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C*********************** Contents ****************************************
C* Principal Components Analysis: C, 638 lines. ****************************
C* Sample input data set (final 36 lines). *********************************
C***************************************************************************
/*********************************/
/* Principal Components Analysis */
/*********************************/
/*********************************************************************/
/* Principal Components Analysis or the Karhunen-Loeve expansion is a
classical method for dimensionality reduction or exploratory data
analysis. One reference among many is: F. Murtagh and A. Heck,
Multivariate Data Analysis, Kluwer Academic, Dordrecht, 1987.
Author:
F. Murtagh
Phone: + 49 89 32006298 (work)
+ 49 89 965307 (home)
Earn/Bitnet: fionn@dgaeso51, fim@dgaipp1s, murtagh@stsci
Span: esomc1::fionn
Internet: murtagh@scivax.stsci.edu
F. Murtagh, Munich, 6 June 1989 */
/*********************************************************************/
#include <stdio.h>
#include <string.h>
#include <math.h>
#define SIGN(a, b) ( (b) < 0 ? -fabs(a) : fabs(a) )
main(argc, argv)
int argc;
char *argv[];
{
FILE *stream;
int n, m, i, j, k, k2;
float **data, **matrix(), **symmat, **symmat2, *vector(), *evals, *interm;
void free_matrix(), free_vector(), corcol(), covcol(), scpcol();
void tred2(), tqli();
float in_value;
char option, *strncpy();
/*********************************************************************
Get from command line:
input data file name, #rows, #cols, option.
Open input file: fopen opens the file whose name is stored in the
pointer argv[argc-1]; if unsuccessful, error message is printed to
stderr.
*********************************************************************/
if (argc != 5)
{
printf("Syntax help: PCA filename #rows #cols option\n\n");
printf("(filename -- give full path name,\n");
printf(" #rows \n");
printf(" #cols -- integer values,\n");
printf(" option -- R (recommended) for correlation analysis,\n");
printf(" V for variance/covariance analysis\n");
printf(" S for SSCP analysis.)\n");
exit(1);
}
n = atoi(argv[2]); /* # rows */
m = atoi(argv[3]); /* # columns */
strncpy(&option,argv[4],1); /* Analysis option */
printf("No. of rows: %d, no. of columns: %d.\n",n,m);
printf("Input file: %s.\n",argv[1]);
if ((stream = fopen(argv[1],"r")) == NULL)
{
fprintf(stderr, "Program %s : cannot open file %s\n",
argv[0], argv[1]);
fprintf(stderr, "Exiting to system.");
exit(1);
/* Note: in versions of DOS prior to 3.0, argv[0] contains the
string "C". */
}
/* Now read in data. */
data = matrix(n, m); /* Storage allocation for input data */
for (i = 1; i <= n; i++)
{
for (j = 1; j <= m; j++)
{
fscanf(stream, "%f", &in_value);
data[i][j] = in_value;
}
}
/* Check on (part of) input data.
for (i = 1; i <= 18; i++) {for (j = 1; j <= 8; j++) {
printf("%7.1f", data[i][j]); } printf("\n"); }
*/
symmat = matrix(m, m); /* Allocation of correlation (etc.) matrix */
/* Look at analysis option; branch in accordance with this. */
switch(option)
{
case 'R':
case 'r':
printf("Analysis of correlations chosen.\n");
corcol(data, n, m, symmat);
/* Output correlation matrix.
for (i = 1; i <= m; i++) {
for (j = 1; j <= 8; j++) {
printf("%7.4f", symmat[i][j]); }
printf("\n"); }
*/
break;
case 'V':
case 'v':
printf("Analysis of variances-covariances chosen.\n");
covcol(data, n, m, symmat);
/* Output variance-covariance matrix.
for (i = 1; i <= m; i++) {
for (j = 1; j <= 8; j++) {
printf("%7.1f", symmat[i][j]); }
printf("\n"); }
*/
break;
case 'S':
case 's':
printf("Analysis of sums-of-squares-cross-products");
printf(" matrix chosen.\n");
scpcol(data, n, m, symmat);
/* Output SSCP matrix.
for (i = 1; i <= m; i++) {
for (j = 1; j <= 8; j++) {
printf("%7.1f", symmat[i][j]); }
printf("\n"); }
*/
break;
default:
printf("Option: %s\n",option);
printf("For option, please type R, V, or S\n");
printf("(upper or lower case).\n");
printf("Exiting to system.\n");
exit(1);
break;
}
/*********************************************************************
Eigen-reduction
**********************************************************************/
/* Allocate storage for dummy and new vectors. */
evals = vector(m); /* Storage alloc. for vector of eigenvalues */
interm = vector(m); /* Storage alloc. for 'intermediate' vector */
symmat2 = matrix(m, m); /* Duplicate of correlation (etc.) matrix */
for (i = 1; i <= m; i++) {
for (j = 1; j <= m; j++) {
symmat2[i][j] = symmat[i][j]; /* Needed below for col. projections */
}
}
tred2(symmat, m, evals, interm); /* Triangular decomposition */
tqli(evals, interm, m, symmat); /* Reduction of sym. trid. matrix */
/* evals now contains the eigenvalues,
columns of symmat now contain the associated eigenvectors. */
printf("\nEigenvalues:\n");
for (j = m; j >= 1; j--) {
printf("%18.5f\n", evals[j]); }
printf("\n(Eigenvalues should be strictly positive; limited\n");
printf("precision machine arithmetic may affect this.\n");
printf("Eigenvalues are often expressed as cumulative\n");
printf("percentages, representing the 'percentage variance\n");
printf("explained' by the associated axis or principal component.)\n");
printf("\nEigenvectors:\n");
printf("(First three; their definition in terms of original vbes.)\n");
for (j = 1; j <= m; j++) {
for (i = 1; i <= 3; i++) {
printf("%12.4f", symmat[j][m-i+1]); }
printf("\n"); }
/* Form projections of row-points on first three prin. components. */
/* Store in 'data', overwriting original data. */
for (i = 1; i <= n; i++) {
for (j = 1; j <= m; j++) {
interm[j] = data[i][j]; } /* data[i][j] will be overwritten */
for (k = 1; k <= 3; k++) {
data[i][k] = 0.0;
for (k2 = 1; k2 <= m; k2++) {
data[i][k] += interm[k2] * symmat[k2][m-k+1]; }
}
}
printf("\nProjections of row-points on first 3 prin. comps.:\n");
for (i = 1; i <= n; i++) {
for (j = 1; j <= 3; j++) {
printf("%12.4f", data[i][j]); }
printf("\n"); }
/* Form projections of col.-points on first three prin. components. */
/* Store in 'symmat2', overwriting what was stored in this. */
for (j = 1; j <= m; j++) {
for (k = 1; k <= m; k++) {
interm[k] = symmat2[j][k]; } /*symmat2[j][k] will be overwritten*/
for (i = 1; i <= 3; i++) {
symmat2[j][i] = 0.0;
for (k2 = 1; k2 <= m; k2++) {
symmat2[j][i] += interm[k2] * symmat[k2][m-i+1]; }
if (evals[m-i+1] > 0.0005) /* Guard against zero eigenvalue */
symmat2[j][i] /= sqrt(evals[m-i+1]); /* Rescale */
else
symmat2[j][i] = 0.0; /* Standard kludge */
}
}
printf("\nProjections of column-points on first 3 prin. comps.:\n");
for (j = 1; j <= m; j++) {
for (k = 1; k <= 3; k++) {
printf("%12.4f", symmat2[j][k]); }
printf("\n"); }
free_matrix(data, n, m);
free_matrix(symmat, m, m);
free_matrix(symmat2, m, m);
free_vector(evals, m);
free_vector(interm, m);
}
/** Correlation matrix: creation ***********************************/
void corcol(data, n, m, symmat)
float **data, **symmat;
int n, m;
/* Create m * m correlation matrix from given n * m data matrix. */
{
float eps = 0.005;
float x, *mean, *stddev, *vector();
int i, j, j1, j2;
/* Allocate storage for mean and std. dev. vectors */
mean = vector(m);
stddev = vector(m);
/* Determine mean of column vectors of input data matrix */
for (j = 1; j <= m; j++)
{
mean[j] = 0.0;
for (i = 1; i <= n; i++)
{
mean[j] += data[i][j];
}
mean[j] /= (float)n;
}
printf("\nMeans of column vectors:\n");
for (j = 1; j <= m; j++) {
printf("%7.1f",mean[j]); } printf("\n");
/* Determine standard deviations of column vectors of data matrix. */
for (j = 1; j <= m; j++)
{
stddev[j] = 0.0;
for (i = 1; i <= n; i++)
{
stddev[j] += ( ( data[i][j] - mean[j] ) *
( data[i][j] - mean[j] ) );
}
stddev[j] /= (float)n;
stddev[j] = sqrt(stddev[j]);
/* The following in an inelegant but usual way to handle
near-zero std. dev. values, which below would cause a zero-
divide. */
if (stddev[j] <= eps) stddev[j] = 1.0;
}
printf("\nStandard deviations of columns:\n");
for (j = 1; j <= m; j++) { printf("%7.1f", stddev[j]); }
printf("\n");
/* Center and reduce the column vectors. */
for (i = 1; i <= n; i++)
{
for (j = 1; j <= m; j++)
{
data[i][j] -= mean[j];
x = sqrt((float)n);
x *= stddev[j];
data[i][j] /= x;
}
}
/* Calculate the m * m correlation matrix. */
for (j1 = 1; j1 <= m-1; j1++)
{
symmat[j1][j1] = 1.0;
for (j2 = j1+1; j2 <= m; j2++)
{
symmat[j1][j2] = 0.0;
for (i = 1; i <= n; i++)
{
symmat[j1][j2] += ( data[i][j1] * data[i][j2]);
}
symmat[j2][j1] = symmat[j1][j2];
}
}
symmat[m][m] = 1.0;
return;
}
/** Variance-covariance matrix: creation *****************************/
void covcol(data, n, m, symmat)
float **data, **symmat;
int n, m;
/* Create m * m covariance matrix from given n * m data matrix. */
{
float *mean, *vector();
int i, j, j1, j2;
/* Allocate storage for mean vector */
mean = vector(m);
/* Determine mean of column vectors of input data matrix */
for (j = 1; j <= m; j++)
{
mean[j] = 0.0;
for (i = 1; i <= n; i++)
{
mean[j] += data[i][j];
}
mean[j] /= (float)n;
}
printf("\nMeans of column vectors:\n");
for (j = 1; j <= m; j++) {
printf("%7.1f",mean[j]); } printf("\n");
/* Center the column vectors. */
for (i = 1; i <= n; i++)
{
for (j = 1; j <= m; j++)
{
data[i][j] -= mean[j];
}
}
/* Calculate the m * m covariance matrix. */
for (j1 = 1; j1 <= m; j1++)
{
for (j2 = j1; j2 <= m; j2++)
{
symmat[j1][j2] = 0.0;
for (i = 1; i <= n; i++)
{
symmat[j1][j2] += data[i][j1] * data[i][j2];
}
symmat[j2][j1] = symmat[j1][j2];
}
}
return;
}
/** Sums-of-squares-and-cross-products matrix: creation **************/
void scpcol(data, n, m, symmat)
float **data, **symmat;
int n, m;
/* Create m * m sums-of-cross-products matrix from n * m data matrix. */
{
int i, j1, j2;
/* Calculate the m * m sums-of-squares-and-cross-products matrix. */
for (j1 = 1; j1 <= m; j1++)
{
for (j2 = j1; j2 <= m; j2++)
{
symmat[j1][j2] = 0.0;
for (i = 1; i <= n; i++)
{
symmat[j1][j2] += data[i][j1] * data[i][j2];
}
symmat[j2][j1] = symmat[j1][j2];
}
}
return;
}
/** Error handler **************************************************/
void erhand(err_msg)
char err_msg[];
/* Error handler */
{
fprintf(stderr,"Run-time error:\n");
fprintf(stderr,"%s\n", err_msg);
fprintf(stderr,"Exiting to system.\n");
exit(1);
}
/** Allocation of vector storage ***********************************/
float *vector(n)
int n;
/* Allocates a float vector with range [1..n]. */
{
float *v;
v = (float *) malloc ((unsigned) n*sizeof(float));
if (!v) erhand("Allocation failure in vector().");
return v-1;
}
/** Allocation of float matrix storage *****************************/
float **matrix(n,m)
int n, m;
/* Allocate a float matrix with range [1..n][1..m]. */
{
int i;
float **mat;
/* Allocate pointers to rows. */
mat = (float **) malloc((unsigned) (n)*sizeof(float*));
if (!mat) erhand("Allocation failure 1 in matrix().");
mat -= 1;
/* Allocate rows and set pointers to them. */
for (i = 1; i <= n; i++)
{
mat[i] = (float *) malloc((unsigned) (m)*sizeof(float));
if (!mat[i]) erhand("Allocation failure 2 in matrix().");
mat[i] -= 1;
}
/* Return pointer to array of pointers to rows. */
return mat;
}
/** Deallocate vector storage *********************************/
void free_vector(v,n)
float *v;
int n;
/* Free a float vector allocated by vector(). */
{
free((char*) (v+1));
}
/** Deallocate float matrix storage ***************************/
void free_matrix(mat,n,m)
float **mat;
int n, m;
/* Free a float matrix allocated by matrix(). */
{
int i;
for (i = n; i >= 1; i--)
{
free ((char*) (mat[i]+1));
}
free ((char*) (mat+1));
}
/** Reduce a real, symmetric matrix to a symmetric, tridiag. matrix. */
void tred2(a, n, d, e)
float **a, *d, *e;
/* float **a, d[], e[]; */
int n;
/* Householder reduction of matrix a to tridiagonal form.
Algorithm: Martin et al., Num. Math. 11, 181-195, 1968.
Ref: Smith et al., Matrix Eigensystem Routines -- EISPACK Guide
Springer-Verlag, 1976, pp. 489-494.
W H Press et al., Numerical Recipes in C, Cambridge U P,
1988, pp. 373-374. */
{
int l, k, j, i;
float scale, hh, h, g, f;
for (i = n; i >= 2; i--)
{
l = i - 1;
h = scale = 0.0;
if (l > 1)
{
for (k = 1; k <= l; k++)
scale += fabs(a[i][k]);
if (scale == 0.0)
e[i] = a[i][l];
else
{
for (k = 1; k <= l; k++)
{
a[i][k] /= scale;
h += a[i][k] * a[i][k];
}
f = a[i][l];
g = f>0 ? -sqrt(h) : sqrt(h);
e[i] = scale * g;
h -= f * g;
a[i][l] = f - g;
f = 0.0;
for (j = 1; j <= l; j++)
{
a[j][i] = a[i][j]/h;
g = 0.0;
for (k = 1; k <= j; k++)
g += a[j][k] * a[i][k];
for (k = j+1; k <= l; k++)
g += a[k][j] * a[i][k];
e[j] = g / h;
f += e[j] * a[i][j];
}
hh = f / (h + h);
for (j = 1; j <= l; j++)
{
f = a[i][j];
e[j] = g = e[j] - hh * f;
for (k = 1; k <= j; k++)
a[j][k] -= (f * e[k] + g * a[i][k]);
}
}
}
else
e[i] = a[i][l];
d[i] = h;
}
d[1] = 0.0;
e[1] = 0.0;
for (i = 1; i <= n; i++)
{
l = i - 1;
if (d[i])
{
for (j = 1; j <= l; j++)
{
g = 0.0;
for (k = 1; k <= l; k++)
g += a[i][k] * a[k][j];
for (k = 1; k <= l; k++)
a[k][j] -= g * a[k][i];
}
}
d[i] = a[i][i];
a[i][i] = 1.0;
for (j = 1; j <= l; j++)
a[j][i] = a[i][j] = 0.0;
}
}
/** Tridiagonal QL algorithm -- Implicit **********************/
void tqli(d, e, n, z)
float d[], e[], **z;
int n;
{
int m, l, iter, i, k;
float s, r, p, g, f, dd, c, b;
void erhand();
for (i = 2; i <= n; i++)
e[i-1] = e[i];
e[n] = 0.0;
for (l = 1; l <= n; l++)
{
iter = 0;
do
{
for (m = l; m <= n-1; m++)
{
dd = fabs(d[m]) + fabs(d[m+1]);
if (fabs(e[m]) + dd == dd) break;
}
if (m != l)
{
if (iter++ == 30) erhand("No convergence in TLQI.");
g = (d[l+1] - d[l]) / (2.0 * e[l]);
r = sqrt((g * g) + 1.0);
g = d[m] - d[l] + e[l] / (g + SIGN(r, g));
s = c = 1.0;
p = 0.0;
for (i = m-1; i >= l; i--)
{
f = s * e[i];
b = c * e[i];
if (fabs(f) >= fabs(g))
{
c = g / f;
r = sqrt((c * c) + 1.0);
e[i+1] = f * r;
c *= (s = 1.0/r);
}
else
{
s = f / g;
r = sqrt((s * s) + 1.0);
e[i+1] = g * r;
s *= (c = 1.0/r);
}
g = d[i+1] - p;
r = (d[i] - g) * s + 2.0 * c * b;
p = s * r;
d[i+1] = g + p;
g = c * r - b;
for (k = 1; k <= n; k++)
{
f = z[k][i+1];
z[k][i+1] = s * z[k][i] + c * f;
z[k][i] = c * z[k][i] - s * f;
}
}
d[l] = d[l] - p;
e[l] = g;
e[m] = 0.0;
}
} while (m != l);
}
}
C***************************************************************************
3.0 3.0 3.0 3.0 3.0 3.0 35.0 45.0
53.0 55.0 58.0 113.0 113.0 86.0 67.0 90.0
3.5 3.5 4.0 4.0 4.5 4.5 46.0 59.0
63.0 58.0 58.0 125.0 126.0 110.0 78.0 97.0
4.0 4.0 4.5 4.5 5.0 5.0 48.0 60.0
68.0 65.0 65.0 123.0 123.0 117.0 87.0 108.0
5.0 5.0 5.0 5.5 5.5 5.5 46.0 63.0
70.0 64.0 63.0 116.0 119.0 115.0 97.0 112.0
6.0 6.0 6.0 6.0 6.5 6.5 51.0 69.0
77.0 70.0 71.0 120.0 122.0 122.0 96.0 123.0
11.0 11.0 11.0 11.0 11.0 11.0 64.0 75.0
81.0 79.0 79.0 112.0 114.0 113.0 98.0 115.0
20.0 20.0 20.0 20.0 20.0 20.0 76.0 86.0
93.0 92.0 91.0 104.0 104.5 107.0 97.5 104.0
30.0 30.0 30.0 30.0 30.1 30.2 84.0 96.0
98.0 99.0 96.0 101.0 102.0 99.0 94.0 99.0
30.0 33.4 36.8 40.0 43.0 45.6 100.0 106.0
106.0 108.0 101.0 99.0 98.0 99.0 95.0 95.0
42.0 44.0 46.0 48.0 50.0 51.0 109.0 111.0
110.0 110.0 103.0 95.5 95.5 95.0 92.5 92.0
60.0 61.7 63.5 65.5 67.3 69.2 122.0 124.0
124.0 121.0 103.0 93.2 92.5 92.2 90.0 90.8
70.0 70.1 70.2 70.3 70.4 70.5 137.0 132.0
134.0 128.0 101.0 91.7 90.2 88.8 87.3 85.8
78.0 77.6 77.2 76.8 76.4 76.0 167.0 159.0
152.0 144.0 103.0 89.8 87.7 85.7 83.7 81.8
98.9 97.8 96.7 95.5 94.3 93.2 183.0 172.0
162.0 152.0 102.0 87.5 85.3 83.3 81.3 79.3
160.0 157.0 155.0 152.0 149.0 147.0 186.0 175.0
165.0 156.0 120.0 87.0 84.9 82.8 80.8 79.0
272.0 266.0 260.0 254.0 248.0 242.0 192.0 182.0
170.0 159.0 131.0 88.0 85.8 83.7 81.6 79.6
382.0 372.0 362.0 352.0 343.0 333.0 205.0 192.0
178.0 166.0 138.0 86.2 84.0 82.0 79.8 77.5
770.0 740.0 710.0 680.0 650.0 618.0 226.0 207.0
195.0 180.0 160.0 82.9 80.2 77.7 75.2 72.7
C***************************************************************************
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