int main(int argc, char *argv []) {
if(populate_env_variable(REF_ERROR_CODES_FILE, "L2_ERROR_CODES_FILE")) {
printf("\nUnable to populate [REF_ERROR_CODES_FILE] variable with corresponding environment variable. Routine will proceed without error handling\n");
}
if (argc != 2) {
if(populate_env_variable(SPTS_BLURB_FILE, "L2_SPTS_BLURB_FILE")) {
RETURN_FLAG = 1;
} else {
print_file(SPTS_BLURB_FILE);
}
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATTR", -1, "Status flag for L2 sptrace routine", ERROR_CODES_FILE_WRITE_ACCESS);
return 1;
} else {
// ***********************************************************************
// Redefine routine input parameters
int order = strtol(argv[1], NULL, 0);
// ***********************************************************************
// Open [SPFIND_OUTPUTF_PEAKS_FILE] input file
FILE *inputfile;
if (!check_file_exists(SPFIND_OUTPUTF_PEAKS_FILE)) {
inputfile = fopen(SPFIND_OUTPUTF_PEAKS_FILE , "r");
} else {
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATTR", -2, "Status flag for L2 sptrace routine", ERROR_CODES_FILE_WRITE_ACCESS);
return 1;
}
// ***********************************************************************
// Find some [SPFIND_OUTPUTF_PEAKS_FILE] input file details
char input_string [150];
int row_count = 0;
while(!feof(inputfile)) {
memset(input_string, '\0', sizeof(char)*150);
fgets(input_string, 150, inputfile);
if (strtol(&input_string[0], NULL, 0) > 0) { // check the line begins with a positive number (usable)
row_count++;
}
}
rewind(inputfile);
// ***********************************************************************
// Store [SPFIND_OUTPUTF_PEAKS_FILE] data
double x_coords[row_count];
memset(x_coords, 0, sizeof(double)*(row_count));
double y_coords[row_count];
memset(y_coords, 0, sizeof(double)*(row_count));
double coord_x, coord_y;
int idx = 0;
while(!feof(inputfile)) {
memset(input_string, '\0', sizeof(char)*150);
fgets(input_string, 150, inputfile);
if (strtol(&input_string[0], NULL, 0) > 0) { // check the line begins with a positive number (usable)
sscanf(input_string, "%lf\t%lf\n", &coord_x, &coord_y);
x_coords[idx] = coord_x;
y_coords[idx] = coord_y;
idx++;
}
}
// ***********************************************************************
// Perform a few checks to ensure the input tracing parameters
// are sensible
if ((order < SPTRACE_VAR_POLYORDER_LO) || (order > SPTRACE_VAR_POLYORDER_HI)) { // Check [order] is within config limits
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATTR", -3, "Status flag for L2 sptrace routine", ERROR_CODES_FILE_WRITE_ACCESS);
fclose(inputfile);
return 1;
}
// ***********************************************************************
// Create [SPTRACE_OUTPUTF_TRACES_FILE] output file and print a few
// parameters
FILE *outputfile;
outputfile = fopen(SPTRACE_OUTPUTF_TRACES_FILE, FILE_WRITE_ACCESS);
if (!outputfile) {
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATTR", -4, "Status flag for L2 sptrace routine", ERROR_CODES_FILE_WRITE_ACCESS);
fclose(inputfile);
return 1;
}
char timestr [80];
memset(timestr, '\0', sizeof(char)*80);
find_time(timestr);
fprintf(outputfile, "#### %s ####\n\n", SPTRACE_OUTPUTF_TRACES_FILE);
fprintf(outputfile, "# Lists the trace coefficients and corresponding chi-squareds found using the sptrace program.\n\n");
fprintf(outputfile, "# Run datetime:\t\t%s\n", timestr);
fprintf(outputfile, "# Polynomial Order:\t%d\n\n", order);
// ***********************************************************************
// Fit and store results to [SPTRACE_OUTPUTF_TRACES_FILE] file
double coeffs[order];
double this_chi_squared;
if (calc_least_sq_fit(order, row_count, x_coords, y_coords, coeffs, &this_chi_squared)) { // reversed [coord_y] and [coord_x] as want to find x = f(y) not y = f(x)
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATTR", -5, "Status flag for L2 frtrace routine", ERROR_CODES_FILE_WRITE_ACCESS);
fclose(inputfile);
fclose(outputfile);
return 1;
}
int ii;
for (ii=0; ii<=order; ii++) {
fprintf(outputfile, SPTRACE_VAR_ACCURACY_COEFFS, coeffs[ii]);
fprintf(outputfile, "\t");
}
fprintf(outputfile, SPTRACE_VAR_ACCURACY_CHISQ, this_chi_squared);
fprintf(outputfile, "\n");
fprintf(outputfile, "%d", EOF);
printf("\nFitting results");
printf("\n--------------------\n");
printf("\nχ2:\t\t\t%.2f\n", this_chi_squared);
// ***********************************************************************
// Perform a few checks to ensure the chi squareds are sensible
if ((this_chi_squared < SPTRACE_VAR_CHISQUARED_MIN) || (this_chi_squared > SPTRACE_VAR_CHISQUARED_MAX)) { // comparing doubles but accuracy isn't a necessity so don't need gsl_fcmp function
RETURN_FLAG = 2;
}
// ***********************************************************************
// Close [SPFIND_OUTPUTF_PEAKS_FILE] input file and
// [SPTRACE_OUTPUTF_TRACES_FILE] output file
if (fclose(inputfile)) {
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATTR", -6, "Status flag for L2 sptrace routine", ERROR_CODES_FILE_WRITE_ACCESS);
return 1;
}
if (fclose(outputfile)) {
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATTR", -7, "Status flag for L2 sptrace routine", ERROR_CODES_FILE_WRITE_ACCESS);
return 1;
}
// Write success to [ERROR_CODES_FILE]
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATTR", RETURN_FLAG, "Status flag for L2 sptrace routine", ERROR_CODES_FILE_WRITE_ACCESS);
return 0;
}
}
int main(int argc, char *argv []) {
if(populate_env_variable(REF_ERROR_CODES_FILE, "L2_ERROR_CODES_FILE")) {
printf("\nUnable to populate [REF_ERROR_CODES_FILE] variable with corresponding environment variable. Routine will proceed without error handling\n");
}
if (argc != 15) {
if(populate_env_variable(SPF_BLURB_FILE, "L2_SPF_BLURB_FILE")) {
RETURN_FLAG = 1;
} else {
print_file(SPF_BLURB_FILE);
}
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATFI", -1, "Status flag for L2 spfind routine", ERROR_CODES_FILE_WRITE_ACCESS);
return 1;
} else {
// ***********************************************************************
// Redefine routine input parameters
char *target_f = strdup(argv[1]);
int bin_size_px = strtol(argv[2], NULL, 0);
double bg_percentile = strtod(argv[3], NULL);
double clip_sigma = strtod(argv[4], NULL);
int median_filter_width_px = strtol(argv[5], NULL, 0);
double min_SNR = strtod(argv[6], NULL);
int min_spatial_width_px = strtol(argv[7], NULL, 0);
int finding_window_lo_px = strtol(argv[8], NULL, 0);
int finding_window_hi_px = strtol(argv[9], NULL, 0);
int max_centering_num_px = strtol(argv[10], NULL, 0);
int centroid_half_window_size_px = strtol(argv[11], NULL, 0);
int min_used_bins = strtol(argv[12], NULL, 0);
int window_x_lo = strtol(argv[13], NULL, 0);
int window_x_hi = strtol(argv[14], NULL, 0);
// ***********************************************************************
// Open target file (ARG 1), get parameters and perform any data format
// checks
fitsfile *target_f_ptr;
int target_f_maxdim = 2, target_f_status = 0, target_f_bitpix, target_f_naxis;
long target_f_naxes [2] = {1,1};
if(!fits_open_file(&target_f_ptr, target_f, IMG_READ_ACCURACY, &target_f_status)) {
if(!populate_img_parameters(target_f, target_f_ptr, target_f_maxdim, &target_f_bitpix, &target_f_naxis, target_f_naxes, &target_f_status, "TARGET FRAME")) {
if (target_f_naxis != 2) { // any data format checks here
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATFI", -2, "Status flag for L2 spfind routine", ERROR_CODES_FILE_WRITE_ACCESS);
free(target_f);
if(fits_close_file(target_f_ptr, &target_f_status)) fits_report_error (stdout, target_f_status);
return 1;
}
} else {
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATFI", -3, "Status flag for L2 spfind routine", ERROR_CODES_FILE_WRITE_ACCESS);
fits_report_error(stdout, target_f_status);
free(target_f);
if(fits_close_file(target_f_ptr, &target_f_status)) fits_report_error (stdout, target_f_status);
return 1;
}
} else {
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATFI", -4, "Status flag for L2 spfind routine", ERROR_CODES_FILE_WRITE_ACCESS);
fits_report_error(stdout, target_f_status);
free(target_f);
return 1;
}
// ***********************************************************************
// Set the range limits
int cut_x [2] = {window_x_lo, window_x_hi};
int cut_y [2] = {1, target_f_naxes[1]};
// ***********************************************************************
// Set parameters used when reading data from target file (ARG 1)
long fpixel [2] = {cut_x[0], cut_y[0]};
long nxelements = (cut_x[1] - cut_x[0]) + 1;
long nyelements = (cut_y[1] - cut_y[0]) + 1;
// ***********************************************************************
// Create arrays to store pixel values from target fits file (ARG 1)
double target_f_pixels [nxelements];
// ***********************************************************************
// Get target fits file (ARG 1) values and store in 2D array
int ii;
double target_frame_values [nyelements][nxelements];
memset(target_frame_values, 0, sizeof(double)*nxelements*nyelements);
for (fpixel[1] = cut_y[0]; fpixel[1] <= cut_y[1]; fpixel[1]++) {
memset(target_f_pixels, 0, sizeof(double)*nxelements);
if(!fits_read_pix(target_f_ptr, TDOUBLE, fpixel, nxelements, NULL, target_f_pixels, NULL, &target_f_status)) {
for (ii=0; ii<nxelements; ii++) {
target_frame_values[fpixel[1]-1][ii] = target_f_pixels[ii];
}
} else {
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATFI", -5, "Status flag for L2 spfind routine", ERROR_CODES_FILE_WRITE_ACCESS);
fits_report_error(stdout, target_f_status);
free(target_f);
if(fits_close_file(target_f_ptr, &target_f_status)) fits_report_error (stdout, target_f_status);
return 1;
}
}
// FIND VALUES OF PEAK CENTROID ALONG DISPERSION AXIS
// ***********************************************************************
// 1. Bin array according to bin width given by [bin_size_px]
int disp_nelements = nxelements, spat_nelements = nyelements;
int disp_nelements_binned = (int)floor(disp_nelements/bin_size_px);
double this_frame_values_binned[spat_nelements][disp_nelements_binned];
memset(this_frame_values_binned, 0, sizeof(double)*spat_nelements*disp_nelements_binned);
double this_bin_value;
int bin_number = 0;
int jj;
for (jj=0; jj<spat_nelements; jj++) {
this_bin_value = 0;
bin_number = 0;
for (ii=0; ii<disp_nelements; ii++) {
if (ii % bin_size_px == 0 && ii != 0) {
this_frame_values_binned[jj][bin_number] = this_bin_value;
bin_number++;
this_bin_value = 0;
}
this_bin_value += target_frame_values[jj][ii];
}
}
printf("\nFinding peaks");
printf("\n-------------------------------------\n");
double peaks[disp_nelements_binned];
int num_bins_used = 0;
for (ii=0; ii<disp_nelements_binned; ii++) {
// 1a. Establish if any target flux is in this bin
// First find the mean/sd of the [bg_percentile]th lowest valued pixels as an initial parameters for sigma clip
double this_spat_values[spat_nelements];
double this_spat_values_sorted[spat_nelements];
for (jj=0; jj<spat_nelements; jj++) {
this_spat_values[jj] = this_frame_values_binned[jj][ii];
}
memcpy(this_spat_values_sorted, this_spat_values, sizeof(double)*spat_nelements);
gsl_sort(this_spat_values_sorted, 1, spat_nelements);
int bg_nelements = (int)floor(spat_nelements*bg_percentile);
double bg_values [bg_nelements];
int idx = 0;
for (jj=0; jj<spat_nelements; jj++) {
if (this_spat_values_sorted[jj] != 0) { // avoid 0s set from median filter edges
bg_values[idx] = this_spat_values_sorted[jj];
idx++;
if (idx == bg_nelements)
break;
}
}
if (idx != bg_nelements) {
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATFI", -6, "Status flag for L2 spfind routine", ERROR_CODES_FILE_WRITE_ACCESS);
free(target_f);
if(fits_close_file(target_f_ptr, &target_f_status)) fits_report_error (stdout, target_f_status);
return 1;
}
double start_mean = gsl_stats_mean(bg_values, 1, bg_nelements);
double start_sd = gsl_stats_sd(bg_values, 1, bg_nelements);
// 1b. Iterative sigma clip around dataset with the initial guess
int retain_indexes[spat_nelements];
double final_mean, final_sd;
int final_num_retained_indexes;
printf("\nBin:\t\t\t\t%d", ii);
printf("\nStart mean:\t\t\t%f", start_mean);
printf("\nStart SD:\t\t\t%f", start_sd);
iterative_sigma_clip(this_spat_values, spat_nelements, clip_sigma, retain_indexes, start_mean, start_sd, &final_mean, &final_sd, &final_num_retained_indexes, FALSE);
printf("\nFinal mean:\t\t\t%f", final_mean);
printf("\nFinal SD:\t\t\t%f", final_sd);
// 2. Smooth array with median filter
double this_spat_values_smoothed[spat_nelements];
memset(this_spat_values_smoothed, 0, sizeof(double)*spat_nelements);
median_filter(this_spat_values, this_spat_values_smoothed, spat_nelements, median_filter_width_px);
// 3. Ascertain if this bin contains target flux
int num_pixels_contain_target_flux = 0;
for (jj=0; jj<spat_nelements-1; jj++) {
if (this_spat_values_smoothed[jj] > final_mean + final_sd*min_SNR) {
num_pixels_contain_target_flux++;
}
}
printf("\nNum pixels (target):\t\t%d", num_pixels_contain_target_flux);
printf("\nDoes bin contain target flux?\t");
if (num_pixels_contain_target_flux >= min_spatial_width_px) {
printf("Yes\n");
} else {
printf("No\n");
peaks[ii] = -1;
continue;
}
// 3. Take derivatives
double this_spat_values_der[spat_nelements-1];
memset(this_spat_values_der, 0, sizeof(double)*spat_nelements-1);
for (jj=1; jj<spat_nelements; jj++) {
this_spat_values_der[jj-1] = this_frame_values_binned[jj][ii] - this_frame_values_binned[jj-1][ii];
}
// 4. Smooth derivatives
double this_spat_values_der_smoothed[spat_nelements-1];
memcpy(this_spat_values_der_smoothed, this_spat_values_der, sizeof(double)*spat_nelements-1);
median_filter(this_spat_values_der, this_spat_values_der_smoothed, spat_nelements-1, median_filter_width_px);
// 5. Pick most positive gradient from window, retaining proper index
double this_spat_values_der_smoothed_windowed[spat_nelements-1];
memcpy(this_spat_values_der_smoothed_windowed, this_spat_values_der_smoothed, sizeof(double)*spat_nelements-1);
for (jj=0; jj<spat_nelements; jj++) {
if (jj >= finding_window_lo_px && jj <= finding_window_hi_px) {
this_spat_values_der_smoothed_windowed[jj] = this_spat_values_der_smoothed_windowed[jj];
} else {
this_spat_values_der_smoothed_windowed[jj] = -1;
}
}
size_t this_pk_idx = gsl_stats_max_index(this_spat_values_der_smoothed_windowed, 1, spat_nelements-1);
printf("Start peak index:\t\t%d\n", this_pk_idx);
// 6. Using this index, walk through centering window [max_centering_num_px] and find derivative turnover point
printf("Found turnover:\t\t\t");
bool found_turnover = FALSE;
for (jj=this_pk_idx; jj<this_pk_idx+max_centering_num_px; jj++) {
if (this_spat_values_der_smoothed[jj] < 0.) {
this_pk_idx = jj;
found_turnover = TRUE;
break;
}
}
if (found_turnover) {
printf("Yes\n");
printf("End peak index:\t\t\t%d\n", this_pk_idx);
} else {
printf("No\n");
peaks[ii] = -1;
continue;
}
// 7. Get parabolic centroid using the full centroid window [centroid_half_window_size_px]
double this_pk_window_idxs[1 + (2*centroid_half_window_size_px)];
double this_pk_window_vals[1 + (2*centroid_half_window_size_px)];
memset(this_pk_window_idxs, 0, sizeof(double)*(1 + (2*centroid_half_window_size_px)));
memset(this_pk_window_vals, 0, sizeof(double)*(1 + (2*centroid_half_window_size_px)));
idx = 0;
for (jj=this_pk_idx-centroid_half_window_size_px; jj<=this_pk_idx+centroid_half_window_size_px; jj++) {
this_pk_window_idxs[idx] = jj;
this_pk_window_vals[idx] = this_frame_values_binned[jj][ii];
idx++;
}
int order = 2;
double coeffs [order+1];
memset(coeffs, 0, sizeof(double)*order+1);
double chi_squared;
if (calc_least_sq_fit(2, 1 + (2*centroid_half_window_size_px), this_pk_window_idxs, this_pk_window_vals, coeffs, &chi_squared)) {
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATFI", -7, "Status flag for L2 spfind routine", ERROR_CODES_FILE_WRITE_ACCESS);
free(target_f);
if(fits_close_file(target_f_ptr, &target_f_status)) fits_report_error (stdout, target_f_status);
return 1;
}
double fitted_peak_idx = -coeffs[1]/(2*coeffs[2]);
printf("Fitted peak index:\t\t%f\n", fitted_peak_idx);
// 8. Ensure fitted peak location is within finding window
printf("Is fitted peak within window?\t");
if (fitted_peak_idx > finding_window_lo_px && fitted_peak_idx < finding_window_hi_px) {
printf("Yes\n");
num_bins_used++;
} else {
printf("No\n");
peaks[ii] = -1;
continue;
}
peaks[ii] = fitted_peak_idx;
/*for (jj=0; jj<spat_nelements-1; jj++) {
printf("%d\t%f\t%f\n", jj, this_spat_values_der_smoothed[jj], this_spat_values_der[jj]);
}*/ // DEBUG
}
printf("\nNum bins used:\t%d\n", num_bins_used);
if (num_bins_used < min_used_bins) {
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATFI", -8, "Status flag for L2 spfind routine", ERROR_CODES_FILE_WRITE_ACCESS);
free(target_f);
if(fits_close_file(target_f_ptr, &target_f_status)) fits_report_error (stdout, target_f_status);
return 1;
}
// ***********************************************************************
// Create [FRFIND_OUTPUTF_PEAKS_FILE] output file and print a few
// parameters
FILE *outputfile;
outputfile = fopen(SPFIND_OUTPUTF_PEAKS_FILE, FILE_WRITE_ACCESS);
if (!outputfile) {
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATFI", -9, "Status flag for L2 spfind routine", ERROR_CODES_FILE_WRITE_ACCESS);
free(target_f);
if(fits_close_file(target_f_ptr, &target_f_status)) fits_report_error (stdout, target_f_status);
return 1;
}
char timestr [80];
memset(timestr, '\0', sizeof(char)*80);
find_time(timestr);
fprintf(outputfile, "#### %s ####\n\n", SPFIND_OUTPUTF_PEAKS_FILE);
fprintf(outputfile, "# Lists the coordinates of the peaks found using the spfind routine.\n\n");
fprintf(outputfile, "# Run filename:\t%s\n", target_f);
fprintf(outputfile, "# Run datetime:\t%s\n\n", timestr);
for (ii=0; ii<disp_nelements_binned; ii++) {
if (peaks[ii] == -1)
continue;
fprintf(outputfile, "%f\t%f\n", cut_x[0]+(ii*bin_size_px) + (double)bin_size_px/2., peaks[ii]);
}
fprintf(outputfile, "%d", EOF);
// ***********************************************************************
// Clean up heap memory
free(target_f);
// ***********************************************************************
// Close [FRFIND_OUTPUTF_PEAKS_FILE] output file and target file (ARG 1)
if (fclose(outputfile)) {
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATFI", -10, "Status flag for L2 spfind routine", ERROR_CODES_FILE_WRITE_ACCESS);
if(fits_close_file(target_f_ptr, &target_f_status)) fits_report_error (stdout, target_f_status);
return 1;
}
if(fits_close_file(target_f_ptr, &target_f_status)) {
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATFI", -11, "Status flag for L2 spfind routine", ERROR_CODES_FILE_WRITE_ACCESS);
fits_report_error (stdout, target_f_status);
return 1;
}
// ***********************************************************************
// Write success to [ERROR_CODES_FILE]
write_key_to_file(ERROR_CODES_FILE, REF_ERROR_CODES_FILE, "L2STATFI", RETURN_FLAG, "Status flag for L2 spfind routine", ERROR_CODES_FILE_WRITE_ACCESS);
return 0;
}
}
