multipers 2.2.3__cp311-cp311-win_amd64.whl → 2.3.0__cp311-cp311-win_amd64.whl

multipers/function_rips.pyx

@@ -1,105 +1,105 @@
-# cimport multipers.tensor as mt
-from libc.stdint cimport intptr_t, uint16_t, uint32_t, int32_t
-from libcpp.vector cimport vector
-from libcpp cimport bool, int, float
-from libcpp.utility cimport pair, tuple
-from typing import Optional,Iterable,Callable
-
-import numpy as np
-cimport numpy as cnp
-cnp.import_array()
-
-ctypedef double value_type 
-python_value_type=np.float64
-
-ctypedef int32_t indices_type # uint fails for some reason
-python_indices_type=np.int32
-
-ctypedef int32_t tensor_dtype
-python_tensor_dtype = np.int32
-
-ctypedef pair[vector[vector[indices_type]], vector[tensor_dtype]] signed_measure_type
-
-
-from multipers.simplex_tree_multi import SimplexTreeMulti_Ff64
-from gudhi.simplex_tree import SimplexTree
-
-cdef extern from "multi_parameter_rank_invariant/function_rips.h" namespace "Gudhi::multiparameter::function_rips":
-	void compute_function_rips_surface_python(const intptr_t, tensor_dtype* , const vector[indices_type], indices_type,indices_type, bool, bool, indices_type) except + nogil
-	signed_measure_type compute_function_rips_signed_measure_python(const intptr_t, tensor_dtype* , const vector[indices_type], indices_type,indices_type, bool, bool, indices_type) except + nogil
-	pair[vector[value_type],int] get_degree_rips_st_python(const intptr_t,const intptr_t, const vector[int]) except + nogil
-
-
-import multipers.grids as mpg
-
-
-
-def get_degree_rips(st, vector[int] degrees, grid_strategy="exact", resolution=0):
-	assert isinstance(st,SimplexTree), "Input has to be a Gudhi simplextree for now."
-	assert st.dimension() == 1, "Simplextree has to be of dimension 1. You can use the `prune_above_dimension` method."
-	degree_rips_st = SimplexTreeMulti_Ff64(num_parameters=degrees.size())
-	cdef intptr_t simplextree_ptr = st.thisptr
-	cdef intptr_t st_multi_ptr = degree_rips_st.thisptr
-	cdef pair[vector[value_type],int] out
-	with nogil:
-		out = get_degree_rips_st_python(simplextree_ptr, st_multi_ptr, degrees)
-	filtrations = np.asarray(out.first)
-	cdef int max_degree = out.second
-	cdef bool inf_flag = filtrations[-1] == np.inf
-	if inf_flag:
-		filtrations = filtrations[:-1]
-	filtrations, = mpg.compute_grid([filtrations],strategy=grid_strategy,resolution=resolution)
-	if inf_flag:
-		filtrations = np.concatenate([filtrations, [np.inf]])
-	degree_rips_st.grid_squeeze([filtrations]*degree_rips_st.num_parameters, inplace=True, coordinate_values=True)
-	degree_rips_st.filtration_grid = [filtrations, np.asarray(degrees)[::-1]]
-	degree_rips_st._is_function_simplextree=True
-	return degree_rips_st,max_degree
-
-def function_rips_surface(st_multi, vector[indices_type] homological_degrees, bool mobius_inversion=True, bool zero_pad=False, indices_type n_jobs=0):
-	assert st_multi.is_squeezed, "Squeeze first !"
-	cdef intptr_t st_multi_ptr = st_multi.thisptr
-	cdef indices_type I = len(st_multi.filtration_grid[0])
-	cdef indices_type J = st_multi.num_parameters
-	container_shape = (homological_degrees.size(),I,J)
-	container_array = np.ascontiguousarray(np.zeros(container_shape, dtype=python_tensor_dtype).flatten())
-	assert len(container_array) < np.iinfo(np.uint32).max, "Too large container. Raise an issue on github if you encounter this issue. (Due to tensor's operator[])"
-	cdef tensor_dtype[::1] container = container_array
-	cdef tensor_dtype* container_ptr = &container[0]
-	with nogil:
-		compute_function_rips_surface_python(st_multi_ptr,container_ptr, homological_degrees, I,J, mobius_inversion, zero_pad, n_jobs)
-	filtration_grid = st_multi.filtration_grid
-	if filtration_grid[0][-1] == np.inf:
-		filtration_grid[0][-1] = filtration_grid[0][-2]
-	return filtration_grid, container_array.reshape(container_shape)
-
-
-
-def function_rips_signed_measure(st_multi, vector[indices_type] homological_degrees, bool mobius_inversion=True, bool zero_pad=False, indices_type n_jobs=0, bool reconvert = True):
-	assert st_multi.is_squeezed
-	cdef intptr_t st_multi_ptr = st_multi.thisptr
-	cdef indices_type I = len(st_multi.filtration_grid[0])
-	cdef indices_type J = st_multi.num_parameters
-	container_shape = (homological_degrees.size(),I,J)
-	container_array = np.ascontiguousarray(np.zeros(container_shape, dtype=python_tensor_dtype).flatten())
-	assert len(container_array) < np.iinfo(np.uint32).max, "Too large container. Raise an issue on github if you encounter this issue. (Due to tensor's operator[])"
-	cdef tensor_dtype[::1] container = container_array
-	cdef tensor_dtype* container_ptr = &container[0]
-	cdef signed_measure_type out 
-	# TODO nogil
-	with nogil:
-		out = compute_function_rips_signed_measure_python(st_multi_ptr,container_ptr, homological_degrees, I,J, mobius_inversion, zero_pad, n_jobs)
-	pts, weights = np.asarray(out.first, dtype=int).reshape(-1, 3), np.asarray(out.second, dtype=int)
-
-	degree_indices = [np.argwhere(pts[:,0] == degree_index).flatten() for degree_index, degree in enumerate(homological_degrees)] ## TODO : maybe optimize
-	sms = [(pts[id,1:],weights[id]) for id in degree_indices]
-	if not reconvert: return sms
-
-	grid_conversion = st_multi.filtration_grid
-	for degree_index,(pts,weights) in enumerate(sms):
-		coords = np.empty(shape=pts.shape, dtype=float)
-		for i in range(coords.shape[1]):
-			coords[:,i] = np.asarray(grid_conversion[i])[pts[:,i]]
-		sms[degree_index]=(coords, weights)
-	
-	return sms
+# cimport multipers.tensor as mt
+from libc.stdint cimport intptr_t, uint16_t, uint32_t, int32_t
+from libcpp.vector cimport vector
+from libcpp cimport bool, int, float
+from libcpp.utility cimport pair, tuple
+from typing import Optional,Iterable,Callable
+
+import numpy as np
+cimport numpy as cnp
+cnp.import_array()
+
+ctypedef double value_type 
+python_value_type=np.float64
+
+ctypedef int32_t indices_type # uint fails for some reason
+python_indices_type=np.int32
+
+ctypedef int32_t tensor_dtype
+python_tensor_dtype = np.int32
+
+ctypedef pair[vector[vector[indices_type]], vector[tensor_dtype]] signed_measure_type
+
+
+from multipers.simplex_tree_multi import SimplexTreeMulti_Ff64
+from gudhi.simplex_tree import SimplexTree
+
+cdef extern from "multi_parameter_rank_invariant/function_rips.h" namespace "Gudhi::multiparameter::function_rips":
+	void compute_function_rips_surface_python(const intptr_t, tensor_dtype* , const vector[indices_type], indices_type,indices_type, bool, bool, indices_type) except + nogil
+	signed_measure_type compute_function_rips_signed_measure_python(const intptr_t, tensor_dtype* , const vector[indices_type], indices_type,indices_type, bool, bool, indices_type) except + nogil
+	pair[vector[value_type],int] get_degree_rips_st_python(const intptr_t,const intptr_t, const vector[int]) except + nogil
+
+
+import multipers.grids as mpg
+
+
+
+def get_degree_rips(st, vector[int] degrees, grid_strategy="exact", resolution=0):
+	assert isinstance(st,SimplexTree), "Input has to be a Gudhi simplextree for now."
+	assert st.dimension() == 1, "Simplextree has to be of dimension 1. You can use the `prune_above_dimension` method."
+	degree_rips_st = SimplexTreeMulti_Ff64(num_parameters=degrees.size())
+	cdef intptr_t simplextree_ptr = st.thisptr
+	cdef intptr_t st_multi_ptr = degree_rips_st.thisptr
+	cdef pair[vector[value_type],int] out
+	with nogil:
+		out = get_degree_rips_st_python(simplextree_ptr, st_multi_ptr, degrees)
+	filtrations = np.asarray(out.first)
+	cdef int max_degree = out.second
+	cdef bool inf_flag = filtrations[-1] == np.inf
+	if inf_flag:
+		filtrations = filtrations[:-1]
+	filtrations, = mpg.compute_grid([filtrations],strategy=grid_strategy,resolution=resolution)
+	if inf_flag:
+		filtrations = np.concatenate([filtrations, [np.inf]])
+	degree_rips_st.grid_squeeze([filtrations]*degree_rips_st.num_parameters, inplace=True, coordinate_values=True)
+	degree_rips_st.filtration_grid = [filtrations, np.asarray(degrees)[::-1]]
+	degree_rips_st._is_function_simplextree=True
+	return degree_rips_st,max_degree
+
+def function_rips_surface(st_multi, vector[indices_type] homological_degrees, bool mobius_inversion=True, bool zero_pad=False, indices_type n_jobs=0):
+	assert st_multi.is_squeezed, "Squeeze first !"
+	cdef intptr_t st_multi_ptr = st_multi.thisptr
+	cdef indices_type I = len(st_multi.filtration_grid[0])
+	cdef indices_type J = st_multi.num_parameters
+	container_shape = (homological_degrees.size(),I,J)
+	container_array = np.ascontiguousarray(np.zeros(container_shape, dtype=python_tensor_dtype).flatten())
+	assert len(container_array) < np.iinfo(np.uint32).max, "Too large container. Raise an issue on github if you encounter this issue. (Due to tensor's operator[])"
+	cdef tensor_dtype[::1] container = container_array
+	cdef tensor_dtype* container_ptr = &container[0]
+	with nogil:
+		compute_function_rips_surface_python(st_multi_ptr,container_ptr, homological_degrees, I,J, mobius_inversion, zero_pad, n_jobs)
+	filtration_grid = st_multi.filtration_grid
+	if filtration_grid[0][-1] == np.inf:
+		filtration_grid[0][-1] = filtration_grid[0][-2]
+	return filtration_grid, container_array.reshape(container_shape)
+
+
+
+def function_rips_signed_measure(st_multi, vector[indices_type] homological_degrees, bool mobius_inversion=True, bool zero_pad=False, indices_type n_jobs=0, bool reconvert = True):
+	assert st_multi.is_squeezed
+	cdef intptr_t st_multi_ptr = st_multi.thisptr
+	cdef indices_type I = len(st_multi.filtration_grid[0])
+	cdef indices_type J = st_multi.num_parameters
+	container_shape = (homological_degrees.size(),I,J)
+	container_array = np.ascontiguousarray(np.zeros(container_shape, dtype=python_tensor_dtype).flatten())
+	assert len(container_array) < np.iinfo(np.uint32).max, "Too large container. Raise an issue on github if you encounter this issue. (Due to tensor's operator[])"
+	cdef tensor_dtype[::1] container = container_array
+	cdef tensor_dtype* container_ptr = &container[0]
+	cdef signed_measure_type out 
+	# TODO nogil
+	with nogil:
+		out = compute_function_rips_signed_measure_python(st_multi_ptr,container_ptr, homological_degrees, I,J, mobius_inversion, zero_pad, n_jobs)
+	pts, weights = np.asarray(out.first, dtype=int).reshape(-1, 3), np.asarray(out.second, dtype=int)
+
+	degree_indices = [np.argwhere(pts[:,0] == degree_index).flatten() for degree_index, degree in enumerate(homological_degrees)] ## TODO : maybe optimize
+	sms = [(pts[id,1:],weights[id]) for id in degree_indices]
+	if not reconvert: return sms
+
+	grid_conversion = st_multi.filtration_grid
+	for degree_index,(pts,weights) in enumerate(sms):
+		coords = np.empty(shape=pts.shape, dtype=float)
+		for i in range(coords.shape[1]):
+			coords[:,i] = np.asarray(grid_conversion[i])[pts[:,i]]
+		sms[degree_index]=(coords, weights)
+	
+	return sms