#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>

#include <lib/algo/avl_tree.h>
#include <lib/algo/flood_fill.h>
#include <lib/bool.h>
#include <lib/color.h>
#include <lib/dir.h>
#include <lib/file.h>
#include <lib/lib.h>
#include <lib/mem/galloc.h>
#include <lib/monad.h>
#include <lib/png.h>
#include <lib/seg/mask_data.h>
#include <lib/seg/util.h>
#include <lib/time.h>

int main(int arg_count, char **arg_value) {
  char cli_option;
  char *process_directory = NULL;
  char *png_output_file_fullpath = "../out.png";
  char *bin_output_file_fullpath = "../out.bin";
  size_t closeup_pixel_count = 10;
  size_t minimum_mask_area_threshold = 500;
  size_t minimum_mask_perimeter_threshold = 0;
  bool_t suppress_outputs_b = FALSE;
  //-----------------------------------------------
  //-GET-COMMAND-LINE-ARGUMENTS--------------------
  //-----------------------------------------------
  while ((cli_option = getopt(arg_count, arg_value, "d:b:p:n:sA:P:")) != -1) {
    switch (cli_option) {
    case 's':
      suppress_outputs_b = TRUE;
      break;
    case 'A':
      minimum_mask_area_threshold = atoi(optarg);
      break;
    case 'P':
      minimum_mask_perimeter_threshold = atoi(optarg);
      break;
    case 'd':
      if (!suppress_outputs_b) {
        printf("Parse Directory: %s\n", optarg);
      }
      process_directory = optarg;
      break;
    case 'b':
      if (!suppress_outputs_b) {
        printf("Bin File: %s\n", optarg);
      }
      bin_output_file_fullpath = optarg;
      break;
    case 'p':
      if (!suppress_outputs_b) {
        printf("PNG File: %s\n", optarg);
      }
      png_output_file_fullpath = optarg;
      break;
    case 'n':
      if (!suppress_outputs_b) {
        printf("Closeup Size: %d\n", atoi(optarg));
      }
      closeup_pixel_count = atoi(optarg);
      break;
    case ':':
      if (!suppress_outputs_b) {
        printf("Option requires value\n");
      }
      break;
    case '?':
      if (!suppress_outputs_b) {
        printf("Unknown option: %c\n", optopt);
      }
      break;
    }
  }
  for (; optind < arg_count; optind++) {
    if (!suppress_outputs_b) {
      printf("Extra arguments: %s\n", arg_value[optind]);
    }
  }
  TIME(ts_g_start);
  //-----------------------------------------------
  //-PROCESS-FILES-IN-DIRECTORY--------------------
  //-----------------------------------------------
  char **file_list = NULL;
  MaskData_t starting_label = 1;
  Mask *masks_im = NULL;
  // Expect a directory to be passed as the first argument
  if (process_directory != NULL) {
    // Ensure the directory exists
    if (is_directory(process_directory)) {
      // List files in the ddirectory
      file_list = list_directory(process_directory);
      if (file_list != NULL) {
        for (size_t index = 0; file_list[index] != NULL; index++) {
          char *fname = file_list[index];
          if (is_tif_ext(fname) == FALSE) {
            g_free(file_list[index]);
            continue;
          }
          // If we have a tiff file
          //  1. Convert to labels
          //  2. Find contiguous regions
          //  3. Combine with current total mask
          //  4. Free up allocations made in this process
          char *fpath = full_path(process_directory, fname);
          if (fpath == NULL) {
            g_free(file_list[index]);
            continue;
          }
          if (!suppress_outputs_b) {
            printf("Loading %s...\n", fpath);
          }
          //-----------------------------------------------
          //-PROCESS-TIFF-TO-LABELS------------------------
          //-----------------------------------------------
          Mask *file_im = tif_to_labels(fpath, &starting_label);
          if (file_im == NULL) {
            g_free(fpath);
            g_free(file_list[index]);
            continue;
          }
          //-----------------------------------------------
          //-COMBINE-LABELS-TO-GLOBAL-MASK-----------------
          //-----------------------------------------------
          masks_im = combine_masks(masks_im, file_im);
          free_image_mask(file_im);
          g_free(fpath);
          g_free(file_list[index]);
        }
        g_free(file_list);
      }
    }
  }
  if (masks_im == NULL) {
    fprintf(stderr, "No masks found!\n");
    return 1;
  }

  uint32_t width = (uint32_t)masks_im->width;
  uint32_t height = (uint32_t)masks_im->height;

  //-----------------------------------------------
  //-FIND-CONTIGUOUS-REGIONS-----------------------
  //-----------------------------------------------
  reduce_contiguous_regions(masks_im, &starting_label);
  if (!suppress_outputs_b) {
    printf("%u labels found\n", starting_label - 1);
    printf("Mask dimensions: %u %u\n", width, height);
  }
  //-----------------------------------------------
  //-FILTER-SMALL-REGIONS-OUT----------------------
  //-----------------------------------------------
  TIME(ts_filter_start);
  filter_small_masks(masks_im, minimum_mask_area_threshold,
                     minimum_mask_perimeter_threshold);
  TIME(ts_filter_end);
  if (!suppress_outputs_b) {
    printf("Removing small labels took %f ms\n",
           1000 * diff_time(&ts_filter_end, &ts_filter_start));
  }
  //-----------------------------------------------
  //-FIND-CONTIGUOUS-REGIONS-----------------------
  //-----------------------------------------------
  //--to-make-labels-span-1-to-n-------------------
  //-----------------------------------------------
  reduce_contiguous_regions(masks_im, &starting_label);
  if (!suppress_outputs_b) {
    printf("%u remaining labels found\n", starting_label - 1);
    printf("Mask dimensions: %u %u\n", width, height);
  }
#ifdef AVL_INFO
  //-----------------------------------------------
  //-OPTIONAL:-------------------------------------
  //-GET-MASK-META-INFORMATION---------------------
  //-----------------------------------------------
  AVLNode *root = NULL;
  root = get_mask_data(masks_im);
  if (!silent) {
    printf("Inorder traversal of AVL tree: ");
    print_label(root);
    printf("\n");
  }
  free_avl_tree_nodes(root);
#endif
  //-----------------------------------------------
  //-CLOSE-UP-SMALL-GAPS-BETWEEN-REGIONS-----------
  //-----------------------------------------------
  TIME(ts_start);
  closeup(masks_im, closeup_pixel_count);
  TIME(ts_end);
  if (!suppress_outputs_b) {
    printf("Closing (%lu) up took %f ms\n", closeup_pixel_count,
           1000 * diff_time(&ts_end, &ts_start));
  }
  //-----------------------------------------------
  //-END-OF-PROCESSING-----------------------------
  //-----------------------------------------------

  //-----------------------------------------------
  //-SAVE-MASK-AS-BINARY-AND-PNG-------------------
  //-----------------------------------------------
  if (masks_im != NULL) {
    Bitmap *bitmap = image_mask_data_to_bitmap(masks_im);
    if (bitmap != NULL) {
      save_png(bitmap, png_output_file_fullpath);
      g_free(bitmap);
    }
    write_array(bin_output_file_fullpath, masks_im->image[0],
                width * height * sizeof(MaskData_t));
    free_image_mask(masks_im);
  }
  TIME(ts_g_end);
  if (!suppress_outputs_b) {
    printf("Finished in %f ms\n", 1000 * diff_time(&ts_g_end, &ts_g_start));
  }
  printf("Outstanding allocations: %zu\n", g_outstanding_allocations());
  return 0;
}