static double path_length(Int_Arraylist *path, int width, int height, double zscale)
{
if (path->length < 2) {
return 0.0;
}
coordinate_3d_t coord1, coord2;
int sub[3];
Stack_Util_Coord(path->array[0], width, height, sub, sub+1, sub+2);
Set_Coordinate_3d(coord1, sub[0], sub[1], sub[2]);
double dist = 0.0;
int k;
for (k = 1; k < path->length; k++) {
Stack_Util_Coord(path->array[k], width, height, sub, sub+1,
sub+2);
Set_Coordinate_3d(coord2, sub[0], sub[1], sub[2]);
dist += Coordinate_3d_Distance(coord1, coord2);
Coordinate_3d_Copy(coord1, coord2);
}
return dist;
}
int Stack_Label_Object_Dist_N(Stack *stack, IMatrix *chord, int seed,
int flag, int label, double max_dist,
int n_nbr)
{
BOOL is_owner = FALSE;
if (chord == NULL) {
chord = Make_3d_IMatrix(stack->width, stack->height, stack->depth);
is_owner = TRUE;
} else {
if (chord->ndim != 3) {
THROW(ERROR_DATA_TYPE);
}
if ((stack->width != chord->dim[0]) || (stack->height != chord->dim[1])
|| (stack->depth != chord->dim[2])) {
THROW(ERROR_DATA_COMPTB);
}
}
if (flag >= 0) {
if (stack->array[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 */
for (i = 0; i < npixel; i++) {
chord->array[i] = -1;
}
int obj_size = 0;
int next = c;
BOOL do_label = TRUE;
double max_dist_square = max_dist * max_dist;
stack->array[seed] = label;
int neighbor[26];
Stack_Neighbor_Offset(n_nbr, stack->width, stack->height, neighbor);
#define STACK_LABEL_OBJECT_DIST_N_UPDATE_QUEUE \
{ \
nb = c + neighbor[i]; \
Stack_Util_Coord(nb, stack->width, stack->height, &nx, &ny, &nz); \
/*process unlabeled white neighbors*/ \
dx = nx - cx; \
dy = ny - cy; \
dz = nz - cz; \
if (dx * dx + dy * dy + dz * dz > max_dist_square) { \
do_label = FALSE; \
} else { \
do_label = TRUE; \
} \
\
if ((((flag < 0) && (stack->array[nb] != label)) || \
(stack->array[nb] == flag)) && \
(chord->array[nb] == -1) && (do_label == TRUE)) { \
chord->array[next] = nb; \
next = nb; \
stack->array[nb] = label; \
} \
}
int x, y, z;
int cx, cy, cz;
int nx, ny, nz;
int dx, dy, dz;
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;
Stack_Util_Coord(seed, stack->width, stack->height, &cx, &cy, &cz);
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_DIST_N_UPDATE_QUEUE;
}
} else {
for (i = 0; i < n_nbr; i++) {
if (is_in_bound[i]) {
STACK_LABEL_OBJECT_DIST_N_UPDATE_QUEUE;
}
}
}
c = chord->array[c]; /* move to next voxel */
obj_size++;
} while (c >= 0);
if (is_owner == TRUE) {
Kill_IMatrix(chord);
}
return obj_size;
}
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);
}
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;
}
int Stack_Label_Object_Level_N(Stack *stack, IMatrix *chord, int seed,
int flag, int label, Stack *code, int max,
int n_nbr)
{
BOOL is_owner = FALSE;
if (chord == NULL) {
chord = Make_3d_IMatrix(stack->width, stack->height, stack->depth);
is_owner = TRUE;
} else {
if (chord->ndim != 3) {
THROW(ERROR_DATA_TYPE);
}
if ((stack->width != chord->dim[0]) || (stack->height != chord->dim[1])
|| (stack->depth != chord->dim[2])) {
THROW(ERROR_DATA_COMPTB);
}
}
if (stack->array[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 */
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 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);
if (is_owner == TRUE) {
Kill_IMatrix(chord);
}
return obj_size;
}
/**
* Stack_Build_Seed_Graph_Gg() allows users to build a seed graph using
* approximate geodesdic distances. The workspace should be created by
* Make_Objlabel_Workspace_Gg() and initialized by Init_Objlabel_Workspace_Gg()
* if necessary.
*/
Graph* Stack_Build_Seed_Graph_Gg(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;
}
int i, j, k;
uint16 *level = (uint16 *) ow->u;
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_GG(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; \
level[checking_voxel] = level[queue_head[i]] + 1; \
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);*/ \
double dist = level[checking_voxel] + level[queue_head[i]]; \
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_GG(1);
} else {
STACK_SEED_GRAPH_UPDATE_QUEUE_GG(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 */
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;
}
Int_Arraylist *Stack_Route(const Stack *stack, int start[], int end[],
Stack_Graph_Workspace *sgw)
{
if (sgw->gw == NULL) {
sgw->gw = New_Graph_Workspace();
}
if (sgw->range == NULL) {
double dist = Geo3d_Dist(start[0], start[1], start[2], end[0], end[1],
end[2]);
int margin[3];
int i = 0;
for (i = 0; i < 3; ++i) {
margin[i] = iround(dist - abs(end[i] - start[i] + 1));
if (margin[i] < 0) {
margin[i] = 0;
}
}
Stack_Graph_Workspace_Set_Range(sgw, start[0], end[0], start[1], end[1],
start[2], end[2]);
Stack_Graph_Workspace_Expand_Range(sgw, margin[0], margin[0],
margin[1], margin[1], margin[2], margin[2]);
Stack_Graph_Workspace_Validate_Range(sgw, stack->width, stack->height,
stack->depth);
}
int swidth = sgw->range[1] - sgw->range[0] + 1;
int sheight = sgw->range[3] - sgw->range[2] + 1;
int sdepth = sgw->range[5] - sgw->range[4] + 1;
int start_index = Stack_Util_Offset(start[0] - sgw->range[0],
start[1] - sgw->range[2],
start[2] - sgw->range[4],
swidth, sheight, sdepth);
int end_index = Stack_Util_Offset(end[0] - sgw->range[0],
end[1] - sgw->range[2],
end[2] - sgw->range[4],
swidth, sheight, sdepth);
if (start_index > end_index) {
int tmp;
SWAP2(start_index, end_index, tmp);
}
ASSERT(start_index >= 0, "Invalid starting index.");
ASSERT(end_index >= 0, "Invalid ending index.");
tic();
Graph *graph = Stack_Graph_W(stack, sgw);
ptoc();
tic();
int *path = NULL;
switch (sgw->sp_option) {
case 0:
path = Graph_Shortest_Path_E(graph, start_index, end_index, sgw->gw);
break;
case 1:
{
//printf("%g\n", sgw->intensity[start_index]);
sgw->intensity[end_index] = 4012;
sgw->intensity[start_index] = 4012;
path = Graph_Shortest_Path_Maxmin(graph, start_index, end_index,
sgw->intensity, sgw->gw);
}
break;
}
sgw->value = sgw->gw->dlist[end_index];
Kill_Graph(graph);
if (isinf(sgw->value)) {
return NULL;
}
#ifdef _DEBUG_2
{
Graph_Update_Edge_Table(graph, sgw->gw);
Stack *stack = Make_Stack(GREY, swidth, sheight, sdepth);
Zero_Stack(stack);
int nvoxel = (int) Stack_Voxel_Number(stack);
int index = end_index;
printf("%d -> %d\n", start_index, end_index);
while (index >= 0) {
if (index < nvoxel) {
stack->array[index] = 255;
}
int x, y, z;
Stack_Util_Coord(index, swidth, sheight, &x, &y, &z);
printf("%d (%d, %d, %d), %g\n", index, x, y, z, sgw->gw->dlist[index]);
index = path[index];
}
Write_Stack("../data/test2.tif", stack);
Kill_Stack(stack);
}
#endif
Int_Arraylist *offset_path =
Parse_Stack_Shortest_Path(path, start_index, end_index,
stack->width, stack->height, sgw);
int org_start = Stack_Util_Offset(start[0], start[1], start[2], stack->width,
stack->height, stack->depth);
if (org_start != offset_path->array[0]) {
iarray_reverse(offset_path->array, offset_path->length);
}
int org_end = Stack_Util_Offset(end[0], end[1], end[2], stack->width,
stack->height, stack->depth);
//printf("%d, %d\n", org_end, offset_path->array[offset_path->length -]);
ASSERT(org_start == offset_path->array[0], "Wrong path head.");
if (org_end != offset_path->array[offset_path->length - 1]) {
printf("debug here\n");
}
ASSERT(org_end == offset_path->array[offset_path->length - 1],
"Wrong path tail.");
ptoc();
return offset_path;
}