multipers 2.3.3b6__cp313-cp313-macosx_10_13_x86_64.whl

multipers/ml/one.py

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+from sklearn.base import BaseEstimator, TransformerMixin
+import gudhi as gd
+from os.path import exists
+import networkx as nx
+from joblib import Parallel, delayed
+import numpy as np
+from tqdm import tqdm
+from warnings import warn
+from sklearn.neighbors import KernelDensity
+from typing import Iterable
+from gudhi.representations import Landscape
+from gudhi.representations.vector_methods import PersistenceImage
+from gudhi.representations.kernel_methods import SlicedWassersteinDistance
+
+
+from types import FunctionType
+def get_simplextree(x)->gd.SimplexTree:
+	if isinstance(x, gd.SimplexTree):
+		return x
+	if isinstance(x, FunctionType):
+		return x()
+	if len(x) == 3 and isinstance(x[0],FunctionType):
+		f,args, kwargs = x
+		return f(*args,**kwargs)
+	raise TypeError("Not a valid SimplexTree")
+def get_simplextrees(X)->Iterable[gd.SimplexTree]:
+	if len(X) == 2 and isinstance(X[0], FunctionType):
+		f,data = X
+		return (f(x) for x in data)
+	if len(X) == 0: return []
+	if not isinstance(X[0], gd.SimplexTree):
+		raise TypeError
+	return X
+	
+
+
+
+############## INTERVALS (for sliced wasserstein)
+class Graph2SimplexTree(BaseEstimator,TransformerMixin):
+	def __init__(self, f:str="ricciCurvature",dtype=gd.SimplexTree, reverse_filtration:bool=False):
+		super().__init__()
+		self.f=f # filtration to search in graph
+		self.dtype = dtype # If None, will delay the computation in the pipe (for parallelism)
+		self.reverse_filtration = reverse_filtration # reverses the filtration #TODO
+	def fit(self, X, y=None):
+		return self
+	def transform(self,X:list[nx.Graph]):
+		def todo(graph, f=self.f) -> gd.SimplexTree: # TODO : use batch insert
+			st = gd.SimplexTree()
+			for i in graph.nodes:	st.insert([i], graph.nodes[i][f])
+			for u,v in graph.edges:	st.insert([u,v], graph[u][v][f])
+			return st
+		return [todo, X] if self.dtype is None else Parallel(n_jobs=-1, prefer="threads")(delayed(todo)(graph) for graph in X)
+
+
+class PointCloud2SimplexTree(BaseEstimator,TransformerMixin):
+	def __init__(self, delayed:bool = False, threshold = np.inf):
+		super().__init__()
+		self.delayed = delayed
+		self.threshold=threshold
+	@staticmethod
+	def _get_point_cloud_diameter(x):
+		from scipy.spatial import distance_matrix
+		return np.max(distance_matrix(x,x))
+	def fit(self, X, y=None):
+		if self.threshold < 0:
+			self.threshold = max(self._get_point_cloud_diameter(x) for x in X)
+		return self
+	def transform(self,X:list[nx.Graph]):
+		def todo(point_cloud) -> gd.SimplexTree: # TODO : use batch insert
+			st = gd.AlphaComplex(points=point_cloud).create_simplex_tree(max_alpha_square = self.threshold**2)
+			return st
+		return [todo, X] if self.delayed is None else Parallel(n_jobs=-1, prefer="threads")(delayed(todo)(point_cloud) for point_cloud in X)
+
+
+
+#################### FILVEC
+def get_filtration_values(g:nx.Graph, f:str)->np.ndarray:
+	filtrations_values = [
+		g.nodes[node][f] for node in g.nodes
+	]+[
+		g[u][v][f] for u,v in g.edges
+	]
+	return np.array(filtrations_values)
+def graph2filvec(g:nx.Graph, f:str, range:tuple, bins:int)->np.ndarray:
+    fs = get_filtration_values(g, f)
+    return np.histogram(fs, bins=bins,range=range)[0]
+class FilvecGetter(BaseEstimator, TransformerMixin):
+	def __init__(self, f:str="ricciCurvature",quantile:float=0., bins:int=100, n_jobs:int=1):
+		super().__init__()
+		self.f=f
+		self.quantile=quantile
+		self.bins=bins
+		self.range:tuple[float]|None=None
+		self.n_jobs=n_jobs
+	def fit(self, X, y=None):
+		filtration_values = np.concatenate(Parallel(n_jobs=self.n_jobs)(delayed(get_filtration_values)(g,f=self.f) for g in X))
+		self.range= tuple(np.quantile(filtration_values, [self.quantile, 1-self.quantile]))
+		return self
+	def transform(self,X):
+		if self.range == None:
+			print("Fit first")
+			return
+		return Parallel(n_jobs=self.n_jobs)(delayed(graph2filvec)(g,f=self.f, range=self.range, bins=self.bins) for g in X)
+
+
+
+
+############# Filvec from SimplexTree
+# Input list of [list of diagrams], outputs histogram of persitence values (x and y coord mixed) 
+def simplextree2hist(simplextree, range:tuple[float, float], bins:int, density:bool)->np.ndarray: #TODO : Anything to histogram
+	filtration_values = np.array([f for s,f in simplextree.get_simplices()])
+	return np.histogram(filtration_values, bins=bins,range=range, density=density)[0]
+class SimplexTree2Histogram(BaseEstimator, TransformerMixin):
+	def __init__(self, quantile:float=0., bins:int=100, n_jobs:int=1, progress:bool=False, density:bool=True):
+		super().__init__()
+		self.range:np.ndarray | None=None
+		self.quantile:float=quantile
+		self.bins:int=bins
+		self.n_jobs=n_jobs
+		self.density=density
+		self.progress = progress
+		# self.max_dimension=None # TODO: maybe use it
+	def fit(self, X, y=None): # X:list[diagrams]
+		if len(X) == 0:	return self
+		if type(X[0]) is gd.SimplexTree: # If X contains simplextree : nothing to do
+			data = X
+			to_st = lambda x : x
+		else: # otherwise we assume that we retrieve simplextrees using f,data = X; simplextrees = (f(x) for x in data)
+			# assert len(X) == 2
+			to_st, data = X
+		persistence_values = np.array([f for st in data for s,f in to_st(st).get_simplices()])
+		persistence_values = persistence_values[persistence_values<np.inf]
+		self.range = np.quantile(persistence_values, [self.quantile, 1-self.quantile])
+		return self
+	def transform(self,X):
+		if len(X) == 0:	return self
+		if type(X[0]) is gd.SimplexTree: # If X contains simplextree : nothing to do
+			if self.n_jobs > 1:
+				warn("Cannot pickle simplextrees, reducing to 1 thread to compute the simplextrees")
+			return [simplextree2hist(g,range=self.range, bins=self.bins, density=self.density) for g in tqdm(X, desc="Computing diagrams", disable=not self.progress)]
+		else: # otherwise we assume that we retrieve simplextrees using f,data = X; simplextrees = (f(x) for x in data)
+			to_st, data = X # asserts len(X) == 2
+			def pickle_able_todo(x, **kwargs):
+				simplextree = to_st(x)
+				return simplextree2hist(simplextree=simplextree, **kwargs)
+		return Parallel(n_jobs=self.n_jobs)(delayed(pickle_able_todo)(g,range=self.range, bins=self.bins, density=self.density) for g in tqdm(data, desc="Computing simplextrees and their diagrams", disable=not self.progress))
+
+
+
+
+############# PERVEC
+# Input list of [list of diagrams], outputs histogram of persitence values (x and y coord mixed) 
+def dgm2pervec(dgms, range:tuple[float, float], bins:int)->np.ndarray: #TODO : Anything to histogram
+	dgm_union = np.concatenate([dgm.flatten() for dgm in dgms]).flatten()
+	return np.histogram(dgm_union, bins=bins,range=range)[0]
+class Dgm2Histogram(BaseEstimator, TransformerMixin):
+	def __init__(self, quantile:float=0., bins:int=100, n_jobs:int=1):
+		super().__init__()
+		self.range:np.ndarray | None=None
+		self.quantile:float=quantile
+		self.bins:int=bins
+		self.n_jobs=n_jobs
+	def fit(self, X, y=None): # X:list[diagrams]
+		persistence_values = np.concatenate([dgm.flatten() for dgms in X for dgm in dgms], axis=0).flatten()
+		persistence_values = persistence_values[persistence_values<np.inf]
+		self.range = np.quantile(persistence_values, [self.quantile, 1-self.quantile])
+		return self
+	def transform(self,X):
+		return Parallel(n_jobs=self.n_jobs)(delayed(dgm2pervec)(g,range=self.range, bins=self.bins) for g in X)
+
+
+
+
+
+
+
+################# SignedMeasureImage
+class Dgms2SignedMeasureImage(BaseEstimator, TransformerMixin):
+	def __init__(self, ranges:None|Iterable[Iterable[float]]=None, resolution:int=100, quantile:float=0, bandwidth:float=1, kernel:str="gaussian") -> None:
+		super().__init__()
+		self.ranges=ranges
+		self.resolution=resolution
+		self.quantile = quantile
+		self.bandwidth = bandwidth
+		self.kernel = kernel
+	def fit(self, X, y=None): # X:list[diagrams]
+		num_degrees = len(X[0])
+		persistence_values = [np.concatenate([dgms[i].flatten() for dgms in X], axis=0) for i in range(num_degrees)] # values per degree
+		persistence_values = [degrees_values[(-np.inf<degrees_values) * (degrees_values<np.inf)] for degrees_values in persistence_values] # non-trivial values
+		quantiles = [np.quantile(degree_values, [self.quantile, 1-self.quantile]) for degree_values in persistence_values] # quantiles 
+		self.ranges = np.array([np.linspace(start=[a], stop=[b], num=self.resolution) for a,b in quantiles])
+		return self
+
+	def _dgm2smi(self, dgms:Iterable[np.ndarray]):
+		smi = np.concatenate(
+				[
+					KernelDensity(bandwidth=self.bandwidth, kernel=self.kernel).fit(dgm[:,[0]]).score_samples(range)
+					- KernelDensity(bandwidth=self.bandwidth).fit(dgm[:,[1]]).score_samples(range)
+					for dgm, range in zip(dgms, self.ranges)
+				],
+			axis=0)
+		return smi
+		
+	def transform(self,X): # X is a list (data) of list of diagrams
+		assert self.ranges is not None
+		out = Parallel(n_jobs=1, prefer="threads")(
+			delayed(Dgms2SignedMeasureImage._dgm2smi)(self=self, dgms=dgms)
+			for dgms in X
+			)
+
+		return out
+
+
+
+################# SignedMeasureHistogram
+class Dgms2SignedMeasureHistogram(BaseEstimator, TransformerMixin):
+	def __init__(self, ranges:None|list[tuple[float,float]]=None, bins:int=100, quantile:float=0) -> None:
+		super().__init__()
+		self.ranges=ranges
+		self.bins=bins
+		self.quantile = quantile
+	def fit(self, X, y=None): # X:list[diagrams]
+		num_degrees = len(X[0])
+		persistence_values = [np.concatenate([dgms[i].flatten() for dgms in X], axis=0) for i in range(num_degrees)] # values per degree
+		persistence_values = [degrees_values[(-np.inf<degrees_values) * (degrees_values<np.inf)] for degrees_values in persistence_values] # non-trivial values
+		self.ranges = [np.quantile(degree_values, [self.quantile, 1-self.quantile]) for degree_values in persistence_values] # quantiles 
+		return self
+	def transform(self,X): # X is a list (data) of list of diagrams
+		assert self.ranges is not None
+		out = [
+			np.concatenate(
+				[np.histogram(dgm[:,0], bins=self.bins,range=range)[0] - np.histogram(dgm[:,1], bins=self.bins,range=range)[0]
+				for dgm, range in zip(dgms, self.ranges)]
+			)
+		for dgms in X]
+		return out
+
+
+
+
+
+
+
+
+################## Signed Measure Kernel 1D
+# input : list of [list of diagrams], outputs: the kernel to feed to an svm
+
+# TODO : optimize ?
+## TODO : np.triu
+class Dgms2SignedMeasureDistance(BaseEstimator, TransformerMixin):
+	def __init__(self, n_jobs:int=1, distance_matrix_path:str|None=None, progress:bool = False) -> None:
+		super().__init__()
+		self.degrees:list[int]|None=None
+		self.X:None|list[np.ndarray] = None
+		self.n_jobs=n_jobs
+		self.distance_matrix_path = distance_matrix_path
+		self.progress=progress
+	def fit(self, X:list[np.ndarray], y=None):
+		if len(X) <= 0:
+			warn("Fit a nontrivial vector")
+			return
+		self.X = X
+		self.degrees = list(range(len(X[0]))) # Assumes that all x \in X have the same number of diagrams
+		return self
+	
+	@staticmethod
+	def wasserstein_1(a:np.ndarray,b:np.ndarray)->float:
+		return np.abs(np.sort(a) - np.sort(b)).mean() # norm 1
+	@staticmethod
+	def OSWdistance(mu:list[np.ndarray], nu:list[np.ndarray], dim:int)->float:
+		return Dgms2SignedMeasureDistance.wasserstein_1(np.hstack([mu[dim][:,0], nu[dim][:,1]]), np.hstack([nu[dim][:,0], mu[dim][:,1]])) # TODO : check: do we want to sum the kernels or the distances ? add weights ?
+	@staticmethod
+	def _ds(mu:list[np.ndarray], nus:list[list[np.ndarray]], dim:int): # mu and nu are lists of diagrams seen as signed measures (birth = +, death = -)
+		return [Dgms2SignedMeasureDistance.OSWdistance(mu,nu, dim) for nu in nus]
+	
+	def transform(self,X): # X is a list (data) of list of diagrams
+		if self.X is None or self.degrees is None:
+			warn("Fit first !")
+			return np.array([[]])
+		# Cannot use sklearn / scipy, measures don't have the same size, -> no numpy array
+		# from sklearn.metrics import pairwise_distances
+		# distances = pairwise_distances(X, self.X, metric = OSWdistance, n_jobs=self.n_jobs)
+		# from scipy.spatial.distance import cdist
+		# distances = cdist(X, self.X, metric=self.OSWdistance)
+		distances_matrices = []
+		if not self.distance_matrix_path is None:
+			for degree in self.degrees:
+				with tqdm(X, desc=f"Computing distance matrix of degree {degree}") as diagrams_iterator:
+					matrix_path = f"{self.distance_matrix_path}_{degree}"
+					if exists(matrix_path):
+						distance_matrix = np.load(open(matrix_path, "rb"))
+					else:
+						distance_matrix = np.array(Parallel(n_jobs=self.n_jobs)(delayed(self._ds)(mu, self.X, degree) for mu in diagrams_iterator))
+						np.save(open(matrix_path, "wb"), distance_matrix)
+					distances_matrices.append(distance_matrix)
+		else:
+			for degree in self.degrees:
+				with tqdm(X, desc=f"Computing distance matrix of degree {degree}") as diagrams_iterator:
+					distances_matrices.append(np.array(Parallel(n_jobs=self.n_jobs, prefer="threads")(delayed(self._ds)(mu, self.X, degree) for mu in diagrams_iterator)))
+		return np.asarray(distances_matrices)
+		# kernels = [np.exp(-distance_matrix / (2*self.sigma**2)) for distance_matrix in distances_matrices]
+		# return np.sum(kernels, axis=0)
+
+
+
+
+
+## Wrapper for SW, in order to take as an input a list of (list of diagrams)
+class Dgms2SWK(BaseEstimator, TransformerMixin):
+	def __init__(self, num_directions:int=10, bandwidth:float=1.0, n_jobs:int=1, distance_matrix_path:str|None = None, progress:bool = False) -> None:
+		super().__init__()
+		self.num_directions:int=num_directions
+		self.bandwidth:float = bandwidth
+		self.n_jobs=n_jobs
+		self.SW_:list = []
+		self.distance_matrix_path = distance_matrix_path
+		self.progress = progress
+	def fit(self, X:list[list[np.ndarray]], y=None):
+		# Assumes that all x \in X have the same size
+		self.SW_ = [
+			SlicedWassersteinDistance(num_directions=self.num_directions, n_jobs = self.n_jobs) for _ in range(len(X[0]))
+		]
+		for i, sw in enumerate(self.SW_):
+			self.SW_[i]=sw.fit([dgms[i] for dgms in X]) # TODO : check : Not sure copy is necessary here
+		return self
+	def transform(self,X)->np.ndarray:
+		if not self.distance_matrix_path is None:
+			distance_matrices = []
+			for i in range(len(self.SW_)):
+				SW_i_path = f"{self.distance_matrix_path}_{i}"
+				if exists(SW_i_path):
+					distance_matrices.append(np.load(open(SW_i_path, "rb"))) 
+				else:
+					distance_matrix = self.SW_[i].transform([dgms[i] for dgms in X])
+					np.save(open(SW_i_path, "wb"), distance_matrix)
+		else:
+			distance_matrices = [sw.transform([dgms[i] for dgms in X]) for i, sw in enumerate(self.SW_)]
+		kernels = [np.exp(-distance_matrix / (2*self.bandwidth**2)) for distance_matrix in distance_matrices]
+		return np.sum(kernels, axis=0) # TODO fix this, we may want to sum the distances instead of the kernels. 
+
+
+class Dgms2SlicedWassersteinDistanceMatrices(BaseEstimator, TransformerMixin):
+	def __init__(self, num_directions:int=10, n_jobs:int=1) -> None:
+		super().__init__()
+		self.num_directions:int=num_directions
+		self.n_jobs=n_jobs
+		self.SW_:list = []
+	def fit(self, X:list[list[np.ndarray]], y=None):
+		# Assumes that all x \in X have the same size
+		self.SW_ = [
+			SlicedWassersteinDistance(num_directions=self.num_directions, n_jobs = self.n_jobs) for _ in range(len(X[0]))
+		]
+		for i, sw in enumerate(self.SW_):
+			self.SW_[i]=sw.fit([dgms[i] for dgms in X]) # TODO : check : Not sure copy is necessary here
+		return self
+	
+	@staticmethod
+	def _get_distance(diagrams, SWD):
+		return SWD.transform(diagrams)
+	def transform(self,X):
+		distance_matrices = Parallel(n_jobs = self.n_jobs)(delayed(self._get_distance)([dgms[degree] for dgms in X], swd) for degree, swd in enumerate(self.SW_))		
+		return np.asarray(distance_matrices)
+
+
+
+# Gudhi simplexTree to list of diagrams
+class SimplexTree2Dgm(BaseEstimator, TransformerMixin):
+	def __init__(self, degrees:list[int]|None = None, extended:list[int]|bool=[], n_jobs=1, progress:bool=False, threshold:float=np.inf) -> None:
+		super().__init__()
+		self.extended:list[int]|bool = False if not extended else extended if type(extended) is list else [0,2,5,7] # extended persistence.
+		# There are 4 diagrams per dimension then, the list of ints acts as a filter, on which to consider,
+		#  eg., [0,2, 5,7] is Ord0, Ext+0, Rel1, Ext-1
+		self.degrees:list[int] = degrees if degrees else list(range((max(self.extended) // 4)+1))  if self.extended else [0] # homological degrees
+		self.n_jobs=n_jobs 
+		self.progress = progress # progress bar
+		self.threshold = threshold # Threshold value
+		return
+	def fit(self, X:list[gd.SimplexTree], y=None):
+		if self.threshold <= 0:
+			self.threshold = max( (abs(f) for simplextree in get_simplextrees(X) for s,f in simplextree.get_simplices()) )  ## MAX FILTRATION VALUE
+			print(f"Setting threshold to {self.threshold}.")
+		return self
+	def transform(self,X:list[gd.SimplexTree]):
+		# Todo computes the diagrams
+		def reshape(dgm:np.ndarray|list)->np.ndarray:
+			out = np.array(dgm) if len(dgm) > 0 else np.empty((0,2)) 
+			if self.threshold != np.inf:
+				out[out>self.threshold] = self.threshold
+				out[out<-self.threshold] = -self.threshold
+			return out
+		def todo_standard(st):
+			st.compute_persistence()
+			return [reshape(st.persistence_intervals_in_dimension(d)) for d in self.degrees]
+		def todo_extended(st):
+			st.extend_filtration()
+			dgms = st.extended_persistence()
+#			print(dgms, self.degrees)
+			return [reshape([bar for j,dgm in enumerate(dgms) for d, bar in dgm if d in self.degrees and j+4*d in self.extended])]
+		todo = todo_extended if self.extended else todo_standard
+
+		if isinstance(X[0],gd.SimplexTree): # simplextree aren't pickleable, no parallel
+			# if self.n_jobs != 1:	warn("Cannot parallelize. Use dtype=None in previous pipe.")
+			return Parallel(n_jobs=self.n_jobs, prefer="threads")(delayed(todo)(x) for x in tqdm(X, disable=not self.progress, desc="Computing diagrams"))
+		else:
+			to_st = X[0]# if to_st is None else to_st 
+			dataset = X[1]# if to_st is None else X
+			pickleable_todo = lambda x : todo(to_st(x))
+			return Parallel(n_jobs=self.n_jobs, prefer="threads")(delayed(pickleable_todo)(x) for x in tqdm(dataset, disable=not self.progress, desc="Computing simplextrees and diagrams"))
+		warn("Bad input.")
+		return
+
+# Shuffles a diagram shaped array. Input : list of (list of diagrams), output, list of (list of shuffled diagrams)
+class DiagramShuffle(BaseEstimator, TransformerMixin):
+	def __init__(self, ) -> None:
+		super().__init__()
+		return
+	def fit(self, X:list[list[np.ndarray]], y=None):
+		return self
+	def transform(self,X:list[list[np.ndarray]]):
+		def shuffle(dgm):
+			shape = dgm.shape
+			dgm = dgm.flatten()
+			np.random.shuffle(dgm)
+			dgm = dgm.reshape(shape)
+			return dgm
+		def todo(dgms):
+			return [shuffle(dgm) for dgm in dgms]
+		return [todo(dgm) for dgm in X]
+
+
+class Dgms2Landscapes(BaseEstimator, TransformerMixin):
+	def __init__(self, num:int=5, resolution:int=100,  n_jobs:int=1) -> None:
+		super().__init__()
+		self.degrees:list[int] = []
+		self.num:int= num
+		self.resolution:int = resolution
+		self.landscapes:list[Landscape]= []
+		self.n_jobs=n_jobs
+		return
+	def fit(self, X, y=None):
+		if len(X) == 0:	return self
+		self.degrees = list(range(len(X[0])))
+		self.landscapes = []
+		for dim in self.degrees:
+			self.landscapes.append(Landscape(num_landscapes=self.num,resolution=self.resolution).fit([dgms[dim] for dgms in X]))
+		return self
+	def transform(self,X):
+		if len(X) == 0:	return []
+		return np.concatenate([landscape.transform([dgms[degree] for dgms in X]) for degree, landscape in enumerate(self.landscapes)], axis=1)
+
+class Dgms2Image(BaseEstimator, TransformerMixin):
+	def __init__(self, bandwidth:float=1, resolution:tuple[int,int]=(20,20),  n_jobs:int=1) -> None:
+		super().__init__()
+		self.degrees:list[int] = []
+		self.bandwidth:float= bandwidth
+		self.resolution = resolution
+		self.PI:list[PersistenceImage]= []
+		self.n_jobs=n_jobs
+		return
+	def fit(self, X, y=None):
+		if len(X) == 0:	return self
+		self.degrees = list(range(len(X[0])))
+		self.PI = []
+		for dim in self.degrees:
+			self.PI.append(PersistenceImage(bandwidth=self.bandwidth,resolution=self.resolution).fit([dgms[dim] for dgms in X]))
+		return self
+	def transform(self,X):
+		if len(X) == 0:	return []
+		return np.concatenate([pers_image.transform([dgms[degree] for dgms in X]) for degree, pers_image in enumerate(self.PI)], axis=1)
+
+