1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
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;
}
|
