#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <time.h>
#include "constants.h"
#include "struct_TAC_in.h"
#include "parse_in_akc.h"
#include "get_tac_akc.h"
#include "find_MAT_akc.h"
#include "fit_sv_akc.h"
#include "write_data_akc.h"

/* C source code name: Plant_main_akc.c */
/* edit, e.g., with emacs. compile with Makefile  */

/* By: Alexander K. Converse, University of Wisconsin-Madison */
/* Created: 25 May 2012 */
/* Modified: 3 March 2014 */

/* Purpose: Fit plant TACs with model  */
/* 20120518 Model based on McKay et al. Plant, Cell and Environment (198) 11:851-861 */
/* 	B(t+dt) = dt* sv(M(t)-B(t)) + B(t)    (B = trapped, M = free) */
/* 	B(infinite) =  B(end of scan) */
/* 	see plant_McKay_akc_c_flow_20120518.pdf */

/* usage: $McKay_akc_dev input_file.txt output_file.txt */

struct TAC_t TAC_in;
struct ROI chosenROI;
struct ROI allROIs[MAXROIS];

int main(int argc, char *argv[])
{
  int i;
  int j;
  int MAT;
  int returnVal;
  char const *inputFile;
  char const *outputFile;

  // Check for correct input arguments
  if (argc < 3) {
    printf("Not enough input arguments\n");
    printf("Usage: ./Plant_main_akc.c input_file.txt output_file.txt");
    printf("Exiting program\n");
    return 0;
  }

  inputFile = argv[1];
  outputFile = argv[2];

  // Check that strings are valid file names
  if ((strlen(outputFile) < 5) || strlen(inputFile) < 5) {
    printf("Input argument doesn't have correct file extension\n");
    printf("Usage: ./Plant_main_akc.c input_file.txt output_file.txt\n");
    printf("Exiting program\n");
    return 0;
  }
  
  // Initialize a structure to hold information from input file
  struct TAC_t *TAC_ptr;
  TAC_ptr = &TAC_in;

  printf("input file: %s\n", inputFile);

  // Store input file information in structure called TAC_t
  returnVal = parse_in_akc(TAC_ptr, inputFile);
  if (returnVal == 0) {
    return 0;
  }

  MAT = TAC_in.MAT;

  // Loop through each ROI
  for (i = 0; i < TAC_in.nROIs; ++i) {
    // Find the ith ROI and store its data in allROIs[i]
    get_tac_akc(TAC_ptr, &allROIs[i], i);
    // Find optimum SV
    fit_sv_akc(i, &allROIs[i], TAC_ptr, MAT);
    // Calculate model information based on optimum sv
    find_MAT_akc(i, 0, &allROIs[i], TAC_ptr, allROIs[i].sv, MAT);

    // Write identifying information at top of file
    if (i == 0) {
      write_header_akc(&TAC_in, outputFile, MAT);
    }
    // Write ROI name, position, sv, MAT
    write_ROIData_akc(&allROIs[i], &TAC_in, outputFile, i);
  }

  // Write time, observed, bound, free, bound+free
  for (i = 0; i < TAC_in.nROIs; ++i) { 
    write_ModelData_akc(&allROIs[i], &TAC_in, outputFile, i);
  }

  printf("\nEnd Plant_main_akc.c\n");

  return 1;
}