int Stack_Label_Largest_Object_W(Stack *stack, int flag, int label,
Objlabel_Workspace *ow)
{
TZ_ASSERT(ow->chord != NULL, "NULL chord is not allowed. Wait for fix.");
TZ_ASSERT(ow->conn <= 26, "Invalid neighborhood system.");
STACK_OBJLABEL_OPEN_WORKSPACE(stack, ow);
int small_label = label;
int large_label = small_label + 1;
int nvoxel = Stack_Voxel_Number(stack);
int i;
if (ow->init_chord == TRUE) {
for (i = 0; i < nvoxel; i++) {
ow->chord->array[i] = -1;
}
ow->init_chord = FALSE;
}
int obj_size = 0;
int max_size = 0;
ow->seed = -1;
int large_seed = -1;
PROGRESS_BEGIN("Labeling object");
for (i = 0; i < nvoxel; i++) {
if (stack->array[i] == flag) {
PROGRESS_STATUS(i / (nvoxel / 100 + 1));
obj_size = Stack_Label_Object_W(stack, i, flag, small_label, ow);
if (obj_size > max_size) { /* update the largest object */
if (large_seed >= 0) { /* relabel the previous largest object */
stack_label_object_by_chord(stack, ow->chord, small_label,
large_seed);
}
#ifdef _DEBUG_
printf("%d\n", obj_size);
if (obj_size > 10000) {
printf("debug here\n");
}
#endif
stack_label_object_by_chord(stack, ow->chord, large_label, i);
large_seed = i;
max_size = obj_size;
}
PROGRESS_REFRESH;
}
}
PROGRESS_END("done");
ow->seed = large_seed;
STACK_OBJLABEL_CLOSE_WORKSPACE(ow);
return max_size;
}
Stack* Stack_Boundary_Code(Stack *stack, Stack *code, Objlabel_Workspace *ow)
{
STACK_OBJLABEL_OPEN_WORKSPACE(stack, ow);
int nvoxel = Stack_Voxel_Number(stack);
int i;
if (ow->init_chord == TRUE) {
for (i = 0; i < nvoxel; i++) {
ow->chord->array[i] = -1;
}
}
if (code == NULL) {
code = Make_Stack(GREY16, stack->width, stack->height, stack->depth);
}
Zero_Stack(code);
int neighbor[26];
int is_in_bound[26];
int nbound;
BOOL is_boundary = FALSE;
Stack_Neighbor_Offset(ow->conn, stack->width, stack->height, neighbor);
int prev_seed = -1;
int offset = 0;
int x, y, z;
cwidth = stack->width - 1;
cheight = stack->height - 1;
cdepth = stack->depth - 1;
uint16 *code_array = (uint16 *) code->array;
for (z = 0; z < stack->depth; z++) {
for (y = 0; y < stack->height; y++) {
for (x = 0; x < stack->width; x++) {
is_boundary = FALSE;
if (stack->array[offset] == 1) {
nbound = Stack_Neighbor_Bound_Test(ow->conn, cwidth, cheight,
cdepth, x, y, z, is_in_bound);
if (nbound < ow->conn) {
is_boundary = TRUE;
} else {
for (i = 0; i < ow->conn; i++) {
if (stack->array[offset + neighbor[i]] == 0) {
is_boundary = TRUE;
break;
}
}
}
}
if (is_boundary == TRUE) {
code_array[offset] = 1;
ow->chord->array[offset] = prev_seed;
prev_seed = offset;
}
offset++;
}
}
}
int entrance = prev_seed;
int area = stack->width * stack->height;
int c;
int prev;
int nb;
int *link = ow->chord->array;
/* generate level field */
while (entrance > 0) {
c = entrance;
prev = -1;
do {
if (code_array[c] == 1) {
Stack_Util_Coord_A(c, stack->width, area, &x, &y, &z);
nbound = Stack_Neighbor_Bound_Test(ow->conn, cwidth, cheight,
cdepth, x, y, z, is_in_bound);
if (nbound < ow->conn) {
for (i = 0; i < ow->conn; i++) {
if (is_in_bound[i]) {
nb = c + neighbor[i];
if (stack->array[nb] && !code_array[nb]) {
code_array[nb] = 2;
link[nb] = prev;
prev = nb;
}
}
}
} else {
for (i = 0; i < nbound; i++) {
nb = c + neighbor[i];
if (stack->array[nb] && !code_array[nb]) {
code_array[nb] = 2;
link[nb] = prev;
prev = nb;
}
}
}
} else {
for (i = 0; i < ow->conn; i++) {
nb = c + neighbor[i];
if (stack->array[nb] && !code_array[nb]) {
code_array[nb] = code_array[c] + 1;
link[nb] = prev;
prev = nb;
}
}
}
c = link[c];
} while (c >= 0);
entrance = prev;
}
STACK_OBJLABEL_CLOSE_WORKSPACE(ow);
return code;
}
void Stack_Build_Seed_Graph(Stack *stack, int *seed, int nseed,
uint8_t **connmat, Objlabel_Workspace *ow)
{
if (stack->kind != GREY16) {
PRINT_EXCEPTION("Unsupported stack kind", "The stack must be GREY16");
return;
}
STACK_OBJLABEL_OPEN_WORKSPACE(stack, ow);
int i, j, k;
int nvoxel = Stack_Voxel_Number(stack);
if (ow->init_chord == TRUE) {
for (i = 0; i < nvoxel; i++) {
ow->chord->array[i] = -1;
}
}
uint16 *mask = (uint16 *) stack->array;
const int conn = 26;
/* each seed has a queue */
int *queue_head = iarray_malloc(nseed); /* queue_head malloced */
int *queue_tail = iarray_malloc(nseed); /* queue_head malloced */
int *queue_length = iarray_malloc(nseed); /* queue_length malloced */
/* At the beginning, each queue has one element, the corresponding seed */
iarraycpy(queue_head, seed, 0, nseed);
iarraycpy(queue_tail, seed, 0, nseed);
for (i = 0; i < nseed; i++) {
queue_length[i] = 1;
}
int neighbor[26];
int bound[26];
int nbound;
int cwidth = stack->width - 1;
int cheight = stack->height - 1;
int cdepth = stack->depth - 1;
BOOL stop = FALSE;
int x, y, z;
Stack_Neighbor_Offset(conn, stack->width, stack->height, neighbor);
#define STACK_SEED_GRAPH_UPDATE_QUEUE(test) \
for (k = 0; k < conn; k++) { \
if (test) { \
int checking_voxel = queue_head[i] + neighbor[k]; \
if ((mask[checking_voxel] > 0) && (mask[checking_voxel] != label)) { \
if (mask[checking_voxel] == 1) { \
ow->chord->array[queue_tail[i]] = checking_voxel; \
queue_tail[i] = checking_voxel; \
mask[checking_voxel] = label; \
queue_length[i]++; \
} else { \
if (mask[checking_voxel] > label) { \
connmat[i][mask[checking_voxel] - 2] = 1; \
} else { \
connmat[mask[checking_voxel] - 2][i] = 1; \
} \
} \
} \
} \
}
while (stop == FALSE) {
stop = TRUE;
for (i = 0; i < nseed; i++) {
if (queue_length[i] > 0) {
int label = i + 2;
for (j = 0; j < queue_length[i]; j++) {
Stack_Util_Coord(queue_head[i], stack->width, stack->height,
&x, &y, &z);
nbound = Stack_Neighbor_Bound_Test(conn, cwidth, cheight, cdepth,
x, y, z, bound);
if (nbound == conn) {
STACK_SEED_GRAPH_UPDATE_QUEUE(1);
/*
for (k = 0; k < conn; k++) {
if (1) {
int checking_voxel = queue_head[i] + neighbor[k];
if ((mask[checking_voxel] > 0) && (mask[checking_voxel] != label)) {
if (mask[checking_voxel] == 1) {
ow->chord->array[queue_tail[i]] = checking_voxel;
queue_tail[i] = checking_voxel;
mask[checking_voxel] = label;
queue_length[i]++;
} else {
if (mask[checking_voxel] > label) {
connmat[mask[checking_voxel] - 2][i] = 1;
} else {
connmat[i][mask[checking_voxel] - 2] = 1;
}
}
}
}
}
*/
} else {
STACK_SEED_GRAPH_UPDATE_QUEUE(bound[k]);
}
}
queue_head[i] = ow->chord->array[queue_head[i]];
queue_length[i]--;
stop = FALSE;
}
}
}
free(queue_head); /* queue_head freed */
free(queue_tail); /* queue_head freed */
free(queue_length); /* queue_length freed */
STACK_OBJLABEL_CLOSE_WORKSPACE(ow);
}
void Stack_Grow_Object_S(Stack *seed, Stack *mask, Objlabel_Workspace *ow)
{
ASSERT(seed->kind = GREY, "GREY stack only");
ASSERT(mask->kind = GREY, "GREY stack only");
STACK_OBJLABEL_OPEN_WORKSPACE(seed, ow);
int i;
int nvoxel = Stack_Voxel_Number(seed);
if (ow->init_chord == TRUE) {
for (i = 0; i < nvoxel; i++) {
ow->chord->array[i] = -1;
}
}
int neighbor[26];
int nbound;
int is_in_bound[26];
int x, y, z;
int offset = 0;
int qbot = -1;
int qtop = -1;
int cwidth = seed->width - 1;
int cheight = seed->height - 1;
int cdepth = seed->depth - 1;
int *queue = ow->chord->array;
int nidx;
int conn = ow->conn;
PROGRESS_BEGIN("Oject growing");
Stack_Neighbor_Offset(conn, seed->width, seed->height, neighbor);
for (z = 0; z < seed->depth; z++) {
PROGRESS_STATUS(z * 90 / seed->depth);
for (y = 0; y < seed->height; y++) {
for (x = 0; x < seed->width; x++) {
if (seed->array[offset] == 1) {
mask->array[offset] = 0;
nbound = Stack_Neighbor_Bound_Test(conn, cwidth, cheight, cdepth,
x, y, z, is_in_bound);
if (nbound < conn) {
for (i = 0; i < conn; i++) {
if (is_in_bound[i]) {
if (seed->array[offset + neighbor[i]] == 0) {
STACK_GROW_OBJECT_ENQUEUE(queue, offset);
break;
}
}
}
} else {
for (i = 0; i < conn; i++) {
if (seed->array[offset + neighbor[i]] == 0) {
STACK_GROW_OBJECT_ENQUEUE(queue, offset);
break;
}
}
}
}
offset++;
}
}
PROGRESS_REFRESH;
}
int area = seed->width * seed->height;
while (qtop >= 0) {
STACK_GROW_OBJECT_DEQUEUE(queue, offset);
STACK_UTIL_COORD(offset, seed->width, area, x, y, z);
nbound = Stack_Neighbor_Bound_Test(conn, cwidth, cheight, cdepth,
x, y, z, is_in_bound);
if (nbound < conn) {
STACK_GROW_OBJECT_ENQUEUE_NEIGHBORS(queue, offset,
(is_in_bound[i] &&
mask->array[nidx] == 1));
} else {
STACK_GROW_OBJECT_ENQUEUE_NEIGHBORS(queue, offset,
(mask->array[nidx] == 1));
}
}
PROGRESS_END("done");
STACK_OBJLABEL_CLOSE_WORKSPACE(ow);
}
int Stack_Label_Large_Objects_W(Stack *stack, int flag, int label, int minsize,
Objlabel_Workspace *ow)
{
ASSERT(label > flag, "label too small");
STACK_OBJLABEL_OPEN_WORKSPACE(stack, ow);
int small_label = label;
int large_label = small_label + 1;
int nvoxel = Stack_Voxel_Number(stack);
int i;
if (ow->init_chord == TRUE) {
for (i = 0; i < nvoxel; i++) {
ow->chord->array[i] = -1;
}
ow->init_chord = FALSE;
}
int obj_size = 0;
int large_object_number = 0;
uint16_t *array16 = (uint16_t*) stack->array;
uint8_t *array8 = (uint8_t*) stack->array;
PROGRESS_BEGIN("Labeling object");
for (i = 0; i < nvoxel; i++) {
BOOL is_flag = FALSE;
if (stack->kind == GREY) {
is_flag = (array8[i] == flag);
} else {
is_flag = (array16[i] == flag);
}
if (is_flag == TRUE) {
PROGRESS_STATUS(i / (nvoxel / 100 + 1));
if (large_label > 255) {
if (stack->kind == GREY) {
Translate_Stack(stack, GREY16, 1);
array16 = (uint16_t*) stack->array;
}
}
obj_size = Stack_Label_Object_W(stack, i, flag, large_label, ow);
if (obj_size < minsize) {
stack_label_object_by_chord(stack, ow->chord, small_label, i);
} else {
large_object_number++;
++large_label;
if (large_label > 65535) {
TZ_WARN(ERROR_DATA_VALUE);
large_label = small_label + 1;
}
}
PROGRESS_REFRESH;
}
}
PROGRESS_END("done");
STACK_OBJLABEL_CLOSE_WORKSPACE(ow);
return large_object_number;
}
int Stack_Label_Object_Level_Nw(Stack *stack, int seed,
int flag, int label, Stack *code, int max,
Objlabel_Workspace *ow)
{
STACK_OBJLABEL_OPEN_WORKSPACE(stack, ow);
if (stack->array[seed] != flag) {
TZ_WARN(ERROR_OTHER);
fprintf(stderr, "The seed does not have the right flag.\n");
return 0;
}
IMatrix *chord = ow->chord;
int npixel = Get_Stack_Size(stack);
int i;
int c = seed; /* center pixel */
int nb; /* neighobr pixel */
for (i = 0; i < npixel; i++) {
chord->array[i] = -1;
}
int obj_size = 0;
int next = c;
uint16 *code_array = NULL;
BOOL do_label = TRUE;
if (code != NULL) {
code_array = (uint16 *)code->array;
}
stack->array[seed] = label;
int n_nbr = ow->conn;
int neighbor[26];
Stack_Neighbor_Offset(n_nbr, stack->width, stack->height, neighbor);
int x, y, z;
int is_in_bound[26];
int n_in_bound = 0;
int cwidth = stack->width - 1;
int cheight = stack->height - 1;
int cdepth = stack->depth - 1;
do {
Stack_Util_Coord(c, stack->width, stack->height, &x, &y, &z);
n_in_bound = Stack_Neighbor_Bound_Test(n_nbr, cwidth, cheight, cdepth,
x, y, z, is_in_bound);
/* add all unlabeled neighbors to the queue*/
if (n_in_bound == n_nbr) { /* no boundary check required */
for (i = 0; i < n_nbr; i++) {
STACK_LABEL_OBJECT_CONSTRAINT_N_UPDATE_QUEUE(stack->array);
}
} else {
for (i = 0; i < n_nbr; i++) {
if (is_in_bound[i]) {
STACK_LABEL_OBJECT_CONSTRAINT_N_UPDATE_QUEUE(stack->array);
}
}
}
c = chord->array[c]; /* move to next voxel */
obj_size++;
if (code == NULL) {
if (obj_size >= max) {
break;
}
}
} while (c >= 0);
STACK_OBJLABEL_CLOSE_WORKSPACE(ow);
return obj_size;
}
Graph* Stack_Label_Field_Neighbor_Graph(Stack *stack, int threshold,
Objlabel_Workspace *ow)
{
TZ_ASSERT(stack->kind == GREY16, "Invalid stack kind");
STACK_OBJLABEL_OPEN_WORKSPACE(stack, ow);
Graph *graph = Make_Graph(0, 1, TRUE);
graph->nvertex = Stack_Max(stack, NULL) + 1;
Graph_Workspace *gw = New_Graph_Workspace();
uint16_t *signal_array = (uint16_t*) stack->array;
int neighbor_offset[26];
int is_in_bound[26];
Stack_Neighbor_Offset(ow->conn, stack->width, stack->height, neighbor_offset);
/* Identify number of objects */
int object_number = 0;
int width = stack->width;
int height = stack->height;
int depth = stack->depth;
size_t voxelNumber = Stack_Voxel_Number(stack);
size_t index;
//Stack *mask = Make_Stack(GREY, width, height, depth);
for (index = 0; index < voxelNumber; ++index) {
if (object_number < signal_array[index]) {
object_number = signal_array[index];
}
if (ow->init_chord == TRUE) {
ow->chord->array[index] = -1;
}
//mask->array[index] = 0;
}
//uint8_t *visited = mask->array;
Int_Arraylist *seed_head = Make_Int_Arraylist(object_number + 1, 0);
Int_Arraylist *seed_tail = Make_Int_Arraylist(object_number + 1, 0);
Int_Arraylist *seed_point = Make_Int_Arraylist(object_number + 1, 0);
int i;
for (i = 0; i < seed_head->length; ++i) {
seed_head->array[i] = -1;
seed_point->array[i] = -1;
seed_tail->array[i] = -1;
}
int *seed_queue = ow->chord->array;
/* Initialize the seeds for each object */
for (index = 0; index < voxelNumber; ++index) {
uint16_t object_label = signal_array[index];
int *current_seed_head = seed_head->array + object_label;
int *current_seed_tail = seed_tail->array + object_label;
int *current_seed_point = seed_point->array + object_label;
int nbound = Stack_Neighbor_Bound_Test_I(ow->conn, width, height, depth,
index, is_in_bound);
if (is_border_voxel(signal_array, index, ow->conn,
neighbor_offset, is_in_bound, nbound) == TRUE) {
//visited[index] = 1;
if (*current_seed_head < 0) {
*current_seed_head = index;
*current_seed_tail = index;
*current_seed_point = *current_seed_head;
} else {
seed_queue[*current_seed_point] = index;
*current_seed_point = index;
}
}
}
int current_level = 0;
/* While the current growing level is below the threshold */
while (current_level < threshold) {
/* Grow each object */
uint16_t object_label;
for (object_label = 1; object_label <= object_number; ++object_label) {
int current_tail = seed_tail->array[object_label];
int new_tail = current_tail;
int seed = seed_head->array[object_label];
while (seed >= 0) {
int nbound = Stack_Neighbor_Bound_Test_I(ow->conn, width, height, depth,
seed, is_in_bound);
int j;
for (j = 0; j < ow->conn; ++j) {
if (nbound == ow->conn || is_in_bound[j]) {
int neighbor_index = seed + neighbor_offset[j];
uint16_t neighbor_label = signal_array[neighbor_index];
if (neighbor_label == 0) {
seed_queue[new_tail] = neighbor_index;
new_tail = neighbor_index;
signal_array[neighbor_index] = object_label;
//visited[neighbor_index] = 1;
} else if (neighbor_label != object_label) {
/* If x-y does not exist */
if (Graph_Edge_Index_U(object_label, neighbor_label, gw)
< 0) {
double weight = current_level * 2;
if (object_label > neighbor_label) {
weight += 1.0;
}
Graph_Add_Weighted_Edge(graph,
object_label, neighbor_label, weight);
Graph_Expand_Edge_Table(object_label, neighbor_label,
graph->nedge - 1, gw);
}
}
}
}
if (seed == current_tail) {
break;
}
seed = seed_queue[seed];
}
if (current_tail >= 0) {
seed_head->array[object_label] = seed_queue[current_tail];
seed_tail->array[object_label] = new_tail;
}
}
++current_level;
}
Kill_Int_Arraylist(seed_head);
Kill_Int_Arraylist(seed_tail);
Kill_Int_Arraylist(seed_point);
Kill_Graph_Workspace(gw);
STACK_OBJLABEL_CLOSE_WORKSPACE(ow);
//Kill_Stack(mask);
return graph;
}
int Stack_Label_Object_W(Stack *stack, int seed, int flag, int label,
Objlabel_Workspace *ow)
{
TZ_ASSERT(stack->kind == GREY || stack->kind == GREY16, "Unsupported kind.");
STACK_OBJLABEL_OPEN_WORKSPACE(stack, ow);
ow->seed = seed;
uint16_t* array16 = (uint16_t*) stack->array;
uint8_t* array8 = (uint8_t*) stack->array;
if (stack->kind == GREY) {
if (stack->array[seed] != flag) {
TZ_WARN(ERROR_OTHER);
fprintf(stderr, "The seed does not have the right flag.\n");
return 0;
}
} else {
if (array16[seed] != flag) {
TZ_WARN(ERROR_OTHER);
fprintf(stderr, "The seed does not have the right flag.\n");
return 0;
}
}
int npixel = Get_Stack_Size(stack);
int i;
int c = seed; /* center pixel */
int nb; /* neighobr pixel */
if (ow->init_chord == TRUE) {
for (i = 0; i < npixel; i++) {
ow->chord->array[i] = -1;
}
}
int obj_size = 0;
int next = c;
if (stack->kind == GREY) {
stack->array[seed] = label;
} else {
array16[seed] = label;
}
int x, y, z;
int is_in_bound[26];
int n_in_bound = 0;
int cwidth = stack->width - 1;
int cheight = stack->height - 1;
int cdepth = stack->depth - 1;
int neighbor[26];
Stack_Neighbor_Offset(ow->conn, stack->width, stack->height, neighbor);
#define STACK_LABEL_OBJECT_N_UPDATE_QUEUE(stack_array) \
{ \
nb = c + neighbor[i]; \
/*process unlabeled white neighbors*/ \
if ((stack_array[nb] == flag) && (ow->chord->array[nb] == -1)) { \
ow->chord->array[next] = nb; \
TZ_ASSERT(ow->chord->array[next] != next, "loop"); \
next = nb; \
stack_array[nb] = label; \
} \
}
int area = stack->width * stack->height;
do {
z = c / area;
if (z > stack->depth) {
n_in_bound = 0;
} else {
y = c % area;
x = y % stack->width;
y = y / stack->width;
if ((x > stack->width) || (y > stack->height)) {
n_in_bound = 0;
} else {
//Stack_Util_Coord(c, stack->width, stack->height, &x, &y, &z);
if ((x > 0) && (x < cwidth) && (y > 0) && (y < cheight) &&
(z > 0) && (z < cdepth)) {
n_in_bound = ow->conn;
} else {
n_in_bound = Stack_Neighbor_Bound_Test_S(ow->conn,
cwidth, cheight, cdepth,
x, y, z, is_in_bound);
}
}
}
/* add all unlabeled neighbors to the queue*/
if (n_in_bound == ow->conn) { /* no boundary check required */
if (stack->kind == GREY) {
for (i = 0; i < ow->conn; i++) {
STACK_LABEL_OBJECT_N_UPDATE_QUEUE(array8);
}
} else {
for (i = 0; i < ow->conn; i++) {
STACK_LABEL_OBJECT_N_UPDATE_QUEUE(array16);
}
}
} else {
for (i = 0; i < ow->conn; i++) {
if (is_in_bound[i]) {
if (stack->kind == GREY) {
STACK_LABEL_OBJECT_N_UPDATE_QUEUE(array8);
} else {
STACK_LABEL_OBJECT_N_UPDATE_QUEUE(array16);
}
}
}
}
c = ow->chord->array[c]; /* move to next voxel */
obj_size++;
} while (c >= 0);
STACK_OBJLABEL_CLOSE_WORKSPACE(ow);
return obj_size;
}
Graph* Stack_Build_Seed_Graph_G(Stack *stack, int *seed, int nseed,
BOOL weighted, Objlabel_Workspace *ow)
{
if (stack->kind != GREY16) {
PRINT_EXCEPTION("Unsupported stack kind", "The stack must be GREY16");
return NULL;
}
STACK_OBJLABEL_OPEN_WORKSPACE(stack, ow);
int i, j, k;
int nvoxel = Stack_Voxel_Number(stack);
if (ow->init_chord == TRUE) {
for (i = 0; i < nvoxel; i++) {
ow->chord->array[i] = -1;
}
}
uint16 *mask = (uint16 *) stack->array;
const int conn = 26;
/* each seed has a queue */
int *queue_head = iarray_malloc(nseed); /* queue_head malloced */
int *queue_tail = iarray_malloc(nseed); /* queue_head malloced */
int *queue_length = iarray_malloc(nseed); /* queue_length malloced */
/* At the beginning, each queue has one element, the corresponding seed */
iarraycpy(queue_head, seed, 0, nseed);
iarraycpy(queue_tail, seed, 0, nseed);
for (i = 0; i < nseed; i++) {
queue_length[i] = 1;
}
int neighbor[26];
int bound[26];
int nbound;
int cwidth = stack->width - 1;
int cheight = stack->height - 1;
int cdepth = stack->depth - 1;
BOOL stop = FALSE;
int x, y, z;
Stack_Neighbor_Offset(conn, stack->width, stack->height, neighbor);
#define STACK_SEED_GRAPH_UPDATE_QUEUE_G(test) \
for (k = 0; k < conn; k++) { \
if (test) { \
int checking_voxel = queue_head[i] + neighbor[k]; \
if ((mask[checking_voxel] > 0) && (mask[checking_voxel] != label)) { \
if (mask[checking_voxel] == 1) { \
ow->chord->array[queue_tail[i]] = checking_voxel; \
queue_tail[i] = checking_voxel; \
mask[checking_voxel] = label; \
queue_length[i]++; \
} else { \
int v1, v2, tmp; \
v1 = i; \
v2 = mask[checking_voxel] - 2; \
ASSERT(v1 != v2, "Bug in Stack_Build_Seed_Graph_G()"); \
if (v1 > v2) { \
SWAP2(v1, v2, tmp); \
} \
if (Graph_Edge_Index(v1, v2, gw) < 0) { \
if (weighted == TRUE) { \
double dist = Stack_Util_Voxel_Distance(seed[v1], seed[v2], stack->width, stack->height); \
Graph_Add_Weighted_Edge(graph, v1, v2, dist); \
} else { \
Graph_Add_Edge(graph, v1, v2); \
} \
Graph_Expand_Edge_Table(v1, v2, graph->nedge -1, gw); \
} \
} \
} \
} \
}
Graph *graph = Make_Graph(nseed, nseed, weighted);
Graph_Workspace *gw = New_Graph_Workspace();
while (stop == FALSE) {
stop = TRUE;
for (i = 0; i < nseed; i++) {
if (queue_length[i] > 0) {
int label = i + 2;
for (j = 0; j < queue_length[i]; j++) {
Stack_Util_Coord(queue_head[i], stack->width, stack->height,
&x, &y, &z);
nbound = Stack_Neighbor_Bound_Test(conn, cwidth, cheight, cdepth,
x, y, z, bound);
if (nbound == conn) {
STACK_SEED_GRAPH_UPDATE_QUEUE_G(1);
} else {
STACK_SEED_GRAPH_UPDATE_QUEUE_G(bound[k]);
}
}
queue_head[i] = ow->chord->array[queue_head[i]];
queue_length[i]--;
stop = FALSE;
}
}
}
free(queue_head); /* queue_head freed */
free(queue_tail); /* queue_head freed */
free(queue_length); /* queue_length freed */
STACK_OBJLABEL_CLOSE_WORKSPACE(ow);
return graph;
}
int main(int argc, char *argv[])
{
#if 0
Stack *stack = Read_Stack("../data/fly_neuron.tif");
Stretch_Stack_Value_Q(stack, 0.99);
Translate_Stack(stack, GREY, 1);
Write_Stack("../data/test.tif", stack);
Kill_Stack(stack);
#endif
#if 0
int idx1, idx2, width, height;
idx1 = 33332;
idx2 = 65535;
width = 111;
height = 112;
printf("%g\n", Stack_Util_Voxel_Distance(idx1, idx2, width, height));
int x1, y1, z1, x2, y2, z2;
Stack_Util_Coord(idx1, width, height, &x1, &y1, &z1);
Stack_Util_Coord(idx2, width, height, &x2, &y2, &z2);
printf("%d, %d, %d\n", x1 - x2, y1 - y2, z1 - z2);
#endif
#if 0
Stack *stack = Read_Stack("../data/fly_neuron.tif");
//Translate_Stack(stack, GREY16, 1);
Image *image = Proj_Stack_Zmax(stack);
Write_Image("../data/test.tif", image);
#endif
#if 0
Stack *stack = Read_Stack("../data/fly_neuron_a1_org.tif");
//stack = Crop_Stack(stack, 256, 256, 0, 512, 512, 170, NULL);
int i;
Stack stack2;
stack2.width = stack->width;
stack2.height = stack->height;
stack2.kind = stack->kind;
stack2.depth = 1;
for (i = 0; i < stack->depth; i++) {
stack2.array = stack->array + i * stack->width * stack->height;
//Stack *locmax = Stack_Locmax_Region(&stack2, 8);
Stack *locmax = Stack_Local_Max(&stack2, NULL, STACK_LOCMAX_SINGLE);
int *hist = Stack_Hist_M(&stack2, locmax);
int low, high;
Int_Histogram_Range(hist, &low, &high);
int thre = Int_Histogram_Triangle_Threshold(hist, low, high);
printf("Threshold: %d\n", thre);
Stack_Threshold_Binarize(&stack2, thre);
Kill_Stack(locmax);
free(hist);
}
//Stack_Bc_Autoadjust(result);
/*
Translate_Stack(stack, COLOR, 1);
Stack_Blend_Mc(stack, result, 0.1);
*/
Write_Stack("../data/test.tif", stack);
#endif
#if 1
Stack *stack = Read_Stack("../data/fly_neuron_crop.tif");
Filter_3d *filter = Gaussian_Filter_3d(1.0, 1.0, 0.5);
Stack *out = Filter_Stack(stack, filter);
Kill_FMatrix(filter)
Write_Stack("../data/test.tif", out);
#endif
#if 0
Stack *stack = Read_Stack("../data/fly_neuron_a2_org.tif");
Stack *locmax = Stack_Locmax_Region(stack, 18);
Stack *mask = Read_Stack("../data/fly_neuron_a2_org/threshold_s.tif");
//Stack_And(locmax, mask, locmax);
Object_3d_List *objs = Stack_Find_Object_N(locmax, NULL, 1, 0, 18);
Zero_Stack(locmax);
int objnum = 0;
while (objs != NULL) {
Object_3d *obj = objs->data;
Voxel_t center;
Object_3d_Central_Voxel(obj, center);
Set_Stack_Pixel(locmax, center[0], center[1], center[2], 0, 1);
objs = objs->next;
objnum++;
}
Write_Stack("../data/fly_neuron_a2_org/locmax.tif", locmax);
printf("objnum: %d\n", objnum);
U8Matrix mat;
mat.ndim = 3;
mat.dim[0] = stack->width;
mat.dim[1] = stack->height;
mat.dim[2] = stack->depth;
mat.array = locmax->array;
dim_type bdim[3];
bdim[0] = 7;
bdim[1] = 7;
bdim[2] = 5;
U8Matrix *mat2 = U8Matrix_Blocksum(&mat, bdim, NULL);
int offset[3];
offset[0] = bdim[0] / 2;
offset[1] = bdim[1] / 2;
offset[2] = bdim[2] / 2;
Crop_U8Matrix(mat2, offset, mat.dim, &mat);
Write_Stack("../data/fly_neuron_a2_org/locmax_sum.tif", locmax);
Stack_Threshold_Binarize(locmax, 6);
Stack *clear_stack = Stack_Majority_Filter_R(locmax, NULL, 26, 4);
Struct_Element *se = Make_Cuboid_Se(3, 3, 3);
Stack *dilate_stack = Stack_Dilate(clear_stack, NULL, se);
Stack *fill_stack = Stack_Fill_Hole_N(dilate_stack, NULL, 1, 4, NULL);
Kill_Stack(dilate_stack);
Stack_Not(fill_stack, fill_stack);
Stack_And(fill_stack, mask, mask);
Write_Stack("../data/test.tif", mask);
#endif
#if 0
Stack *stack = Read_Stack("../data/fly_neuron_t1.tif");
Stack *locmax = Stack_Locmax_Region(stack, 6);
Stack_Label_Objects_Ns(locmax, NULL, 1, 2, 3, 6);
int nvoxel = Stack_Voxel_Number(locmax);
int i;
int s[26];
for (i = 0; i < nvoxel; i++) {
if (locmax->array[i] < 3) {
locmax->array[i] = 0;
} else {
locmax->array[i] = 1;
printf("%u\n", stack->array[i]);
Stack_Neighbor_Sampling_I(stack, 6, i, -1, s);
iarray_print2(s, 6, 1);
}
}
//Stack *locmax = Stack_Local_Max(stack, NULL, STACK_LOCMAX_SINGLE);
Write_Stack("../data/test.tif", locmax);
#endif
#if 0
Stack *stack = Read_Stack("../data/fly_neuron_n1.tif");
Stack *stack2 = Flip_Stack_Y(stack, NULL);
Flip_Stack_Y(stack2, stack2);
if (!Stack_Identical(stack, stack2)) {
printf("bug found\n");
}
Write_Stack("../data/test.tif", stack);
#endif
#if 0
Mc_Stack *stack = Read_Mc_Stack("../data/benchmark/L3_12bit.lsm", -1);
Mc_Stack_Grey16_To_8(stack, 3);
Write_Mc_Stack("../data/test.lsm", stack, "../data/benchmark/L3_12bit.lsm");
#endif
#if 0
//Stack *stack = Read_Stack("../data/C2-Slice06_R1_GR1_B1_L18.tif");
Stack *stack = Read_Stack("../data/fly_neuron_n1/traced.tif");
Print_Stack_Info(stack);
#endif
#if 0
Mc_Stack *stack = Make_Mc_Stack(GREY, 1024, 1024, 1024, 5);
/*
stack.width = 1024;
stack.height = 1024;
stack.depth = 1024;
stack.kind = GREY;
stack.nchannel = 5;
printf("%zd\n", ((size_t)stack.kind * stack.width * stack.height *
stack.depth * stack.nchannel));
*/
#endif
#if 0
Stack *stack = Make_Stack(GREY, 1, 1, 1);
printf("stack usage: %d\n", Stack_Usage());
uint8 *data = stack->array;
stack->array = NULL;
Kill_Stack(stack);
stack = Read_Stack("../data/benchmark/line.tif");
free(data);
printf("stack usage: %d\n", Stack_Usage());
#endif
#if 0
Stack *stack = Read_Stack("../data/test.tif");
int *hist = Stack_Hist(stack);
Print_Int_Histogram(hist);
#endif
#if 0
Stack *stack = Read_Stack("../data/benchmark/mouse_neuron_single/stack.tif");
Stack dst;
dst.text = "\0";
dst.array = stack->array;
Crop_Stack(stack, 0, 0, 0, stack->width - 100, stack->height - 100,
stack->depth - 30, &dst);
Write_Stack("../data/test.tif", &dst);
#endif
#if 0
Stack *stack = Make_Stack(GREY, 5, 5, 3);
Zero_Stack(stack);
Set_Stack_Pixel(stack, 2, 2, 1, 0, 1.0);
Print_Stack_Value(stack);
Stack *out = Stack_Running_Max(stack, 0, NULL);
out = Stack_Running_Max(out, 1, out);
out = Stack_Running_Max(out, 2, out);
Print_Stack_Value(out);
#endif
#if 0
Stack *stack = Read_Stack("../data/benchmark/stack_graph/fork/fork.tif");
Stack *out = Stack_Running_Median(stack, 0, NULL);
Stack_Running_Median(out, 1, out);
//Stack_Running_Max(stack, 0, out);
//Stack_Running_Max(out, 1, out);
Write_Stack("../data/test.tif", out);
Stack *out2 = Stack_Running_Median(stack, 0, NULL);
Stack *out3 = Stack_Running_Median(out2, 1, NULL);
if (Stack_Identical(out, out3)) {
printf("Same in-place and out-place\n");
}
#endif
#if 0
Stack *stack = Read_Stack_U("../data/diadem_d1_147.xml");
printf("%d\n", Stack_Threshold_Quantile(stack, 0.9));
#endif
#if 0
const char *filepath = "/Users/zhaot/Data/Julie/All_tiled_nsyb5_Sum.lsm";
char filename[100];
fname(filepath, filename);
Mc_Stack *stack = Read_Mc_Stack(filepath, -1);
Print_Mc_Stack_Info(stack);
Mc_Stack *tmpstack = Make_Mc_Stack(stack->kind, stack->width, stack->height,
stack->depth / 8, stack->nchannel);
size_t channel_size = stack->kind * stack->width *stack->height
* stack->depth;
size_t channel_size2 = tmpstack->kind * tmpstack->width *tmpstack->height
* tmpstack->depth;
int i;
int k;
uint8_t *array = stack->array;
for (k = 0; k < 8; k++) {
int offset = 0;
int offset2 = 0;
for (i = 0; i < stack->nchannel; i++) {
memcpy(tmpstack->array + offset2, array + offset, channel_size2);
offset += channel_size;
offset2 += channel_size2;
}
array += channel_size2;
char outpath[500];
sprintf(outpath, "../data/test/%s_%03d.lsm", filename, k);
Write_Mc_Stack(outpath, tmpstack, filepath);
}
#endif
#if 0
Stack *stack = Index_Stack(GREY16, 5, 5, 1);
Set_Stack_Pixel(stack, 1, 1, 0, 0, 0);
Set_Stack_Pixel(stack, 1, 2, 0, 0, 0);
Print_Stack_Value(stack);
Stack *out = Stack_Neighbor_Median(stack, 8, NULL);
Print_Stack_Value(out);
#endif
#if 0
Stack *stack = Make_Stack(GREY, 10, 10, 3);
Zero_Stack(stack);
Cuboid_I bound_box;
Set_Stack_Pixel(stack, 1, 1, 1, 0, 1);
Set_Stack_Pixel(stack, 1, 2, 1, 0, 1);
Set_Stack_Pixel(stack, 3, 1, 2, 0, 1);
Stack_Bound_Box(stack, &bound_box);
Print_Cuboid_I(&bound_box);
#endif
#if 0
Stack_Document *doc = Xml_Read_Stack_Document("../data/test.xml");
File_List *list = (File_List*) doc->ci;
Cuboid_I bound_box;
Stack_Bound_Box_F(list, &bound_box);
Print_Cuboid_I(&bound_box);
#endif
#if 0
Stack_Document *doc = Xml_Read_Stack_Document("../data/test.xml");
File_List *list = (File_List*) doc->ci;
Print_File_List(list);
Stack *stack = Read_Image_List_Bounded(list);
Stack *out = stack;
out = Stack_Region_Expand(stack, 8, 1, NULL);
out = Downsample_Stack(out, 4, 4, 0);
Write_Stack("../data/test.tif", out);
#endif
#if 0
Stack_Document *doc = Xml_Read_Stack_Document(
"../data/ting_example_stack/test.xml");
File_List *list = (File_List*) doc->ci;
Print_File_List(list);
int i;
for (i = 0; i < list->file_number; i++) {
Stack *stack = Read_Stack_U(list->file_path[i]);
Stack *ds = Downsample_Stack(stack, 39, 39, 0);
char file_path[500];
sprintf(file_path, "../data/ting_example_stack/thumbnails/tb%05d.tif", i);
Write_Stack(file_path, ds);
Free_Stack(stack);
}
#endif
#if 0
Stack *stack = Read_Stack("../data/test2.tif");
Stack_Threshold_Binarize(stack, 6);
Objlabel_Workspace ow;
STACK_OBJLABEL_OPEN_WORKSPACE(stack, (&ow));
Object_3d *obj = Stack_Find_Largest_Object_N(stack, ow.chord, 1, 26);
//Print_Object_3d(obj);
//printf("%llu\n", obj->size);
double vec[3];
Object_3d_Orientation(obj, vec, MAJOR_AXIS);
double center[3];
Object_3d_Centroid(obj, center);
darray_print2(vec, 3, 1);
double span[2] = {100000, -100000};
for (int i = 0; i < obj->size; i++) {
double proj = Geo3d_Dot_Product(vec[0], vec[1], vec[2],
(double) obj->voxels[i][0] - center[0],
(double) obj->voxels[i][1] - center[1],
(double) obj->voxels[i][2] - center[2]);
if (proj < span[0]) {
span[0] = proj;
}
if (proj > span[1]) {
span[1] = proj;
}
}
darray_print2(span, 2, 1);
double vec2[3];
Object_3d_Orientation(obj, vec2, PLANE_NORMAL);
darray_print2(vec2, 3, 1);
double span2[2] = {100000, -100000};
for (int i = 0; i < obj->size; i++) {
double proj = Geo3d_Dot_Product(vec2[0], vec2[1], vec2[2],
(double) obj->voxels[i][0] - center[0],
(double) obj->voxels[i][1] - center[1],
(double) obj->voxels[i][2] - center[2]);
if (proj < span2[0]) {
span2[0] = proj;
}
if (proj > span2[1]) {
span2[1] = proj;
}
}
darray_print2(span2, 2, 1);
double vec3[3];
Geo3d_Cross_Product(vec[0], vec[1], vec[2], vec2[0], vec2[1], vec2[2],
vec3, vec3+1, vec3+2);
double span3[2] = {100000, -100000};
int i;
for (i = 0; i < obj->size; i++) {
double proj = Geo3d_Dot_Product(vec3[0], vec3[1], vec3[2],
(double) obj->voxels[i][0] - center[0],
(double) obj->voxels[i][1] - center[1],
(double) obj->voxels[i][2] - center[2]);
if (proj < span3[0]) {
span3[0] = proj;
}
if (proj > span3[1]) {
span3[1] = proj;
}
}
darray_print2(span3, 2, 1);
coordinate_3d_t vertex[8];
for (i = 0; i < 8; i++) {
Coordinate_3d_Copy(vertex[i], center);
int j;
for (j = 0; j < 3; j++) {
vertex[i][j] +=
span[0] * vec[j] + span2[0] * vec2[j] + span3[0] * vec3[j];
}
}
for (i = 0; i < 3; i++) {
vertex[1][i] += (span[1] - span[0]) * vec[i];
vertex[2][i] += (span2[1] - span2[0]) * vec2[i];
vertex[3][i] += (span3[1] - span3[0]) * vec3[i];
vertex[4][i] = vertex[1][i] + (span2[1] - span2[0]) * vec2[i];
vertex[5][i] = vertex[2][i] + (span3[1] - span3[0]) * vec3[i];
vertex[6][i] = vertex[3][i] + (span[1] - span[0]) * vec[i];
vertex[7][i] = vertex[5][i] + (span[1] - span[0]) * vec[i];
}
FILE *fp = fopen("../data/test.swc", "w");
fprintf(fp, "%d %d %g %g %g %g %d\n", 1, 2, vertex[0][0], vertex[0][1],
vertex[0][2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 2, 2, vertex[1][0], vertex[1][1],
vertex[1][2], 3.0, 1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 3, 2, vertex[2][0], vertex[2][1],
vertex[2][2], 3.0, 1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 4, 2, vertex[3][0], vertex[3][1],
vertex[3][2], 3.0, 1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 5, 2, vertex[4][0], vertex[4][1],
vertex[4][2], 3.0, 2);
fprintf(fp, "%d %d %g %g %g %g %d\n", 6, 2, vertex[5][0], vertex[5][1],
vertex[5][2], 3.0, 3);
fprintf(fp, "%d %d %g %g %g %g %d\n", 7, 2, vertex[6][0], vertex[6][1],
vertex[6][2], 3.0, 4);
fprintf(fp, "%d %d %g %g %g %g %d\n", 8, 2, vertex[7][0], vertex[7][1],
vertex[7][2], 3.0, 7);
fprintf(fp, "%d %d %g %g %g %g %d\n", 9, 2, vertex[4][0], vertex[4][1],
vertex[4][2], 3.0, 8);
fprintf(fp, "%d %d %g %g %g %g %d\n", 10, 2, vertex[4][0], vertex[4][1],
vertex[4][2], 3.0, 3);
fprintf(fp, "%d %d %g %g %g %g %d\n", 11, 2, vertex[5][0], vertex[5][1],
vertex[5][2], 3.0, 8);
fprintf(fp, "%d %d %g %g %g %g %d\n", 12, 2, vertex[5][0], vertex[5][1],
vertex[5][2], 3.0, 4);
fprintf(fp, "%d %d %g %g %g %g %d\n", 13, 2, vertex[6][0], vertex[6][1],
vertex[6][2], 3.0, 2);
/*
Geo3d_Scalar_Field *field = Make_Geo3d_Scalar_Field(6);
field->points[0][0] = span[0] * vec[0] + center[0];
field->points[0][1] = span[0] * vec[1] + center[1];
field->points[0][2] = span[0] * vec[2] + center[2];
field->points[1][0] = span[1] * vec[0] + center[0];
field->points[1][1] = span[1] * vec[1] + center[1];
field->points[1][2] = span[1] * vec[2] + center[2];
field->points[2][0] = span2[0] * vec2[0] + center[0];
field->points[2][1] = span2[0] * vec2[1] + center[1];
field->points[2][2] = span2[0] * vec2[2] + center[2];
field->points[3][0] = span2[1] * vec2[0] + center[0];
field->points[3][1] = span2[1] * vec2[1] + center[1];
field->points[3][2] = span2[1] * vec2[2] + center[2];
field->points[4][0] = span3[0] * vec3[0] + center[0];
field->points[4][1] = span3[0] * vec3[1] + center[1];
field->points[4][2] = span3[0] * vec3[2] + center[2];
field->points[5][0] = span3[1] * vec3[0] + center[0];
field->points[5][1] = span3[1] * vec3[1] + center[1];
field->points[5][2] = span3[1] * vec3[2] + center[2];
coordinate_3d_t corner[2];
Geo3d_Scalar_Field_Boundbox(field, corner);
darray_print2(corner[0], 3, 1);
darray_print2(corner[1], 3, 1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 1, 2, corner[0][0], corner[0][1],
corner[0][2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 2, 2, corner[1][0], corner[0][1],
corner[0][2], 3.0, 1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 3, 2, corner[1][0], corner[1][1],
corner[0][2], 3.0, 2);
fprintf(fp, "%d %d %g %g %g %g %d\n", 4, 2, corner[0][0], corner[1][1],
corner[0][2], 3.0, 3);
fprintf(fp, "%d %d %g %g %g %g %d\n", 5, 2, corner[0][0], corner[0][1],
corner[0][2], 3.0, 4);
fprintf(fp, "%d %d %g %g %g %g %d\n", 6, 2, corner[0][0], corner[0][1],
corner[1][2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 7, 2, corner[1][0], corner[0][1],
corner[1][2], 3.0, 6);
fprintf(fp, "%d %d %g %g %g %g %d\n", 8, 2, corner[1][0], corner[1][1],
corner[1][2], 3.0, 7);
fprintf(fp, "%d %d %g %g %g %g %d\n", 9, 2, corner[0][0], corner[1][1],
corner[1][2], 3.0, 8);
fprintf(fp, "%d %d %g %g %g %g %d\n", 10, 2, corner[0][0], corner[0][1],
corner[1][2], 3.0, 9);
fprintf(fp, "%d %d %g %g %g %g %d\n", 11, 2, corner[0][0], corner[0][1],
corner[1][2], 3.0, 1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 12, 2, corner[1][0], corner[0][1],
corner[1][2], 3.0, 2);
fprintf(fp, "%d %d %g %g %g %g %d\n", 13, 2, corner[1][0], corner[1][1],
corner[1][2], 3.0, 3);
fprintf(fp, "%d %d %g %g %g %g %d\n", 14, 2, corner[0][0], corner[1][1],
corner[1][2], 3.0, 4);
*/
/*
fprintf(fp, "%d %d %g %g %g %g %d\n", 5, 2, corner[1][0], corner[1][1],
corner[1][2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 6, 2, corner[0][0], corner[1][1],
corner[1][2], 3.0, 6);
fprintf(fp, "%d %d %g %g %g %g %d\n", 7, 2, corner[1][0], corner[0][1],
corner[1][2], 3.0, 7);
fprintf(fp, "%d %d %g %g %g %g %d\n", 8, 2, corner[1][0], corner[1][1],
corner[0][2], 3.0, 7);
fprintf(fp, "%d %d %g %g %g %g %d\n", 12, 2, corner[1][0], corner[1][1],
corner[0][2], 3.0, 2);
fprintf(fp, "%d %d %g %g %g %g %d\n", 9, 2, corner[1][0], corner[1][1],
corner[1][2], 3.0, 6);
fprintf(fp, "%d %d %g %g %g %g %d\n", 10, 2, corner[0][0], corner[1][1],
corner[1][2], 3.0, 3);
fprintf(fp, "%d %d %g %g %g %g %d\n", 11, 2, corner[1][0], corner[0][1],
corner[1][2], 3.0, 4);
fprintf(fp, "%d %d %g %g %g %g %d\n", 12, 2, corner[1][0], corner[1][1],
corner[0][2], 3.0, -1);
*/
fprintf(fp, "%d %d %g %g %g %g %d\n", 21, 2, span[0] * vec[0] + center[0],
span[0] * vec[1] + center[1], span[0] * vec[2] + center[2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 22, 2, span[1] * vec[0] + center[0],
span[1] * vec[1] + center[1], span[1] * vec[2] + center[2], 3.0, 21);
fprintf(fp, "%d %d %g %g %g %g %d\n", 23, 2, span2[0] * vec2[0] + center[0],
span2[0] * vec2[1] + center[1], span2[0] * vec2[2] + center[2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 24, 2, span2[1] * vec2[0] + center[0],
span2[1] * vec2[1] + center[1], span2[1] * vec2[2] + center[2], 3.0, 23);
fprintf(fp, "%d %d %g %g %g %g %d\n", 25, 2, span3[0] * vec3[0] + center[0],
span3[0] * vec3[1] + center[1], span3[0] * vec3[2] + center[2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 26, 2, span3[1] * vec3[0] + center[0],
span3[1] * vec3[1] + center[1], span3[1] * vec3[2] + center[2], 3.0, 25);
fclose(fp);
//double corner[6];
/*
FILE *fp = fopen("../data/test.swc", "w");
fprintf(fp, "%d %d %g %g %g %g %d\n", 1, 2, span[0] * vec[0] + center[0],
span[0] * vec[1] + center[1], span[0] * vec[2] + center[2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 2, 2, span[1] * vec[0] + center[0],
span[1] * vec[1] + center[1], span[1] * vec[2] + center[2], 3.0, 1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 3, 2, span2[0] * vec2[0] + center[0],
span2[0] * vec2[1] + center[1], span2[0] * vec2[2] + center[2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 4, 2, span2[1] * vec2[0] + center[0],
span2[1] * vec2[1] + center[1], span2[1] * vec2[2] + center[2], 3.0, 3);
fprintf(fp, "%d %d %g %g %g %g %d\n", 5, 2, span3[0] * vec3[0] + center[0],
span3[0] * vec3[1] + center[1], span3[0] * vec3[2] + center[2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 6, 2, span3[1] * vec3[0] + center[0],
span3[1] * vec3[1] + center[1], span3[1] * vec3[2] + center[2], 3.0, 5);
fclose(fp);
*/
//calculate corners
//Draw the six line of the corners
/*
Stack *stack2 = Copy_Stack(stack);
Zero_Stack(stack2);
int i = 0;
for (i = 0; i < obj->size; i++) {
stack2->array[Stack_Util_Offset(obj->voxels[i][0], obj->voxels[i][1],
obj->voxels[i][2], stack->width, stack->height, stack->depth)] = 1;
}
Write_Stack("../data/test.tif", stack2);
*/
#endif
#if 0
Stack *stack = Read_Stack("../data/test2.tif");
Stack_Threshold_Binarize(stack, 6);
Objlabel_Workspace ow;
STACK_OBJLABEL_OPEN_WORKSPACE(stack, (&ow));
ow.conn = 26;
ow.init_chord = TRUE;
int obj_size = Stack_Label_Largest_Object_W(stack, 1, 2, &ow);
Object_3d *obj = Make_Object_3d(obj_size, ow.conn);
extract_object(ow.chord, ow.seed, obj);
//Print_Object_3d(obj);
/*
STACK_OBJLABEL_CLOSE_WORKSPACE((&ow));
Objlabel_Workspace *ow = New_Objlabel_Workspace();
ow->conn = 26;
ow->init_chord = TRUE;
STACK_OBJLABEL_OPEN_WORKSPACE(stack, ow);
Stack_Label_Largest_Object_W(stack, 1, 2, ow);
*/
Write_Stack("../data/test3.tif", stack);
#endif
#if 0
Mc_Stack *stack = Read_Mc_Stack("../data/test2.tif", -1);
Print_Mc_Stack_Info(stack);
size_t offset;
size_t voxelNumber = Mc_Stack_Voxel_Number(stack);
uint8_t* arrayc[3] = {NULL, NULL, NULL};
arrayc[0] = stack->array;
arrayc[1] = stack->array + voxelNumber;
arrayc[2] = stack->array + voxelNumber * 2;
for (offset = 0; offset < voxelNumber; ++offset) {
if ((arrayc[0][offset] != 128) || (arrayc[1][offset] != 6) ||
(arrayc[2][offset] != 0)) {
arrayc[0][offset] = 0;
arrayc[1][offset] = 0;
arrayc[2][offset] = 0;
}
}
Write_Mc_Stack("../data/test.tif", stack, NULL);
Kill_Mc_Stack(stack);
#endif
#if 0
Mc_Stack *stack = Read_Mc_Stack("../data/flyem/TEM/slice_figure/segmentation/selected_body.tif", -1);
Print_Mc_Stack_Info(stack);
size_t offset;
size_t voxelNumber = Mc_Stack_Voxel_Number(stack);
Stack *mask = Make_Stack(GREY, stack->width, stack->height, stack->depth);
uint8_t* arrayc[4] = {NULL, NULL, NULL, NULL};
int i;
for (i = 0; i < 4; ++i) {
arrayc[i] = stack->array + voxelNumber * i;
}
for (offset = 0; offset < voxelNumber; ++offset) {
if ((arrayc[0][offset] > 0) || (arrayc[1][offset] > 0) ||
(arrayc[2][offset] > 0) || (arrayc[3][offset] > 0)) {
mask->array[offset] = 1;
} else {
mask->array[offset] = 0;
}
}
mask = Downsample_Stack_Max(mask, 7, 7, 0, NULL);
Write_Stack("../data/test.tif", mask);
#endif
#if 0
Stack *stack = Read_Stack("../data/test2.tif");
size_t offset;
size_t voxelNumber = Stack_Voxel_Number(stack);
color_t *arrayc = (color_t*) stack->array;
for (offset = 0; offset < voxelNumber; ++offset) {
if ((arrayc[offset][0] != 128) || (arrayc[offset][1] != 6) ||
(arrayc[offset][2] != 0)) {
arrayc[offset][0] = 0;
arrayc[offset][1] = 0;
arrayc[offset][2] = 0;
}
}
Write_Stack("../data/test.tif", stack);
#endif
#if 0
Stack *stack = Read_Stack("../data/flyem/TEM/slice_figure/segmentation/selected_body_volume.tif");
Stack *out = Make_Stack(COLOR, stack->width, stack->height, stack->depth);
Zero_Stack(out);
Object_3d_List *objs = Stack_Find_Object_N(stack, NULL, 255, 0, 26);
Print_Object_3d_List_Compact(objs);
uint8_t color[] = {0, 200, 50, 200, 0, 0};
uint8_t *color2 = color;
while (objs != NULL) {
Object_3d *obj = objs->data;
Stack_Draw_Object_C(out, obj, color2[0], color2[1], color2[2]);
color2 += 3;
objs = objs->next;
break;
}
Write_Stack("../data/test.tif", out);
#endif
#if 0
//Stack *stack = Read_Stack("../data/benchmark/binary/2d/btrig2.tif");
Stack *stack = Make_Stack(GREY, 3, 3, 3);
One_Stack(stack);
//Zero_Stack(stack);
//Set_Stack_Pixel(stack, 0, 1, 1, 1, 1);
Set_Stack_Pixel(stack, 0, 1, 1, 1, 0);
Set_Stack_Pixel(stack, 0, 1, 1, 0, 0);
Set_Stack_Pixel(stack, 0, 0, 0, 0, 0);
Set_Stack_Pixel(stack, 0, 0, 2, 0, 0);
Set_Stack_Pixel(stack, 0, 2, 0, 0, 0);
Set_Stack_Pixel(stack, 0, 2, 2, 0, 0);
Set_Stack_Pixel(stack, 0, 0, 0, 2, 0);
Set_Stack_Pixel(stack, 0, 0, 2, 2, 0);
Set_Stack_Pixel(stack, 0, 2, 0, 2, 0);
Set_Stack_Pixel(stack, 0, 2, 2, 2, 0);
//Set_Stack_Pixel(stack, 0, 1, 1, 2, 0);
Stack_Graph_Workspace *sgw = New_Stack_Graph_Workspace();
//Default_Stack_Graph_Workspace(sgw);
sgw->signal_mask = stack;
Graph *graph = Stack_Graph_W(stack, sgw);
sgw->signal_mask = NULL;
//Print_Graph(graph);
//Graph_To_Dot_File(graph, "../data/test.dot");
if (Graph_Has_Hole(graph) == TRUE) {
printf("The graph has a hole.\n");
}
#endif
#if 0
Stack *stack = Read_Stack("../data/flyem/skeletonization/session3/T1_207.tif");
size_t voxel_number = Stack_Voxel_Number(stack);
size_t i;
for (i = 0; i < voxel_number; ++i) {
if (stack->array[i] == 1) {
stack->array[i] = 255;
}
}
Filter_3d *filter = Gaussian_Filter_3d(0.5, 0.5, 0.5);
Stack *out = Filter_Stack(stack, filter);
Write_Stack("../data/test2.tif", out);
#endif
#if 0
Stack *stack = Make_Stack(GREY, 3, 3, 3);
Zero_Stack(stack);
Cuboid_I cuboid;
Cuboid_I_Set_S(&cuboid, 0, 0, 0, 4, 2, 3);
Cuboid_I_Label_Stack(&cuboid, 1, stack);
Print_Stack_Value(stack);
#endif
#if 0
Stack *stack = Make_Stack(GREY, 3, 3, 1);
Zero_Stack(stack);
Set_Stack_Pixel(stack, 1, 1, 0, 0, 1);
Print_Stack_Value(stack);
Stack *out = Downsample_Stack_Max(stack, 2, 2, 2, NULL);
Print_Stack_Value(out);
#endif
#if 0
double t[3] = {1, 2 * 256 + 12, 255 * 256};
printf("%g\n", Stack_Voxel_Weight_C(t));
#endif
#if 0
Stack *stack = Read_Stack_U("../data/vr/label.tif");
Stack_Binarize_Level(stack, 1);
Stack_Label_Large_Objects_N(stack, NULL, 1, 2, 2000, 4);
Stack_Threshold_Binarize(stack, 2);
Write_Stack("../data/vr/label1.tif", stack);
#endif
#if 0
Stack *stack = Read_Stack_U("../data/vr/label.tif");
Stack_Binarize_Level(stack, 5);
Stack_Label_Large_Objects_N(stack, NULL, 1, 2, 5000, 4);
Stack_Threshold_Binarize(stack, 2);
Write_Stack("../data/vr/label5.tif", stack);
#endif
#if 0
Stack *stack = Read_Stack_U("../data/vr/original.tif");
/* Make mask */
Stack *mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(mask);
Stack *overallLabel = Copy_Stack(mask);
Stack *labelStack[5];
size_t voxelNumber = Stack_Voxel_Number(mask);
size_t k;
Struct_Element *se = Make_Disc_Se(5);
int i;
char filePath[100];
for (i = 0; i < 5; ++i) {
sprintf(filePath, "../data/vr/label%d.tif", i + 1);
labelStack[i] = Read_Stack_U(filePath);
//labelStack[i] = Stack_Erode_Fast(labelStack[i], NULL, se);
Stack_Or(mask, labelStack[i], mask);
for (k = 0; k < voxelNumber; ++k) {
if (labelStack[i]->array[k] == 1) {
overallLabel->array[k] = i + 1;
}
}
}
for (k = 0; k < voxelNumber; ++k) {
if (mask->array[k] == 1) {
mask->array[k] = SP_GROW_SOURCE;
}
}
Sp_Grow_Workspace *sgw = New_Sp_Grow_Workspace();
sgw->size = voxelNumber;
Sp_Grow_Workspace_Set_Mask(sgw, mask->array);
sgw->wf = Stack_Voxel_Weight_C;
sgw->sp_option = 1;
tic();
Int_Arraylist *path = Stack_Sp_Grow(stack, NULL, 0, NULL, 0, sgw);
printf("time: %llu\n", toc());
Kill_Int_Arraylist(path);
for (k = 0; k < voxelNumber; ++k) {
if (mask->array[k] == 0) {
int idx = (int) k;
while (overallLabel->array[idx] == 0) {
idx = sgw->path[idx];
}
int label = overallLabel->array[idx];
idx = (int) k;
while (overallLabel->array[idx] == 0) {
overallLabel->array[idx] = label;
idx = sgw->path[idx];
}
}
}
for (k = 0; k < voxelNumber; ++k) {
if (overallLabel->array[k] == 1 || overallLabel->array[k] == 5) {
overallLabel->array[k] = 0;
}
}
Write_Stack("../data/test.tif", overallLabel);
Kill_Stack(stack);
#endif
return 0;
}
