diff options
Diffstat (limited to 'src/lib')
| -rw-r--r-- | src/lib/dir.c | 22 | ||||
| -rw-r--r-- | src/lib/seg/util.c | 149 |
2 files changed, 171 insertions, 0 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; +} |