Modularize

3 files changed, 179 insertions, 175 deletions

diff --git a/src/lib/dir.c b/src/lib/dir.c
index a681d26..be2a2ac 100644
--- a/src/lib/dir.c
+++ b/src/lib/dir.c
@@ -45,3 +45,25 @@ char** list_directory(char* dirname) {
   return NULL;
 }
 
+// Get full path
+char* full_path(char* dir, char* file)
+{
+  char* fpath = NULL;
+  size_t dir_len = strlen(dir);
+  size_t file_len = strlen(file);
+  fpath = (char*)calloc(dir_len+file_len+2,sizeof(char));
+  strcpy(fpath,dir);
+  strcpy(fpath+dir_len+1,file);
+  fpath[dir_len] = '/';
+  return fpath;
+}
+
+// Determines if file name has tif file extension
+bool_t is_tif_ext(char* file_name)
+{
+  size_t file_len = strlen(file_name);
+  if ((file_name[file_len-3] == 't') && (file_name[file_len-2] == 'i') && (file_name[file_len-1] == 'f')) {
+    return TRUE;
+  }
+  return FALSE;
+}
diff --git a/src/lib/seg/util.c b/src/lib/seg/util.c
new file mode 100644
index 0000000..d7b91b1
--- /dev/null
+++ b/src/lib/seg/util.c
@@ -0,0 +1,149 @@
+#include <lib/seg/util.h>
+#include <lib/algo/flood_fill.h>
+#include <tiffio.h>
+#include <assert.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+// Convert x,y coords to linear coordinate
+size_t xy_to_coord(size_t x, size_t y, uint32_t width, uint32_t height)
+{
+  return x + y*width;
+}
+
+// Dilate masks by one 4-connected pixel
+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++) {
+    for (size_t x = 0; x < width; x++) {
+      size_t current_position = xy_to_coord(x, y, width, height);
+      if (mask[current_position] != 0) {
+	new_mask[current_position] = mask[current_position];
+	continue;
+      }
+      size_t proposed_position;
+      if (x != 0) {
+	proposed_position = xy_to_coord(x-1, y, width, height);
+	if (mask[proposed_position] != 0) {
+	  new_mask[current_position] = mask[proposed_position];
+	  continue;
+	}
+      }
+      if ((x+1) != width) {
+	proposed_position = xy_to_coord(x+1, y, width, height);
+	if (mask[proposed_position] != 0) {
+	  new_mask[current_position] = mask[proposed_position];
+	  continue;
+	}
+      }
+      if (y != 0) {
+	proposed_position = xy_to_coord(x, y-1, width, height);
+	if (mask[proposed_position] != 0) {
+	  new_mask[current_position] = mask[proposed_position];
+	  continue;
+	}
+      }
+      if ((y+1) != height) {
+	proposed_position = xy_to_coord(x, y+1, width, height);
+	if (mask[proposed_position] != 0) {
+	  new_mask[current_position] = mask[proposed_position];
+	  continue;
+	}
+      }
+    }
+  }
+  return 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
+uint16_t* combine_masks(uint16_t *destination, uint16_t *extra_labels, uint32_t width, uint32_t height)
+{
+  if (destination == NULL) {
+    destination = (uint16_t*)calloc(width*height, sizeof(uint16_t));
+  }
+  for (size_t y = 0; y < height; y++) {
+    for (size_t x = 0; x < width; x++) {
+      size_t coord = x + y*width;
+      if (destination[coord] == 0) {
+	destination[coord] = extra_labels[coord];
+      }
+    }
+  }
+  return destination;
+}
+
+// Process Tif File to Labels
+//  width, height will be overwritten with image dimensions
+//  starting_label_p will be incremented for each label found in the image
+uint16_t* tif_to_labels(char* tif_file_name, uint32_t *width, uint32_t *height, uint16_t *starting_label_p)
+{
+  //-TIFF-IMAGE-OPEN-------------------------------
+  TIFF *tif = TIFFOpen(tif_file_name, "r");
+  if (!tif) {
+    fprintf(stderr, "Failed to open TIFF file\n");
+    return NULL;
+  }
+
+  //-TIFF-FIND-DIMENSIONS--------------------------
+  size_t channels = 1;
+  TIFFGetField(tif, TIFFTAG_IMAGEWIDTH, width);
+  TIFFGetField(tif, TIFFTAG_IMAGELENGTH, height);
+
+  tmsize_t STRIP_LENGTH = TIFFStripSize(tif);
+  tmsize_t STRIP_COUNT = TIFFNumberOfStrips(tif);
+  if ((*width)*(*height)*3 == STRIP_LENGTH*STRIP_COUNT) {
+    channels = 3;
+  } else if ((*width)*(*height)*4 == STRIP_LENGTH*STRIP_COUNT) {
+    channels = 4;
+  }
+
+  //-TIFF-LOAD-DATA--------------------------------
+  void* buffer = malloc(STRIP_LENGTH*sizeof(uint8_t));
+  if (buffer == NULL) {
+    fprintf(stderr, "Memory allocation error\n");
+    TIFFClose(tif);
+    return NULL;
+  }
+  uint8_t* image_data = calloc((*width)*(*height)*channels,sizeof(uint8_t));
+  if (image_data == NULL) {
+    fprintf(stderr, "Memory allocation error\n");
+    free(buffer);
+    TIFFClose(tif);
+    return NULL;
+  }
+  for (size_t y = 0; y < STRIP_COUNT; y++) {
+    tmsize_t strip_size = TIFFReadRawStrip(tif, y, buffer, STRIP_LENGTH);
+    assert(strip_size == STRIP_LENGTH);
+    for (size_t x = 0; x < STRIP_LENGTH; x++) {
+      image_data[x + y*STRIP_LENGTH] = ((uint8_t*)buffer)[x];
+    }
+  }
+  free(buffer);
+
+  //-FLOOD-FILL-SEGMENTATION-----------------------
+  //-CONTIGUOUS-REGION-FINDING---------------------
+  uint16_t *labels = NULL;
+  labels = (uint16_t*)calloc((*width)*(*height),sizeof(uint16_t));
+  if (labels == NULL) {
+    fprintf(stderr, "Memory allocation error\n");
+    free(image_data);
+    TIFFClose(tif);
+    return NULL;
+  }
+  // Flood fill on each pixel
+  //  Increase label for each success
+  for (size_t y = 0; y < *height; y++) {
+    for (size_t x = 0; x < *width; x++) {
+      size_t coord = x + y*(*width);
+      if(flood(image_data, labels, *width, *height, channels, x, y, &(image_data[coord*channels]), *starting_label_p)) {
+        *starting_label_p += 1;
+      }
+    }
+  }
+  free(image_data);
+  TIFFClose(tif);
+  return labels;
+}
diff --git a/src/main.c b/src/main.c
index 9075dcb..02f5520 100644
--- a/src/main.c
+++ b/src/main.c
@@ -1,187 +1,18 @@
 #include <stdio.h>
 #include <stdlib.h>
-#include <assert.h>
-#include <string.h>
 
 #include <raylib.h>
 
-#include <tiffio.h>
-
 #include <lib/lib.h>
 #include <lib/bool.h>
 #include <lib/dir.h>
 #include <lib/time.h>
 #include <lib/color.h>
 #include <lib/algo/flood_fill.h>
+#include <lib/seg/util.h>
 
 #define OFFSET 16
 
-// Get full path
-char* full_path(char* dir, char* file)
-{
-  char* fpath = NULL;
-  size_t dir_len = strlen(dir);
-  size_t file_len = strlen(file);
-  fpath = (char*)calloc(dir_len+file_len+2,sizeof(char));
-  strcpy(fpath,dir);
-  strcpy(fpath+dir_len+1,file);
-  fpath[dir_len] = '/';
-  return fpath;
-}
-
-// Determines if file name has tif file extension
-bool_t is_tif_ext(char* file_name)
-{
-  size_t file_len = strlen(file_name);
-  if ((file_name[file_len-3] == 't') && (file_name[file_len-2] == 'i') && (file_name[file_len-1] == 'f')) {
-    return TRUE;
-  }
-  return FALSE;
-}
-
-// Convert x,y coords to linear coordinate
-size_t xy_to_coord(size_t x, size_t y, uint32_t width, uint32_t height)
-{
-  return x + y*width;
-}
-
-// Dilate masks by one 4-connected pixel
-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++) {
-    for (size_t x = 0; x < width; x++) {
-      size_t current_position = xy_to_coord(x, y, width, height);
-      if (mask[current_position] != 0) {
-	new_mask[current_position] = mask[current_position];
-	continue;
-      }
-      size_t proposed_position;
-      if (x != 0) {
-	proposed_position = xy_to_coord(x-1, y, width, height);
-	if (mask[proposed_position] != 0) {
-	  new_mask[current_position] = mask[proposed_position];
-	  continue;
-	}
-      }
-      if ((x+1) != width) {
-	proposed_position = xy_to_coord(x+1, y, width, height);
-	if (mask[proposed_position] != 0) {
-	  new_mask[current_position] = mask[proposed_position];
-	  continue;
-	}
-      }
-      if (y != 0) {
-	proposed_position = xy_to_coord(x, y-1, width, height);
-	if (mask[proposed_position] != 0) {
-	  new_mask[current_position] = mask[proposed_position];
-	  continue;
-	}
-      }
-      if ((y+1) != height) {
-	proposed_position = xy_to_coord(x, y+1, width, height);
-	if (mask[proposed_position] != 0) {
-	  new_mask[current_position] = mask[proposed_position];
-	  continue;
-	}
-      }
-    }
-  }
-  return 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
-uint16_t* combine_masks(uint16_t *destination, uint16_t *extra_labels, uint32_t width, uint32_t height)
-{
-  if (destination == NULL) {
-    destination = (uint16_t*)calloc(width*height, sizeof(uint16_t));
-  }
-  for (size_t y = 0; y < height; y++) {
-    for (size_t x = 0; x < width; x++) {
-      size_t coord = x + y*width;
-      if (destination[coord] == 0) {
-	destination[coord] = extra_labels[coord];
-      }
-    }
-  }
-  return destination;
-}
-
-// Process Tif File to Labels
-//  width, height will be overwritten with image dimensions
-//  starting_label_p will be incremented for each label found in the image
-uint16_t* tif_to_labels(char* tif_file_name, uint32_t *width, uint32_t *height, uint16_t *starting_label_p)
-{
-  //-TIFF-IMAGE-OPEN-------------------------------
-  TIFF *tif = TIFFOpen(tif_file_name, "r");
-  if (!tif) {
-    fprintf(stderr, "Failed to open TIFF file\n");
-    return NULL;
-  }
-
-  //-TIFF-FIND-DIMENSIONS--------------------------
-  size_t channels = 1;
-  TIFFGetField(tif, TIFFTAG_IMAGEWIDTH, width);
-  TIFFGetField(tif, TIFFTAG_IMAGELENGTH, height);
-
-  tmsize_t STRIP_LENGTH = TIFFStripSize(tif);
-  tmsize_t STRIP_COUNT = TIFFNumberOfStrips(tif);
-  if ((*width)*(*height)*3 == STRIP_LENGTH*STRIP_COUNT) {
-    channels = 3;
-  } else if ((*width)*(*height)*4 == STRIP_LENGTH*STRIP_COUNT) {
-    channels = 4;
-  }
-
-  //-TIFF-LOAD-DATA--------------------------------
-  void* buffer = malloc(STRIP_LENGTH*sizeof(uint8_t));
-  if (buffer == NULL) {
-    fprintf(stderr, "Memory allocation error\n");
-    TIFFClose(tif);
-    return NULL;
-  }
-  uint8_t* image_data = calloc((*width)*(*height)*channels,sizeof(uint8_t));
-  if (image_data == NULL) {
-    fprintf(stderr, "Memory allocation error\n");
-    free(buffer);
-    TIFFClose(tif);
-    return NULL;
-  }
-  for (size_t y = 0; y < STRIP_COUNT; y++) {
-    tmsize_t strip_size = TIFFReadRawStrip(tif, y, buffer, STRIP_LENGTH);
-    assert(strip_size == STRIP_LENGTH);
-    for (size_t x = 0; x < STRIP_LENGTH; x++) {
-      image_data[x + y*STRIP_LENGTH] = ((uint8_t*)buffer)[x];
-    }
-  }
-  free(buffer);
-
-  //-FLOOD-FILL-SEGMENTATION-----------------------
-  //-CONTIGUOUS-REGION-FINDING---------------------
-  uint16_t *labels = NULL;
-  labels = (uint16_t*)calloc((*width)*(*height),sizeof(uint16_t));
-  if (labels == NULL) {
-    fprintf(stderr, "Memory allocation error\n");
-    free(image_data);
-    TIFFClose(tif);
-    return NULL;
-  }
-  // Flood fill on each pixel
-  //  Increase label for each success
-  for (size_t y = 0; y < *height; y++) {
-    for (size_t x = 0; x < *width; x++) {
-      size_t coord = x + y*(*width);
-      if(flood(image_data, labels, *width, *height, channels, x, y, &(image_data[coord*channels]), *starting_label_p)) {
-        *starting_label_p += 1;
-      }
-    }
-  }
-  free(image_data);
-  TIFFClose(tif);
-  return labels;
-}
-
 int main(int argc, char** argv)
 {
   //-----------------------------------------------
@@ -204,23 +35,25 @@ int main(int argc, char** argv)
 	  if (is_tif_ext(fname) == FALSE) {
 	    free(file_list[index++]);
 	    continue;
-	  } else {
-	    printf("Tiff found!\n");
 	  }
 	  char* fpath = full_path(argv[1], fname);
+	  printf("Loading %s...\n", fpath);
 	  uint16_t *file_labels = tif_to_labels(fpath, &width, &height, &starting_label);
 	  masks = combine_masks(masks, file_labels, width, height);
 	  free(file_labels);
-	  printf("%s\n", fpath);
 	  free(fpath);
-	  printf("%s\n", fname);
 	  free(file_list[index++]);
 	}
 	free(file_list);
       }
     }
   }
-  printf("%u %u\n", width, height);
+  if (masks == NULL) {
+    fprintf(stderr, "No masks found!\n");
+    return 1;
+  }
+  printf("%u labels found\n", starting_label-1);
+  printf("Mask dimensions: %u %u\n", width, height);
   for (uint16_t count = 0; count < 3; count++) {
     uint16_t *new_labels = dilate(masks, width, height);
     free(masks);