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-rw-r--r--src/lib/seg/util.c363
1 files changed, 0 insertions, 363 deletions
diff --git a/src/lib/seg/util.c b/src/lib/seg/util.c
deleted file mode 100644
index 8a5f5e5..0000000
--- a/src/lib/seg/util.c
+++ /dev/null
@@ -1,363 +0,0 @@
- #include <lib/seg/util.h>
-#include <lib/algo/flood_fill.h>
-#include <lib/png.h>
-#include <tiffio.h>
-#include <assert.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-// Suppress Tiff Warnings
-void TiffDummyHandler(const char* module, const char* fmt, va_list ap)
-{
- // ignore errors and warnings (or handle them your own way)
-}
-
-// 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;
-}
-
-// Determine if coordinate is on a mask boundary
-// Assumes mask is (WxH)
-bool_t is_on_mask_boundary(uint16_t* mask, uint32_t width, uint32_t height, size_t x, size_t y)
-{
- size_t starting_coord = xy_to_coord(x, y, width, height);
- size_t proposed_position;
- uint16_t current_value = mask[starting_coord];
-
- // Left neighbor
- if (x != 0) {
- proposed_position = xy_to_coord(x-1, y, width, height);
- if (mask[proposed_position] != current_value) {
- return TRUE;
- }
- }
- // Right neighbor
- if ((x+1) != width) {
- proposed_position = xy_to_coord(x+1, y, width, height);
- if (mask[proposed_position] != current_value) {
- return TRUE;
- }
- }
- if (y != 0) {
- proposed_position = xy_to_coord(x, y-1, width, height);
- if (mask[proposed_position] != current_value) {
- return TRUE;
- }
- }
- if ((y+1) != height) {
- proposed_position = xy_to_coord(x, y+1, width, height);
- if (mask[proposed_position] != current_value) {
- return TRUE;
- }
- }
- return FALSE;
-}
-
-// 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;
-}
-
-// 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 *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;
-}
-
-// 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 *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++) {
- dilate(&new_mask, width, height);
- }
- for (size_t count = 0; count < num_pixels; count++) {
- erode(&new_mask, width, height);
- }
- // Retain original mask at the very least
- for (size_t y = 0; y < height; y++) {
- for (size_t x = 0; x < width; x++) {
- size_t coord = x + y*width;
- if (mask[coord] != 0) {
- if (new_mask[coord] != mask[coord]) {
- new_mask[coord] = mask[coord];
- }
- }
- }
- }
- 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
-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)
-{
- TIFFSetWarningHandler(TiffDummyHandler);
- //-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;
-}
-
-// Convert mask to bitmap
-struct bitmap_t* uint16_to_bitmap(uint16_t* buffer, uint32_t width, uint32_t height)
-{
- struct pixel_t* out_buffer = (struct pixel_t*)calloc(width*height, sizeof(struct pixel_t));
- if (out_buffer == NULL) {
- return NULL;
- }
- struct bitmap_t* bitmap = (struct bitmap_t*)malloc(sizeof(struct bitmap_t));
- if (bitmap == NULL) {
- free(out_buffer);
- 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 red = (buffer[coord] & 0xF00) >> 4*2;
- uint8_t green = (buffer[coord] & 0x0F0) >> 4*1;
- uint8_t blue = (buffer[coord] & 0x00F) >> 4*0;
- out_buffer[coord].red = red | (red << 4);
- out_buffer[coord].green = green | (green << 4);
- out_buffer[coord].blue = blue | (blue << 4);
- }
- }
- bitmap->image_buffer = out_buffer;
- bitmap->width = (size_t)width;
- 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;
- }
-}
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