multipers 1.1.3__cp310-cp310-macosx_11_0_universal2.whl

multipers/multiparameter_module_approximation.pyi

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+
+#########################################################################
+## Small hack for typing
+from multipers.simplex_tree_multi import SimplexTreeMulti
+import numpy as np
+
+
+class PySummand:
+	"""
+	Stores a Summand of a PyModule
+	"""
+
+
+	def get_birth_list(self): # TODO: FIXME
+		...
+	def get_death_list(self):
+		...
+	@property
+	def num_parameters(self)->int:
+		...
+
+
+class PyBox:
+	@property
+	def num_parameters(self)->int:
+		...
+	def contains(self, x)->bool:
+		...
+
+
+	def get(self):
+		...
+	def to_multipers(self):
+		...
+
+class PyMultiDiagramPoint:
+	def get_degree(self):
+		...
+	def get_birth(self):
+		...
+	def get_death(self):
+		...
+
+class PyMultiDiagram:
+	"""
+	Stores the diagram of a PyModule on a line
+	"""
+	def get_points(self, degree:int=-1) -> np.ndarray:
+		...
+	def to_multipers(self, dimension:int):
+		...
+	def __len__(self) -> int:
+		...
+	def __getitem__(self,i:int) -> PyMultiDiagramPoint:
+		...
+class PyMultiDiagrams:
+	"""
+	Stores the barcodes of a PyModule on multiple lines
+	"""
+
+	def to_multipers(self):
+		...
+	def __getitem__(self,i:int):
+		...
+	def __len__(self):
+		...
+	def get_points(self, degree:int=-1):
+		...
+
+	def plot(self, degree:int=-1, min_persistence:float=0):
+		"""
+		Plots the barcodes.
+
+		Parameters
+		----------
+		degree:int=-1
+			Only plots the bars of specified homology degree. Useful when the multidiagrams contains multiple dimenions
+		min_persistence:float=0
+			Only plot bars of length greater than this value. Useful to reduce the time to plot.
+
+		Warning
+		-------
+		If the barcodes are not thresholded, essential barcodes will not be displayed !
+
+		Returns
+		-------
+		Nothing
+		"""
+		...
+
+class PyModule:
+	"""
+	Stores a representation of a n-persistence module.
+	"""
+	def get_module_of_dimension(self, degree:int)->PyModule: # TODO : in c++ ?
+		...
+
+	def __len__(self)->int:
+		...
+	def get_bottom(self):
+		...
+	def get_top(self):
+		...
+	def get_box(self):
+		...
+	@property
+	def num_parameters(self)->int:
+		...
+	def dump(self, path:str|None=None):
+		"""
+		Dumps the module into a pickle-able format.
+		
+		Parameters
+		----------
+		path:str=None (optional) saves the pickled module in specified path
+		
+		Returns
+		-------
+		list of list, encoding the module, which can be retrieved with the function `from_dump`.
+		"""
+		...
+	def __getitem__(self, i:int) -> PySummand:
+		...
+	
+	def plot(self, degree:int=-1,**kwargs)->None:
+		"""Shows the module on a plot. Each color corresponds to an apprimation summand of the module, and its shape corresponds to its support.
+		Only works with 2-parameter modules.
+
+		Parameters
+		----------
+		degree = -1 : integer
+			If positive returns only the image of dimension `dimension`.
+		box=None : of the form [[b_x,b_y], [d_x,d_y]] where b,d are the bottom and top corner of the rectangle.
+			If non-None, will plot the module on this specific rectangle.
+		min_persistence =0 : float
+			Only plots the summand with a persistence above this threshold.
+		separated=False : bool
+			If true, plot each summand in a different plot.
+		alpha=1 : float
+			Transparancy parameter
+		save = False : string
+			if nontrivial, will save the figure at this path
+
+
+		Returns
+		-------
+		The figure of the plot.
+		"""
+		...
+
+	def barcode(self, basepoint, degree:int,*, threshold = False): # TODO direction vector interface
+		"""Computes the barcode of module along a lines.
+
+		Parameters
+		----------
+		basepoint  : vector
+			basepoint of the lines on which to compute the barcodes, i.e. a point on the line
+		degree = -1 : integer
+			Homology degree on which to compute the bars. If negative, every dimension is computed
+		box (default) :
+			box on which to compute the barcodes if basepoints is not specified. Default is a linspace of lines crossing that box.
+		threshold = False : threshold t
+			Resolution of the image(s).
+
+		Warning
+		-------
+		If the barcodes are not thresholded, essential barcodes will not be plot-able.
+
+		Returns
+		-------
+		PyMultiDiagrams
+			Structure that holds the barcodes. Barcodes can be retrieved with a .get_points() or a .to_multipers() or a .plot().
+		"""
+		...
+	def barcodes(self, degree:int, basepoints = None, num=100, box = None,threshold = False):
+		"""Computes barcodes of module along a set of lines.
+
+		Parameters
+		----------
+		basepoints = None : list of vectors
+			basepoints of the lines on which to compute the barcodes.
+		degree = -1 : integer
+			Homology degree on which to compute the bars. If negative, every dimension is computed
+		box (default) :
+			box on which to compute the barcodes if basepoints is not specified. Default is a linspace of lines crossing that box.
+		num:int=100
+			if basepoints is not specified, defines the number of lines to consider.
+		threshold = False : threshold t
+			Resolution of the image(s).
+
+		Warning
+		-------
+		If the barcodes are not thresholded, essential barcodes will not be plot-able.
+
+		Returns
+		-------
+		PyMultiDiagrams
+			Structure that holds the barcodes. Barcodes can be retrieved with a .get_points() or a .to_multipers() or a .plot().
+		"""
+		...
+	def landscape(self, degree:int, k:int=0,box:list|np.ndarray|None=None, resolution:List=[100,100], plot=True):
+		"""Computes the multiparameter landscape from a PyModule. Python interface only bifiltrations.
+
+		Parameters
+		----------
+		degree : integer
+			The homology degree of the landscape.
+		k = 0 : int
+			the k-th landscape
+		resolution = [50,50] : pair of integers
+			Resolution of the image.
+		box = None : in the format [[a,b], [c,d]]
+			If nontrivial, compute the landscape of this box. Default is the PyModule box.
+		plot = True : Boolean
+			If true, plots the images;
+		Returns
+		-------
+		Numpy array
+			The landscape of the module.
+		"""
+		...
+	def landscapes(self, degree:int, ks:list|np.ndarray=[0],box=None, resolution:list|np.ndarray=[100,100], plot=True):
+		"""Computes the multiparameter landscape from a PyModule. Python interface only bifiltrations.
+
+		Parameters
+		----------
+		degree : integer
+			The homology degree of the landscape.
+		ks = 0 : list of int
+			the k-th landscape
+		resolution = [50,50] : pair of integers
+			Resolution of the image.
+		box = None : in the format [[a,b], [c,d]]
+			If nontrivial, compute the landscape of this box. Default is the PyModule box.
+		plot = True : Boolean
+			If true, plots the images;
+		Returns
+		-------
+		Numpy array
+			The landscapes of the module with parameters ks.
+		"""
+		...
+
+
+	def image(self, degree:int = -1, bandwidth:float=0.1, resolution:list=[100,100], normalize:bool=False, plot:bool=True, save:bool=False, dpi:int=200,p:float=1., **kwargs)->np.ndarray:
+		"""Computes a vectorization from a PyModule. Python interface only bifiltrations.
+
+		Parameters
+		----------
+		degree = -1 : integer
+			If positive returns only the image of homology degree `degree`.
+		bandwidth = 0.1 : float
+			Image parameter. TODO : different weights
+		resolution = [100,100] : pair of integers
+			Resolution of the image(s).
+		normalize = True : Boolean
+			Ensures that the image belongs to [0,1].
+		plot = True : Boolean
+			If true, plots the images;
+
+		Returns
+		-------
+		List of Numpy arrays or numpy array
+			The list of images, or the image of fixed dimension.
+		"""
+		...
+
+
+	def euler_char(self, points:list|np.ndarray) -> np.ndarray:
+		""" Computes the Euler Characteristic of the filtered complex at given (multiparameter) time
+
+		Parameters
+		----------
+		points: list[float] | list[list[float]] | np.ndarray
+			List of filtration values on which to compute the euler characteristic.
+			WARNING FIXME : the points have to have the same dimension as the simplextree.	
+
+		Returns
+		-------
+		The list of euler characteristic values
+		"""
+		...
+
+def module_approximation(
+	st:SimplexTreeMulti,
+	max_error:float|None = None,
+	box:list|np.ndarray|None = None,
+	threshold:bool = False,
+	complete:bool = True,
+	multithread:bool = False, 
+	verbose:bool = False,
+	ignore_warning:bool = False,
+	nlines:int = 500,
+	max_dimension=np.inf,
+	boundary = None,
+	filtration = None,
+	**kwargs)->PyModule:
+	"""Computes an interval module approximation of a multiparameter filtration.
+
+	Parameters
+	----------
+	st : n-filtered Simplextree.
+		Defines the n-filtration on which to compute the homology.
+	max_error: positive float
+		Trade-off between approximation and computational complexity.
+		Upper bound of the module approximation, in bottleneck distance, 
+		for interval-decomposable modules.
+	nlines: int
+		Alternative to precision.
+	box : pair of list of floats
+		Defines a rectangle on which to compute the approximation.
+		Format : [x,y], where x,y defines the rectangle {z : x ≤ z ≤ y}
+	threshold: bool
+		When true, intersects the module support with the box.
+	verbose: bool
+		Prints C++ infos.
+	ignore_warning : bool
+		Unless set to true, prevents computing on more than 10k lines. Useful to prevent a segmentation fault due to "infinite" recursion.
+	Returns
+	-------
+	PyModule
+		An interval decomposable module approximation of the module defined by the
+		homology of this multi-filtration.
+	"""
+
+	...
+
+	
+
+def from_dump(dump)->PyModule:
+	"""Retrieves a PyModule from a previous dump.
+
+	Parameters
+	----------
+	dump: either the output of the dump function, or a file containing the output of a dump.
+		The dumped module to retrieve
+
+	Returns
+	-------
+	PyModule
+		The retrieved module.
+	"""
+	...
+
+
+#################################################### DATASETS for test
+
+def noisy_annulus(r1:float=1, r2:float=2, n1:int=1000,n2:int=200, dim:int=2, center:np.ndarray|list|None=None, **kwargs)->np.ndarray:
+	"""Generates a noisy annulus dataset.
+
+	Parameters
+	----------
+	r1 : float.
+		Lower radius of the annulus.
+	r2 : float.
+		Upper radius of the annulus.
+	n1 : int
+		Number of points in the annulus.
+	n2 : int
+		Number of points in the square.
+	dim : int
+		Dimension of the annulus.
+	center: list or array
+		center of the annulus.
+
+	Returns
+	-------
+	numpy array
+		Dataset. size : (n1+n2) x dim
+
+	"""
+	...
+
+def test_module(**kwargs):
+	"""Generates a module from a noisy annulus.
+
+	Parameters
+	----------
+	r1 : float.
+		Lower radius of the annulus.
+	r2 : float.
+		Upper radius of the annulus.
+	n1 : int
+		Number of points in the annulus.
+	n2 : int
+		Number of points in the square.
+	dim : int
+		Dimension of the annulus.
+	center: list or array
+		center of the annulus.
+
+	Returns
+	-------
+	PyModule
+		The associated module.
+
+	"""
+	...
+
+
+##################################################### MMA CONVERSIONS
+
+
+
+
+
+
+############################################# MMA - Matching distances
+
+
+
+
+
+def estimate_matching(b1:PyMultiDiagrams, b2:PyMultiDiagrams)->float:
+	...
+
+
+#### Functions to estimate precision
+def estimate_error(st:SimplexTreeMulti, module:PyModule, degree:int, nlines = 100, verbose:bool =False)->float:
+	"""
+	Given an MMA SimplexTree and PyModule, estimates the bottleneck distance using barcodes given by gudhi.
+	
+	Parameters
+	----------
+	st:SimplexTree
+		The simplextree representing the n-filtered complex. Used to define the gudhi simplextrees on different lines.
+	module:PyModule
+		The module on which to estimate approximation error, w.r.t. the original simplextree st.
+	degree: The homology degree to consider
+	
+	Returns
+	-------
+	The estimation of the matching distance, i.e., the maximum of the sampled bottleneck distances.
+		
+	"""
+	...
+
+
+