sgwt 0.1.0__py3-none-any.whl

sgwt/__init__.py

@@ -0,0 +1,2 @@
+from .main import FastSGWT
+from .kernel import *

sgwt/kernel/__init__.py

@@ -0,0 +1 @@
+from .design import KernelDesign

sgwt/kernel/design.py

@@ -0,0 +1,128 @@
+
+# This is the main class the user interacts with.
+from .kernel import AbstractKernel
+from .fitting import WaveletFitting
+from numpy import log, savez, geomspace
+
+class KernelDesign(AbstractKernel):
+    ''' 
+    Class holding the spectral form of the wavelet function
+    '''
+
+    def __init__(
+            self, 
+            spectrum_range = (1e-7, 1e2),
+            scale_range    = (1e-2, 1e5),
+            pole_min       = 1e-5,
+            nscales        = 10, 
+            npoles         = 10, 
+            nsamples       = 300,
+            order          = 2 
+        ):
+
+        # Scales, Domain, and initial poles
+        s  = self.logsamp(*scale_range   , nscales )   
+        x  = self.logsamp(*spectrum_range, nsamples)  
+        Q0 = self.logsamp(pole_min,spectrum_range[1], npoles  )  
+
+        # Sample the function for all scales
+        # (Scales x lambda)
+        G = self.g(x*s.T, order=order)
+
+        wf = WaveletFitting(
+            domain        = x, 
+            samples       = G, 
+            initial_poles = Q0
+        )
+
+        # Fit and return pole and residues of apporimation
+        R, Q = wf.fit()
+
+        # Calculate the interval of scales on log scale
+        self.ds = log(s[1]/s[0])[0]
+
+        # Assign Poles, residues, scales
+        self.wf  = wf
+        self.__q = Q
+        self.__r = R
+        self.__s = s
+        self.nscales  = nscales 
+        self.npoles   = npoles
+        self.nsamples = nsamples
+
+        # Useful for debugging
+        self.x = x
+        self.G = G
+        
+    def logsamp(self, start, end, N=5):
+        '''
+        Description:
+            Helper sampling function for log scales
+        Parameters:
+            start: first value
+            end: last value
+            N: number of log-spaced values between start and end
+        Returns:
+            Samples array: shape is  (N x 1)
+        '''
+        return geomspace(start, [end],N)
+    
+    
+    def g(self, x, order=1):
+        '''
+        Description:
+            Default kernel function evaluator
+        Parameters:
+            x: domain to evaluate (array)
+            order: higher order -> narrower bandwidth
+        Returns:
+            g(x): same shape as x
+        '''
+        f = 2*x/(1+x**2)
+        return f**order
+    
+    def h(self, x):
+        '''
+        Description:
+            The scaling kerenl h(x) evaluating the 'DC-like' spectrum
+        Parameters:
+            x: domain to evaluate (array)
+        Returns:
+           h(x): same shape as x
+        '''
+        f = 1/(1+x**2)
+        return f
+    
+    def get_approx(self):
+
+        V, R = self.wf.V, self.R
+
+        return V@R
+
+    @property
+    def R(self):
+        '''Residue Matrix where each column is a scale
+        and each row corresponds to a pole '''
+        return self.__r
+
+    @property
+    def Q(self):
+        '''Vector of Poles'''
+        return self.__q
+    
+    @property
+    def scales(self):
+        '''Vector of Scales'''
+        return self.__s
+    
+    def write(self, fname):
+        '''
+        Description:
+            Writes poles & residue model to npz file format.
+            Post-fix .npz not needed, just write desired name.
+        Parameters:
+            fname: Filename/directory if needed
+        Returns:
+            None
+        '''
+        savez(f'{fname}.npz', R=self.R, Q=self.Q, S=self.scales)

sgwt/kernel/fitting.py

@@ -0,0 +1,71 @@
+
+from scipy.linalg import pinv
+
+# This is the native vector fitting tool.
+# No pole allocation in this version.
+
+class WaveletFitting:
+    '''
+    Native vector fitting tool.
+
+    Determines the residues and poles of a discrete
+    set of frequnecy-domain wavelet kernels
+    '''
+
+    def __init__(self, domain, samples, initial_poles):
+        '''
+        Parameters:
+            domain: (log spaced) sample points of signal
+            samples: (on domain) kernel values, each col is different scale
+            initial poles: (log spaced) initial pole locations
+        '''
+
+        # location, samples of VF, and initial poles
+        self.x = domain
+        self.G = samples # scale x lambda
+        self.Q0 = initial_poles
+
+    def eval_pole_matrix(self, Q, x):
+        '''
+        Description:
+            Evaluates the 'pole matrix' over some domain x given poles Q
+        Parameters:
+            Q: Poles array (npoles x 1)
+            x: domain to evaluate (nsamp x 1)
+        Returns:
+            Pole Matrix: shape is  (nsamps x npoles)
+        '''
+        return 1/(x + Q.T)
+    
+    def calc_residues(self, V, G):
+        '''
+        Description:
+            Solves least square problem for residues for given set of poles
+        Parameters:
+            V: 'pole matrix' (use eval_pole_matrix)
+            G: function being approximated
+        Returns:
+            Residue Matrix: shape is  (npoles x nscales)
+        '''
+        # Solve Equation: V@R = G
+        return pinv(V)@G
+    
+    def fit(self):
+        '''
+        Description:
+            Performs VF procedure on signal G.
+        Returns:
+            R, Q: shape is  (npoles x nscales), (npoles x 1)
+        '''
+        
+        # (samples x poles)
+        self.V = self.eval_pole_matrix(self.Q0, self.x)
+
+        # (pole x scale)
+        R = self.calc_residues(self.V, self.G)
+
+        # TODO pole relalocation step here and iterative
+        Q = self.Q0
+
+        return R, Q
+    

sgwt/kernel/kernel.py

@@ -0,0 +1,35 @@
+from abc import ABC, abstractmethod
+
+class AbstractKernel:
+    '''
+    An Abstract SGWT Kernel incase multiple version of the 
+    SGWT transformation are implemented
+    '''
+
+    def __init__(self) -> None:
+        pass
+
+    @abstractmethod
+    def h(self, x):
+        '''
+        Description:
+            The scaling kerenl h(x) evaluating the 'DC-like' spectrum
+        Parameters:
+            Vector x, the spectrum domain to evaluate.
+        Returns:
+            Spectral domain scaling kerenel
+        '''
+
+    @abstractmethod
+    def g(self, x):
+        '''
+        Description:
+            The wavelet generating kernel g(x) evaluating the un-scaled wavelet
+        Parameters:
+            Vector x, the spectrum domain to evaluate.
+        Returns:
+            Spectral domain wavelet kerenel
+        '''
+
+
+

sgwt/main.py

@@ -0,0 +1,93 @@
+from sksparse.cholmod import analyze
+from scipy.sparse import csc_matrix
+
+import numpy as np
+
+class FastSGWT:
+    '''
+    A rational-approximation approach to the SGWT
+    '''
+
+    def __init__(self, L: csc_matrix, kern: str):
+
+        # Sparse Laplacian
+        self.L = L
+
+        # Load Residues, Poles, Scales
+        npzfile = np.load(f'{kern}.npz')
+        self.R, self.Q, self.scales = npzfile['R'], npzfile['Q'], npzfile['S']
+        npzfile.close()
+
+        # Wavelet Constant (scalar mult)
+        ds = np.log(self.scales[1]/self.scales[0])[0]
+        self.C = 1/ds
+
+        # Number of scales
+        self.nscales = len(self.scales)
+
+        # Pre-Factor (Symbolic)
+        self.factor = analyze(L)
+
+    def allocate(self, f):
+        return np.zeros((*f.shape, self.nscales))
+
+    def __call__(self, f):
+        '''
+        Returns
+            W:  Array size (Bus, Time, Scale)
+        '''
+        
+        W = self.allocate(f)
+        F = self.factor
+        L = self.L
+
+        for q, r in zip(self.Q, self.R):
+
+            F.cholesky_inplace(L, q) 
+            W += F(f)[:, :, None]*r   # Almost the entire duration is occupied multiplying here
+
+        return W
+    
+    def singleton(self, f, n):
+        '''
+        Returns
+            Coefficients of f localized at n
+        '''
+        
+        F = self.factor
+        L = self.L
+
+        # LOCALIZATION VECTOR
+        local = np.zeros((L.shape[0], 1))
+        local[n] = 1
+
+        # Singleton Matrix
+        W = np.zeros((L.shape[0], self.nscales))
+
+        # Compute
+        for q, r in zip(self.Q, self.R):
+
+            F.cholesky_inplace(L, q) 
+            W += F(local)*r.T  
+
+        return f.T@W 
+    
+    def inv(self, W):
+        '''
+        Description
+            The inverse SGWT transformation (only one time point for now)
+            And does not support scaling coefficients right now.
+        Parameters
+            W: ndarray of shape (Bus x Times x Scales)
+        '''
+        
+        fact, L = self.factor, self.L
+        f = np.zeros((W.shape[0], W.shape[1]))
+
+        for q, r in zip(self.Q, self.R):
+
+            fact.cholesky_inplace(L, q) 
+            f += fact(W@r) 
+
+        return f/self.C
+    

sgwt-0.1.0.dist-info/LICENSE

@@ -0,0 +1,201 @@
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sgwt-0.1.0.dist-info/METADATA

@@ -0,0 +1,243 @@
+Metadata-Version: 2.1
+Name: sgwt
+Version: 0.1.0
+Summary: A Spectral Graph Wavelet module for sparse networks
+Author-email: Luke Lowery <lukel@tamu.edu>
+License: Apache License
+                                   Version 2.0, January 2004
+                                http://www.apache.org/licenses/
+        
+           TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+        
+           1. Definitions.
+        
+              "License" shall mean the terms and conditions for use, reproduction,
+              and distribution as defined by Sections 1 through 9 of this document.
+        
+              "Licensor" shall mean the copyright owner or entity authorized by
+              the copyright owner that is granting the License.
+        
+              "Legal Entity" shall mean the union of the acting entity and all
+              other entities that control, are controlled by, or are under common
+              control with that entity. For the purposes of this definition,
+              "control" means (i) the power, direct or indirect, to cause the
+              direction or management of such entity, whether by contract or
+              otherwise, or (ii) ownership of fifty percent (50%) or more of the
+              outstanding shares, or (iii) beneficial ownership of such entity.
+        
+              "You" (or "Your") shall mean an individual or Legal Entity
+              exercising permissions granted by this License.
+        
+              "Source" form shall mean the preferred form for making modifications,
+              including but not limited to software source code, documentation
+              source, and configuration files.
+        
+              "Object" form shall mean any form resulting from mechanical
+              transformation or translation of a Source form, including but
+              not limited to compiled object code, generated documentation,
+              and conversions to other media types.
+        
+              "Work" shall mean the work of authorship, whether in Source or
+              Object form, made available under the License, as indicated by a
+              copyright notice that is included in or attached to the work
+              (an example is provided in the Appendix below).
+        
+              "Derivative Works" shall mean any work, whether in Source or Object
+              form, that is based on (or derived from) the Work and for which the
+              editorial revisions, annotations, elaborations, or other modifications
+              represent, as a whole, an original work of authorship. For the purposes
+              of this License, Derivative Works shall not include works that remain
+              separable from, or merely link (or bind by name) to the interfaces of,
+              the Work and Derivative Works thereof.
+        
+              "Contribution" shall mean any work of authorship, including
+              the original version of the Work and any modifications or additions
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+              submitted to Licensor for inclusion in the Work by the copyright owner
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+              to the Licensor or its representatives, including but not limited to
+              communication on electronic mailing lists, source code control systems,
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+              Licensor for the purpose of discussing and improving the Work, but
+              excluding communication that is conspicuously marked or otherwise
+              designated in writing by the copyright owner as "Not a Contribution."
+        
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+           3. Grant of Patent License. Subject to the terms and conditions of
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+              institute patent litigation against any entity (including a
+              cross-claim or counterclaim in a lawsuit) alleging that the Work
+              or a Contribution incorporated within the Work constitutes direct
+              or contributory patent infringement, then any patent licenses
+              granted to You under this License for that Work shall terminate
+              as of the date such litigation is filed.
+        
+           4. Redistribution. You may reproduce and distribute copies of the
+              Work or Derivative Works thereof in any medium, with or without
+              modifications, and in Source or Object form, provided that You
+              meet the following conditions:
+        
+              (a) You must give any other recipients of the Work or
+                  Derivative Works a copy of this License; and
+        
+              (b) You must cause any modified files to carry prominent notices
+                  stating that You changed the files; and
+        
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+        
+           5. Submission of Contributions. Unless You explicitly state otherwise,
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+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# sparse-sgwt
+
+A Collection of SGWT Functions for Large Sparse Networks
+
+## About
+
+Currently under construction at the moment, but a minimum viable code example is available.
+
+## Installation
+
+More details will be added on specific versions for this python implementation.
+
+- Python 3.8
+- scikit-sparse 
+
+
+https://github.com/scikit-sparse/scikit-sparse
+
+
+First
+
+conda install -c conda-forge scikit-sparse
+
+Then we need to enfore these versions for now
+- scipy
+```
+pip install --force-reinstall "scipy<=1.9.1"
+```
+- numpy
+```
+pip install --force-reinstall "numpy<=1.23.2"
+```

sgwt-0.1.0.dist-info/RECORD

@@ -0,0 +1,11 @@
+sgwt/__init__.py,sha256=l-VNUQ3N7XbpLS3zbPRR763ZnhNPDbdDSO5T_BCZ8oQ,49
+sgwt/main.py,sha256=PZs5nJ0fcchCdt50Igo6kqy0oQdKJOib_wJO_XaJvBA,2287
+sgwt/kernel/__init__.py,sha256=bcFpgQO48bRiCmkSqxX5ZG9u_xgASMrSbKoVomfvD20,32
+sgwt/kernel/design.py,sha256=_Db7bUzopx4Pp9YC8q0g2fS1ccCE9x2NhAYN7d4kOZI,3472
+sgwt/kernel/fitting.py,sha256=x5O241TYy8-XsxO-Fp531a_-GVoxnIgmtD1ZYg6_YQQ,2031
+sgwt/kernel/kernel.py,sha256=4PSYqniafLA7Swe9TJWYoh4zJamcOE2TiY_UIiGt0Bs,853
+sgwt-0.1.0.dist-info/LICENSE,sha256=HrhfyXIkWY2tGFK11kg7vPCqhgh5DcxleloqdhrpyMY,11558
+sgwt-0.1.0.dist-info/METADATA,sha256=dBZoXpnH17fNvCu_8Gfol-z1nEHI4NUCvAfHPLRh8VA,13998
+sgwt-0.1.0.dist-info/WHEEL,sha256=iAkIy5fosb7FzIOwONchHf19Qu7_1wCWyFNR5gu9nU0,91
+sgwt-0.1.0.dist-info/top_level.txt,sha256=8LSxEs_qatRESXGTRxf80xaNVoBt5NeSp9jBXQIm23Y,5
+sgwt-0.1.0.dist-info/RECORD,,

sgwt-0.1.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (75.3.2)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

sgwt-0.1.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+sgwt