Simplify execution

2 files changed, 112 insertions, 10 deletions

diff --git a/src/lib/seg/mask_data.c b/src/lib/seg/mask_data.c
index 2f3a51a..8c4b037 100644
--- a/src/lib/seg/mask_data.c
+++ b/src/lib/seg/mask_data.c
@@ -1,4 +1,5 @@
 #include <lib/seg/mask_data.h>
+#include <lib/seg/util.h>
 
 #include <stdio.h>
 
@@ -224,3 +225,39 @@ struct AVLNode* get_small_labels(struct AVLNode* removal_tree, struct AVLNode* l
   }
   return return_tree;
 }
+
+// Get mask label data
+struct AVLNode* get_mask_data(uint16_t* masks, uint32_t width, uint32_t height)
+{
+  struct AVLNode* root = NULL;
+  for (size_t y = 0; y < height; y++) {
+    for (size_t x = 0; x < width; x++) {
+      size_t coord = x + y*width;
+      if (masks[coord] != 0) {
+	root = increase_label_area_alloc(root, masks[coord]);
+	if (is_on_mask_boundary(masks, width, height, x, y)) {
+	  increase_label_perimeter(root, masks[coord]);
+	}
+      }
+    }
+  }
+  return root;
+}
+
+// Filter out small masks in mask
+void filter_small_masks(uint16_t* masks, uint32_t width, uint32_t height, size_t min_area, size_t min_perimeter)
+{
+  struct AVLNode* root = get_mask_data(masks, width, height);
+  struct AVLNode* small_label_tree = NULL;
+  small_label_tree = get_small_labels(NULL, root, min_area, min_perimeter);
+  for (size_t y = 0; y < height; y++) {
+    for (size_t x = 0; x < width; x++) {
+      size_t coord = x + y*width;
+      if (in_uint16_t_tree(small_label_tree, masks[coord])) {
+	masks[coord] = 0;
+      }
+    }
+  }
+  free_avl_tree(small_label_tree);
+  free_avl_tree_nodes(root);
+}
diff --git a/src/lib/seg/util.c b/src/lib/seg/util.c
index 10b8fa8..a45f6c8 100644
--- a/src/lib/seg/util.c
+++ b/src/lib/seg/util.c
@@ -1,4 +1,4 @@
-#include <lib/seg/util.h>
+ #include <lib/seg/util.h>
 #include <lib/algo/flood_fill.h>
 #include <lib/png.h>
 #include <tiffio.h>
@@ -51,7 +51,7 @@ bool_t is_on_mask_boundary(uint16_t* mask, uint32_t width, uint32_t height, size
 }
 
 // Dilate masks by one 4-connected pixel
-uint16_t* dilate(uint16_t* mask, uint32_t width, uint32_t height)
+uint16_t* _dilate(uint16_t* mask, uint32_t width, uint32_t height)
 {
   uint16_t *new_mask = (uint16_t*)calloc(width*height,sizeof(uint16_t));
   for (size_t y = 0; y < height; y++) {
@@ -95,8 +95,18 @@ uint16_t* dilate(uint16_t* mask, uint32_t width, uint32_t height)
   return new_mask;
 }
 
+// Dilate masks by one 4-connected pixel
+void dilate(uint16_t** mask, uint32_t width, uint32_t height)
+{
+  uint16_t *new_mask = _dilate(*mask, width, height);
+  if (new_mask != NULL) {
+    free(*mask);
+    *mask = new_mask;
+  }
+}
+
 // Erode masks by one 4-connected pixel
-uint16_t* erode(uint16_t* mask, uint32_t width, uint32_t height)
+uint16_t* _erode(uint16_t* mask, uint32_t width, uint32_t height)
 {
   uint16_t *new_mask = (uint16_t*)calloc(width*height,sizeof(uint16_t));
   for (size_t y = 0; y < height; y++) {
@@ -141,20 +151,26 @@ uint16_t* erode(uint16_t* mask, uint32_t width, uint32_t height)
   return new_mask;
 }
 
+// Erode masks by one 4-connected pixel
+void erode(uint16_t** mask, uint32_t width, uint32_t height)
+{
+  uint16_t *new_mask = _erode(*mask, width, height);
+  if (new_mask != NULL) {
+    free(*mask);
+    *mask = new_mask;
+  }
+}
+
 // Close up masks by N-pixels
-uint16_t* closeup(uint16_t* mask, uint32_t width, uint32_t height, size_t num_pixels)
+uint16_t* _closeup(uint16_t* mask, uint32_t width, uint32_t height, size_t num_pixels)
 {
   uint16_t *new_mask = (uint16_t*)calloc(width*height,sizeof(uint16_t));
   memcpy(new_mask, mask, width*height*sizeof(uint16_t));
   for (size_t count = 0; count < num_pixels; count++) {
-    uint16_t *new_labels = dilate(new_mask, width, height);
-    free(new_mask);
-    new_mask = new_labels;
+    dilate(&new_mask, width, height);
   }
   for (size_t count = 0; count < num_pixels; count++) {
-    uint16_t *new_labels = erode(new_mask, width, height);
-    free(new_mask);
-    new_mask = new_labels;
+    erode(&new_mask, width, height);
   }
   // Retain original mask at the very least
   for (size_t y = 0; y < height; y++) {
@@ -170,6 +186,17 @@ uint16_t* closeup(uint16_t* mask, uint32_t width, uint32_t height, size_t num_pi
   return new_mask;
 }
 
+// Close up masks by N-pixels
+//  Update pointer
+void closeup(uint16_t** mask, uint32_t width, uint32_t height, size_t num_pixels)
+{
+  uint16_t *new_mask = _closeup(*mask, width, height, num_pixels);
+  if (new_mask != NULL) {
+    free(*mask);
+    *mask = new_mask;
+  }
+}
+
 // Combine Label Masks
 // For all empty spaces in the destination, put the extra label if it exists
 // Allocates an array if destination is unallocated
@@ -290,3 +317,41 @@ struct bitmap_t* uint16_to_bitmap(uint16_t* buffer, uint32_t width, uint32_t hei
   bitmap->height = (size_t)height;
   return bitmap;
 }
+
+// Reduce a mask to the contiguous regions
+uint16_t* _reduce_contiguous_regions(uint16_t* masks, uint32_t width, uint32_t height, uint16_t* total_labels)
+{
+  uint16_t starting_label = 1;
+  uint16_t* new_masks = (uint16_t*)calloc(width*height, sizeof(uint16_t));
+  if (new_masks == NULL) {
+    return NULL;
+  }
+  for (size_t y = 0; y < height; y++) {
+    for (size_t x = 0; x < width; x++) {
+      size_t coord = x + y*width;
+      uint8_t channels = 2; // uint16_t = 2*uint8_t
+      if (flood((uint8_t*)masks, new_masks, width, height, channels, x, y, &(((uint8_t*)masks)[coord*channels]), starting_label)) {
+	starting_label++;
+      }
+    }
+  }
+  if (total_labels != NULL) {
+    *total_labels = starting_label;
+  }
+  return new_masks;
+}
+
+// Reduce a mask to the contiguous regions
+//  Automatically update pointer to contiguous mask
+//  Freeing previous mask
+void reduce_contiguous_regions(uint16_t** masks_p, uint32_t width, uint32_t height, uint16_t* total_labels)
+{
+  if (masks_p == NULL) {
+    return;
+  }
+  uint16_t* new_masks = _reduce_contiguous_regions(*masks_p, width, height, total_labels);
+  if (new_masks != NULL) {
+    free(*masks_p);
+    *masks_p = new_masks;
+  }
+}