fast & efficient least squares fit algorithm in C? - c

I am trying to implement a linear least squares fit onto 2 arrays of data: time vs amplitude. The only technique I know so far is to test all of the possible m and b points in (y = m*x+b) and then find out which combination fits my data best so that it has the least error. However, I think iterating so many combinations is sometimes useless because it tests out everything. Are there any techniques to speed up the process that I don't know about? Thanks.

Try this code. It fits y = mx + b to your (x,y) data.
The arguments to linreg are
linreg(int n, REAL x[], REAL y[], REAL* b, REAL* m, REAL* r)
n = number of data points
x,y = arrays of data
*b = output intercept
*m = output slope
*r = output correlation coefficient (can be NULL if you don't want it)
The return value is 0 on success, !=0 on failure.
Here's the code
#include "linreg.h"
#include <stdlib.h>
#include <math.h> /* math functions */
//#define REAL float
#define REAL double
inline static REAL sqr(REAL x) {
return x*x;
}
int linreg(int n, const REAL x[], const REAL y[], REAL* m, REAL* b, REAL* r){
REAL sumx = 0.0; /* sum of x */
REAL sumx2 = 0.0; /* sum of x**2 */
REAL sumxy = 0.0; /* sum of x * y */
REAL sumy = 0.0; /* sum of y */
REAL sumy2 = 0.0; /* sum of y**2 */
for (int i=0;i<n;i++){
sumx += x[i];
sumx2 += sqr(x[i]);
sumxy += x[i] * y[i];
sumy += y[i];
sumy2 += sqr(y[i]);
}
REAL denom = (n * sumx2 - sqr(sumx));
if (denom == 0) {
// singular matrix. can't solve the problem.
*m = 0;
*b = 0;
if (r) *r = 0;
return 1;
}
*m = (n * sumxy - sumx * sumy) / denom;
*b = (sumy * sumx2 - sumx * sumxy) / denom;
if (r!=NULL) {
*r = (sumxy - sumx * sumy / n) / /* compute correlation coeff */
sqrt((sumx2 - sqr(sumx)/n) *
(sumy2 - sqr(sumy)/n));
}
return 0;
}
Example
You can run this example online.
int main()
{
int n = 6;
REAL x[6]= {1, 2, 4, 5, 10, 20};
REAL y[6]= {4, 6, 12, 15, 34, 68};
REAL m,b,r;
linreg(n,x,y,&m,&b,&r);
printf("m=%g b=%g r=%g\n",m,b,r);
return 0;
}
Here is the output
m=3.43651 b=-0.888889 r=0.999192
Here is the Excel plot and linear fit (for verification).
All values agree exactly with the C code above (note C code returns r while Excel returns R**2).

There are efficient algorithms for least-squares fitting; see Wikipedia for details. There are also libraries that implement the algorithms for you, likely more efficiently than a naive implementation would do; the GNU Scientific Library is one example, but there are others under more lenient licenses as well.

From Numerical Recipes: The Art of Scientific Computing in (15.2) Fitting Data to a Straight Line:
Linear Regression:
Consider the problem of fitting a set of N data points (xi, yi) to a straight-line model:
Assume that the uncertainty: sigmai associated with each yi and that the xi’s (values of the dependent variable) are known exactly. To measure how well the model agrees with the data, we use the chi-square function, which in this case is:
The above equation is minimized to determine a and b. This is done by finding the derivative of the above equation with respect to a and b, equate them to zero and solve for a and b. Then we estimate the probable uncertainties in the estimates of a and b, since obviously the measurement errors in the data must introduce some uncertainty in the determination of those parameters. Additionally, we must estimate the goodness-of-fit of the data to the
model. Absent this estimate, we have not the slightest indication that the parameters a and b in the model have any meaning at all.
The below struct performs the mentioned calculations:
struct Fitab {
// Object for fitting a straight line y = a + b*x to a set of
// points (xi, yi), with or without available
// errors sigma i . Call one of the two constructors to calculate the fit.
// The answers are then available as the variables:
// a, b, siga, sigb, chi2, and either q or sigdat.
int ndata;
double a, b, siga, sigb, chi2, q, sigdat; // Answers.
vector<double> &x, &y, &sig;
// Constructor.
Fitab(vector<double> &xx, vector<double> &yy, vector<double> &ssig)
: ndata(xx.size()), x(xx), y(yy), sig(ssig), chi2(0.), q(1.), sigdat(0.)
{
// Given a set of data points x[0..ndata-1], y[0..ndata-1]
// with individual standard deviations sig[0..ndata-1],
// sets a,b and their respective probable uncertainties
// siga and sigb, the chi-square: chi2, and the goodness-of-fit
// probability: q
Gamma gam;
int i;
double ss=0., sx=0., sy=0., st2=0., t, wt, sxoss; b=0.0;
for (i=0;i < ndata; i++) { // Accumulate sums ...
wt = 1.0 / SQR(sig[i]); //...with weights
ss += wt;
sx += x[i]*wt;
sy += y[i]*wt;
}
sxoss = sx/ss;
for (i=0; i < ndata; i++) {
t = (x[i]-sxoss) / sig[i];
st2 += t*t;
b += t*y[i]/sig[i];
}
b /= st2; // Solve for a, b, sigma-a, and simga-b.
a = (sy-sx*b) / ss;
siga = sqrt((1.0+sx*sx/(ss*st2))/ss);
sigb = sqrt(1.0/st2); // Calculate chi2.
for (i=0;i<ndata;i++) chi2 += SQR((y[i]-a-b*x[i])/sig[i]);
if (ndata>2) q=gam.gammq(0.5*(ndata-2),0.5*chi2); // goodness of fit
}
// Constructor.
Fitab(vector<double> &xx, vector<double> &yy)
: ndata(xx.size()), x(xx), y(yy), sig(xx), chi2(0.), q(1.), sigdat(0.)
{
// As above, but without known errors (sig is not used).
// The uncertainties siga and sigb are estimated by assuming
// equal errors for all points, and that a straight line is
// a good fit. q is returned as 1.0, the normalization of chi2
// is to unit standard deviation on all points, and sigdat
// is set to the estimated error of each point.
int i;
double ss,sx=0.,sy=0.,st2=0.,t,sxoss;
b=0.0; // Accumulate sums ...
for (i=0; i < ndata; i++) {
sx += x[i]; // ...without weights.
sy += y[i];
}
ss = ndata;
sxoss = sx/ss;
for (i=0;i < ndata; i++) {
t = x[i]-sxoss;
st2 += t*t;
b += t*y[i];
}
b /= st2; // Solve for a, b, sigma-a, and sigma-b.
a = (sy-sx*b)/ss;
siga=sqrt((1.0+sx*sx/(ss*st2))/ss);
sigb=sqrt(1.0/st2); // Calculate chi2.
for (i=0;i<ndata;i++) chi2 += SQR(y[i]-a-b*x[i]);
if (ndata > 2) sigdat=sqrt(chi2/(ndata-2));
// For unweighted data evaluate typical
// sig using chi2, and adjust
// the standard deviations.
siga *= sigdat;
sigb *= sigdat;
}
};
where struct Gamma:
struct Gamma : Gauleg18 {
// Object for incomplete gamma function.
// Gauleg18 provides coefficients for Gauss-Legendre quadrature.
static const Int ASWITCH=100; When to switch to quadrature method.
static const double EPS; // See end of struct for initializations.
static const double FPMIN;
double gln;
double gammp(const double a, const double x) {
// Returns the incomplete gamma function P(a,x)
if (x < 0.0 || a <= 0.0) throw("bad args in gammp");
if (x == 0.0) return 0.0;
else if ((Int)a >= ASWITCH) return gammpapprox(a,x,1); // Quadrature.
else if (x < a+1.0) return gser(a,x); // Use the series representation.
else return 1.0-gcf(a,x); // Use the continued fraction representation.
}
double gammq(const double a, const double x) {
// Returns the incomplete gamma function Q(a,x) = 1 - P(a,x)
if (x < 0.0 || a <= 0.0) throw("bad args in gammq");
if (x == 0.0) return 1.0;
else if ((Int)a >= ASWITCH) return gammpapprox(a,x,0); // Quadrature.
else if (x < a+1.0) return 1.0-gser(a,x); // Use the series representation.
else return gcf(a,x); // Use the continued fraction representation.
}
double gser(const Doub a, const Doub x) {
// Returns the incomplete gamma function P(a,x) evaluated by its series representation.
// Also sets ln (gamma) as gln. User should not call directly.
double sum,del,ap;
gln=gammln(a);
ap=a;
del=sum=1.0/a;
for (;;) {
++ap;
del *= x/ap;
sum += del;
if (fabs(del) < fabs(sum)*EPS) {
return sum*exp(-x+a*log(x)-gln);
}
}
}
double gcf(const Doub a, const Doub x) {
// Returns the incomplete gamma function Q(a, x) evaluated
// by its continued fraction representation.
// Also sets ln (gamma) as gln. User should not call directly.
int i;
double an,b,c,d,del,h;
gln=gammln(a);
b=x+1.0-a; // Set up for evaluating continued fraction
// by modified Lentz’s method with with b0 = 0.
c=1.0/FPMIN;
d=1.0/b;
h=d;
for (i=1;;i++) {
// Iterate to convergence.
an = -i*(i-a);
b += 2.0;
d=an*d+b;
if (fabs(d) < FPMIN) d=FPMIN;
c=b+an/c;
if (fabs(c) < FPMIN) c=FPMIN;
d=1.0/d;
del=d*c;
h *= del;
if (fabs(del-1.0) <= EPS) break;
}
return exp(-x+a*log(x)-gln)*h; Put factors in front.
}
double gammpapprox(double a, double x, int psig) {
// Incomplete gamma by quadrature. Returns P(a,x) or Q(a, x),
// when psig is 1 or 0, respectively. User should not call directly.
int j;
double xu,t,sum,ans;
double a1 = a-1.0, lna1 = log(a1), sqrta1 = sqrt(a1);
gln = gammln(a);
// Set how far to integrate into the tail:
if (x > a1) xu = MAX(a1 + 11.5*sqrta1, x + 6.0*sqrta1);
else xu = MAX(0.,MIN(a1 - 7.5*sqrta1, x - 5.0*sqrta1));
sum = 0;
for (j=0;j<ngau;j++) { // Gauss-Legendre.
t = x + (xu-x)*y[j];
sum += w[j]*exp(-(t-a1)+a1*(log(t)-lna1));
}
ans = sum*(xu-x)*exp(a1*(lna1-1.)-gln);
return (psig?(ans>0.0? 1.0-ans:-ans):(ans>=0.0? ans:1.0+ans));
}
double invgammp(Doub p, Doub a);
// Inverse function on x of P(a,x) .
};
const Doub Gamma::EPS = numeric_limits<Doub>::epsilon();
const Doub Gamma::FPMIN = numeric_limits<Doub>::min()/EPS
and stuct Gauleg18:
struct Gauleg18 {
// Abscissas and weights for Gauss-Legendre quadrature.
static const Int ngau = 18;
static const Doub y[18];
static const Doub w[18];
};
const Doub Gauleg18::y[18] = {0.0021695375159141994,
0.011413521097787704,0.027972308950302116,0.051727015600492421,
0.082502225484340941, 0.12007019910960293,0.16415283300752470,
0.21442376986779355, 0.27051082840644336, 0.33199876341447887,
0.39843234186401943, 0.46931971407375483, 0.54413605556657973,
0.62232745288031077, 0.70331500465597174, 0.78649910768313447,
0.87126389619061517, 0.95698180152629142};
const Doub Gauleg18::w[18] = {0.0055657196642445571,
0.012915947284065419,0.020181515297735382,0.027298621498568734,
0.034213810770299537,0.040875750923643261,0.047235083490265582,
0.053244713977759692,0.058860144245324798,0.064039797355015485
0.068745323835736408,0.072941885005653087,0.076598410645870640,
0.079687828912071670,0.082187266704339706,0.084078218979661945,
0.085346685739338721,0.085983275670394821};
and, finally fuinction Gamma::invgamp():
double Gamma::invgammp(double p, double a) {
// Returns x such that P(a,x) = p for an argument p between 0 and 1.
int j;
double x,err,t,u,pp,lna1,afac,a1=a-1;
const double EPS=1.e-8; // Accuracy is the square of EPS.
gln=gammln(a);
if (a <= 0.) throw("a must be pos in invgammap");
if (p >= 1.) return MAX(100.,a + 100.*sqrt(a));
if (p <= 0.) return 0.0;
if (a > 1.) {
lna1=log(a1);
afac = exp(a1*(lna1-1.)-gln);
pp = (p < 0.5)? p : 1. - p;
t = sqrt(-2.*log(pp));
x = (2.30753+t*0.27061)/(1.+t*(0.99229+t*0.04481)) - t;
if (p < 0.5) x = -x;
x = MAX(1.e-3,a*pow(1.-1./(9.*a)-x/(3.*sqrt(a)),3));
} else {
t = 1.0 - a*(0.253+a*0.12); and (6.2.9).
if (p < t) x = pow(p/t,1./a);
else x = 1.-log(1.-(p-t)/(1.-t));
}
for (j=0;j<12;j++) {
if (x <= 0.0) return 0.0; // x too small to compute accurately.
err = gammp(a,x) - p;
if (a > 1.) t = afac*exp(-(x-a1)+a1*(log(x)-lna1));
else t = exp(-x+a1*log(x)-gln);
u = err/t;
// Halley’s method.
x -= (t = u/(1.-0.5*MIN(1.,u*((a-1.)/x - 1))));
// Halve old value if x tries to go negative.
if (x <= 0.) x = 0.5*(x + t);
if (fabs(t) < EPS*x ) break;
}
return x;
}

Here is my version of a C/C++ function that does simple linear regression. The calculations follow the wikipedia article on simple linear regression. This is published as a single-header public-domain (MIT) library on github: simple_linear_regression. The library (.h file) is tested to work on Linux and Windows, and from C and C++ using -Wall -Werror and all -std versions supported by clang/gcc.
#define SIMPLE_LINEAR_REGRESSION_ERROR_INPUT_VALUE -2
#define SIMPLE_LINEAR_REGRESSION_ERROR_NUMERIC -3
int simple_linear_regression(const double * x, const double * y, const int n, double * slope_out, double * intercept_out, double * r2_out) {
double sum_x = 0.0;
double sum_xx = 0.0;
double sum_xy = 0.0;
double sum_y = 0.0;
double sum_yy = 0.0;
double n_real = (double)(n);
int i = 0;
double slope = 0.0;
double denominator = 0.0;
if (x == NULL || y == NULL || n < 2) {
return SIMPLE_LINEAR_REGRESSION_ERROR_INPUT_VALUE;
}
for (i = 0; i < n; ++i) {
sum_x += x[i];
sum_xx += x[i] * x[i];
sum_xy += x[i] * y[i];
sum_y += y[i];
sum_yy += y[i] * y[i];
}
denominator = n_real * sum_xx - sum_x * sum_x;
if (denominator == 0.0) {
return SIMPLE_LINEAR_REGRESSION_ERROR_NUMERIC;
}
slope = (n_real * sum_xy - sum_x * sum_y) / denominator;
if (slope_out != NULL) {
*slope_out = slope;
}
if (intercept_out != NULL) {
*intercept_out = (sum_y - slope * sum_x) / n_real;
}
if (r2_out != NULL) {
denominator = ((n_real * sum_xx) - (sum_x * sum_x)) * ((n_real * sum_yy) - (sum_y * sum_y));
if (denominator == 0.0) {
return SIMPLE_LINEAR_REGRESSION_ERROR_NUMERIC;
}
*r2_out = ((n_real * sum_xy) - (sum_x * sum_y)) * ((n_real * sum_xy) - (sum_x * sum_y)) / denominator;
}
return 0;
}
Usage example:
#define SIMPLE_LINEAR_REGRESSION_IMPLEMENTATION
#include "simple_linear_regression.h"
#include <stdio.h>
/* Some data that we want to find the slope, intercept and r2 for */
static const double x[] = { 1.47, 1.50, 1.52, 1.55, 1.57, 1.60, 1.63, 1.65, 1.68, 1.70, 1.73, 1.75, 1.78, 1.80, 1.83 };
static const double y[] = { 52.21, 53.12, 54.48, 55.84, 57.20, 58.57, 59.93, 61.29, 63.11, 64.47, 66.28, 68.10, 69.92, 72.19, 74.46 };
int main() {
double slope = 0.0;
double intercept = 0.0;
double r2 = 0.0;
int res = 0;
res = simple_linear_regression(x, y, sizeof(x) / sizeof(x[0]), &slope, &intercept, &r2);
if (res < 0) {
printf("Error: %s\n", simple_linear_regression_error_string(res));
return res;
}
printf("slope: %f\n", slope);
printf("intercept: %f\n", intercept);
printf("r2: %f\n", r2);
return 0;
}

The original example above worked well for me with slope and offset but I had a hard time with the corr coef. Maybe I don't have my parenthesis working the same as the assumed precedence? Anyway, with some help of other web pages I finally got values that match the linear trend-line in Excel. Thought I would share my code using Mark Lakata's variable names. Hope this helps.
double slope = ((n * sumxy) - (sumx * sumy )) / denom;
double intercept = ((sumy * sumx2) - (sumx * sumxy)) / denom;
double term1 = ((n * sumxy) - (sumx * sumy));
double term2 = ((n * sumx2) - (sumx * sumx));
double term3 = ((n * sumy2) - (sumy * sumy));
double term23 = (term2 * term3);
double r2 = 1.0;
if (fabs(term23) > MIN_DOUBLE) // Define MIN_DOUBLE somewhere as 1e-9 or similar
r2 = (term1 * term1) / term23;

as an assignment I had to code in C a simple linear regression using RMSE loss function. The program is dynamic and you can enter your own values and choose your own loss function which is for now limited to Root Mean Square Error. But first here are the algorithms I used:
now the code... you need gnuplot to display the chart, sudo apt install gnuplot
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <sys/types.h>
#define BUFFSIZE 64
#define MAXSIZE 100
static double vector_x[MAXSIZE] = {0};
static double vector_y[MAXSIZE] = {0};
static double vector_predict[MAXSIZE] = {0};
static double max_x;
static double max_y;
static double mean_x;
static double mean_y;
static double teta_0_intercept;
static double teta_1_grad;
static double RMSE;
static double r_square;
static double prediction;
static char intercept[BUFFSIZE];
static char grad[BUFFSIZE];
static char xrange[BUFFSIZE];
static char yrange[BUFFSIZE];
static char lossname_RMSE[BUFFSIZE] = "Simple Linear Regression using RMSE'";
static char cmd_gnu_0[BUFFSIZE] = "set title '";
static char cmd_gnu_1[BUFFSIZE] = "intercept = ";
static char cmd_gnu_2[BUFFSIZE] = "grad = ";
static char cmd_gnu_3[BUFFSIZE] = "set xrange [0:";
static char cmd_gnu_4[BUFFSIZE] = "set yrange [0:";
static char cmd_gnu_5[BUFFSIZE] = "f(x) = (grad * x) + intercept";
static char cmd_gnu_6[BUFFSIZE] = "plot f(x), 'data.temp' with points pointtype 7";
static char const *commands_gnuplot[] = {
cmd_gnu_0,
cmd_gnu_1,
cmd_gnu_2,
cmd_gnu_3,
cmd_gnu_4,
cmd_gnu_5,
cmd_gnu_6,
};
static size_t size;
static void user_input()
{
printf("Enter x,y vector size, MAX = 100\n");
scanf("%lu", &size);
if (size > MAXSIZE) {
printf("Wrong input size is too big\n");
user_input();
}
printf("vector's size is %lu\n", size);
size_t i;
for (i = 0; i < size; i++) {
printf("Enter vector_x[%ld] values\n", i);
scanf("%lf", &vector_x[i]);
}
for (i = 0; i < size; i++) {
printf("Enter vector_y[%ld] values\n", i);
scanf("%lf", &vector_y[i]);
}
}
static void display_vector()
{
size_t i;
for (i = 0; i < size; i++){
printf("vector_x[%lu] = %lf\t", i, vector_x[i]);
printf("vector_y[%lu] = %lf\n", i, vector_y[i]);
}
}
static void concatenate(char p[], char q[]) {
int c;
int d;
c = 0;
while (p[c] != '\0') {
c++;
}
d = 0;
while (q[d] != '\0') {
p[c] = q[d];
d++;
c++;
}
p[c] = '\0';
}
static void compute_mean_x_y()
{
size_t i;
double tmp_x = 0.0;
double tmp_y = 0.0;
for (i = 0; i < size; i++) {
tmp_x += vector_x[i];
tmp_y += vector_y[i];
}
mean_x = tmp_x / size;
mean_y = tmp_y / size;
printf("mean_x = %lf\n", mean_x);
printf("mean_y = %lf\n", mean_y);
}
static void compute_teta_1_grad()
{
double numerator = 0.0;
double denominator = 0.0;
double tmp1 = 0.0;
double tmp2 = 0.0;
size_t i;
for (i = 0; i < size; i++) {
numerator += (vector_x[i] - mean_x) * (vector_y[i] - mean_y);
}
for (i = 0; i < size; i++) {
tmp1 = vector_x[i] - mean_x;
tmp2 = tmp1 * tmp1;
denominator += tmp2;
}
teta_1_grad = numerator / denominator;
printf("teta_1_grad = %lf\n", teta_1_grad);
}
static void compute_teta_0_intercept()
{
teta_0_intercept = mean_y - (teta_1_grad * mean_x);
printf("teta_0_intercept = %lf\n", teta_0_intercept);
}
static void compute_prediction()
{
size_t i;
for (i = 0; i < size; i++) {
vector_predict[i] = teta_0_intercept + (teta_1_grad * vector_x[i]);
printf("y^[%ld] = %lf\n", i, vector_predict[i]);
}
printf("\n");
}
static void compute_RMSE()
{
compute_prediction();
double error = 0;
size_t i;
for (i = 0; i < size; i++) {
error = (vector_predict[i] - vector_y[i]) * (vector_predict[i] - vector_y[i]);
printf("error y^[%ld] = %lf\n", i, error);
RMSE += error;
}
/* mean */
RMSE = RMSE / size;
/* square root mean */
RMSE = sqrt(RMSE);
printf("\nRMSE = %lf\n", RMSE);
}
static void compute_loss_function()
{
int input = 0;
printf("Which loss function do you want to use?\n");
printf(" 1 - RMSE\n");
scanf("%d", &input);
switch(input) {
case 1:
concatenate(cmd_gnu_0, lossname_RMSE);
compute_RMSE();
printf("\n");
break;
default:
printf("Wrong input try again\n");
compute_loss_function(size);
}
}
static void compute_r_square(size_t size)
{
double num_err = 0.0;
double den_err = 0.0;
size_t i;
for (i = 0; i < size; i++) {
num_err += (vector_y[i] - vector_predict[i]) * (vector_y[i] - vector_predict[i]);
den_err += (vector_y[i] - mean_y) * (vector_y[i] - mean_y);
}
r_square = 1 - (num_err/den_err);
printf("R_square = %lf\n", r_square);
}
static void compute_predict_for_x()
{
double x = 0.0;
printf("Please enter x value\n");
scanf("%lf", &x);
prediction = teta_0_intercept + (teta_1_grad * x);
printf("y^ if x = %lf -> %lf\n",x, prediction);
}
static void compute_max_x_y()
{
size_t i;
double tmp1= 0.0;
double tmp2= 0.0;
for (i = 0; i < size; i++) {
if (vector_x[i] > tmp1) {
tmp1 = vector_x[i];
max_x = vector_x[i];
}
if (vector_y[i] > tmp2) {
tmp2 = vector_y[i];
max_y = vector_y[i];
}
}
printf("vector_x max value %lf\n", max_x);
printf("vector_y max value %lf\n", max_y);
}
static void display_model_line()
{
sprintf(intercept, "%0.7lf", teta_0_intercept);
sprintf(grad, "%0.7lf", teta_1_grad);
sprintf(xrange, "%0.7lf", max_x + 1);
sprintf(yrange, "%0.7lf", max_y + 1);
concatenate(cmd_gnu_1, intercept);
concatenate(cmd_gnu_2, grad);
concatenate(cmd_gnu_3, xrange);
concatenate(cmd_gnu_3, "]");
concatenate(cmd_gnu_4, yrange);
concatenate(cmd_gnu_4, "]");
printf("grad = %s\n", grad);
printf("intercept = %s\n", intercept);
printf("xrange = %s\n", xrange);
printf("yrange = %s\n", yrange);
printf("cmd_gnu_0: %s\n", cmd_gnu_0);
printf("cmd_gnu_1: %s\n", cmd_gnu_1);
printf("cmd_gnu_2: %s\n", cmd_gnu_2);
printf("cmd_gnu_3: %s\n", cmd_gnu_3);
printf("cmd_gnu_4: %s\n", cmd_gnu_4);
printf("cmd_gnu_5: %s\n", cmd_gnu_5);
printf("cmd_gnu_6: %s\n", cmd_gnu_6);
/* print plot */
FILE *gnuplot_pipe = (FILE*)popen("gnuplot -persistent", "w");
FILE *temp = (FILE*)fopen("data.temp", "w");
/* create data.temp */
size_t i;
for (i = 0; i < size; i++)
{
fprintf(temp, "%f %f \n", vector_x[i], vector_y[i]);
}
/* display gnuplot */
for (i = 0; i < 7; i++)
{
fprintf(gnuplot_pipe, "%s \n", commands_gnuplot[i]);
}
}
int main(void)
{
printf("===========================================\n");
printf("INPUT DATA\n");
printf("===========================================\n");
user_input();
display_vector();
printf("\n");
printf("===========================================\n");
printf("COMPUTE MEAN X:Y, TETA_1 TETA_0\n");
printf("===========================================\n");
compute_mean_x_y();
compute_max_x_y();
compute_teta_1_grad();
compute_teta_0_intercept();
printf("\n");
printf("===========================================\n");
printf("COMPUTE LOSS FUNCTION\n");
printf("===========================================\n");
compute_loss_function();
printf("===========================================\n");
printf("COMPUTE R_square\n");
printf("===========================================\n");
compute_r_square(size);
printf("\n");
printf("===========================================\n");
printf("COMPUTE y^ according to x\n");
printf("===========================================\n");
compute_predict_for_x();
printf("\n");
printf("===========================================\n");
printf("DISPLAY LINEAR REGRESSION\n");
printf("===========================================\n");
display_model_line();
printf("\n");
return 0;
}

Look at Section 1 of this paper. This section expresses a 2D linear regression as a matrix multiplication exercise. As long as your data is well-behaved, this technique should permit you to develop a quick least squares fit.
Depending on the size of your data, it might be worthwhile to algebraically reduce the matrix multiplication to simple set of equations, thereby avoiding the need to write a matmult() function. (Be forewarned, this is completely impractical for more than 4 or 5 data points!)

The fastest, most efficient way to solve least squares, as far as I am aware, is to subtract (the gradient)/(the 2nd order gradient) from your parameter vector. (2nd order gradient = i.e. the diagonal of the Hessian.)
Here is the intuition:
Let's say you want to optimize least squares over a single parameter. This is equivalent to finding the vertex of a parabola. Then, for any random initial parameter, x0, the vertex of the loss function is located at x0 - f(1) / f(2). That's because adding - f(1) / f(2) to x will always zero out the derivative, f(1).
Side note: Implementing this in Tensorflow, the solution appeared at w0 - f(1) / f(2) / (number of weights), but I'm not sure if that's due to Tensorflow or if it's due to something else..

Related

Logistic regression code stops working above ~43,500 generated observations

Having some difficulty troubleshooting code I wrote in C to perform a logistic regression. While it seems to work on smaller, semi-randomized datasets, it stops working (e.g. assigning proper probabilities of belonging to class 1) at around the point where I pass 43,500 observations (determined by tweaking the number of observations created. When creating the 150 features used in the code, I do create the first two as a function of the number of observations, so I'm not sure if maybe that's the issue here, though I am using double precision. Maybe there's an overflow somewhere in the code?
The below code should be self-contained; it generates m=50,000 observations with n=150 features. Setting m below 43,500 should return "Percent class 1: 0.250000", setting to 44,000 or above will return "Percent class 1: 0.000000", regardless of what max_iter (number of times we sample m observations) is set to.
The first feature is set to 1.0 divided by the total number of observations, if class 0 (first 75% of observations), or the index of the observation divided by the total number of observations otherwise.
The second feature is just index divided by total number of observations.
All other features are random.
The logistic regression is intended to use stochastic gradient descent, randomly selecting an observation index, computing the gradient of the loss with the predicted y using current weights, and updating weights with the gradient and learning rate (eta).
Using the same initialization with Python and NumPy, I still get the proper results, even above 50,000 observations.
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <time.h>
// Compute z = w * x + b
double dlc( int n, double *X, double *coef, double intercept )
{
double y_pred = intercept;
for (int i = 0; i < n; i++)
{
y_pred += X[i] * coef[i];
}
return y_pred;
}
// Compute y_hat = 1 / (1 + e^(-z))
double sigmoid( int n, double alpha, double *X, double *coef, double beta, double intercept )
{
double y_pred;
y_pred = dlc(n, X, coef, intercept);
y_pred = 1.0 / (1.0 + exp(-y_pred));
return y_pred;
}
// Stochastic gradient descent
void sgd( int m, int n, double *X, double *y, double *coef, double *intercept, double eta, int max_iter, int fit_intercept, int random_seed )
{
double *gradient_coef, *X_i;
double y_i, y_pred, resid;
int idx;
double gradient_intercept = 0.0, alpha = 1.0, beta = 1.0;
X_i = (double *) malloc (n * sizeof(double));
gradient_coef = (double *) malloc (n * sizeof(double));
for ( int i = 0; i < n; i++ )
{
coef[i] = 0.0;
gradient_coef[i] = 0.0;
}
*intercept = 0.0;
srand(random_seed);
for ( int epoch = 0; epoch < max_iter; epoch++ )
{
for ( int run = 0; run < m; run++ )
{
// Randomly sample an observation
idx = rand() % m;
for ( int i = 0; i < n; i++ )
{
X_i[i] = X[n*idx+i];
}
y_i = y[idx];
// Compute y_hat
y_pred = sigmoid( n, alpha, X_i, coef, beta, *intercept );
resid = -(y_i - y_pred);
// Compute gradients and adjust weights
for (int i = 0; i < n; i++)
{
gradient_coef[i] = X_i[i] * resid;
coef[i] -= eta * gradient_coef[i];
}
if ( fit_intercept == 1 )
{
*intercept -= eta * resid;
}
}
}
}
int main(void)
{
double *X, *y, *coef, *y_pred;
double intercept;
double eta = 0.05;
double alpha = 1.0, beta = 1.0;
long m = 50000;
long n = 150;
int max_iter = 20;
long class_0 = (long)(3.0 / 4.0 * (double)m);
double pct_class_1 = 0.0;
clock_t test_start;
clock_t test_end;
double test_time;
printf("Constructing variables...\n");
X = (double *) malloc (m * n * sizeof(double));
y = (double *) malloc (m * sizeof(double));
y_pred = (double *) malloc (m * sizeof(double));
coef = (double *) malloc (n * sizeof(double));
// Initialize classes
for (int i = 0; i < m; i++)
{
if (i < class_0)
{
y[i] = 0.0;
}
else
{
y[i] = 1.0;
}
}
// Initialize observation features
for (int i = 0; i < m; i++)
{
if (i < class_0)
{
X[n*i] = 1.0 / (double)m;
}
else
{
X[n*i] = (double)i / (double)m;
}
X[n*i + 1] = (double)i / (double)m;
for (int j = 2; j < n; j++)
{
X[n*i + j] = (double)(rand() % 100) / 100.0;
}
}
// Fit weights
printf("Running SGD...\n");
test_start = clock();
sgd( m, n, X, y, coef, &intercept, eta, max_iter, 1, 42 );
test_end = clock();
test_time = (double)(test_end - test_start) / CLOCKS_PER_SEC;
printf("Time taken: %f\n", test_time);
// Compute y_hat and share of observations predicted as class 1
printf("Making predictions...\n");
for ( int i = 0; i < m; i++ )
{
y_pred[i] = sigmoid( n, alpha, &X[i*n], coef, beta, intercept );
}
printf("Printing results...\n");
for ( int i = 0; i < m; i++ )
{
//printf("%f\n", y_pred[i]);
if (y_pred[i] > 0.5)
{
pct_class_1 += 1.0;
}
// Troubleshooting print
if (i < 10 || i > m - 10)
{
printf("%g\n", y_pred[i]);
}
}
printf("Percent class 1: %f", pct_class_1 / (double)m);
return 0;
}
For reference, here is my (presumably) equivalent Python code, which returns the correct percent of identified classes at more than 50,000 observations:
import numpy as np
import time
def sigmoid(x):
return 1 / (1 + np.exp(-x))
class LogisticRegressor:
def __init__(self, eta, init_runs, fit_intercept=True):
self.eta = eta
self.init_runs = init_runs
self.fit_intercept = fit_intercept
def fit(self, x, y):
m, n = x.shape
self.coef = np.zeros((n, 1))
self.intercept = np.zeros((1, 1))
for epoch in range(self.init_runs):
for run in range(m):
idx = np.random.randint(0, m)
x_i = x[idx:idx+1, :]
y_i = y[idx]
y_pred_i = sigmoid(x_i.dot(self.coef) + self.intercept)
gradient_w = -(x_i.T * (y_i - y_pred_i))
self.coef -= self.eta * gradient_w
if self.fit_intercept:
gradient_b = -(y_i - y_pred_i)
self.intercept -= self.eta * gradient_b
def predict_proba(self, x):
m, n = x.shape
y_pred = np.ones((m, 2))
y_pred[:,1:2] = sigmoid(x.dot(self.coef) + self.intercept)
y_pred[:,0:1] -= y_pred[:,1:2]
return y_pred
def predict(self, x):
return np.round(sigmoid(x.dot(self.coef) + self.intercept))
m = 50000
n = 150
class1 = int(3.0 / 4.0 * m)
X = np.random.rand(m, n)
y = np.zeros((m, 1))
for obs in range(m):
if obs < class1:
continue
else:
y[obs,0] = 1
for obs in range(m):
if obs < class1:
X[obs, 0] = 1.0 / float(m)
else:
X[obs, 0] = float(obs) / float(m)
X[obs, 1] = float(obs) / float(m)
logit = LogisticRegressor(0.05, 20)
start_time = time.time()
logit.fit(X, y)
end_time = time.time()
print(round(end_time - start_time, 2))
y_pred = logit.predict(X)
print("Percent:", y_pred.sum() / len(y_pred))
The issue is here:
// Randomly sample an observation
idx = rand() % m;
... in light of the fact that the OP's RAND_MAX is 32767. This is exacerbated by the fact that all of the class 0 observations are at the end.
All samples will be drawn from the first 32768 observations, and when the total number of observations is greater than that, the proportion of class 0 observations among those that can be sampled is less than 0.25. At 43691 total observations, there are no class 0 observations among those that can be sampled.
As a secondary issue, rand() % m does not yield a wholly uniform distribution if m does not evenly divide RAND_MAX + 1, though the effect of this issue will be much more subtle.
Bottom line: you need a better random number generator.
At minimum, you could consider combining the bits from two calls to rand() to yield an integer with sufficient range, but you might want to consider getting a third-party generator. There are several available.
Note: OP reports "m=50,000 observations with n=150 features.", so perhaps this is not the issue for OP, but I'll leave this answer up for reference when OP tries larger tasks.
A potential issue:
long overflow
m * n * sizeof(double) risks overflow when long is 32-bit and m*n > LONG_MAX (or about 46,341 if m, n are the same).
OP does report
A first step is to perform the multiplication using size_t math where we gain at least 1 more bit in the calculation.
// m * n * sizeof(double)
sizeof(double) * m * n
Yet unless OP's size_t is more than 32-bit, we still have trouble.
IAC, I recommend to use size_t for array sizing and indexing.
Check allocations for failure too.
Since RAND_MAX may be too small and array indexing should be done using size_t math, consider a helper function to generate a random index over the entire size_t range.
// idx = rand() % m;
size_t idx = rand_size_t() % (size_t)m;
If stuck with the standard rand(), below is a helper function to extend its range as needed.
It uses the real nifty IMAX_BITS(m).
#include <assert.h>
#include <limits.h>
#include <stdint.h>
#include <stdlib.h>
// https://stackoverflow.com/a/4589384/2410359
/* Number of bits in inttype_MAX, or in any (1<<k)-1 where 0 <= k < 2040 */
#define IMAX_BITS(m) ((m)/((m)%255+1) / 255%255*8 + 7-86/((m)%255+12))
// Test that RAND_MAX is a power of 2 minus 1
_Static_assert((RAND_MAX & 1) && ((RAND_MAX/2 + 1) & (RAND_MAX/2)) == 0, "RAND_MAX is not a Mersenne number");
#define RAND_MAX_WIDTH (IMAX_BITS(RAND_MAX))
#define SIZE_MAX_WIDTH (IMAX_BITS(SIZE_MAX))
size_t rand_size_t(void) {
size_t index = (size_t) rand();
for (unsigned i = RAND_MAX_WIDTH; i < SIZE_MAX_WIDTH; i += RAND_MAX_WIDTH) {
index <<= RAND_MAX_WIDTH;
index ^= (size_t) rand();
}
return index;
}
Further considerations can replace the rand_size_t() % (size_t)m with a more uniform distribution.
As has been determined elsewhere, the problem is due to the implementation's RAND_MAX value being too small.
Assuming 32-bit ints, a slightly better PRNG function can be implemented in the code, such as this C implementation of the minstd_rand() function from C++:
#define MINSTD_RAND_MAX 2147483646
// Code assumes `int` is at least 32 bits wide.
static unsigned int minstd_seed = 1;
static void minstd_srand(unsigned int seed)
{
seed %= 2147483647;
// zero seed is bad!
minstd_seed = seed ? seed : 1;
}
static int minstd_rand(void)
{
minstd_seed = (unsigned long long)minstd_seed * 48271 % 2147483647;
return (int)minstd_seed;
}
Another problem is that expressions of the form rand() % m produce a biased result when m does not divide (unsigned int)RAND_MAX + 1. Here is an unbiased function that returns a random integer from 0 to le inclusive, making use of the minstd_rand() function defined earlier:
static int minstd_rand_max(int le)
{
int r;
if (le < 0)
{
r = le;
}
else if (le >= MINSTD_RAND_MAX)
{
r = minstd_rand();
}
else
{
int rm = MINSTD_RAND_MAX - le + MINSTD_RAND_MAX % (le + 1);
while ((r = minstd_rand()) > rm)
{
}
r /= (rm / (le + 1) + 1);
}
return r;
}
(Actually, it does still have a very small bias because minstd_rand() will never return 0.)
For example, replace rand() % 100 with minstd_rand_max(99), and replace rand() % m with minstd_rand_max(m - 1). Also replace srand(random_seed) with minstd_srand(random_seed).

Trapezoidal Integration in C

I am trying to compute the integral of the function f(x)=(1-x^2)^(1/2) from x=0 to x=1. The answer should be approximately pi/4. I am currently getting 2.
My current implementation of the trapezoidal rule is the following:
double
def_integral(double *f, double *x, int n)
{
double F;
for (int i = 0 ; i < n ; i++) {
F += 0.5 * ( x[i+1] - x[i] ) * ( f[i] + f[i+1] );
}
return F;
}
I'm creating N divisions to approximate the area under the curve between x_1=0 and x_N=1 by looping through i to N with x_i = i / N.
int
main(int argc, char **argv)
{
int N = 1000;
double f_x[N];
double x[N];
for (int i = 0 ; i <= N ; i++) {
double x = i * 1. / N;
f_x[i] = sqrt(1. - pow(x, 2.));
//printf("%.2f %.5f\n", x, f_x[i]); //uncomment if you wanna see function values
}
double F_x = def_integral(f_x, x, N);
printf("The integral is %g\n", F_x);
}
The result of 2 that I am currently getting should be dependent on the number of N division, however, no matter if I make N=10000 or N=100, I still get 2.
Any suggestions?
In this for loop, you forgot updatin array x as well.
for (int i = 0 ; i <= N ; i++) {
double x = i * 1. / N;
f_x[i] = sqrt(1. - pow(x, 2.));
//printf("%.2f %.5f\n", x, f_x[i]); //uncomment if you wanna see function values
}
So, for loop should be replaced by
for (int i = 0 ; i <= N ; i++) {
double xi = i * 1. / N;
x[i] = xi;
f_x[i] = sqrt(1. - pow(xi , 2.));
//printf("%.2f %.5f\n", x, f_x[i]); //uncomment if you wanna see function values
}
In your main code, you call def_integral with a double (x) and in the function an array of x (double * x) is expected. Perhaps (it is what I suppose), the problem comes from the fact you formula needs x(i+1)-x(i) but you use a constant step. Indeed, x(i+1)-x(i)=step_x is constant so you do not need each x(i) but only value : 1./N
Other remark, with a constant step, your formula could be simplified to : F_x=step_x* ( 0.5*f_x(x0)+ f_x(x1)+...+f_x(xn-1)+ 0.5*f_x(xn) ) . It helps to simplify the code and to write a better efficient one.
Everything is commented in the code above. I hope it could help you. Best regards.
#include <stdio.h>
#include <math.h>
double
def_integral(double *f, double step_x, int n)
{
double F;
for (int i = 0 ; i < n ; i++) {
F += 0.5 * ( step_x ) * ( f[i] + f[i+1] );
}
return F;
}
int main()
{
int N = 1001; // 1001 abscissas means 1000 intervalls (see comment on array size and indices)
double f_x[N]; // not needed for the simplified algorithm
double step_x = 1. / N; // x(i+1)-x(i) is constant
for (int i = 0 ; i < N ; i++) { // Note : i<N and not i<=N
double xi = i * step_x; // abscissa calculation
f_x[i] = sqrt((1. - xi )*(1. + xi )); // cf chux comment
}
double F_x = def_integral(f_x, step_x, N);
printf("The integral is %.10g\n", F_x);
// simplified algorithm
// F_x=step_x*( 0.5*f_x(x0)+f_x(x1)+...+f_x(xn-1)+0.5f_x(xn) )
double xi;
xi=0; // x(0)
F_x=0.5*sqrt((1. - xi )*(1. + xi ));
for (int i=1 ; i<=N-1 ; i++) {
xi=step_x*i;
F_x+=sqrt((1. - xi )*(1. + xi ));
}
xi=step_x*N;
F_x+=0.5*sqrt((1. - xi )*(1. + xi ));
F_x=step_x*F_x;
printf("The integral is %.10g\n", F_x);
}

Euler's method for neuroscience in C [closed]

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I need to estimate for my internship the firing rate of neurons that follows an ODE. I code at first in python and it goes pretty well but for better performance, my supervisor told to write the same code in C. However, I never coded in C so I am a very beginner and the file in which i want to have the values for the firing rate is full of zero... Can someone help me ?
Thank you very much
So here is my python code :
import numpy as np
import matplotlib.pyplot as plt
from math import cos, sin, sqrt, pi, exp as cos, sin, sqrt, pi, exp
#parameters
eps = 0.05
f = 0.215
mu = 1.1
D = 0.001
DeltaT = 0.01
timewindow = 40
num_points = int(timewindow/DeltaT)
T = np.linspace(0, timewindow, num_points)
#signal
s = [sin(2*3.14*f*t) for t in T]
N=30000
compteur=np.zeros(num_points)
v = np.zeros((num_points,N))
samples = np.random.normal(0, 1, (num_points,N))
for i in range(1,num_points):
for j in range(N):
v[i,j] = v[i-1,j] + DeltaT *(-v[i-1,j]+ mu + eps*s[i-1]) + \
sqrt(2*D*DeltaT)*samples[i,j]
if v[i,j]>1:
v[i,j]=0
compteur[i]+=1/DeltaT/N
plt.plot(T,compteur)
plt.show()
and here is my "translation" in C :
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#define PI 3.1415926536
float s(float x, float);
double AWGN_generator();
FILE* fopen(const char* nomDuFichier, const char* modeOuverture);
int fclose(FILE* pointeurSurFichier);
int main(int argc, char *argv[])
{
//parameters
double eps = 0.05;
float f = 0.215 ;
double mu = 1.1 ;
double D = 0.001 ;
int time_window = 90;
int num_points = 1000;
long num_neurons = 1000;
double deltaT = time_window/num_points;
int i ;
//time
double Time[num_points] ;
Time[0]= 0.0;
for (i = 1 ; i < num_points ; i++ )
{ Time[i] = Time[i-1] + deltaT;
}
//opening file for saving data
FILE* fichier = NULL;
fichier = fopen("challala.txt", "w");
if (fichier != NULL)
{
double v[num_points][num_neurons] ;
memset(v, 0, num_points*num_neurons*sizeof(long) );
long compteur[num_points];
memset( compteur, 0, num_points*sizeof(long) );
int pos_1 ;
int pos_2 ;
//Euler's method
for (pos_1 = 1 ; pos_1 < num_points ; pos_1 ++)
{
for (pos_2 = 0 ; pos_2<num_neurons ; pos_2 ++)
{
float t = Time[pos_1-1] ;
v[pos_1][pos_2] = v[pos_1-1][pos_2] + deltaT *(-v[pos_1-1]
[pos_2]+ mu + eps*s(t, f))+ sqrt(2*D*deltaT)*AWGN_generator();
if (v[pos_1][pos_2]>1)
{
v[pos_1][pos_2]=0 ;
compteur[pos_1]+=1/deltaT/num_neurons ;
}
}
fprintf(fichier, "%ld",compteur[pos_1]);
}
fclose(fichier);
printf("ca a marche test.txt");
}
else
{
// On affiche un message d'erreur si on veut
printf("Impossible d'ouvrir le fichier test.txt");
}
return 0;
}
float s(float x, float f)
{
return sin(2*M_PI*f*x);
}
double AWGN_generator()
{/* Generates additive white Gaussian Noise samples with zero mean and a
standard deviation of 1. */
double temp1;
double temp2;
double result;
int p;
p = 1;
while( p > 0 )
{
temp2 = ( rand() / ( (double)RAND_MAX ) ); /* rand() function generates an
integer between 0 and
RAND_MAX,
which is defined in
stdlib.h.
*/
if ( temp2 == 0 )
{// temp2 is >= (RAND_MAX / 2)
p = 1;
}// end if
else
{// temp2 is < (RAND_MAX / 2)
p = -1;
}// end else
}// end while()
temp1 = cos( ( 2.0 * (double)PI ) * rand() / ( (double)RAND_MAX ) );
result = sqrt( -2.0 * log( temp2 ) ) * temp1;
return result; // return the generated random sample to the caller
}
Code repaired as able with old code commented out. See comments for change details.
Need to see challala.txt for a definitive test.
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
// Why use a coarse approximation?
//#define PI 3.1415926536
#define PI 3.1415926535897932384626433832795
// Let us stick to double only.
//float s(float x, float);
double s(double x, double);
// Add void, else declaration does not check the parameters.
//double AWGN_generator();
double AWGN_generator(void);
// These should have already been declared in <stdio.h>
// FILE* fopen(const char* nomDuFichier, const char* modeOuverture);
// int fclose(FILE* pointeurSurFichier);
int main(int argc, char *argv[]) {
//parameters
double eps = 0.05;
// float f = 0.215;
double f = 0.215;
double mu = 1.1;
double D = 0.001;
int time_window = 90;
// Unclear why `int/long` used here. size_t would be idiomatic for array sizing.
int num_points = 1000;
long num_neurons = 1000;
// Avoid integer division when a FP quotinet is desired
// double deltaT = time_window / num_points;
double deltaT = 1.0*time_window / num_points;
int i;
//time
double Time[num_points];
Time[0] = 0.0;
for (i = 1; i < num_points; i++)
{
Time[i] = Time[i - 1] + deltaT;
}
//opening file for saving data
FILE* fichier = NULL;
fichier = fopen("challala.txt", "w");
if (fichier != NULL) {
double v[num_points][num_neurons];
// zero fill use wrong type in sizeof.
// Avoid type in sizeof, better to use sizeof object
// memset(v, 0, num_points * num_neurons * sizeof(long));
memset(v, 0, sizeof v);
// Let us use FP here.
//long compteur[num_points];
double compteur[num_points];
memset(compteur, 0, sizeof compteur);
int pos_1;
int pos_2;
//Euler's method
for (pos_1 = 1; pos_1 < num_points; pos_1++)
{
for (pos_2 = 0; pos_2 < num_neurons; pos_2++) {
// float t = Time[pos_1 - 1];
double t = Time[pos_1 - 1];
v[pos_1][pos_2] = v[pos_1 - 1][pos_2]
+ deltaT * (-v[pos_1 - 1][pos_2] + mu + eps * s(t, f))
+ sqrt(2 * D * deltaT) * AWGN_generator();
if (v[pos_1][pos_2] > 1) {
v[pos_1][pos_2] = 0;
compteur[pos_1] += 1 / deltaT / num_neurons;
}
}
// Change of type
// fprintf(fichier, "%ld", compteur[pos_1]);
fprintf(fichier, " %g", compteur[pos_1]);
}
fclose(fichier);
printf("ca a marche test.txt");
} else {
// Was not the file another name?
// printf("Impossible d'ouvrir le fichier test.txt");
printf("Impossible d'ouvrir le fichier \"%s\"\n", challala.txt);
}
return 0;
}
//float s(float x, float f) {
double s(double x, double f) {
// M_PI is not defined in the standard C library, although common in extensions.
//return sin(2 * M_PI * f * x);
return sin(2 * PI * f * x);
}
double AWGN_generator() {
double temp1;
double temp2;
double result;
int p;
p = 1;
while (p > 0) {
temp2 = (rand() / ((double) RAND_MAX));
if (temp2 == 0) { // temp2 is >= (RAND_MAX / 2)
p = 1;
} // end if
else { // temp2 is < (RAND_MAX / 2)
p = -1;
} // end else
} // end while()
temp1 = cos((2.0 * (double) PI) * rand() / ((double) RAND_MAX));
result = sqrt(-2.0 * log(temp2)) * temp1;
return result; // return the generated random sample to the caller
}
Minor and advanced numeric issue:
Realize that quotient 1.0*time_window / num_points maybe be a little different than mathematical expected due to finite precision of double. This is, at worst, expected to be a very small amount, maybe about 0.5 parts in 253.
Yet the repetitive additions accumulate the error.
double deltaT = 1.0*time_window / num_points;
int i;
double Time[num_points];
Time[0] = 0.0;
for (i = 1; i < num_points; i++) {
Time[i] = Time[i - 1] + deltaT;
}
To avoid that accumulated error, code can re-calculate Time[i] anew on each iteration.
double deltaT = 1.0*time_window / num_points;
double Time[num_points];
for (int i = 0; i < num_points; i++) {
Time[i] = deltaT*i;
}
Of course, such small errors are often ignorable, but mayne not when num_points is large enough. This happens when your good code is applied to ever larger tasks.
regarding the following 3 statements
int time_window = 90;
int num_points = 1000;
double deltaT = time_window/num_points;
Since time_window and num_points are integers, the division is performed as an integer divide.
In an integer divide, all fractions are truncated.
the expression: time_window/num_points is actually:
90 / 1000
the resulting fraction has everything right of the decimal point truncated, so the result is 0
so: Time[0] + 0 results in 0.0.
The same (calculated) value: 0.0 is then propagated thorough the whole array
suggest changing:
int time_window = 90;
int num_points = 1000;
to
double time_window = 90.0;
double num_points = 1000.0;
regarding:
memset(v, 0, num_points*num_neurons*sizeof(long) );
this statement may (or may not) perform the desired functionality. It depends on if the size of double is the same as the size of long
Suggest using:
memset( v, 0, sizeof( v ) );

Poisson calculation (erlang C)

i posted this before, user told me to post it on codereview. i did, and they closed it...so one more time here: (i deleted the old question)
I have these formulas:
and I need the Poisson formulas for the erlangC formula:
I tried to rebuild the formulas in C:
double getPoisson(double m, double u, bool cumu)
{
double ret = 0;
if(!cumu)
{
ret = (exp(-u)*pow(u,m)) / (factorial(m));
}
else
{
double facto = 1;
double ehu = exp(-u);
for(int i = 0; i < m; i++)
{
ret = ret + (ehu * pow(u,i)) / facto;
facto *= (i+1);
}
}
return ret;
}
The Erlang C Formula:
double getErlangC(double m, double u, double p)
{
double numerator = getPoisson(m, u, false);
double denominator = getPoisson(m, u, false) + (1-p) * getPoisson(m, u, true);
return numerator/denominator;
}
The main problem is, the m parameter in getPoisson is a big value (>170)
so it wants to calculate >170! but it cannot handle it. I think the primitive data types are too small to work correctly, or what do you say?
BTW: This is the factorial function I use for the first Poisson:
double factorial(double n)
{
if(n >= 1)
return n*factorial(n-1);
else
return 1;
}
Some samples:
Input:
double l = getErlangC(50, 48, 0.96);
printf("%g", l);
Output:
0.694456 (correct)
Input:
double l = getErlangC(100, 96, 0.96);
printf("%g", l);
Output:
0.5872811 (correct)
if i use a value higher than 170 for the first parameter (m) of getErlangC like:
Input:
double l = getErlangC(500, 487, 0.974);
printf("%g", l);
Output:
naN (incorrect)
Excepted:
0.45269
How's my approach? Would be there a better way to calculate Poisson and erlangC?
Some Info: Excel has the POISSON Function, and on Excel it works perfekt... would there be a way to see the algorithm(code) EXCEL uses for POISSON?
(pow(u, m)/factorial(m)) can be expressed as a recursive loop with each element shown as u/n where each n is an element of m!.
double ratio(double u, int n)
{
if(n > 0)
{
// Avoid the ratio overflow by calculating each ratio element
double val;
val = u/n;
return val*ratio(u, n-1);
}
else
{
// Avoid division by 0 as power and factorial of 0 are 1
return 1;
}
}
Note that if you want to avoid recursion, you can do it as a loop as well
double ratio(double u, int n)
{
int i;
// Avoid the ratio overflow by calculating each ratio element
// default the ratio to 1 for n == 0
double val = 1;
// calculate the next n-1 ratios and put them into the total
for (i = 1; i<=n; i++)
{
// Put in the next element of the ratio
val *= u/i;
}
// return the final value of the ratio
return val;
}
To cope with values exceeding the double range, re-code to use the log of values. Downside- some precision loss.
Precision can be re-gained with improved code, but here is something that at least copes with the range issues.
Slight variant of OP's code follows: Used for comparison.
long double factorial(unsigned m) {
long double f = 1.0;
while (m > 0) {
f *= m;
m--;
}
return f;
}
double getPoisson(unsigned m, double u, bool cumu) {
double ret = 0;
if (!cumu) {
ret = (double) ((exp(-u) * pow(u, m)) / (factorial(m)));
} else {
double facto = 1;
double ehu = exp(-u);
for (unsigned i = 0; i < m; i++) {
ret = ret + (ehu * pow(u, i)) / facto;
facto *= (i + 1);
}
}
return ret;
}
double getErlang(unsigned m, double u, double p) {
double numerator = getPoisson(m, u, false);
double denominator = numerator + (1.0 - p) * getPoisson(m, u, true);
return numerator / denominator;
}
Suggested changes
#ifdef M_PI
#define MY_PI M_PI
#else
#define MY_PI 3.1415926535897932384626433832795
#endif
// log of n!
//
// Gosper Approximation of Stirling's Approximation
// http://mathworld.wolfram.com/StirlingsApproximation.html
// n! about= sqrt(pi*(2*n + 1/3.)) * pow(n,n) * exp(-n)
static double ln_factorial(unsigned n) {
if (n <= 1) return 0.0;
double x = n;
return log(sqrt(MY_PI * (2 * x + 1 / 3.0))) + log(x) * x - x;
}
double getPoisson_2(unsigned m, double u, bool cumu) {
double ret = 0.0;
if (cumu) {
// Simplify term calculation. `mul` does not get too large nor small.
double mul = exp(-u);
for (unsigned i = 0; i < m; i++) {
ret += mul;
mul *= u/(i + 1);
// printf("ret:% 10e mul:% 10e\n", ret, mul);
}
} else {
// ret = (exp(-u) * pow(u, m)) / (factorial(m));
double ln_ret = -u + log(u) * m - ln_factorial(m);
return exp(ln_ret);
}
return ret;
}
double getErlang_2(unsigned m, double u, double p) {
double numerator = getPoisson_2(m, u, false);
double denominator = numerator + (1 - p) * getPoisson_2(m, u, true);
return numerator / denominator;
}
Test code
void ErTest(unsigned m, double u, double p, double expect) {
printf("m:%4u u:% 14e p:% 14e", m, u, p);
printf(" E0:% 14e", expect);
double y1 = getErlang(m, u, p);
printf(" E1:% 14e", y1);
double y2 = getErlang_2(m, u, p);
printf(" E2:% 14e", y2);
puts("");
}
int main(void) {
ErTest(50, 48, 0.96, 0.694456);
ErTest(100, 96, 0.96, 0.5872811);
ErTest(500, 487, 0.974, 0.45269);
}
m: 50 u: 4.800000e+01 p: 9.600000e-01 E0: 6.944560e-01 E1: 6.944556e-01 E2: 6.944562e-01
m: 100 u: 9.600000e+01 p: 9.600000e-01 E0: 5.872811e-01 E1: 5.872811e-01 E2: 5.872813e-01
m: 500 u: 4.870000e+02 p: 9.740000e-01 E0: 4.526900e-01 E1: nan E2: 4.464746e-01
Your large recursive factorial is a problem as it might produce a stack overflow as well as a value overflow. pow might also get large.
Here's a way to combine things incrementally:
double
getPoisson(double m, double u, bool cumu)
{
double sum = 0;
double facto = 1;
double u_i = 1;
double ehu = exp(-u);
double cur = ehu;
// u_i -- pow(u,i)
// cur -- current/last term in series
// sum -- sum of terms
for (int i = 0; i < m; i++) {
cur = (ehu * u_i) / facto;
sum += cur;
u_i *= u;
facto *= (i + 1);
}
return cumu ? sum : cur;
}
The above is "okay", but still might overflow some values because of the u_i and facto terms.
Here is an alternate that combines the terms as a ratio. It is less likely to overflow:
double
getPoisson(double m, double u, bool cumu)
{
double sum = 0;
double ehu = exp(-u);
double cur = ehu;
double ratio = 1;
// cur -- current/last term in series
// sum -- sum of terms
// ratio -- u^i / factorial(i)
for (int i = 0; i < m; i++) {
cur = ehu * ratio;
sum += cur;
ratio *= u;
ratio /= (i + 1);
}
return cumu ? sum : cur;
}
The above might still produce some large values. If so, you might have to use long double, quadmath, or multiprecision arithmetic. Or, come up with an "analog" of the equation/algorithm.

Realtime Band-Limited Impulse Train Synthesis using SDL mixer

I'm trying to implement a audio synthesizer using this technique:
https://ccrma.stanford.edu/~stilti/papers/blit.pdf
I'm doing it in standard C, using SDL2_Mixer library.
This is my BLIT function implementation:
double blit(double angle, double M, double P) {
double x = M * angle / P;
double denom = (M * sin(M_PI * angle / P));
if (denom < 1)
return (M / P) * cos(M_PI * x) / cos(M_PI * x / M);
else {
double numerator = sin(M_PI * x);
return (M / P) * numerator / denom;
}
}
The idea is to combine it to generate a square wave, following the paper instructions. I setted up SDL2_mixer with this configuration:
SDL_AudioSpec *desired, *obtained;
SDL_AudioSpec *hardware_spec;
desired = (SDL_AudioSpec*)malloc(sizeof(SDL_AudioSpec));
obtained = (SDL_AudioSpec*)malloc(sizeof(SDL_AudioSpec));
desired->freq=44100;
desired->format=AUDIO_U8;
desired->channels=1;
desired->samples=2048;
desired->callback=create_rect;
desired->userdata=NULL;
And here's my create_rect function. It creates a bipolar impulse train, then it integrates it's value to generate a band-limited rect function.
void create_rect(void *userdata, Uint8 *stream, int len) {
static double angle = 0;
static double integral = 0;
int i = 0;
// This is the freq of my tone
double f1 = tone_table[current_wave.note];
// Sample rate
double fs = 44100;
// Pulse
double P = fs / f1;
int M = 2 * floor(P / 2) + 1;
double oldbipolar = 0;
double bipolar = 0;
for(i = 0; i < len; i++) {
if (++angle > P)
angle -= P;
double angle2 = angle + floor(P/2);
if (angle2 > P)
angle2 -= P;
bipolar = blit(angle2, M, P) - blit(angle, M, P);
integral += (bipolar + old bipolar) * 0.5;
oldbipolar = bipolar;
*stream++ = (integral + 0.5) * 127;
}
}
My problem is: the resulting wave is quite ok, but after few seconds it starts to make noises. I tried to plot the result, and here's it:
Any idea?
EDIT: Here's a plot of the bipolar BLIT before integrating it:

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