuff)]
+
+cdef inline KFlat_i64 python_2_KFlat_i64(int64_t[:,:] filtrations) noexcept nogil:
+    cdef vector[double] f = vector[double](filtrations.shape[0] * filtrations.shape[1])
+    cdef int k = 0;
+    for i in range(filtrations.shape[0]):
+        for j in range(filtrations.shape[1]):
+            f[k] = filtrations[i,j]
+            k = k + 1
+    cdef KFlat_i64 out = KFlat_i64(f.begin(), f.end(), filtrations.shape[1])
+    out.simplify()
+    return out
+
+cdef inline vector[KFlat_i64] python_2_vect_KFlat_i64(int64_t[:,:] filtrations) noexcept nogil:
+    # cdef double[:,:] filtrations = np.asarray(filtrations_, dtype=np.float64)
+    cdef vector[KFlat_i64] out
+    cdef vector[int64_t] f = vector[int64_t](filtrations.shape[1])
+    out.reserve(filtrations.shape[0])
+    for i in range(filtrations.shape[0]):
+        for j in range(filtrations.shape[1]):
+          f[j] = filtrations[i,j]
+        out.emplace_back(f)
+    return out
+cdef inline Flat_i64_2_python(Flat_i64* x, bool copy=False, bool raw=False):
+  cdef Py_ssize_t k = dereference(x).num_generators()
+
+
+  cdef int num_parameters = 2
+
+  cdef int64_t[:] data_view = <int64_t[:k]>(&(dereference(x)(0,0)))
+  numpy_view = np.asarray(data_view, dtype=np.int64)
+  if raw:
+    return numpy_view
+  return np.concatenate([numpy_view[:,None], np.arange(k, dtype=np.int64)[:,None]], axis=1)
+
+
+cdef inline  vect_Flat_i64_2_python(vector[Flat_i64]& x, bool copy = False, bool raw=False):
+  cdef Py_ssize_t num_stuff = x.size()
+  return [Flat_i64_2_python(&(x[i]), copy=copy, raw=raw) for i in range(num_stuff)]
+
+
+
+cdef inline Flat_i64 python_2_Flat_i64(int64_t[:] filtration) noexcept nogil:
+  cdef int num_parameters = filtration.shape[0]
+  cdef Flat_i64 out = Flat_i64(num_parameters) 
+  cdef int64_t* x
+  for i in range(num_parameters):
+    x = &out(0,i)
+    x[0] = filtration[i]
+  return out
+
+cdef inline vector[Flat_i64] python_2_vect_Flat_i64(int64_t[:,:] filtrations) noexcept nogil:
+    # cdef double[:,:] filtrations = np.asarray(filtrations_, dtype=np.float64)
+    cdef vector[Flat_i64] out
+    cdef vector[int64_t] f = vector[int64_t](filtrations.shape[1])
+    out.reserve(filtrations.shape[0])
+    for i in range(filtrations.shape[0]):
+        for j in range(filtrations.shape[1]):
+          f[j] = filtrations[i,j]
+        out.emplace_back(f)
+    return out
+cdef inline KFlat_f32_2_python(KFlat_f32* x, bool copy=False, bool raw=False):
+  cdef Py_ssize_t k = dereference(x).num_generators()
+
+
+  cdef int num_parameters = 2
+
+  cdef float[:] data_view = <float[:k]>(&(dereference(x)(0,0)))
+  numpy_view = np.asarray(data_view, dtype=np.float32)
+  if raw:
+    return numpy_view
+  return np.concatenate([numpy_view[:,None], np.arange(k, dtype=np.float32)[:,None]], axis=1)
+
+
+cdef inline  vect_KFlat_f32_2_python(vector[KFlat_f32]& x, bool copy = False, bool raw=False):
+  cdef Py_ssize_t num_stuff = x.size()
+  return [KFlat_f32_2_python(&(x[i]), copy=copy, raw=raw) for i in range(num_stuff)]
+
+cdef inline KFlat_f32 python_2_KFlat_f32(float[:,:] filtrations) noexcept nogil:
+    cdef vector[double] f = vector[double](filtrations.shape[0] * filtrations.shape[1])
+    cdef int k = 0;
+    for i in range(filtrations.shape[0]):
+        for j in range(filtrations.shape[1]):
+            f[k] = filtrations[i,j]
+            k = k + 1
+    cdef KFlat_f32 out = KFlat_f32(f.begin(), f.end(), filtrations.shape[1])
+    out.simplify()
+    return out
+
+cdef inline vector[KFlat_f32] python_2_vect_KFlat_f32(float[:,:] filtrations) noexcept nogil:
+    # cdef double[:,:] filtrations = np.asarray(filtrations_, dtype=np.float64)
+    cdef vector[KFlat_f32] out
+    cdef vector[float] f = vector[float](filtrations.shape[1])
+    out.reserve(filtrations.shape[0])
+    for i in range(filtrations.shape[0]):
+        for j in range(filtrations.shape[1]):
+          f[j] = filtrations[i,j]
+        out.emplace_back(f)
+    return out
+cdef inline Flat_f32_2_python(Flat_f32* x, bool copy=False, bool raw=False):
+  cdef Py_ssize_t k = dereference(x).num_generators()
+
+
+  cdef int num_parameters = 2
+
+  cdef float[:] data_view = <float[:k]>(&(dereference(x)(0,0)))
+  numpy_view = np.asarray(data_view, dtype=np.float32)
+  if raw:
+    return numpy_view
+  return np.concatenate([numpy_view[:,None], np.arange(k, dtype=np.float32)[:,None]], axis=1)
+
+
+cdef inline  vect_Flat_f32_2_python(vector[Flat_f32]& x, bool copy = False, bool raw=False):
+  cdef Py_ssize_t num_stuff = x.size()
+  return [Flat_f32_2_python(&(x[i]), copy=copy, raw=raw) for i in range(num_stuff)]
+
+
+
+cdef inline Flat_f32 python_2_Flat_f32(float[:] filtration) noexcept nogil:
+  cdef int num_parameters = filtration.shape[0]
+  cdef Flat_f32 out = Flat_f32(num_parameters) 
+  cdef float* x
+  for i in range(num_parameters):
+    x = &out(0,i)
+    x[0] = filtration[i]
+  return out
+
+cdef inline vector[Flat_f32] python_2_vect_Flat_f32(float[:,:] filtrations) noexcept nogil:
+    # cdef double[:,:] filtrations = np.asarray(filtrations_, dtype=np.float64)
+    cdef vector[Flat_f32] out
+    cdef vector[float] f = vector[float](filtrations.shape[1])
+    out.reserve(filtrations.shape[0])
+    for i in range(filtrations.shape[0]):
+        for j in range(filtrations.shape[1]):
+          f[j] = filtrations[i,j]
+        out.emplace_back(f)
+    return out
 cdef inline KFlat_f64_2_python(KFlat_f64* x, bool copy=False, bool raw=False):
   cdef Py_ssize_t k = dereference(x).num_generators()
 
@@ -663,6 +815,148 @@ cdef inline vector[Contiguous_i32] python_2_vect_Contiguous_i32(int32_t[:,:] fil
           f[j] = filtrations[i,j]
         out.emplace_back(f)
     return out
+cdef inline KContiguous_i64_2_python(KContiguous_i64* x, bool copy=False, bool raw=False):
+  cdef Py_ssize_t k = dereference(x).num_generators()
+
+
+  cdef Py_ssize_t p = dereference(x).num_parameters()
+  if dereference(x).is_finite():
+    duplicate = 0
+  else:
+    duplicate = p
+  # TODO  : make it contiguous
+  return [_ff21cview2_i64(&(dereference(x)(i,0)), p, duplicate, copy=copy) for i in range(k)]
+
+
+cdef inline  vect_KContiguous_i64_2_python(vector[KContiguous_i64]& x, bool copy = False, bool raw=False):
+  cdef Py_ssize_t num_stuff = x.size()
+  return [KContiguous_i64_2_python(&(x[i]), copy=copy, raw=raw) for i in range(num_stuff)]
+
+cdef inline KContiguous_i64 python_2_KContiguous_i64(int64_t[:,:] filtrations) noexcept nogil:
+    cdef vector[double] f = vector[double](filtrations.shape[0] * filtrations.shape[1])
+    cdef int k = 0;
+    for i in range(filtrations.shape[0]):
+        for j in range(filtrations.shape[1]):
+            f[k] = filtrations[i,j]
+            k = k + 1
+    cdef KContiguous_i64 out = KContiguous_i64(f.begin(), f.end(), filtrations.shape[1])
+    out.simplify()
+    return out
+
+cdef inline vector[KContiguous_i64] python_2_vect_KContiguous_i64(int64_t[:,:] filtrations) noexcept nogil:
+    # cdef double[:,:] filtrations = np.asarray(filtrations_, dtype=np.float64)
+    cdef vector[KContiguous_i64] out
+    cdef vector[int64_t] f = vector[int64_t](filtrations.shape[1])
+    out.reserve(filtrations.shape[0])
+    for i in range(filtrations.shape[0]):
+        for j in range(filtrations.shape[1]):
+          f[j] = filtrations[i,j]
+        out.emplace_back(f)
+    return out
+# Assumes it's contiguous
+cdef inline Contiguous_i64_2_python(Contiguous_i64* x, bool copy=False, bool raw=False):
+  cdef Py_ssize_t num_parameters = dereference(x).num_parameters()
+  if not dereference(x).is_finite():
+    return np.full(shape=num_parameters, fill_value=dereference(x)(0,0))
+  cdef int64_t[:] x_view = <int64_t[:num_parameters]>(&(dereference(x)(0,0)))
+  return np.array(x_view) if copy else np.asarray(x_view)
+
+cdef inline  vect_Contiguous_i64_2_python(vector[Contiguous_i64]& x, bool copy = False, bool raw=False):
+  cdef Py_ssize_t num_stuff = x.size()
+  return [Contiguous_i64_2_python(&(x[i]), copy=copy, raw=raw) for i in range(num_stuff)]
+
+
+
+cdef inline Contiguous_i64 python_2_Contiguous_i64(int64_t[:] filtration) noexcept nogil:
+  cdef int num_parameters = filtration.shape[0]
+  cdef Contiguous_i64 out = Contiguous_i64(num_parameters) 
+  cdef int64_t* x
+  for i in range(num_parameters):
+    x = &out(0,i)
+    x[0] = filtration[i]
+  return out
+
+cdef inline vector[Contiguous_i64] python_2_vect_Contiguous_i64(int64_t[:,:] filtrations) noexcept nogil:
+    # cdef double[:,:] filtrations = np.asarray(filtrations_, dtype=np.float64)
+    cdef vector[Contiguous_i64] out
+    cdef vector[int64_t] f = vector[int64_t](filtrations.shape[1])
+    out.reserve(filtrations.shape[0])
+    for i in range(filtrations.shape[0]):
+        for j in range(filtrations.shape[1]):
+          f[j] = filtrations[i,j]
+        out.emplace_back(f)
+    return out
+cdef inline KContiguous_f32_2_python(KContiguous_f32* x, bool copy=False, bool raw=False):
+  cdef Py_ssize_t k = dereference(x).num_generators()
+
+
+  cdef Py_ssize_t p = dereference(x).num_parameters()
+  if dereference(x).is_finite():
+    duplicate = 0
+  else:
+    duplicate = p
+  # TODO  : make it contiguous
+  return [_ff21cview2_f32(&(dereference(x)(i,0)), p, duplicate, copy=copy) for i in range(k)]
+
+
+cdef inline  vect_KContiguous_f32_2_python(vector[KContiguous_f32]& x, bool copy = False, bool raw=False):
+  cdef Py_ssize_t num_stuff = x.size()
+  return [KContiguous_f32_2_python(&(x[i]), copy=copy, raw=raw) for i in range(num_stuff)]
+
+cdef inline KContiguous_f32 python_2_KContiguous_f32(float[:,:] filtrations) noexcept nogil:
+    cdef vector[double] f = vector[double](filtrations.shape[0] * filtrations.shape[1])
+    cdef int k = 0;
+    for i in range(filtrations.shape[0]):
+        for j in range(filtrations.shape[1]):
+            f[k] = filtrations[i,j]
+            k = k + 1
+    cdef KContiguous_f32 out = KContiguous_f32(f.begin(), f.end(), filtrations.shape[1])
+    out.simplify()
+    return out
+
+cdef inline vector[KContiguous_f32] python_2_vect_KContiguous_f32(float[:,:] filtrations) noexcept nogil:
+    # cdef double[:,:] filtrations = np.asarray(filtrations_, dtype=np.float64)
+    cdef vector[KContiguous_f32] out
+    cdef vector[float] f = vector[float](filtrations.shape[1])
+    out.reserve(filtrations.shape[0])
+    for i in range(filtrations.shape[0]):
+        for j in range(filtrations.shape[1]):
+          f[j] = filtrations[i,j]
+        out.emplace_back(f)
+    return out
+# Assumes it's contiguous
+cdef inline Contiguous_f32_2_python(Contiguous_f32* x, bool copy=False, bool raw=False):
+  cdef Py_ssize_t num_parameters = dereference(x).num_parameters()
+  if not dereference(x).is_finite():
+    return np.full(shape=num_parameters, fill_value=dereference(x)(0,0))
+  cdef float[:] x_view = <float[:num_parameters]>(&(dereference(x)(0,0)))
+  return np.array(x_view) if copy else np.asarray(x_view)
+
+cdef inline  vect_Contiguous_f32_2_python(vector[Contiguous_f32]& x, bool copy = False, bool raw=False):
+  cdef Py_ssize_t num_stuff = x.size()
+  return [Contiguous_f32_2_python(&(x[i]), copy=copy, raw=raw) for i in range(num_stuff)]
+
+
+
+cdef inline Contiguous_f32 python_2_Contiguous_f32(float[:] filtration) noexcept nogil:
+  cdef int num_parameters = filtration.shape[0]
+  cdef Contiguous_f32 out = Contiguous_f32(num_parameters) 
+  cdef float* x
+  for i in range(num_parameters):
+    x = &out(0,i)
+    x[0] = filtration[i]
+  return out
+
+cdef inline vector[Contiguous_f32] python_2_vect_Contiguous_f32(float[:,:] filtrations) noexcept nogil:
+    # cdef double[:,:] filtrations = np.asarray(filtrations_, dtype=np.float64)
+    cdef vector[Contiguous_f32] out
+    cdef vector[float] f = vector[float](filtrations.shape[1])
+    out.reserve(filtrations.shape[0])
+    for i in range(filtrations.shape[0]):
+        for j in range(filtrations.shape[1]):
+          f[j] = filtrations[i,j]
+        out.emplace_back(f)
+    return out
 cdef inline KContiguous_f64_2_python(KContiguous_f64* x, bool copy=False, bool raw=False):
   cdef Py_ssize_t k = dereference(x).num_generators()
 

{multipers-2.3.5b4 → multipers-2.4.0}/multipers/filtrations/__init__.py

@@ -6,6 +6,7 @@ from .filtrations import (
     DelaunayLowerstar,
     RipsCodensity,
     RipsLowerstar,
+    RhomboidBifiltration,
 )
 
 __all__ = [
@@ -16,4 +17,5 @@ __all__ = [
     "DelaunayLowerstar",
     "RipsCodensity",
     "RipsLowerstar",
+    "RhomboidBifiltration",
 ]