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Parallel Colt is a multithreaded version of Colt - a library for high performance scientific computing in Java. It contains efficient algorithms for data analysis, linear algebra, multi-dimensional arrays, Fourier transforms, statistics and histogramming.

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/*
Copyright (C) 1999 CERN - European Organization for Nuclear Research.
Permission to use, copy, modify, distribute and sell this software and its documentation for any purpose 
is hereby granted without fee, provided that the above copyright notice appear in all copies and 
that both that copyright notice and this permission notice appear in supporting documentation. 
CERN makes no representations about the suitability of this software for any purpose. 
It is provided "as is" without expressed or implied warranty.
 */
package cern.colt.matrix.tfloat.algo.decomposition;

import cern.colt.matrix.tfloat.FloatFactory1D;
import cern.colt.matrix.tfloat.FloatFactory2D;
import cern.colt.matrix.tfloat.FloatMatrix1D;
import cern.colt.matrix.tfloat.FloatMatrix2D;
import cern.colt.matrix.tfloat.algo.DenseFloatAlgebra;
import cern.colt.matrix.tfloat.algo.FloatProperty;

/**
 * Eigenvalues and eigenvectors of a real matrix A.
 * 

* If A is symmetric, then A = V*D*V' where the eigenvalue matrix * D is diagonal and the eigenvector matrix V is orthogonal. * I.e. A = V.mult(D.mult(transpose(V))) and * V.mult(transpose(V)) equals the identity matrix. * *

* If A is not symmetric, then the eigenvalue matrix D is * block diagonal with the real eigenvalues in 1-by-1 blocks and any complex * eigenvalues, lambda + i*mu, in 2-by-2 blocks, * [lambda, mu; -mu, lambda]. The columns of V represent the * eigenvectors in the sense that A*V = V*D, i.e. * A.mult(V) equals V.mult(D). The matrix V may be badly * conditioned, or even singular, so the validity of the equation * A = V*D*inverse(V) depends upon Algebra.cond(V). */ public class DenseFloatEigenvalueDecomposition implements java.io.Serializable { static final long serialVersionUID = 1020; /** * Row and column dimension (square matrix). * * @serial matrix dimension. */ private int n; /** * Symmetry flag. * * @serial internal symmetry flag. */ private boolean issymmetric; /** * Arrays for internal storage of eigenvalues. * * @serial internal storage of eigenvalues. */ private float[] d, e; /** * Array for internal storage of eigenvectors. * * @serial internal storage of eigenvectors. */ private float[][] V; /** * Array for internal storage of nonsymmetric Hessenberg form. * * @serial internal storage of nonsymmetric Hessenberg form. */ private float[][] H; /** * Working storage for nonsymmetric algorithm. * * @serial working storage for nonsymmetric algorithm. */ private float[] ort; // Complex scalar division. private transient float cdivr, cdivi; /** * Constructs and returns a new eigenvalue decomposition object; The * decomposed matrices can be retrieved via instance methods of the returned * decomposition object. Checks for symmetry, then constructs the eigenvalue * decomposition. * * @param A * A square matrix. * @throws IllegalArgumentException * if A is not square. */ public DenseFloatEigenvalueDecomposition(FloatMatrix2D A) { FloatProperty.DEFAULT.checkSquare(A); n = A.columns(); V = new float[n][n]; d = new float[n]; e = new float[n]; issymmetric = FloatProperty.DEFAULT.isSymmetric(A); if (issymmetric) { for (int i = 0; i < n; i++) { for (int j = 0; j < n; j++) { V[i][j] = A.getQuick(i, j); } } // Tridiagonalize. tred2(); // Diagonalize. tql2(); } else { H = new float[n][n]; ort = new float[n]; for (int j = 0; j < n; j++) { for (int i = 0; i < n; i++) { H[i][j] = A.getQuick(i, j); } } // Reduce to Hessenberg form. orthes(); // Reduce Hessenberg to real Schur form. hqr2(); } } private void cdiv(float xr, float xi, float yr, float yi) { float r, d; if (Math.abs(yr) > Math.abs(yi)) { r = yi / yr; d = yr + r * yi; cdivr = (xr + r * xi) / d; cdivi = (xi - r * xr) / d; } else { r = yr / yi; d = yi + r * yr; cdivr = (r * xr + xi) / d; cdivi = (r * xi - xr) / d; } } /** * Returns the block diagonal eigenvalue matrix, D. * * @return D */ public FloatMatrix2D getD() { float[][] D = new float[n][n]; for (int i = 0; i < n; i++) { for (int j = 0; j < n; j++) { D[i][j] = 0.0f; } D[i][i] = d[i]; if (e[i] > 0) { D[i][i + 1] = e[i]; } else if (e[i] < 0) { D[i][i - 1] = e[i]; } } return FloatFactory2D.dense.make(D); } /** * Returns the imaginary parts of the eigenvalues. * * @return imag(diag(D)) */ public FloatMatrix1D getImagEigenvalues() { return FloatFactory1D.dense.make(e); } /** * Returns the real parts of the eigenvalues. * * @return real(diag(D)) */ public FloatMatrix1D getRealEigenvalues() { return FloatFactory1D.dense.make(d); } /** * Returns the eigenvector matrix, V * * @return V */ public FloatMatrix2D getV() { return FloatFactory2D.dense.make(V); } /** * Nonsymmetric reduction from Hessenberg to real Schur form. */ private void hqr2() { // This is derived from the Algol procedure hqr2, // by Martin and Wilkinson, Handbook for Auto. Comp., // Vol.ii-Linear Algebra, and the corresponding // Fortran subroutine in EISPACK. // Initialize int nn = this.n; int n = nn - 1; int low = 0; int high = nn - 1; float eps = (float) Math.pow(2.0, -23.0); float exshift = 0.0f; float p = 0, q = 0, r = 0, s = 0, z = 0, t, w, x, y; // Store roots isolated by balanc and compute matrix norm float norm = 0.0f; for (int i = 0; i < nn; i++) { if (i < low | i > high) { d[i] = H[i][i]; e[i] = 0.0f; } for (int j = Math.max(i - 1, 0); j < nn; j++) { norm = norm + Math.abs(H[i][j]); } } // Outer loop over eigenvalue index int iter = 0; while (n >= low) { // Look for single small sub-diagonal element int l = n; while (l > low) { s = Math.abs(H[l - 1][l - 1]) + Math.abs(H[l][l]); if (s == 0.0f) { s = norm; } if (Math.abs(H[l][l - 1]) < eps * s) { break; } l--; } // Check for convergence // One root found if (l == n) { H[n][n] = H[n][n] + exshift; d[n] = H[n][n]; e[n] = 0.0f; n--; iter = 0; // Two roots found } else if (l == n - 1) { w = H[n][n - 1] * H[n - 1][n]; p = (H[n - 1][n - 1] - H[n][n]) / 2.0f; q = p * p + w; z = (float) Math.sqrt(Math.abs(q)); H[n][n] = H[n][n] + exshift; H[n - 1][n - 1] = H[n - 1][n - 1] + exshift; x = H[n][n]; // Real pair if (q >= 0) { if (p >= 0) { z = p + z; } else { z = p - z; } d[n - 1] = x + z; d[n] = d[n - 1]; if (z != 0.0f) { d[n] = x - w / z; } e[n - 1] = 0.0f; e[n] = 0.0f; x = H[n][n - 1]; s = Math.abs(x) + Math.abs(z); p = x / s; q = z / s; r = (float) Math.sqrt(p * p + q * q); p = p / r; q = q / r; // Row modification for (int j = n - 1; j < nn; j++) { z = H[n - 1][j]; H[n - 1][j] = q * z + p * H[n][j]; H[n][j] = q * H[n][j] - p * z; } // Column modification for (int i = 0; i <= n; i++) { z = H[i][n - 1]; H[i][n - 1] = q * z + p * H[i][n]; H[i][n] = q * H[i][n] - p * z; } // Accumulate transformations for (int i = low; i <= high; i++) { z = V[i][n - 1]; V[i][n - 1] = q * z + p * V[i][n]; V[i][n] = q * V[i][n] - p * z; } // Complex pair } else { d[n - 1] = x + p; d[n] = x + p; e[n - 1] = z; e[n] = -z; } n = n - 2; iter = 0; // No convergence yet } else { // Form shift x = H[n][n]; y = 0.0f; w = 0.0f; if (l < n) { y = H[n - 1][n - 1]; w = H[n][n - 1] * H[n - 1][n]; } // Wilkinson's original ad hoc shift if (iter == 10) { exshift += x; for (int i = low; i <= n; i++) { H[i][i] -= x; } s = Math.abs(H[n][n - 1]) + Math.abs(H[n - 1][n - 2]); x = y = 0.75f * s; w = -0.4375f * s * s; } // MATLAB's new ad hoc shift if (iter == 30) { s = (y - x) / 2.0f; s = s * s + w; if (s > 0) { s = (float) Math.sqrt(s); if (y < x) { s = -s; } s = x - w / ((y - x) / 2.0f + s); for (int i = low; i <= n; i++) { H[i][i] -= s; } exshift += s; x = y = w = 0.964f; } } iter = iter + 1; // (Could check iteration count here.) // Look for two consecutive small sub-diagonal elements int m = n - 2; while (m >= l) { z = H[m][m]; r = x - z; s = y - z; p = (r * s - w) / H[m + 1][m] + H[m][m + 1]; q = H[m + 1][m + 1] - z - r - s; r = H[m + 2][m + 1]; s = Math.abs(p) + Math.abs(q) + Math.abs(r); p = p / s; q = q / s; r = r / s; if (m == l) { break; } if (Math.abs(H[m][m - 1]) * (Math.abs(q) + Math.abs(r)) < eps * (Math.abs(p) * (Math.abs(H[m - 1][m - 1]) + Math.abs(z) + Math.abs(H[m + 1][m + 1])))) { break; } m--; } for (int i = m + 2; i <= n; i++) { H[i][i - 2] = 0.0f; if (i > m + 2) { H[i][i - 3] = 0.0f; } } // Float QR step involving rows l:n and columns m:n for (int k = m; k <= n - 1; k++) { boolean notlast = (k != n - 1); if (k != m) { p = H[k][k - 1]; q = H[k + 1][k - 1]; r = (notlast ? H[k + 2][k - 1] : 0.0f); x = Math.abs(p) + Math.abs(q) + Math.abs(r); if (x != 0.0f) { p = p / x; q = q / x; r = r / x; } } if (x == 0.0f) { break; } s = (float) Math.sqrt(p * p + q * q + r * r); if (p < 0) { s = -s; } if (s != 0) { if (k != m) { H[k][k - 1] = -s * x; } else if (l != m) { H[k][k - 1] = -H[k][k - 1]; } p = p + s; x = p / s; y = q / s; z = r / s; q = q / p; r = r / p; // Row modification for (int j = k; j < nn; j++) { p = H[k][j] + q * H[k + 1][j]; if (notlast) { p = p + r * H[k + 2][j]; H[k + 2][j] = H[k + 2][j] - p * z; } H[k][j] = H[k][j] - p * x; H[k + 1][j] = H[k + 1][j] - p * y; } // Column modification for (int i = 0; i <= Math.min(n, k + 3); i++) { p = x * H[i][k] + y * H[i][k + 1]; if (notlast) { p = p + z * H[i][k + 2]; H[i][k + 2] = H[i][k + 2] - p * r; } H[i][k] = H[i][k] - p; H[i][k + 1] = H[i][k + 1] - p * q; } // Accumulate transformations for (int i = low; i <= high; i++) { p = x * V[i][k] + y * V[i][k + 1]; if (notlast) { p = p + z * V[i][k + 2]; V[i][k + 2] = V[i][k + 2] - p * r; } V[i][k] = V[i][k] - p; V[i][k + 1] = V[i][k + 1] - p * q; } } // (s != 0) } // k loop } // check convergence } // while (n >= low) // Backsubstitute to find vectors of upper triangular form if (norm == 0.0f) { return; } for (n = nn - 1; n >= 0; n--) { p = d[n]; q = e[n]; // Real vector if (q == 0) { int l = n; H[n][n] = 1.0f; for (int i = n - 1; i >= 0; i--) { w = H[i][i] - p; r = 0.0f; for (int j = l; j <= n; j++) { r = r + H[i][j] * H[j][n]; } if (e[i] < 0.0f) { z = w; s = r; } else { l = i; if (e[i] == 0.0f) { if (w != 0.0f) { H[i][n] = -r / w; } else { H[i][n] = -r / (eps * norm); } // Solve real equations } else { x = H[i][i + 1]; y = H[i + 1][i]; q = (d[i] - p) * (d[i] - p) + e[i] * e[i]; t = (x * s - z * r) / q; H[i][n] = t; if (Math.abs(x) > Math.abs(z)) { H[i + 1][n] = (-r - w * t) / x; } else { H[i + 1][n] = (-s - y * t) / z; } } // Overflow control t = Math.abs(H[i][n]); if ((eps * t) * t > 1) { for (int j = i; j <= n; j++) { H[j][n] = H[j][n] / t; } } } } // Complex vector } else if (q < 0) { int l = n - 1; // Last vector component imaginary so matrix is triangular if (Math.abs(H[n][n - 1]) > Math.abs(H[n - 1][n])) { H[n - 1][n - 1] = q / H[n][n - 1]; H[n - 1][n] = -(H[n][n] - p) / H[n][n - 1]; } else { cdiv(0.0f, -H[n - 1][n], H[n - 1][n - 1] - p, q); H[n - 1][n - 1] = cdivr; H[n - 1][n] = cdivi; } H[n][n - 1] = 0.0f; H[n][n] = 1.0f; for (int i = n - 2; i >= 0; i--) { float ra, sa, vr, vi; ra = 0.0f; sa = 0.0f; for (int j = l; j <= n; j++) { ra = ra + H[i][j] * H[j][n - 1]; sa = sa + H[i][j] * H[j][n]; } w = H[i][i] - p; if (e[i] < 0.0f) { z = w; r = ra; s = sa; } else { l = i; if (e[i] == 0) { cdiv(-ra, -sa, w, q); H[i][n - 1] = cdivr; H[i][n] = cdivi; } else { // Solve complex equations x = H[i][i + 1]; y = H[i + 1][i]; vr = (d[i] - p) * (d[i] - p) + e[i] * e[i] - q * q; vi = (d[i] - p) * 2.0f * q; if (vr == 0.0f & vi == 0.0f) { vr = eps * norm * (Math.abs(w) + Math.abs(q) + Math.abs(x) + Math.abs(y) + Math.abs(z)); } cdiv(x * r - z * ra + q * sa, x * s - z * sa - q * ra, vr, vi); H[i][n - 1] = cdivr; H[i][n] = cdivi; if (Math.abs(x) > (Math.abs(z) + Math.abs(q))) { H[i + 1][n - 1] = (-ra - w * H[i][n - 1] + q * H[i][n]) / x; H[i + 1][n] = (-sa - w * H[i][n] - q * H[i][n - 1]) / x; } else { cdiv(-r - y * H[i][n - 1], -s - y * H[i][n], z, q); H[i + 1][n - 1] = cdivr; H[i + 1][n] = cdivi; } } // Overflow control t = Math.max(Math.abs(H[i][n - 1]), Math.abs(H[i][n])); if ((eps * t) * t > 1) { for (int j = i; j <= n; j++) { H[j][n - 1] = H[j][n - 1] / t; H[j][n] = H[j][n] / t; } } } } } } // Vectors of isolated roots for (int i = 0; i < nn; i++) { if (i < low | i > high) { for (int j = i; j < nn; j++) { V[i][j] = H[i][j]; } } } // Back transformation to get eigenvectors of original matrix for (int j = nn - 1; j >= low; j--) { for (int i = low; i <= high; i++) { z = 0.0f; for (int k = low; k <= Math.min(j, high); k++) { z = z + V[i][k] * H[k][j]; } V[i][j] = z; } } } /** * Nonsymmetric reduction to Hessenberg form. */ private void orthes() { // This is derived from the Algol procedures orthes and ortran, // by Martin and Wilkinson, Handbook for Auto. Comp., // Vol.ii-Linear Algebra, and the corresponding // Fortran subroutines in EISPACK. int low = 0; int high = n - 1; for (int m = low + 1; m <= high - 1; m++) { // Scale column. float scale = 0.0f; for (int i = m; i <= high; i++) { scale = scale + Math.abs(H[i][m - 1]); } if (scale != 0.0f) { // Compute Householder transformation. float h = 0.0f; for (int i = high; i >= m; i--) { ort[i] = H[i][m - 1] / scale; h += ort[i] * ort[i]; } float g = (float) Math.sqrt(h); if (ort[m] > 0) { g = -g; } h = h - ort[m] * g; ort[m] = ort[m] - g; // Apply Householder similarity transformation // H = (I-u*u'/h)*H*(I-u*u')/h) for (int j = m; j < n; j++) { float f = 0.0f; for (int i = high; i >= m; i--) { f += ort[i] * H[i][j]; } f = f / h; for (int i = m; i <= high; i++) { H[i][j] -= f * ort[i]; } } for (int i = 0; i <= high; i++) { float f = 0.0f; for (int j = high; j >= m; j--) { f += ort[j] * H[i][j]; } f = f / h; for (int j = m; j <= high; j++) { H[i][j] -= f * ort[j]; } } ort[m] = scale * ort[m]; H[m][m - 1] = scale * g; } } // Accumulate transformations (Algol's ortran). for (int i = 0; i < n; i++) { for (int j = 0; j < n; j++) { V[i][j] = (i == j ? 1.0f : 0.0f); } } for (int m = high - 1; m >= low + 1; m--) { if (H[m][m - 1] != 0.0f) { for (int i = m + 1; i <= high; i++) { ort[i] = H[i][m - 1]; } for (int j = m; j <= high; j++) { float g = 0.0f; for (int i = m; i <= high; i++) { g += ort[i] * V[i][j]; } // Float division avoids possible underflow g = (g / ort[m]) / H[m][m - 1]; for (int i = m; i <= high; i++) { V[i][j] += g * ort[i]; } } } } } /** * Returns a String with (propertyName, propertyValue) pairs. Useful for * debugging or to quickly get the rough picture. For example, * *

     * 	 rank          : 3
     * 	 trace         : 0
     * 
     * 
*/ public String toString() { StringBuffer buf = new StringBuffer(); String unknown = "Illegal operation or error: "; buf.append("---------------------------------------------------------------------\n"); buf.append("EigenvalueDecomposition(A) --> D, V, realEigenvalues, imagEigenvalues\n"); buf.append("---------------------------------------------------------------------\n"); buf.append("realEigenvalues = "); try { buf.append(String.valueOf(this.getRealEigenvalues())); } catch (IllegalArgumentException exc) { buf.append(unknown + exc.getMessage()); } buf.append("\nimagEigenvalues = "); try { buf.append(String.valueOf(this.getImagEigenvalues())); } catch (IllegalArgumentException exc) { buf.append(unknown + exc.getMessage()); } buf.append("\n\nD = "); try { buf.append(String.valueOf(this.getD())); } catch (IllegalArgumentException exc) { buf.append(unknown + exc.getMessage()); } buf.append("\n\nV = "); try { buf.append(String.valueOf(this.getV())); } catch (IllegalArgumentException exc) { buf.append(unknown + exc.getMessage()); } return buf.toString(); } /** * Symmetric tridiagonal QL algorithm. */ private void tql2() { // This is derived from the Algol procedures tql2, by // Bowdler, Martin, Reinsch, and Wilkinson, Handbook for // Auto. Comp., Vol.ii-Linear Algebra, and the corresponding // Fortran subroutine in EISPACK. for (int i = 1; i < n; i++) { e[i - 1] = e[i]; } e[n - 1] = 0.0f; float f = 0.0f; float tst1 = 0.0f; float eps = (float) Math.pow(2.0, -23.0); for (int l = 0; l < n; l++) { // Find small subdiagonal element tst1 = Math.max(tst1, Math.abs(d[l]) + Math.abs(e[l])); int m = l; while (m < n) { if (Math.abs(e[m]) <= eps * tst1) { break; } m++; } // If m == l, d[l] is an eigenvalue, // otherwise, iterate. if (m > l) { int iter = 0; do { iter = iter + 1; // (Could check iteration count here.) // Compute implicit shift float g = d[l]; float p = (d[l + 1] - g) / (2.0f * e[l]); float r = DenseFloatAlgebra.hypot(p, 1.0f); if (p < 0) { r = -r; } d[l] = e[l] / (p + r); d[l + 1] = e[l] * (p + r); float dl1 = d[l + 1]; float h = g - d[l]; for (int i = l + 2; i < n; i++) { d[i] -= h; } f = f + h; // Implicit QL transformation. p = d[m]; float c = 1.0f; float c2 = c; float c3 = c; float el1 = e[l + 1]; float s = 0.0f; float s2 = 0.0f; for (int i = m - 1; i >= l; i--) { c3 = c2; c2 = c; s2 = s; g = c * e[i]; h = c * p; r = DenseFloatAlgebra.hypot(p, e[i]); e[i + 1] = s * r; s = e[i] / r; c = p / r; p = c * d[i] - s * g; d[i + 1] = h + s * (c * g + s * d[i]); // Accumulate transformation. for (int k = 0; k < n; k++) { h = V[k][i + 1]; V[k][i + 1] = s * V[k][i] + c * h; V[k][i] = c * V[k][i] - s * h; } } p = -s * s2 * c3 * el1 * e[l] / dl1; e[l] = s * p; d[l] = c * p; // Check for convergence. } while (Math.abs(e[l]) > eps * tst1); } d[l] = d[l] + f; e[l] = 0.0f; } // Sort eigenvalues and corresponding vectors. for (int i = 0; i < n - 1; i++) { int k = i; float p = d[i]; for (int j = i + 1; j < n; j++) { if (d[j] < p) { k = j; p = d[j]; } } if (k != i) { d[k] = d[i]; d[i] = p; for (int j = 0; j < n; j++) { p = V[j][i]; V[j][i] = V[j][k]; V[j][k] = p; } } } } /** * Symmetric Householder reduction to tridiagonal form. */ private void tred2() { // This is derived from the Algol procedures tred2 by // Bowdler, Martin, Reinsch, and Wilkinson, Handbook for // Auto. Comp., Vol.ii-Linear Algebra, and the corresponding // Fortran subroutine in EISPACK. for (int j = 0; j < n; j++) { d[j] = V[n - 1][j]; } // Householder reduction to tridiagonal form. for (int i = n - 1; i > 0; i--) { // Scale to avoid under/overflow. float scale = 0.0f; float h = 0.0f; for (int k = 0; k < i; k++) { scale = scale + Math.abs(d[k]); } if (scale == 0.0f) { e[i] = d[i - 1]; for (int j = 0; j < i; j++) { d[j] = V[i - 1][j]; V[i][j] = 0.0f; V[j][i] = 0.0f; } } else { // Generate Householder vector. for (int k = 0; k < i; k++) { d[k] /= scale; h += d[k] * d[k]; } float f = d[i - 1]; float g = (float) Math.sqrt(h); if (f > 0) { g = -g; } e[i] = scale * g; h = h - f * g; d[i - 1] = f - g; for (int j = 0; j < i; j++) { e[j] = 0.0f; } // Apply similarity transformation to remaining columns. for (int j = 0; j < i; j++) { f = d[j]; V[j][i] = f; g = e[j] + V[j][j] * f; for (int k = j + 1; k <= i - 1; k++) { g += V[k][j] * d[k]; e[k] += V[k][j] * f; } e[j] = g; } f = 0.0f; for (int j = 0; j < i; j++) { e[j] /= h; f += e[j] * d[j]; } float hh = f / (h + h); for (int j = 0; j < i; j++) { e[j] -= hh * d[j]; } for (int j = 0; j < i; j++) { f = d[j]; g = e[j]; for (int k = j; k <= i - 1; k++) { V[k][j] -= (f * e[k] + g * d[k]); } d[j] = V[i - 1][j]; V[i][j] = 0.0f; } } d[i] = h; } // Accumulate transformations. for (int i = 0; i < n - 1; i++) { V[n - 1][i] = V[i][i]; V[i][i] = 1.0f; float h = d[i + 1]; if (h != 0.0f) { for (int k = 0; k <= i; k++) { d[k] = V[k][i + 1] / h; } for (int j = 0; j <= i; j++) { float g = 0.0f; for (int k = 0; k <= i; k++) { g += V[k][i + 1] * V[k][j]; } for (int k = 0; k <= i; k++) { V[k][j] -= g * d[k]; } } } for (int k = 0; k <= i; k++) { V[k][i + 1] = 0.0f; } } for (int j = 0; j < n; j++) { d[j] = V[n - 1][j]; V[n - 1][j] = 0.0f; } V[n - 1][n - 1] = 1.0f; e[0] = 0.0f; } }




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