double single_file_correlate(std::string directory, std::string fname,rarray<double,1> predictPS){
// Read in detection signal, do the Fourier transform and compute the power spectrum
data_cols detection = readcols(directory,fname);
rarray<std::complex<double>,1> detection_FT = FT(detection.signal);
rarray<double,1> detectPS = powerspectrum(detection_FT);
return correlation_coeffecient(predictPS,detectPS);
}
int main(int argc, char *argv[])
{
/* Important definitions */
// Lengths
size_t N = 0; // Length of time series
size_t M = 0; // Length of sampling vector (number of frequencies)
// Filenames
char inname[100];
char outname[100];
// Sampling
double low, high, rate;
// Frequency of window function
double winfreq = 0;
// Options
int quiet = 0;
int unit = 1;
int prep = 1;
int autosamp = 0;
int fast = 0;
int useweight = 0;
int windowmode = 0;
int Nclean = 0;
int filter = 0;
/* Process command line arguments and return line count of the input file */
N = cmdarg(argc, argv, inname, outname, &quiet, &unit, &prep, &low, &high,\
&rate, &autosamp, &fast, &useweight, &windowmode, &winfreq,\
&Nclean, &filter, NULL, NULL);
// Pretty print
if ( quiet == 0 || fast == 1 ){
if ( windowmode == 0 && useweight != 0 )
printf("\nCalculating the weighted power spectrum of \"%s\" ...\n",\
inname);
else if ( windowmode == 0 )
printf("\nCalculating the power spectrum of \"%s\" ...\n", inname);
else
printf("\nCalculating the window function of \"%s\" ...\n", inname);
}
/* Read data (and weights) from the input file */
if ( quiet == 0 ) printf(" - Reading input\n");
double* time = malloc(N * sizeof(double));
double* flux = malloc(N * sizeof(double));
double* weight = malloc(N * sizeof(double));
readcols(inname, time, flux, weight, N, useweight, unit, quiet);
// Do if fast-mode and window-mode is not activated
if ( fast == 0 && windowmode == 0 ) {
// Calculate Nyquist frequency
double* dt = malloc(N-1 * sizeof(double));
double nyquist;
arr_diff(time, dt, N);
nyquist = 1.0 / (2.0 * arr_median(dt, N-1)) * 1e6; // microHz !
free(dt);
// Calculate suggested sampling (4 times oversampling)
double minsamp;
minsamp = 1.0e6 / (4 * (time[N-1] - time[0])); // microHz !
// Display info?
if ( quiet == 0 ){
printf(" -- INFO: Length of time series = %li\n", N);
printf(" -- INFO: Nyquist frequency = %.2lf microHz\n", nyquist);
printf(" -- INFO: Suggested minimum sampling = %.3lf microHz\n",\
minsamp);
}
// Apply automatic sampling?
if ( autosamp != 0 ) {
low = 5.0;
high = nyquist;
rate = minsamp;
}
}
/* Prepare for power spectrum */
// Calculate proper frequency range for window-function-mode
double limit = 0;
if ( windowmode != 0 ) {
limit = low;
low = winfreq - limit;
high = winfreq + limit;
}
// Get length of sampling vector
M = arr_util_getstep(low, high, rate);
// Fill sampling vector with cyclic frequencies
double* freq = malloc(M * sizeof(double));
arr_init_linspace(freq, low, rate, M);
// Initialise arrays for data storage
double* power = malloc(M * sizeof(double));
double* alpha = malloc(M * sizeof(double));
double* beta = malloc(M * sizeof(double));
/* Calculate power spectrum OR window function */
if ( windowmode == 0 ) {
// Subtract the mean to avoid "zero-frequency" problems
if ( prep != 0 ) {
if ( quiet == 0 ){
printf(" - Subtracting the mean from time series\n");
}
arr_sca_add(flux, -arr_mean(flux, N), N);
}
else {
if ( quiet == 0 )
printf(" - Time series used *without* mean subtraction!\n");
}
// Display info
if ( quiet == 0 ){
printf(" - Calculating fourier transform\n");
if ( autosamp != 0 ) {
printf(" -- NB: Using automatic sampling!\n");
printf(" -- INFO: Auto-sampling (in microHz): %.2lf to %.2lf"\
" in steps of %.4lf\n", low, high, rate);
}
else {
printf(" -- INFO: Sampling (in microHz): %.2lf to %.2lf in"\
" steps of %.4lf\n", low, high, rate);
}
printf(" -- INFO: Number of sampling frequencies = %li\n", M);
}
// Calculate power spectrum with or without weights
fourier(time, flux, weight, freq, N, M, power, alpha, beta, useweight);
}
else {
if ( quiet == 0 ){
printf(" - Calculating window function\n");
printf(" -- INFO: Window frequency = %.2lf microHz\n", winfreq);
printf(" -- INFO: Sampling in the range +/- %.2lf microHz in" \
" steps of %.4lf microHz\n", limit, rate);
printf(" -- INFO: Number of sampling frequencies = %li\n", M);
}
// Calculate spectral window with or without weights
windowfunction(time, freq, weight, N, M, winfreq, power, useweight);
if ( quiet == 0 )
printf(" - Sum of spectral window = %.4lf\n", arr_sum(power, M));
// Move frequencies to the origin
arr_sca_add(freq, -winfreq, M);
}
/* Write data to file */
if ( quiet == 0 ) printf(" - Saving to file \"%s\"\n", outname);
writecols(outname, freq, power, M);
/* Free data */
free(time);
free(flux);
free(weight);
free(freq);
free(power);
free(alpha);
free(beta);
/* Done! */
if ( quiet == 0 || fast ==1 ) printf("Done!\n\n");
return 0;
}
int main(int argc, char *argv[])
{
/* Important definitions */
// Lengths
size_t N = 0; // Length of time series
size_t M = 0; // Length of sampling vector (number of frequencies)
// Filenames
char inname[100];
char outname[100];
char logname[100];
// Sampling
double low, high, rate;
// Options
int quiet = 0;
int unit = 1;
int prep = 1;
int autosamp = 0;
int fast = 0;
int useweight = 0;
int Nclean = 1;
int filter = 0;
/* Process command line arguments and return line count of the input file */
N = cmdarg(argc, argv, inname, outname, &quiet, &unit, &prep, &low, &high,\
&rate, &autosamp, &fast, &useweight, NULL, NULL, &Nclean,\
&filter, NULL, NULL);
// Pretty print
if ( quiet == 0 || fast == 1){
if ( useweight != 0 )
printf("\nCLEANing the time series \"%s\" using weights...\n",\
inname);
else
printf("\nCLEANing the time series \"%s\" without weights...\n",\
inname);
}
/* Read data (and weights) from the input file */
if ( quiet == 0 ) printf(" - Reading input\n");
double* time = malloc(N * sizeof(double));
double* flux = malloc(N * sizeof(double));
double* weight = malloc(N * sizeof(double));
readcols(inname, time, flux, weight, N, useweight, unit, quiet);
// Do if fast-mode is not activated
if ( fast == 0 ) {
// Calculate Nyquist frequency
double* dt = malloc(N-1 * sizeof(double));
double nyquist;
arr_diff(time, dt, N);
nyquist = 1.0 / (2.0 * arr_median(dt, N-1)) * 1e6; // microHz !
free(dt);
// Automatic or manual sampling?
int oversamp;
if ( autosamp != 0 ) {
low = 5.0;
high = nyquist;
oversamp = 4;
}
else {
oversamp = (int) rate;
}
// Calculate N times oversampling (in microHz!)
double minsamp = 1.0e6 / (oversamp * (time[N-1] - time[0]));
rate = minsamp;
// Display info?
if ( quiet == 0 ){
printf(" -- INFO: Length of time series = %li\n", N);
printf(" -- INFO: Nyquist frequency = %.2lf microHz\n", nyquist);
printf(" -- INFO: Using %i times oversampling = %.3lf microHz\n",\
oversamp, minsamp);
}
}
else {
// Only set the N times oversampling
int oversamp = (int) rate;
double minsamp = 1.0e6 / (oversamp * (time[N-1] - time[0]));
rate = minsamp;
}
/* Prepare for power spectrum */
// Get length of sampling vector
M = arr_util_getstep(low, high, rate);
// Fill sampling vector with cyclic frequencies
double* freq = malloc(M * sizeof(double));
arr_init_linspace(freq, low, rate, M);
if ( quiet == 0 )
printf(" -- INFO: Number of sampling frequencies = %li\n", M);
// Subtract the mean to avoid "zero-frequency" problems
double fmean = 0;
if ( prep != 0 ) {
if ( quiet == 0 ) printf(" - Subtracting the mean from time series\n");
fmean = arr_mean(flux, N);
arr_sca_add(flux, -fmean, N);
}
else {
if ( quiet == 0 )
printf(" - Time series used *without* mean subtraction!\n");
}
/* Prepare file for writing the CLEAN-output */
// Create log-file
strcpy(logname, outname);
strcat(logname, ".cleanlog");
FILE* logfile = fopen(logname, "w");
// Write header
fprintf(logfile, "# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"\
"~~~~~~~~~~\n");
fprintf(logfile, "# Log of CLEAN on \"%s\"\n", inname);
fprintf(logfile, "# Interval: [%.2lf, %.2lf] microHz\n", low, high);
fprintf(logfile, "# Finding %i frequencies\n", Nclean);
fprintf(logfile, "# \n");
fprintf(logfile, "# %8s %11s %11s %12s %12s\n", "Number", "Frequency",\
"Power", "Alpha", "Beta");
fprintf(logfile, "# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"\
"~~~~~~~~~~\n");
/* Find and clean peaks */
// Init variables
double fmax, alpmax, betmax, powmax;
// Display info
if ( quiet == 0 ) {
printf(" - CLEANing %i frequencies in the range %.1lf to %.1lf"\
" microHz\n", Nclean, low, high);
printf("\n %9s %11s %11s\n", "Number", "Frequency", "Power");
}
// Enter CLEAN-loop
for (int i = 0; i < Nclean; ++i) {
// Display progress
if ( quiet == 0 ) printf(" %6i", i+1);
// Reset variables
fmax = 0;
alpmax = 0;
betmax = 0;
powmax = 0;
// Call with or without weights
fouriermax(time, flux, weight, freq, N, M, &fmax, &alpmax, &betmax,\
useweight);
// Calculate the power and write to log
powmax = alpmax*alpmax + betmax*betmax;
fprintf(logfile, " %6i %15.6lf %12.6lg %12.6lf %12.6lf\n", i+1, fmax,\
powmax, alpmax, betmax);
if ( quiet == 0) printf(" %15.6lf %12.6lg \n", fmax, powmax);
// Remove frequency from time series
for (int j = 0; j < N; ++j) {
flux[j] = flux[j] - alpmax * sin( PI2micro*fmax * time[j] ) - \
betmax * cos( PI2micro*fmax * time[j] );
}
}
// Final touch
fclose(logfile);
if ( quiet == 0 ) printf("\n");
/* Write CLEANed time series to file */
if ( quiet == 0 ) printf(" - Saving to file \"%s\"\n", outname);
// Add the mean to the time series data again
if ( prep != 0 ) arr_sca_add(flux, fmean, N);
// Save to file
writecols3(outname, time, flux, weight, N, useweight, unit);
/* Free data */
free(time);
free(flux);
free(weight);
free(freq);
/* Done! */
if ( quiet == 0 || fast ==1 ) printf("Done!\n\n");
return 0;
}
