#include <stdio.h>
#include <math.h>
#include <stddef.h>
#include <stdlib.h>
#include <string.h>
#include "nrutil.c"
#include "nrutil.h"
#include "UVStruct.c"
#include "UVFile.c"
#include "UVCommon.c"
#include "Brewer.c"

void main(void)

{
	int i;
	int n_col, n_file, n_row, ok;
	int cy, dark_cy, day;
	float dark, time, wl, mic, sig;
	float **data;
	char st[64];
	char sch_file[20], in_file[20], out_file[20], prev_file[20];
	
	struct scan_header AES;
	
	FILE *fp_sch, *fp_in, *fp_out, *fp_data;
	
	data = matrix(1, 275, 1, 3);		
	
	printf("Scan Schedule File: ");		// schedule of scans
	scanf("%s", &sch_file);	
	
	fp_sch = fopen(sch_file, "r");		
	fp_in = fopen("test.txt", "r");
	
	fp_data = fopen("96FE.AES", "w");	// compilation of header data
	fprintf(fp_data, "Header:\n");
	fprintf(fp_data, "Number_of_columns\t26\n");
	fprintf(fp_data, "Labels:\n");
	fprintf(fp_data, "File\tInstrument\tSource\tLocation\tEnvironment\t");
	fprintf(fp_data, "Year\tDay\tDate\tOperation\tMeasurement_type\t");
	fprintf(fp_data, "Measurement_purpose\t");
	fprintf(fp_data, "Number_of_scans\tNumber_of_columns\t");
	fprintf(fp_data, "Number_of_rows\tStart_time\tStop_time\t");
	fprintf(fp_data, "Start_wavelength\tStop_wavelength\tIncrement_wavelength\t");
	fprintf(fp_data, "Dead_time\tIntegration_time\tDark_signal\tFilter_temperature\t");
	fprintf(fp_data, "Comments\tData_file\tAnalysis_file\n");
	fprintf(fp_data, "\t\t\t\t\t\t\t\t\t\t\t\t\t\t");
	fprintf(fp_data, "[UTC]\t[UTC]\t[nm]\t[nm]\t[nm]\t[ns]\t[s]\t[p_s^-1]\t[C]\n");
	fprintf(fp_data, "Data:\n");
	
	fscanf(fp_sch, "%s %s %d", &st, &st, &n_col);	// read schedule file header
	do{
		fscanf(fp_sch, "%s", &st);
	} while(strcmp(st, "Data:") != 0);
	
	while(fscanf(fp_sch, "%s", &in_file) != EOF){	// read schedule file info.
		strcpy(AES.data_file, in_file);
		fscanf(fp_sch, "%d", &i);
		fscanf(fp_sch, "%s", AES.inst);
		fscanf(fp_sch, "%s", AES.source);
		fscanf(fp_sch, "%s", AES.locat);
		fscanf(fp_sch, "%s", AES.envir);
		fscanf(fp_sch, "%s", AES.operat);
		fscanf(fp_sch, "%s", AES.meas_type);
		fscanf(fp_sch, "%s", AES.meas_purp);
		fscanf(fp_sch, "%s", AES.comments);
		printf("%s\n", AES.data_file);
		
		fp_in = fopen(in_file, "r");				//open in_file
		
		while(fscanf(fp_in, "%s", &st) != EOF){
			for(i = 1; i <= 6; i++){				// load info. from data file
				fscanf(fp_in, "%s", &st);
			}
			fscanf(fp_in, "%s %f", &st, &AES.dead_time);
			fscanf(fp_in, "%s %d", &st, &cy);
			for(i = 1; i <= 7; i++){
				fscanf(fp_in, "%s", &st);
			}
			fscanf(fp_in, "%f", &AES.filter_temp);
			for(i = 1; i <= 4; i++){
				fscanf(fp_in, "%s", &st);
			}
			fscanf(fp_in, "%f", &dark);
			fscanf(fp_in, "%s", &st);
			n_row = 1;
			while(strcmp(st, "end") != 0){				// load data
				sscanf(st, "%f,%f,%f,%f,%f", &time, &wl, &mic, &mic, &sig);
				data[n_row][1] = wl/10.0;
				data[n_row][2] = sig;
				if(n_row == 1){ 
					AES.start_time = time/60.0;
					AES.start_wl = wl/10.0;
				}
				AES.stop_time = time/60.0;
				AES.stop_wl = wl/10.0;
				n_row++;
				fscanf(fp_in, "%s", &st);
			}
			n_row--;
		
			AES.inc_wl = (AES.stop_wl - AES.start_wl)/(float)(n_row - 1);
			AES.dark_sig = dark/(float)(40/cy);
			AES.int_time = 0.2294*cy;
			AES.filter_temp = AES.filter_temp*18.64 - 33.27;
			
			for(i = 1; i <= n_row; i++){					// reduce signal data
				data[i][2] = 4.0*(data[i][2] - AES.dark_sig);
				if(data[i][2] != 0){
					data[i][3] = 1.0/(float)sqrt(fabs(data[i][2]));
				}
				else{
					data[i][3] = 0;
				}
				data[i][2] /= AES.int_time;
				data[i][2] = nlexp(data[i][2], AES.dead_time);
			}
			
			AES.dark_sig *= 4.0/AES.int_time;
			sscanf(in_file, "%2s%3d%2d.%3d", &st, &AES.day, &AES.year, &i);	// read day
			if(AES.start_time < 6.0) AES.day++;
			AES.year += 1900;
			day_to_date(AES.year, AES.day, AES.date);
			
			n_file = 1;								// create formatted file
			do{
				sprintf(out_file, "96%03dF%02d.AES", AES.day, n_file);
				ok = file_exist(out_file);
				n_file++;
			} while(ok == 1);
			
			fp_out = fopen(out_file, "w");			// store header in files
			printf("%s\t%.5f\n", out_file, AES.start_time);
			fprintf(fp_data, "%s\t", out_file);
			fprintf(fp_out, "Header:\n");
			fprintf(fp_out, "Instrument\t%s\n", AES.inst);
			fprintf(fp_data, "%s\t", AES.inst);
			fprintf(fp_out, "Source\t%s\n", AES.source);
			fprintf(fp_data, "%s\t", AES.source);
			fprintf(fp_out, "Location\t%s\n", AES.locat);
			fprintf(fp_data, "%s\t", AES.locat);
			fprintf(fp_out, "Environment\t%s\n", AES.envir);
			fprintf(fp_data, "%s\t", AES.envir);
			fprintf(fp_out, "Year\t%d\n", AES.year);
			fprintf(fp_data, "%d\t", AES.year);
			fprintf(fp_out, "Day\t%d\n", AES.day);
			fprintf(fp_data, "%d\t", AES.day);
			fprintf(fp_out, "Date\t%s\n", AES.date);
			fprintf(fp_data, "%s\t", AES.date);
			fprintf(fp_out, "Operation\t%s\n", AES.operat);
			fprintf(fp_data, "%s\t", AES.operat);
			fprintf(fp_out, "Measurement_type\t%s\n", AES.meas_type);
			fprintf(fp_data, "%s\t", AES.meas_type);
			fprintf(fp_out, "Measurement_purpose\t%s\n", AES.meas_purp);
			fprintf(fp_data, "%s\t", AES.meas_purp);
			fprintf(fp_out, "Number_of_scans\t1\n");
			fprintf(fp_data, "1\t");
			fprintf(fp_out, "Number_of_columns\t3\n");
			fprintf(fp_data, "3\t");
			fprintf(fp_out, "Number_of_rows\t%d\n", n_row);
			fprintf(fp_data, "%d\t", n_row);
			fprintf(fp_out, "Start_time\t%.5f\t[UTC]\n", AES.start_time);
			fprintf(fp_data, "%.5f\t", AES.start_time);
			fprintf(fp_out, "Stop_time\t%.5f\t[UTC]\n", AES.stop_time);
			fprintf(fp_data, "%.5f\t", AES.stop_time);
			fprintf(fp_out, "Start_wavelength\t%.2f\t[nm]\n", AES.start_wl);
			fprintf(fp_data, "%.2f\t", AES.start_wl);		
			fprintf(fp_out, "Stop_wavelength\t%.2f\t[nm]\n", AES.stop_wl);
			fprintf(fp_data, "%.2f\t", AES.stop_wl);
			fprintf(fp_out, "Increment_wavelength\t%.2f\t[nm]\n", AES.inc_wl);
			fprintf(fp_data, "%.2f\t", AES.inc_wl);
			fprintf(fp_out, "Dead_time\t%.1f\t[ns]\n", AES.dead_time*1e9);
			fprintf(fp_data, "%.1f\t", AES.dead_time*1e9);
			fprintf(fp_out, "Integration_time\t%.4f\t[s]\n", AES.int_time);
			fprintf(fp_data, "%.4f\t", AES.int_time);
			fprintf(fp_out, "Dark_signal\t%.2f\t[p_s^-1]\n", AES.dark_sig);
			fprintf(fp_data, "%.2f\t", AES.dark_sig);
			fprintf(fp_out, "Filter_temperature\t%.2f\t[C]\n", AES.filter_temp);
			fprintf(fp_data, "%.2f\t", AES.filter_temp);
			fprintf(fp_out, "Comments\t%s\n", AES.comments);
			fprintf(fp_data, "%s\t", AES.comments);
			fprintf(fp_out, "Data_file\t%s\n", AES.data_file);
			fprintf(fp_data, "%s\t", AES.data_file);
			fprintf(fp_out, "Analysis_program\tFmt_96AES_S.c\n");
			fprintf(fp_data, "Fmt_96AES_S.c\n");
			fprintf(fp_out, "Labels:\n");
			fprintf(fp_out, "Wavelength\tSignal\tdS/S\n");
			fprintf(fp_out, "[nm]\t[p_s^-1]\n");
			fprintf(fp_out, "Data:\n");
			for(i = 1; i <= n_row; i++){				// store data
				fprintf(fp_out, "%.2f\t%.4f\t%.4f\n", data[i][1], data[i][2], data[i][3]);
			}
			
			fclose(fp_out);
		}
		fclose(fp_in);	
	}
	fclose(fp_sch);	
	fclose(fp_data);	
}