From ffeadedd0510cb7194058c8c66c21b57f6fa02f2 Mon Sep 17 00:00:00 2001
From: Christian C <cc@localhost>
Date: Wed, 5 Mar 2025 20:30:01 -0800
Subject: Cleanup

TODO: Create erosion function for filling gaps
---
 src/main.c | 25 ++++++++++++++++++++-----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/src/main.c b/src/main.c
index fa09a86..5746cd8 100644
--- a/src/main.c
+++ b/src/main.c
@@ -17,7 +17,7 @@
 
 #define OFFSET 16
 
-#define N_DILATIONS 3
+#define N_DILATIONS 0
 
 #define MIN_AREA 200
 #define MIN_PERIMETER 50
@@ -33,11 +33,15 @@ int main(int argc, char** argv)
   uint32_t width, height;
   uint16_t starting_label = 1;
   uint16_t *masks = NULL;
+  // Expect a directory to be passed as the first argument
   if (argc > 1) {
+    // Ensure the directory exists
     if (is_directory(argv[1])) {
+      // List files in the ddirectory
       file_list = list_directory(argv[1]);
       if (file_list) {
 	size_t index = 0;
+	// For each file
 	while (1) {
 	  char* fname = file_list[index];
 	  if (fname == NULL) {
@@ -47,9 +51,23 @@ int main(int argc, char** argv)
 	    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(argv[1], fname);
+	  if (fpath == NULL) {
+	    free(file_list[index++]);
+	    continue;
+	  }
 	  printf("Loading %s...\n", fpath);
 	  uint16_t *file_labels = tif_to_labels(fpath, &width, &height, &starting_label);
+	  if (file_labels == NULL) {
+	    free(fpath);
+	    free(file_list[index++]);
+	    continue;
+	  }
 	  masks = combine_masks(masks, file_labels, width, height);
 	  free(file_labels);
 	  free(fpath);
@@ -119,9 +137,6 @@ int main(int argc, char** argv)
   struct AVLNode* small_label_tree = NULL;
   small_label_tree = get_small_labels(NULL, root, MIN_AREA, MIN_PERIMETER);
 
-  print_in_order_uint16_t(small_label_tree);
-  printf("\n");
-
   // Remove the small labels
   for (size_t y = 0; y < height; y++) {
     for (size_t x = 0; x < width; x++) {
@@ -155,7 +170,7 @@ int main(int argc, char** argv)
   labels = masks;
   masks = temp;
   free(labels);
-  printf("%u labels found\n", starting_label-1);
+  printf("%u remaining labels found\n", starting_label-1);
   printf("Mask dimensions: %u %u\n", width, height);
   // Regenerate information after relabeling
   root = NULL;
-- 
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