int main(int argc, char* argv[])
{ Range params[3] = { {0.0, 1.0, 0.2},
{0.5, 6.5, 0.4},
{-M_PI/4.0, M_PI/4.0, M_PI/36.0} };
Array *bank = Build_Line_Detectors( params[0], params[1], params[2],
7, 2*7+3 );
{ float *p,*d,sum=0.0;
d = (float*) bank->data;
p = d + bank->strides_px[0];
while( p-- > d )
sum += *p;
printf("sum: %g\n",sum);
if( sum > 0.01 )
printf("Mean is not zero: The image is probably too small to support the detector\n");
}
{ Stack stk, *t;
stk.kind = 4;
stk.width = bank->shape[0];
stk.height = bank->shape[1];
stk.depth = bank->strides_px[0] / bank->strides_px[3];
stk.array = (uint8*) bank->data;
Scale_Stack_To_Range( &stk, 0, 0, 255 );
t = Translate_Stack( &stk, GREY8 , 0 );
Write_Stack( "bank.tif", t );
Free_Stack(t);
}
Free_Array( bank );
return 0;
}
/*
* bwdist - build a distance map for a binary stack
*
* bwdist [-b<int>] infile -o outfile
*
* -i: inverse the image
* -b: byte number for output file (1 (default) or 2)
* -sq: build square distance map
*/
int main(int argc, char *argv[])
{
static char *Spec[] = {"<image:string> -o <string>",
"[-b<int> | -sq] [-i] [--plane]",
NULL};
Process_Arguments(argc, argv, Spec, 1);
char *image_file = Get_String_Arg("image");
Stack *stack = Read_Stack(image_file);
if (Is_Arg_Matched("-i")) {
Stack_Not(stack, stack);
}
Stack *distmap = NULL;
if (!Is_Arg_Matched("-sq")) {
distmap = Stack_Bwdist_L(stack, NULL, NULL);
Kill_Stack(stack);
int kind = GREY;
if (Is_Arg_Matched("-b")) {
kind = Get_Int_Arg("-b");
}
stack = Scale_Float_Stack((float *) distmap->array, distmap->width,
distmap->height, distmap->depth, kind);
Kill_Stack(distmap);
distmap = stack;
} else {
if (Is_Arg_Matched("--plane")) {
distmap = Stack_Bwdist_L_U16P(stack, NULL, 0);
Translate_Stack(distmap, GREY, 1);
} else {
distmap = Stack_Bwdist_L_U16(stack, NULL, 0);
}
Kill_Stack(stack);
}
char *out_file = Get_String_Arg("-o");
Write_Stack(out_file, distmap);
Kill_Stack(distmap);
return 1;
}
int main(int argc, char* argv[])
{
#if 0
Stack *stack = Read_Stack("../data/binimg.tif");
Set_Matlab_Path("/Applications/MATLAB74/bin/matlab");
Stack *dist = Stack_Bwdist(stack);
Stack* seeds = Stack_Local_Max(dist, NULL, STACK_LOCMAX_ALTER1);
Stack *out = Scale_Double_Stack((double *) dist->array, stack->width,
stack->height, stack->depth, GREY);
Translate_Stack(out, COLOR, 1);
Rgb_Color color;
Set_Color(&color, 255, 0, 0);
Stack_Label_Bwc(out, seeds, color);
Print_Stack_Info(dist);
Write_Stack("../data/test.tif", out);
#endif
#if 0
Stack *stack = Read_Stack("../data/benchmark/sphere_bw.tif");
//Stack *stack = Read_Stack("../data/sphere_data.tif");
//Stack_Not(stack, stack);
int i;
/*
uint8 *array = stack->array + 512 * 600;
for (i = 1; i < 512; i++) {
array[i] = 1;
}
*/
//stack->depth = 50;
/*
long int *label = (long int *) malloc(sizeof(long int) *
Stack_Voxel_Number(stack));
*/
tic();
Stack *out = Stack_Bwdist_L_U16(stack, NULL, 0);
uint16 *out_array = (uint16 *) out->array;
printf("%llu\n", toc());
//int *hist = Stack_Hist(out);
//Print_Int_Histogram(hist);
Stack *out2 = Stack_Bwdist_L(stack, NULL, NULL);
float *out2_array = (float *) out2->array;
int n = Stack_Voxel_Number(out);
int t = 0;
int x, y, z;
for (i = 0; i < n; i++) {
uint16 d2 = (uint16) out2_array[i];
if (out_array[i] != d2){
int area = stack->width * stack->height;
STACK_UTIL_COORD(i, stack->width, area, x, y, z);
printf("(%d %d %d)", x, y, z);
printf("%d %d %d\n", out_array[i], d2, stack->array[i]);
t++;
}
}
printf("%d error\n", t);
# if 0
//Translate_Stack(out, GREY, 1);
float *out_array = (float *) out->array;
int i;
int n = Stack_Voxel_Number(out);
/*
for (i = 0; i < n; i++) {
out_array[i] = sqrt(out_array[i]);
}
Stack *out2 = Scale_Float_Stack((float *)out->array, out->width, out->height,
out->depth, GREY);
*/
Stack *out2 = Make_Stack(GREY, out->width, out->height, out->depth);
for (i = 0; i < n; i++) {
out2->array[i] = (uint8) round(sqrt(out_array[i]));
}
Write_Stack("../data/test.tif", out2);
# endif
Write_Stack("../data/test.tif", out);
Kill_Stack(out);
Kill_Stack(out2);
#endif
#if 1
Stack *stack = Read_Stack("../data/system/29.tif");
Print_Stack_Info(stack);
tic();
Stack *out = Stack_Bwdist_L_U16P(stack, NULL, 0);
ptoc();
Stack *golden = Read_Stack("../data/system/29_dist2.tif");
printf("Checking result ...\n");
if (Stack_Identical(out, golden) == FALSE) {
printf("Result unmatched.\n");
} else {
printf("Good.\n");
}
#endif
return 0;
}
int main(int argc, char* argv[])
{ Range params[3] = { {0.0, 1.0, 0.1},
{0.5, 4.5, 0.5},
{-M_PI/4.0, M_PI/4.0, M_PI/72.0} };
Array *bank = Build_Harmonic_Line_Detectors(
params[0],
params[1],
params[2],
7,
2*7+3);
{ float *p,*d,sum=0.0;
d = (float*) bank->data;
p = d + bank->strides_px[0];
while( p-- > d )
sum += ( *p - round(*p) )*10.0;;
printf("sum: %g\n",sum);
if( sum > 0.01 )
printf("Mean is not zero: The image is probably too small to support the detector\n");
}
{ Stack stk, *lbl, *t;
float *d;
int i;
d = (float*) bank->data;
stk.kind = 4;
stk.width = bank->shape[0];
stk.height = bank->shape[1];
stk.depth = bank->strides_px[0] / bank->strides_px[3];
stk.array = (uint8*) bank->data;
lbl = Make_Stack(stk.kind, stk.width, stk.height, stk.depth);
{ int j,labels[NLABELS] = {2,3/*,5,7*/};
d = (float*) bank->data;
i = bank->strides_px[0];
while( i-- )
{ float v = d[i];
int l = lround(v);
int cnt = 0;
( (float*) stk.array )[i] = (v-l)*10.0;
( (float*) lbl->array )[i] = 0;
for(j=0;j<NLABELS;j++)
if( l > 0.0 )
if( ((int)l) % labels[j] == 0 )
{ ( (float*) lbl->array )[i] += (j+1);
cnt++;
}
if(cnt)
( (float*) lbl->array )[i] /= cnt;
}
}
Scale_Stack_To_Range( &stk, 0, 0, 255 );
Scale_Stack_To_Range( lbl, 0, 0, 255 );
t = Translate_Stack( &stk, GREY8 , 0 );
Free_Stack(t);
Write_Stack( "evaltest5_weights.tif", t );
t = Translate_Stack( lbl, GREY8 , 0 );
Write_Stack( "evaltest5_labels.tif", t );
Free_Stack(t);
Free_Stack(lbl);
}
Free_Array( bank );
return 0;
}
int main(int argc, char *argv[])
{
static char *Spec[] = {"[-t]", NULL};
Process_Arguments(argc, argv, Spec, 1);
if (Is_Arg_Matched("-t")) {
/* Example test */
Stack *stack = Make_Stack(GREY, 7, 7, 1);
One_Stack(stack);
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->conn = 26;
ws->mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(ws->mask);
/* set seeds */
Set_Stack_Pixel(ws->mask, 1, 1, 0, 0, 1.0);
Set_Stack_Pixel(ws->mask, 1, 5, 0, 0, 2.0);
Set_Stack_Pixel(ws->mask, 3, 3, 0, 0, 3.0);
Set_Stack_Pixel(ws->mask, 5, 1, 0, 0, 4.0);
Set_Stack_Pixel(ws->mask, 5, 5, 0, 0, 5.0);
/* set stack values */
Set_Stack_Pixel(stack, 1, 1, 0, 0, 3.0);
Set_Stack_Pixel(stack, 1, 5, 0, 0, 3.0);
Set_Stack_Pixel(stack, 3, 3, 0, 0, 3.0);
Set_Stack_Pixel(stack, 5, 1, 0, 0, 3.0);
Set_Stack_Pixel(stack, 5, 5, 0, 0, 3.0);
Stack *out = Stack_Watershed(stack, ws);
//Write_Stack("../data/test/watershed/golden/watershed1.tif", out);
char *golden_file = "../data/test/watershed/golden/watershed1.tif";
if (fexist(golden_file)) {
Stack *golden = Read_Stack(golden_file);
if (Stack_Identical(out, golden) == FALSE) {
Print_Stack_Value(stack);
Print_Stack_Value(out);
Print_Stack_Value(golden);
PRINT_EXCEPTION("Bug?", "Conflict with golden.");
return 1;
}
Kill_Stack(stack);
Kill_Stack(out);
Kill_Stack(golden);
Kill_Stack_Watershed_Workspace(ws);
} else {
printf("%s cannot be found.\n", golden_file);
}
char *test_file = "../data/benchmark/rice_label.tif";
if (fexist(test_file)) {
stack = Read_Stack_U(test_file);
ws = Make_Stack_Watershed_Workspace(stack);
ws->mask = Copy_Stack(stack);
ws->conn = 26;
One_Stack(stack);
out = Stack_Watershed(stack, ws);
//Write_Stack("../data/test/watershed/golden/watershed2.tif", out);
Stack *golden = Read_Stack("../data/test/watershed/golden/watershed2.tif");
if (Stack_Identical(out, golden) == FALSE) {
PRINT_EXCEPTION("Bug?", "Conflict with golden.");
return 1;
}
} else {
printf("%s cannot be found.\n", test_file);
}
printf(":) Testing passed.\n");
return 0;
}
#if 0
/* Initialize */
Watershed_3d *watershed = New_Watershed_3d();
Watershed_3d_Workspace *ws = New_Watershed_3d_Workspace();
ws->conn = 26;
/* Initialize stack */
Stack *stack = Read_Stack("../data/fly_neuron/dist.tif");
int nvoxel = Stack_Voxel_Number(stack);
int i;
uint16 *array16 = (uint16 *)stack->array;
for (i = 0; i < nvoxel; i++) {
array16[i] = 0xFFFF - array16[i];
}
/* Add mask to ignore dark voxels */
ws->mask = Copy_Stack(stack);
//Translate_Stack(stack, GREY, 1);
//stack->array = stack->array + stack->width * stack->height * 100;
//stack->depth = 1;
// ws->mask = Copy_Stack(stack);
//Stack_Binarize(ws->mask);
// ws->mask = NULL;
//Write_Stack("../data/dist.tif", stack);
//Stack *stack2 = Copy_Stack(stack);
# if 0
Build_3D_Watershed(stack, watershed, ws);
Write_Stack("../data/test.tif", watershed->labels);
# endif
# if 0
Image_View iv = Image_View_Stack(stack2);
Watershed_Test *watershed2 = Build_2D_Watershed_Test(&(iv.image), 0);
Write_Image("../data/test2.tif", watershed2->labels);
# endif
#endif
#if 0
Image *image = Read_Image("../data/Ring15.tif_Sub1200_Original_inv.tif");
Watershed_2D *ws = Build_2D_Watershed(image, 0);
Image *result = Color_Watersheds(ws, image);
Write_Image("../data/test.tif", result);
Kill_Image(image);
#endif
#if 0
Stack *stack = Make_Stack(GREY, 7, 7, 1);
One_Stack(stack);
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->conn = 26;
ws->mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(ws->mask);
Set_Stack_Pixel(ws->mask, 1, 1, 0, 0, 1.0);
Set_Stack_Pixel(ws->mask, 1, 5, 0, 0, 2.0);
Set_Stack_Pixel(ws->mask, 3, 3, 0, 0, 3.0);
Set_Stack_Pixel(ws->mask, 5, 1, 0, 0, 4.0);
Set_Stack_Pixel(ws->mask, 5, 5, 0, 0, 5.0);
Set_Stack_Pixel(stack, 1, 1, 0, 0, 3.0);
Set_Stack_Pixel(stack, 1, 5, 0, 0, 3.0);
Set_Stack_Pixel(stack, 3, 3, 0, 0, 3.0);
Set_Stack_Pixel(stack, 5, 1, 0, 0, 3.0);
Set_Stack_Pixel(stack, 5, 5, 0, 0, 3.0);
Stack *out = Stack_Watershed(stack, ws);
Print_Stack_Value(out);
#endif
#if 0
Stack *stack = Make_Stack(GREY, 3, 3, 1);
One_Stack(stack);
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->conn = 26;
ws->mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(ws->mask);
Set_Stack_Pixel(ws->mask, 0, 0, 0, 0, 1.0);
Set_Stack_Pixel(ws->mask, 2, 2, 0, 0, 2.0);
Set_Stack_Pixel(stack, 0, 0, 0, 0, 5.0);
Set_Stack_Pixel(stack, 2, 2, 0, 0, 3.0);
Set_Stack_Pixel(stack, 0, 2, 0, 0, 2.0);
//Set_Stack_Pixel(stack, 1, 1, 0, 0, 2.0);
Set_Stack_Pixel(stack, 1, 2, 0, 0, 2.0);
Set_Stack_Pixel(stack, 2, 0, 0, 0, 2.0);
Set_Stack_Pixel(stack, 2, 1, 0, 0, 2.0);
Print_Stack_Value(stack);
ws->start_level = 6;
Stack *out = Stack_Watershed(stack, ws);
Print_Stack_Value(out);
#endif
#if 0
Stack *stack = Read_Stack_U("../data/benchmark/rice_label.tif");
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->mask = Copy_Stack(stack);
ws->conn = 26;
One_Stack(stack);
tic();
Stack *out = Stack_Watershed(stack, ws);
printf("%lld\n", toc());
Write_Stack("../data/test.tif", out);
#endif
#if 0
Stack *stack = Read_Stack_U("../data/diadem_d1_147.xml");
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(ws->mask);
ws->conn = 26;
const int *dx = Stack_Neighbor_X_Offset(ws->conn);
const int *dy = Stack_Neighbor_X_Offset(ws->conn);
const int *dz = Stack_Neighbor_X_Offset(ws->conn);
int seed[3];
String_Workspace *sw = New_String_Workspace();
char *line = NULL;
FILE *fp = fopen("../data/diadem_d1_root_z.txt", "r");
int k = 1;
while ((line = Read_Line(fp, sw)) != NULL) {
int n;
String_To_Integer_Array(line, seed, &n);
double maxv = -1;
if (n == 3) {
maxv = Get_Stack_Pixel(stack, seed[0], seed[1], seed[2], 0);
printf("%g\n", maxv);
int i;
for (i = 0; i < ws->conn; i++) {
if (maxv < Get_Stack_Pixel(stack, seed[0] + dx[i], seed[1] + dy[i],
seed[2] + dz[i], 0)) {
maxv = Get_Stack_Pixel(stack, seed[0] + dx[i], seed[1] + dy[i],
seed[2] + dz[i], 0);
}
}
//Set_Stack_Pixel(stack, seed[0], seed[1], seed[2], 0, maxv);
Set_Stack_Pixel(ws->mask, seed[0], seed[1], seed[2], 0, k);
for (i = 0; i < ws->conn; i++) {
//Set_Stack_Pixel(stack, seed[0] + dx[i], seed[1] + dy[i],
// seed[2] + dz[i], 0, maxv);
Set_Stack_Pixel(ws->mask, seed[0] + dx[i], seed[1] + dy[i],
seed[2] + dz[i], 0, k);
}
k++;
}
}
fclose(fp);
Kill_String_Workspace(sw);
/*
Set_Stack_Pixel(ws->mask, 19, 605, 112, 0, 1.0);
Set_Stack_Pixel(ws->mask, 28, 565, 112, 0, 1.0);
*/
Stack_Watershed_Infer_Parameter(stack, ws);
tic();
Stack *out = Stack_Watershed(stack, ws);
printf("%lld\n", toc());
Write_Stack("../data/diadem_d1_147_label.tif", out);
static const uint8 Color_Map[][3] = {
{0, 0, 0},
{0, 224, 64}, {32, 64, 128}, {64, 64, 0}, {64, 128, 64},
{96, 64, 128}, {64, 0, 0}, {128, 200, 64}, {160, 128, 128},
{192, 0, 0}, {192, 160, 64}, {224, 64, 128}, {224, 224, 192}};
Translate_Stack(out, COLOR, 1);
size_t nvoxel = Stack_Voxel_Number(out);
size_t i;
color_t *arrayc = (color_t*) out->array;
for (i = 0; i < nvoxel; i++) {
arrayc[i][2] = Color_Map[arrayc[i][0]][2];
arrayc[i][1] = Color_Map[arrayc[i][0]][1];
arrayc[i][0] = Color_Map[arrayc[i][0]][0];
}
Write_Stack("../data/diadem_d1_147_paint.tif", out);
#endif
#if 0
Stack *stack = Read_Stack_U("../data/diadem_d1_146.xml");
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
Stack *mask = Read_Stack("../data/test3.tif");
ws->mask = Crop_Stack(mask, 252, -937, 2, 1024, 1024, 63, NULL);
ws->conn = 26;
Stack_Watershed_Infer_Parameter(stack, ws);
tic();
Stack *out = Stack_Watershed(stack, ws);
printf("%lld\n", toc());
Write_Stack("../data/test2.tif", out);
#endif
#if 0
Stack *stack = Make_Stack(GREY, 7, 7, 1);
One_Stack(stack);
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->conn = 26;
ws->mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(ws->mask);
Set_Stack_Pixel(ws->mask, 1, 1, 0, 0, 1.0);
Set_Stack_Pixel(ws->mask, 1, 5, 0, 0, 2.0);
Set_Stack_Pixel(ws->mask, 3, 3, 0, 0, 3.0);
Set_Stack_Pixel(ws->mask, 5, 1, 0, 0, 4.0);
Set_Stack_Pixel(ws->mask, 5, 5, 0, 0, 5.0);
Set_Stack_Pixel(stack, 1, 1, 0, 0, 3.0);
Set_Stack_Pixel(stack, 1, 5, 0, 0, 3.0);
Set_Stack_Pixel(stack, 3, 3, 0, 0, 3.0);
Set_Stack_Pixel(stack, 5, 1, 0, 0, 3.0);
Set_Stack_Pixel(stack, 5, 5, 0, 0, 3.0);
Stack *out = Stack_Watershed(stack, ws);
Print_Stack_Value(out);
Stack *out2 = Stack_Region_Border_Shrink(out, ws);
Print_Stack_Value(out2);
#endif
#if 0
Stack *stack = Read_Stack("../data/diadem_d1_013_label.tif");
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
//ws->conn = 26;
Stack *out = Stack_Region_Border_Shrink(stack, ws);
Write_Stack("../data/test.tif", out);
#endif
#if 0
Stack *stack = Make_Stack(GREY, 1, 1, 19);
One_Stack(stack);
stack->array[3] = 5;
stack->array[4] = 5;
stack->array[7] = 5;
stack->array[8] = 5;
stack->array[10] = 4;
stack->array[11] = 5;
stack->array[12] = 5;
stack->array[13] = 4;
stack->array[16] = 5;
stack->array[17] = 5;
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->conn = 26;
ws->mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(ws->mask);
Print_Stack_Value(stack);
Stack_Watershed_Zgap_Barrier(stack, ws->mask);
Print_Stack_Value(ws->mask);
#endif
#if 0
Stack *stack = Read_Stack("../data/diadem_d1_047_label.tif");
Stack_Binarize(stack);
Stack *stack2 = Stack_Bwdist_L_U16(stack, NULL, 0);
Write_Stack("../data/test.tif", stack2);
#endif
#if 0
char stack_path[100];
char mask_path[100];
strcpy(stack_path, "../data/diadem_d1_064.xml");
strcpy(mask_path, stack_path);
strsplit(mask_path, '.', -1);
sprintf(mask_path, "%s_label.tif", mask_path);
if (!fexist(stack_path)) {
fprintf(stderr, "Cannot find %s\n", stack_path);
return 1;
}
printf("Processing %s\n", stack_path);
Stack *stack = Read_Stack_U(stack_path);
Stack *mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(mask);
int conn = 26;
const int *dx = Stack_Neighbor_X_Offset(conn);
const int *dy = Stack_Neighbor_X_Offset(conn);
const int *dz = Stack_Neighbor_X_Offset(conn);
int seed[3];
String_Workspace *sw = New_String_Workspace();
char *line = NULL;
FILE *fp = fopen("../data/064.seeds.txt", "r");
int k = 1;
/* label seeds */
while ((line = Read_Line(fp, sw)) != NULL) {
int n;
String_To_Integer_Array(line, seed, &n);
double maxv = -1;
if (n == 3) {
maxv = Get_Stack_Pixel(stack, seed[0], seed[1], seed[2], 0);
int i;
for (i = 0; i < conn; i++) {
if (maxv < Get_Stack_Pixel(stack, seed[0] + dx[i], seed[1] + dy[i],
seed[2] + dz[i], 0)) {
maxv = Get_Stack_Pixel(stack, seed[0] + dx[i], seed[1] + dy[i],
seed[2] + dz[i], 0);
}
}
Set_Stack_Pixel(mask, seed[0], seed[1], seed[2], 0, k);
for (i = 0; i < conn; i++) {
Set_Stack_Pixel(mask, seed[0] + dx[i], seed[1] + dy[i],
seed[2] + dz[i], 0, k);
}
k++;
}
}
fclose(fp);
Kill_String_Workspace(sw);
Stack_Running_Median(stack, 0, stack);
Stack_Running_Median(stack, 1, stack);
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->mask = mask;
Filter_3d *filter = Gaussian_Filter_3d(2.0, 2.0, 1.5);
Stack *filtered_stack = Filter_Stack(stack, filter);
Stack_Watershed_Zgap_Barrier(filtered_stack, ws->mask);
Stack_Running_Max(ws->mask, 0, ws->mask);
Stack_Running_Max(ws->mask, 1, ws->mask);
//Write_Stack("../data/test.tif", ws->mask);
Kill_Stack(filtered_stack);
filtered_stack = NULL;
FMatrix *dm = Mexihat_3D1_F(2.0, NULL, 2);
//FMatrix *dm = Mexihat_3D_F(2.0, NULL);
FMatrix_Negative(dm);
filtered_stack = Filter_Stack(stack, dm);
Stack_Threshold_Common(filtered_stack, 0, 65535);
Stack_Binarize(filtered_stack);
Translate_Stack(filtered_stack, GREY, 1);
{
int i, j, k;
int offset = 0;
uint16 *array = (uint16*) stack->array;
for (k = 0; k < stack->depth; k++) {
for (j = 0; j < stack->height; j++) {
for (i = 0; i < stack->width; i++) {
if (filtered_stack != NULL) {
if (filtered_stack->array[offset] == 1) {
ws->mask->array[offset] = STACK_WATERSHED_BARRIER;
}
}
array[offset++] += k * 2;
}
}
}
}
Kill_Stack(filtered_stack);
Stack_Watershed_Infer_Parameter(stack, ws);
ws->conn = 6;
double weights[26] = {0.5, 0.5, 1.0, 1.0, 0.2, 0.2, 0.75, 0.75, 0.75, 0.75,
0.35, 0.35, 0.35, 0.35, 0.6, 0.6, 0.6, 0.6,
0.45, 0.45, 0.45, 0.45,
0.45, 0.45, 0.45, 0.45};
ws->weights = weights;
ws->weights = NULL;
if (ws->weights != NULL) {
ws->min_level /= 3;
}
Stack_Running_Median(stack, 0, stack);
Stack_Running_Median(stack, 1, stack);
Stack *out = Stack_Watershed(stack, ws);
strcpy(mask_path, stack_path);
strsplit(mask_path, '.', -1);
sprintf(mask_path, "%s_label.tif", mask_path);
Write_Stack("../data/test.tif", out);
#endif
#if 0
Stack *stack = Read_Stack("../data/test/soma2.tif");
int thre = Stack_Find_Threshold_A(stack, THRESHOLD_LOCMAX_TRIANGLE);
Filter_3d *filter = Gaussian_Filter_3d(1.0, 1.0, 0.5);
Stack *out = Filter_Stack(stack, filter);
stack = Copy_Stack(out);
Stack_Threshold_Binarize(out, thre);
Stack *out2 = Stack_Bwdist_L_U16P(out, NULL, 0);
int nvoxel = Stack_Voxel_Number(out);
uint16_t *dist_array = (uint16_t*) out2->array;
int i;
for (i = 0; i < nvoxel; i++) {
dist_array[i] = sqrt(dist_array[i]);
}
Write_Stack("../data/labmeeting13/distp.tif", out2);
#endif
#if 0
//Stack *stack = Read_Stack("../data/test/soma2.tif");
Stack *stack = Read_Stack("/Users/zhaot/Data/jinny/slice7_2to34ds_soma_c2.tif");
int thre = Stack_Find_Threshold_A(stack, THRESHOLD_LOCMAX_TRIANGLE);
Filter_3d *filter = Gaussian_Filter_3d(1.0, 1.0, 0.5);
Stack *out = Filter_Stack(stack, filter);
stack = Copy_Stack(out);
Stack_Threshold_Binarize(out, thre);
Stack *out2 = Stack_Bwdist_L_U16P(out, NULL, 0);
/*
out = Stack_Locmax_Region(out2, 26);
*/
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(ws->mask);
size_t nvoxel = Stack_Voxel_Number(stack);
size_t offset;
uint16_t *dist_array = (uint16_t*) out2->array;
for (offset = 0; offset < nvoxel; offset++) {
if (/*(out->array[offset] == 1) && */(dist_array[offset] > 1000)) {
ws->mask->array[offset] = 1;
}
}
//Objlabel_Workspace *ow = New_Objlabel_Workspace();
//Stack_Label_Large_Objects_W(ws->mask, 1, 2, 10, ow);
//Stack_Label_Objects_N(ws->mask, NULL, 1, 2, 26);
Object_3d_List *objs = Stack_Find_Object(ws->mask, 1, 100);
Zero_Stack(ws->mask);
Stack_Draw_Objects_Bw(ws->mask, objs, -255);
printf("%g\n", Stack_Max(ws->mask, NULL));
/*
Write_Stack("../data/test.tif", ws->mask);
return 1;
*/
ws->min_level = thre;
ws->start_level = 65535;
Stack *out3 = Stack_Watershed(stack, ws);
/*
Write_Stack("../data/labmeeting13/watershed.tif", out3);
return 1;
*/
for (offset = 0; offset < nvoxel; offset++) {
if (dist_array[offset] < 300) {
out3->array[offset] = 0;
}
}
int nregion = Stack_Max(out3, NULL);
Kill_Stack(out2);
Stack *filtered = Copy_Stack(stack);
Kill_Stack(stack);
ws->conn = 8;
stack = Stack_Region_Border_Shrink(out3, ws);
out2 = Stack_Region_Expand(stack, 4, 30, NULL);
for (offset = 0; offset < nvoxel; offset++) {
if (out->array[offset] == 0) {
out2->array[offset] = 0;
}
}
Write_Stack("../data/test2.tif", out2);
Kill_Stack(stack);
//stack = Read_Stack("../data/test/soma2.tif");
stack = Read_Stack("/Users/zhaot/Data/jinny/slice7_2to34ds_soma_c2.tif");
Translate_Stack(stack, COLOR, 1);
int i;
double h = 0.0;
double s = 1.0;
for (i = 0; i < nregion; i++) {
Stack_Label_Color_L(stack, out2, i+1, h+=0.35, s, filtered);
/*
Rgb_Color color;
Set_Color_Jet(&color, i*3);
Stack_Label_Level(stack, out2, i+1, color);
*/
}
Write_Stack("../data/test.tif", stack);
#endif
#if 0
Stack *stack = Read_Stack("../data/leaktest/leak3.tif");
Stack *distmap = Stack_Bwdist_L_U16P(stack, NULL, 0);
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->mask = Copy_Stack(distmap);
Stack_Threshold_Binarize(ws->mask, 10);
Translate_Stack(ws->mask, GREY, 1);
Object_3d_List *objs = Stack_Find_Object(ws->mask, 1, 100);
Zero_Stack(ws->mask);
Stack_Draw_Objects_Bw(ws->mask, objs, -255);
ws->min_level = 1;
ws->start_level = 65535;
Stack *out3 = Stack_Watershed(distmap, ws);
Write_Stack("../data/test.tif", out3);
#endif
#if 0
Stack *stack = Read_Stack("../data/benchmark/two_disk.tif");
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->conn = 26;
Stack *out = Stack_Watershed(stack, ws);
Write_Stack("../data/test.tif", out);
#endif
return 0;
}
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_Objects_N(Stack *stack, IMatrix *chord,
int flag, int label, int n_nbr)
{
TZ_ASSERT(label > flag, "Invalid label");
int start_label = label;
BOOL is_owner = FALSE;
STACK_OBJLABEL_CHECK_CHORD(stack, chord, is_owner);
int nvoxel = Stack_Voxel_Number(stack);
int nobj = 0;
int i;
Objlabel_Workspace ow;
Default_Objlabel_Workspace(&ow);
ow.conn = n_nbr;
ow.chord = chord;
ow.init_chord = FALSE;
for (i = 0; i < nvoxel; i++) {
ow.chord->array[i] = -1;
}
PROGRESS_BEGIN("Labeling object");
uint16_t *array16 = (uint16_t*) stack->array;
uint8_t *array8 = (uint8_t*) stack->array;
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) {
if (label > 255) {
if (stack->kind == GREY) {
Translate_Stack(stack, GREY16, 1);
array16 = (uint16_t*) stack->array;
}
}
PROGRESS_STATUS(i / (nvoxel / 100 + 1));
Stack_Label_Object_W(stack, i, flag, label, &ow);
label++;
if (label > 65535) {
TZ_WARN(ERROR_DATA_VALUE);
label = start_label;
}
nobj++;
PROGRESS_REFRESH;
}
}
PROGRESS_END("done");
if (is_owner == TRUE) {
Kill_IMatrix(chord);
}
return nobj;
}
int main()
{
/* Read stack */
Stack *stack = Read_Stack("../data/fly_neuron.tif");
double z_scale = 1.0;
/* New a bifold segment */
Local_Bifold_Neuroseg *locbn = New_Local_Bifold_Neuroseg();
/*
Set_Local_Bifold_Neuroseg(locbn, 2, 2, 2, 2, 30, 0.5,
TZ_PI_2, TZ_PI_2, -TZ_PI_2, 0,
461, 296, 144); //fly_neuron.tif
*/
Set_Local_Bifold_Neuroseg(locbn, 2, 2, 2, 2, 40, 0.5,
TZ_PI_2, TZ_PI_2, TZ_PI_2, TZ_PI_2,
290, 304, 112); //fly_neuron.tif
/*
Set_Local_Bifold_Neuroseg(locbn, 2, 2, 2, 2, 30, 0.5,
TZ_PI_2, TZ_PI_2, -TZ_PI_2, 0,
320, 164, 148); //fly_neuron.tif
*/
/*
Set_Local_Bifold_Neuroseg(locbn, 3, 3, 3, 3, 30, 0.5,
TZ_PI_2, TZ_PI_2, -TZ_PI_2, 0,
262, 136, 141); //fly_neuron2.tif
*/
/*
Set_Local_Bifold_Neuroseg(locbn, 3, 3, 3, 3, 30, 0.5,
TZ_PI_2, TZ_PI_2, -TZ_PI_2, 0,
236, 396, 143); //fly_neuron2.tif
*/
/* fit */
int var_index[LOCAL_BIFOLD_NEUROSEG_NPARAM];
int nvar = Local_Bifold_Neuroseg_Var_Mask_To_Index
(BIFOLD_NEUROSEG_VAR_MASK_R |
BIFOLD_NEUROSEG_VAR_MASK_KNOT |
BIFOLD_NEUROSEG_VAR_MASK_ORIENTATION2 |
BIFOLD_NEUROSEG_VAR_MASK_ORIENTATION, NEUROPOS_VAR_MASK_NONE, var_index);
Fit_Local_Bifold_Neuroseg(locbn, stack, var_index, nvar, z_scale, NULL);
Print_Local_Bifold_Neuroseg(locbn);
/* Generate field */
Geo3d_Scalar_Field *field = Local_Bifold_Neuroseg_Field(locbn, 1.0, NULL);
Delete_Local_Bifold_Neuroseg(locbn);
/* Draw it in a stack */
Stack *label = Make_Stack(FLOAT32, stack->width, stack->height, stack->depth);
Zero_Stack(label);
double coef[] = {0.1, 255.0};
double range[] = {0.0, 10000.0};
Geo3d_Scalar_Field_Draw_Stack(field, label, coef, range);
/* Turn the stack to GREY type */
Translate_Stack(label, GREY, 1);
/* Make canvas */
Translate_Stack(stack, COLOR, 1);
/* Label the canvas */
Stack_Label_Color(stack, label, 5.0, 1.0, label);
/* Save the stack */
Write_Stack("../data/test.tif", stack);
/* clean up */
Kill_Geo3d_Scalar_Field(field);
Kill_Stack(stack);
Kill_Stack(label);
return 0;
}
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 main(int argc, char *argv[])
{
static char *Spec[] = {"<input:string> -o <string>",
"[-count <int>] [-dist <int>] [-minobj <int>]", NULL};
Process_Arguments(argc, argv, Spec, 1);
Stack *input = Read_Stack(Get_String_Arg("input"));
int nregion = Stack_Max(input, NULL);
int nvoxel = Stack_Voxel_Number(input);
int i;
Stack *stack = Make_Stack(GREY, Stack_Width(input), Stack_Height(input),
Stack_Depth(input));
Stack *out = Make_Stack(GREY, Stack_Width(input), Stack_Height(input),
Stack_Depth(input));
Zero_Stack(out);
int nobj = 0;
for (i = 1; i <= nregion; i++) {
int j;
int count = 0;
for (j = 0; j < nvoxel; j++) {
stack->array[j] = (input->array[j] == i);
}
Stack *out3 = NULL;
int maxcount = 100000;
if (Is_Arg_Matched("-count")) {
maxcount = Get_Int_Arg("-count");
}
if (count > maxcount) {
out3 = Copy_Stack(stack);
Stack_Addc_M(out3, nobj);
nobj++;
} else {
Stack *distmap = Stack_Bwdist_L_U16P(stack, NULL, 0);
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->mask = Copy_Stack(distmap);
int mindist = 10;
if (Is_Arg_Matched("-dist")) {
mindist = Get_Int_Arg("-dist");
}
Stack_Threshold_Binarize(ws->mask, mindist);
Translate_Stack(ws->mask, GREY, 1);
int minobj = 100;
if (Is_Arg_Matched("-minobj")) {
minobj = Get_Int_Arg("-minobj");
}
Object_3d_List *objs = Stack_Find_Object(ws->mask, 1, minobj);
Zero_Stack(ws->mask);
Stack_Draw_Objects_Bw(ws->mask, objs, -255);
ws->min_level = 1;
ws->start_level = 65535;
out3 = Stack_Watershed(distmap, ws);
Stack_Addc_M(out3, nobj);
nobj += Object_3d_List_Length(objs);
Kill_Stack(distmap);
Kill_Stack_Watershed_Workspace(ws);
Kill_Object_3d_List(objs);
}
Stack_Add(out, out3, out);
Kill_Stack(out3);
}
printf("number of regions: %d\n", nobj);
Write_Stack(Get_String_Arg("-o"), out);
char cmd[500];
sprintf(cmd, "touch %s_done", Get_String_Arg("-o"));
system(cmd);
return 0;
}
int main()
{
#if 0
char *filepath = "../data/fly_neuron_n2/graph_d.swc";
Neuron_Structure *ns = Neuron_Structure_From_Swc_File(filepath);
Neuron_Component_Arraylist *comp_array =
Neuron_Structure_Branch_Point(ns);
filepath = "../data/fly_neuron_n2.tif";
Stack *stack = Read_Stack(filepath);
Translate_Stack(stack, COLOR, 1);
int i;
Stack_Draw_Workspace *ws = New_Stack_Draw_Workspace();
for (i = 0; i < comp_array->length; i++) {
Neuron_Component_Draw_Stack(comp_array->array + i, stack, ws);
}
Kill_Stack_Draw_Workspace(ws);
Write_Stack("../data/test.tif", stack);
#endif
#if 0
Stack *stack = NULL;
Locseg_Chain *chain1 = Read_Locseg_Chain("../data/fly_neuron_n3/chain0.tb");
Locseg_Chain *chain2 = Read_Locseg_Chain("../data/fly_neuron_n3/chain10.tb");
Connection_Test_Workspace *ws = New_Connection_Test_Workspace();
Connection_Test_Workspace_Read_Resolution(ws, "../data/fly_neuron_n1.res");
Neurocomp_Conn conn;
conn.mode = NEUROCOMP_CONN_HL;
Locseg_Chain_Connection_Test(chain1, chain2, stack, 1.0, &conn, ws);
Print_Neurocomp_Conn(&conn);
#endif
#if 0
Locseg_Chain **chain = (Locseg_Chain**) malloc(sizeof(Locseg_Chain*) * 3);
chain[0] = Read_Locseg_Chain("../data/mouse_single_org/chain4.tb");
chain[1] = Read_Locseg_Chain("../data/mouse_single_org/chain19.tb");
chain[2] = Read_Locseg_Chain("../data/mouse_single_org/chain64.tb");
Stack *signal = Read_Stack("../data/mouse_single_org.tif");
Connection_Test_Workspace *ctw = New_Connection_Test_Workspace();
FILE *fp = fopen("../data/mouse_single_org.res", "r");
darray_fscanf(fp, ctw->resolution, 3);
Neuron_Component *chain_array = Make_Neuron_Component_Array(3);
int i;
for (i = 0; i < 3; i++) {
Set_Neuron_Component(chain_array + i,
NEUROCOMP_TYPE_LOCSEG_CHAIN, chain[i]);
}
Neuron_Structure *ns = Locseg_Chain_Comp_Neurostruct(chain_array,
3, signal, 1.0, ctw);
Graph *graph = ns->graph;
Process_Neuron_Structure(ns);
Print_Neuron_Structure(ns);
Neuron_Structure_Crossover_Test(ns, 0.5375);
printf("\ncross over changed: \n");
Print_Neuron_Structure(ns);
#endif
#if 0
Neuron_Structure *ns = Make_Neuron_Structure(5);
Set_Neuron_Component(ns->comp, NEUROCOMP_TYPE_GEO3D_CIRCLE,
New_Geo3d_Circle());
Set_Neuron_Component(ns->comp + 1, NEUROCOMP_TYPE_GEO3D_CIRCLE,
New_Geo3d_Circle());
Set_Neuron_Component(ns->comp + 2, NEUROCOMP_TYPE_GEO3D_CIRCLE,
New_Geo3d_Circle());
Set_Neuron_Component(ns->comp + 3, NEUROCOMP_TYPE_GEO3D_CIRCLE,
New_Geo3d_Circle());
Set_Neuron_Component(ns->comp + 4, NEUROCOMP_TYPE_GEO3D_CIRCLE,
New_Geo3d_Circle());
NEUROCOMP_GEO3D_CIRCLE(ns->comp)->radius = 1.5;
NEUROCOMP_GEO3D_CIRCLE(ns->comp + 1)->radius = 2.5;
NEUROCOMP_GEO3D_CIRCLE(ns->comp + 2)->radius = 3.5;
NEUROCOMP_GEO3D_CIRCLE(ns->comp + 3)->radius = 4.5;
NEUROCOMP_GEO3D_CIRCLE(ns->comp + 4)->radius = 5.5;
ns->graph = Make_Graph(5, 4, 0);
//Graph_Add_Edge(ns->graph, 0, 1);
Graph_Add_Edge(ns->graph, 1, 3);
Graph_Add_Edge(ns->graph, 1, 4);
Graph_Add_Edge(ns->graph, 0, 2);
Graph_Set_Directed(ns->graph, TRUE);
Print_Graph(ns->graph);
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns, 1.0, NULL);
Print_Swc_Tree(tree);
Swc_Tree_To_Dot_File(tree, "../data/test2.dot");
#endif
#if 0
int n;
Neuron_Component *chain_array = Dir_Locseg_Chain_Nc("../data/fly_neuron_n22",
"^chain.*\\.tb",
&n, NULL);
Neuron_Structure *ns =
Locseg_Chain_Comp_Neurostruct(chain_array, n, NULL, 1.0, NULL);
Process_Neuron_Structure(ns);
Neuron_Structure* ns2=
Neuron_Structure_Locseg_Chain_To_Circle(ns);
Neuron_Structure_To_Tree(ns2);
Graph_To_Dot_File(ns2->graph, "../data/test.dot");
Swc_Tree *tree =
Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, NULL);
Swc_Tree_Remove_Zigzag(tree);
//Swc_Tree_Tune_Fork(tree);
//Print_Swc_Tree(tree);
Write_Swc_Tree("../data/test.swc", tree);
#endif
#if 0
Graph *graph = Neuron_Structure_Import_Xml_Graph("../data/mouse_single_org/trueconn2.xml");
Graph_Normalize_Edge(graph);
Graph_Remove_Duplicated_Edge(graph);
Graph *graph2 = Neuron_Structure_Import_Xml_Graph("../data/mouse_single_org/conn.xml");
Graph_Normalize_Edge(graph2);
Graph_Remove_Duplicated_Edge(graph2);
Graph_Workspace *gw = New_Graph_Workspace();
int n = Graph_Edge_Count(graph, graph2->edges, graph2->nedge, gw);
printf("fp: %d\n", graph2->nedge - n);
printf("tp: %d\n", n);
printf("fn: %d\n", graph->nedge - n);
double p = (double) n / graph2->nedge;
double r = (double) n / graph->nedge;
printf("precision: %g\n", p);
printf("recall: %g\n", r);
printf("F-measure: %g\n", 2.0 * (p * r) / (p + r));
#endif
#if 0
Neuron_Structure *ns = Make_Neuron_Structure(2);
Local_Neuroseg *locseg = New_Local_Neuroseg();
Locseg_Chain *chain1 = New_Locseg_Chain();
Locseg_Chain_Add(chain1, locseg, NULL, DL_TAIL);
Set_Neuron_Component(ns->comp, NEUROCOMP_TYPE_LOCSEG_CHAIN, chain1);
Locseg_Chain *chain2 = New_Locseg_Chain();
locseg = New_Local_Neuroseg();
double bottom[3] = {10, 10, 5};
double top[3] = {5, 5, 5};
Local_Neuroseg_Set_Bottom_Top(locseg, bottom, top);
Locseg_Chain_Add(chain2, locseg, NULL, DL_TAIL);
Set_Neuron_Component(ns->comp + 1, NEUROCOMP_TYPE_LOCSEG_CHAIN, chain2);
Neurocomp_Conn *conn = New_Neurocomp_Conn();
Connection_Test_Workspace *ctw = New_Connection_Test_Workspace();
Locseg_Chain_Connection_Test(chain2, chain1, NULL, 1.0, conn, ctw);
Neuron_Structure_Add_Conn(ns, 1, 0, conn);
Print_Neuron_Structure(ns);
Neuron_Structure *ns2 =
Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
Neuron_Structure_To_Swc_File(ns2, "../data/test.swc");
#endif
#if 0
int n;
Locseg_Chain **chain_array = Dir_Locseg_Chain_Nd("../data/diadem_a1_part3",
"^chain.*\\.tb", &n, NULL);
/*
Locseg_Chain **chain_array =
Locseg_Chain_Import_List("../data/diadem_a1_part2/good_tube.txt", &n);
*/
//n = 100;
/*
Locseg_Chain **chain_array =
(Locseg_Chain**) malloc(sizeof(Locseg_Chain*) * 2);
n = 2;
chain_array[0] = Read_Locseg_Chain("../data/diadem_a1_part2/chain58.tb");
chain_array[1] = Read_Locseg_Chain("../data/diadem_a1_part2/chain154.tb");
*/
Stack *stack = Read_Stack("../data/diadem_a1_part3.tif");
Stack *mask = Make_Stack(GREY, stack->width, stack->height, stack->depth);
Zero_Stack(mask);
Sp_Grow_Workspace *sgw = New_Sp_Grow_Workspace();
sgw->size = Stack_Voxel_Number(stack);
sgw->resolution[0] = 0.0375 * 2.0;
sgw->resolution[1] = 0.0375 * 2.0;
sgw->resolution[2] = 0.33;
Sp_Grow_Workspace_Set_Mask(sgw, mask->array);
sgw->wf = Stack_Voxel_Weight_S;
Stack_Sp_Grow_Infer_Parameter(sgw, stack);
Neuron_Structure *ns =
Locseg_Chain_Sp_Grow_Reconstruct(chain_array, n, stack, 1.0, sgw);
Print_Neuron_Structure(ns);
Graph_To_Dot_File(ns->graph, "../data/test.dot");
//Neuron_Structure_To_Swc_File(ns, "../data/test.swc");
Neuron_Structure *ns2 =
Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
//double root[3] = {31, 430, 0};
double root[3] = {1221, 449, 8.5};
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, root);
Swc_Tree_Clean_Root(tree);
Swc_Tree_Resort_Id(tree);
Write_Swc_Tree("../data/test.swc", tree);
#endif
#if 0
int n;
Locseg_Chain **chain_array = Dir_Locseg_Chain_Nd("../data/diadem_e1",
"^chain.*\\.tb", &n, NULL);
//n = 100;
/*
Locseg_Chain **chain_array =
(Locseg_Chain**) malloc(sizeof(Locseg_Chain*) * 2);
n = 2;
chain_array[0] = Read_Locseg_Chain("../data/diadem_a1_part2/chain58.tb");
chain_array[1] = Read_Locseg_Chain("../data/diadem_a1_part2/chain154.tb");
*/
Stack *stack = Read_Stack("../data/diadem_e1.tif");
Stack *mask = Make_Stack(GREY, stack->width, stack->height, stack->depth);
Zero_Stack(mask);
Sp_Grow_Workspace *sgw = New_Sp_Grow_Workspace();
sgw->size = Stack_Voxel_Number(stack);
sgw->resolution[0] = 0.3296485;
sgw->resolution[1] = 0.3296485;
sgw->resolution[2] = 1.0;
Sp_Grow_Workspace_Set_Mask(sgw, mask->array);
sgw->wf = Stack_Voxel_Weight_S;
Stack_Sp_Grow_Infer_Parameter(sgw, stack);
Neuron_Structure *ns =
Locseg_Chain_Sp_Grow_Reconstruct(chain_array, n, stack, 1.0, sgw);
Print_Neuron_Structure(ns);
//Neuron_Structure_To_Swc_File(ns, "../data/test.swc");
Neuron_Structure *ns2 =
Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
Graph_To_Dot_File(ns2->graph, "../data/test.dot");
double root[3] = {31, 430, 0};
//double root[3] = {4882, 1797, 19};
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, root);
//Swc_Tree_Clean_Root(tree);
Swc_Tree_Resort_Id(tree);
Write_Swc_Tree("../data/test2.swc", tree);
#endif
#if 0
int n;
Locseg_Chain **chain_array =
Dir_Locseg_Chain_Nd("../data/benchmark/stack_graph/fork", "^chain.*\\.tb",
&n, NULL);
Stack *stack = Read_Stack("../data/benchmark/stack_graph/fork/fork.tif");
Stack *mask = Make_Stack(GREY, stack->width, stack->height, stack->depth);
Zero_Stack(mask);
Sp_Grow_Workspace *sgw = New_Sp_Grow_Workspace();
sgw->size = Stack_Voxel_Number(stack);
Sp_Grow_Workspace_Set_Mask(sgw, mask->array);
sgw->wf = Stack_Voxel_Weight_S;
Stack_Sp_Grow_Infer_Parameter(sgw, stack);
Neuron_Structure *ns =
Locseg_Chain_Sp_Grow_Reconstruct(chain_array, n, stack, 1.0, sgw);
Neuron_Structure *ns2 =
Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, NULL);
//Swc_Tree_Clean_Root(tree);
Swc_Tree_Resort_Id(tree);
Write_Swc_Tree("../data/test.swc", tree);
#endif
#if 0
int n = 3;
Locseg_Chain **chain_array =
(Locseg_Chain**) malloc(sizeof(Locseg_Chain) * n);
chain_array[0] = Read_Locseg_Chain("/Users/zhaot/Work/neurolabi/data/benchmark/stack_graph/fork/chain0.tb");
chain_array[1] = Read_Locseg_Chain("/Users/zhaot/Work/neurolabi/data/benchmark/stack_graph/fork/chain1.tb");
chain_array[2] = New_Locseg_Chain();
printf("%d\n", Locseg_Chain_Is_Empty(chain_array[2]));
Stack *stack = Read_Stack("../data/benchmark/stack_graph/fork/fork.tif");
Stack *mask = Make_Stack(GREY, stack->width, stack->height, stack->depth);
Zero_Stack(mask);
Sp_Grow_Workspace *sgw = New_Sp_Grow_Workspace();
sgw->size = Stack_Voxel_Number(stack);
Sp_Grow_Workspace_Set_Mask(sgw, mask->array);
sgw->wf = Stack_Voxel_Weight_S;
Stack_Sp_Grow_Infer_Parameter(sgw, stack);
Neuron_Structure *ns =
Locseg_Chain_Sp_Grow_Reconstruct(chain_array, n, stack, 1.0, sgw);
Neuron_Structure *ns2 =
Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, NULL);
//Swc_Tree_Clean_Root(tree);
Swc_Tree_Remove_Zigzag(tree);
Swc_Tree_Resort_Id(tree);
Write_Swc_Tree("../data/test2.swc", tree);
#endif
#if 0
Neuron_Structure *ns = New_Neuron_Structure();
ns->graph = New_Graph();
Graph_Add_Edge(ns->graph, 0, 1);
Graph_Add_Edge(ns->graph, 0, 2);
Graph_Add_Edge(ns->graph, 2, 3);
Graph_Add_Edge(ns->graph, 2, 4);
Graph_Add_Edge(ns->graph, 4, 5);
Graph_Add_Edge(ns->graph, 5, 6);
ns->conn = (Neurocomp_Conn*) malloc(sizeof(Neurocomp_Conn) * ns->graph->nedge);
ns->conn[0].info[0] = 0;
ns->conn[0].info[1] = 0;
ns->conn[0].cost = 0.0;
ns->conn[0].mode = NEUROCOMP_CONN_LINK;
ns->conn[1].info[0] = 1;
ns->conn[1].info[1] = 1;
ns->conn[1].cost = 0.0;
ns->conn[1].mode = NEUROCOMP_CONN_LINK;
ns->conn[2].info[0] = 0;
ns->conn[2].info[1] = 0;
ns->conn[2].cost = 0.0;
ns->conn[2].mode = NEUROCOMP_CONN_LINK;
ns->conn[3].info[0] = 1;
ns->conn[3].info[1] = 0;
ns->conn[3].cost = 1.0;
ns->conn[3].mode = NEUROCOMP_CONN_HL;
ns->conn[4].info[0] = 0;
ns->conn[4].info[1] = 1;
ns->conn[4].cost = 0.0;
ns->conn[4].mode = NEUROCOMP_CONN_LINK;
ns->conn[5].info[0] = 1;
ns->conn[5].info[1] = 1;
ns->conn[5].cost = 1.0;
ns->conn[5].mode = NEUROCOMP_CONN_LINK;
Neuron_Structure_Merge_Locseg_Chain(ns);
#endif
#if 0
Neuron_Structure *ns = New_Neuron_Structure();
ns->graph = New_Graph();
ns->comp = Dir_Locseg_Chain_Nc("../data/diadem_e3", "^chain.*\\.tb",
&(ns->graph->nvertex), NULL);
Graph_Add_Edge(ns->graph, 0, 1);
Graph_Add_Edge(ns->graph, 0, 2);
Graph_Add_Edge(ns->graph, 2, 3);
Graph_Add_Edge(ns->graph, 3, 4);
Graph_Add_Edge(ns->graph, 4, 5);
ns->conn = (Neurocomp_Conn*) malloc(sizeof(Neurocomp_Conn) * ns->graph->nedge);
ns->conn[0].info[0] = 0;
ns->conn[0].info[1] = 0;
ns->conn[0].cost = 0.0;
ns->conn[0].mode = NEUROCOMP_CONN_LINK;
ns->conn[1].info[0] = 0;
ns->conn[1].info[1] = 0;
ns->conn[1].cost = 0.0;
ns->conn[1].mode = NEUROCOMP_CONN_LINK;
ns->conn[2].info[0] = 0;
ns->conn[2].info[1] = 0;
ns->conn[2].cost = 1.0;
ns->conn[2].mode = NEUROCOMP_CONN_LINK;
ns->conn[3].info[0] = 0;
ns->conn[3].info[1] = 0;
ns->conn[3].cost = 2.0;
ns->conn[3].mode = NEUROCOMP_CONN_LINK;
ns->conn[4].info[0] = 0;
ns->conn[4].info[1] = 0;
ns->conn[4].cost = 0.0;
ns->conn[4].mode = NEUROCOMP_CONN_LINK;
int i;
for (i = 0; i < ns->graph->nvertex; i++) {
printf("%d ", Locseg_Chain_Length(NEUROCOMP_LOCSEG_CHAIN(ns->comp+i)));
}
printf("\n");
Neuron_Structure_Merge_Locseg_Chain(ns);
for (i = 0; i < ns->graph->nvertex; i++) {
printf("%d ", Locseg_Chain_Length(NEUROCOMP_LOCSEG_CHAIN(ns->comp+i)));
}
printf("\n");
#endif
#if 0
int n;
Locseg_Chain **chain_array = Dir_Locseg_Chain_Nd("../data/diadem_e1",
"^chain.*\\.tb", &n, NULL);
Stack *stack = Read_Stack("../data/diadem_e1.tif");
Stack *mask = Make_Stack(GREY, stack->width, stack->height, stack->depth);
Zero_Stack(mask);
Sp_Grow_Workspace *sgw = New_Sp_Grow_Workspace();
sgw->size = Stack_Voxel_Number(stack);
sgw->resolution[0] = 0.3296485;
sgw->resolution[1] = 0.3296485;
sgw->resolution[2] = 1.0;
Sp_Grow_Workspace_Set_Mask(sgw, mask->array);
sgw->wf = Stack_Voxel_Weight_S;
Stack_Sp_Grow_Infer_Parameter(sgw, stack);
Neuron_Structure *ns =
Locseg_Chain_Sp_Grow_Reconstruct(chain_array, n, stack, 1.0, sgw);
Neuron_Structure_Merge_Locseg_Chain(ns);
int i;
char filepath[100];
for (i = 0; i < ns->graph->nvertex; i++) {
Locseg_Chain_Regularize(NEUROCOMP_LOCSEG_CHAIN(ns->comp+i));
if (Locseg_Chain_Is_Empty(NEUROCOMP_LOCSEG_CHAIN(ns->comp+i)) == FALSE) {
sprintf(filepath, "../data/tmp/chain%d.tb", i);
Write_Locseg_Chain(filepath, NEUROCOMP_LOCSEG_CHAIN(ns->comp+i));
}
}
#endif
#if 0
Stack *stack = Read_Stack("../data/benchmark/fork2/fork2.tif");
Neuron_Structure *ns = New_Neuron_Structure();
ns->graph = New_Graph();
ns->comp = Dir_Locseg_Chain_Nc("../data/benchmark/fork2/tubes",
"^chain.*\\.tb", &(ns->graph->nvertex), NULL);
coordinate_3d_t roots[3];
roots[0][0] = 51;
roots[0][1] = 23;
roots[0][2] = 60;
roots[1][0] = 51;
roots[1][1] = 23;
roots[1][2] = 40;
roots[2][0] = 25;
roots[2][1] = 76;
roots[2][2] = 60;
Neuron_Structure_Break_Root(ns, roots, 3);
Neuron_Structure_Load_Root(ns, roots, 3);
Connection_Test_Workspace *ctw = New_Connection_Test_Workspace();
ctw->dist_thre = 100.0;
ctw->sp_test = FALSE;
Locseg_Chain_Comp_Neurostruct_W(ns, stack, 1.0, ctw);
Process_Neuron_Structure(ns);
Neuron_Structure_To_Tree(ns);
/*
Neuron_Structure_Remove_Conn(ns, 0, 2);
Neuron_Structure_Remove_Conn(ns, 2, 0);
*/
Neuron_Structure_Remove_Negative_Conn(ns);
Neuron_Structure* ns2= NULL;
ns2 = Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
Neuron_Structure_To_Tree(ns2);
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, NULL);
Swc_Tree_Resort_Id(tree);
Write_Swc_Tree("../data/test3.swc", tree);
#endif
#if 1
Stack *stack = NULL;
Locseg_Chain *chain1 = Read_Locseg_Chain("../data/benchmark/diadem/diadem_e1/chain22.tb");
Locseg_Chain *chain2 = Read_Locseg_Chain("../data/benchmark/diadem/diadem_e1/chain0.tb");
Connection_Test_Workspace *ws = New_Connection_Test_Workspace();
Connection_Test_Workspace_Read_Resolution(ws, "../data/diadem_e3.res");
Neurocomp_Conn conn;
conn.mode = NEUROCOMP_CONN_HL;
Locseg_Chain_Connection_Test(chain1, chain2, stack, 1.0, &conn, ws);
Print_Neurocomp_Conn(&conn);
#endif
return 0;
}
/*
* trace_neuron - trace neuron from given seeds
*
* trace_neuron [!wtr] seed_file -Dsave_dir
* -r: write intermediate results
*
*/
int main(int argc, char* argv[])
{
static char *Spec[] = {
"[!wtr] [-canvas <string>] [-mask <string>] [-res <string>] [-minr <int>]",
"-minlen <double>",
" <image:string> -S<string> -D<string>",
NULL};
Process_Arguments(argc, argv, Spec, 1);
char *dir = Get_String_Arg("-D");
char file_path[100];
sprintf(file_path, "%s/%s", dir, Get_String_Arg("-S"));
printf("%s\n", file_path);
Geo3d_Scalar_Field *seed = Read_Geo3d_Scalar_Field(file_path);
int idx;
sprintf(file_path, "%s/%s.bn", dir, "max_r");
double max_r;
int tmp;
if (fexist(file_path)) {
darray_read2(file_path, &max_r, &tmp);
} else {
max_r = darray_max(seed->values, seed->size, &idx);
}
printf("%g\n", max_r);
max_r *= 1.5;
/*
sprintf(file_path, "%s/%s", dir, "soma0.bn");
if (!fexist(file_path)) {
max_r *= 2.0;
}
*/
Set_Neuroseg_Max_Radius(max_r);
Stack *signal = Read_Stack(Get_String_Arg("image"));
dim_type dim[3];
dim[0] = signal->width;
dim[1] = signal->height;
dim[2] = signal->depth;
/*
IMatrix *chord = Make_IMatrix(dim, 3);
Stack *code = Make_Stack(GREY16,
signal->width, signal->height, signal->depth);
*/
Rgb_Color color;
Set_Color(&color, 255, 0, 0);
Stack *canvas = NULL;
char trace_file_path[100];
sprintf(trace_file_path, "%s/%s", dir, Get_String_Arg("-canvas"));
if (fexist(trace_file_path) == 1) {
canvas = Read_Stack((char *) trace_file_path);
} else {
canvas = Copy_Stack(signal);
Stretch_Stack_Value_Q(canvas, 0.999);
Translate_Stack(canvas, COLOR, 1);
}
Stack *traced = NULL;
char trace_mask_path[100];
sprintf(trace_mask_path, "%s/%s", dir, Get_String_Arg("-mask"));
if (fexist(trace_mask_path) == 1) {
traced = Read_Stack((char *) trace_mask_path);
} else {
traced = Make_Stack(GREY, signal->width, signal->height, signal->depth);
One_Stack(traced);
}
//Object_3d *obj = NULL;
int seed_offset = -1;
Neurochain *chain = NULL;
double z_scale = 1.0;
if (Is_Arg_Matched("-res")) {
sprintf(file_path, "%s", Get_String_Arg("-res"));
if (fexist(file_path)) {
double res[3];
int length;
darray_read2(file_path, res, &length);
if (res[0] != res[1]) {
perror("Different X-Y resolutions.");
TZ_ERROR(ERROR_DATA_VALUE);
}
z_scale = res[0] / res[2];
}
}
//sprintf(file_path, "%s/%s", dir, Get_String_Arg("-M"));
//Stack *stack = Read_Stack(file_path);
tic();
FILE *fp = NULL;
char chain_file_path[100];
char vrml_file_path[100];
double min_chain_length = 25.0;
if (Is_Arg_Matched("-minlen")) {
min_chain_length = Get_Double_Arg("-minlen");
}
int *indices = iarray_malloc(seed->size);
double *values = darray_malloc(seed->size);
int i;
Local_Neuroseg *locseg = (Local_Neuroseg *)
malloc(seed->size * sizeof(Local_Neuroseg));
int index = 0;
for (i = 0; i < seed->size; i++) {
printf("-----------------------------> seed: %d / %d\n", i, seed->size);
indices[i] = i;
index = i;
int x = (int) seed->points[index][0];
int y = (int) seed->points[index][1];
int z = (int) seed->points[index][2];
double width = seed->values[index];
chain = New_Neurochain();
seed_offset = Stack_Util_Offset(x, y, z, signal->width, signal->height,
signal->depth);
if (width < 3.0) {
width += 0.5;
}
Set_Neuroseg(&(locseg[i].seg), width, width, 12.0,
0.0, 0.0, 0.0);
double cpos[3];
cpos[0] = x;
cpos[1] = y;
cpos[2] = z;
cpos[2] *= z_scale;
Set_Neuroseg_Position(&(locseg[i]), cpos, NEUROSEG_CENTER);
Stack_Fit_Score fs;
fs.n = 1;
fs.options[0] = 1;
values[i] = Local_Neuroseg_Orientation_Search_C(&(locseg[i]), signal, z_scale, &fs);
}
darray_qsort(values, indices, seed->size);
/*
for (i = 0; i < seed->size; i++) {
indices[i] = i;
}
darraycpy(values, seed->values, 0, seed->size);
darray_qsort(values, indices, seed->size);
*/
int counter = 0;
// for (i = seed->size - 1; i >= seed->size - 231; i--) {
for (i = seed->size - 1; i >= 0; i--) {
index = indices[i];
printf("-----------------------------> seed: %d / %d\n", i, seed->size);
sprintf(chain_file_path, "%s/chain%d.bn", dir, index);
sprintf(vrml_file_path, "%s/chain%d.wrl", dir, index);
if (fexist(chain_file_path) == 1) {
chain = Read_Neurochain(chain_file_path);
if (Neurochain_Geolen(chain) >= min_chain_length) {
Write_Neurochain_Vrml(vrml_file_path, chain);
Neurochain_Label(canvas, chain, z_scale);
Neurochain_Erase_E(traced, chain, z_scale, 0,
Neurochain_Length(chain, FORWARD),
1.5, 0.0);
}
Free_Neurochain(chain);
printf("chain exists\n");
continue;
}
int x = (int) seed->points[index][0];
int y = (int) seed->points[index][1];
int z = (int) seed->points[index][2];
if (*STACK_PIXEL_8(traced, x, y, z, 0) == 0) {
printf("traced \n");
continue;
}
double width = seed->values[index];
if (width > max_r) {
printf("too thick\n");
continue;
}
if (Is_Arg_Matched("-minr")) {
int max_level = (int) (width + 0.5);
if (max_level <= Get_Int_Arg("-minr")) {
printf("too thin\n");
continue;
}
}
/*
seed_offset = Stack_Util_Offset(x, y, z, signal->width, signal->height,
signal->depth);
*/
chain = New_Neurochain();
/*
Stack_Level_Code_Constraint(stack, code, chord->array, &seed_offset, 1,
max_level + 1);
Voxel_t v;
v[0] = x;
v[1] = y;
v[2] = z;
Stack *tmp_stack = Copy_Stack(stack);
obj = Stack_Grow_Object_Constraint(tmp_stack, 1, v, chord, code,
max_level);
Free_Stack(tmp_stack);
Print_Object_3d_Info(obj);
double vec[3];
Object_3d_Orientation_Zscale(obj, vec, MAJOR_AXIS, z_scale);
double theta, psi;
Geo3d_Vector obj_vec;
Set_Geo3d_Vector(&obj_vec, vec[0], vec[1], vec[2]);
Geo3d_Vector_Orientation(&obj_vec, &theta, &psi);
*/
/*
if (width < 3.0) {
width += 0.5;
}
Set_Neuroseg(&(chain->locseg.seg), width, width, 12.0,
0.0, 0.0, 0.0);
double cpos[3];
cpos[0] = x;
cpos[1] = y;
cpos[2] = z;
cpos[2] *= z_scale;
//Set_Neuroseg_Position(&(chain->locseg), cpos, NEUROSEG_BOTTOM);
Set_Neuroseg_Position(&(chain->locseg), cpos, NEUROSEG_CENTER);
Stack_Fit_Score fs;
fs.n = 1;
fs.options[0] = 1;
Local_Neuroseg_Orientation_Search_C(&(chain->locseg), signal, z_scale,
&fs);
//fs.options[0] = 1;
*/
Copy_Local_Neuroseg(&(chain->locseg), &(locseg[index]));
Neurochain *chain_head = chain;
if (Initialize_Tracing(signal, chain, NULL, z_scale) >= MIN_SCORE) {
if ((Neuroseg_Hit_Traced(&(chain->locseg), traced, z_scale) == FALSE) &&
(chain->locseg.seg.r1 < max_r) &&
(chain->locseg.seg.r2 < max_r)) {
//Initialize_Tracing(signal, chain, NULL, z_scale);
chain = Trace_Neuron2(signal, chain, BOTH, traced, z_scale, 500);
//Neurochain *chain_head = Neurochain_Head(chain);
chain_head = Neurochain_Remove_Overlap_Segs(chain);
chain_head = Neurochain_Remove_Turn_Ends(chain_head, 0.5);
/*
if (i == seed->size - 231) {
Print_Neurochain(chain_head);
}
*/
fp = fopen(chain_file_path, "w");
Neurochain_Fwrite(chain_head, fp);
fclose(fp);
if (Neurochain_Geolen(chain_head) >= min_chain_length) {
Write_Neurochain_Vrml(vrml_file_path, chain_head);
Neurochain_Erase_E(traced, chain_head, z_scale, 0,
Neurochain_Length(chain_head, FORWARD),
1.5, 0.0);
Neurochain_Label(canvas, chain_head, z_scale);
counter += Neurochain_Length(chain_head, FORWARD);
if (counter > 500) {
if (Is_Arg_Matched("-r")) {
Write_Stack((char *) trace_mask_path, traced);
}
if (Is_Arg_Matched("-r")) {
Write_Stack((char *) trace_file_path, canvas);
}
counter = 0;
}
}
}
}
Free_Neurochain(chain_head);
//Kill_Object_3d(obj);
}
Write_Stack((char *) trace_file_path, canvas);
if (Is_Arg_Matched("-r")) {
Write_Stack((char *) trace_mask_path, traced);
}
Kill_Geo3d_Scalar_Field(seed);
printf("Time passed: %lld\n", toc());
return 0;
}
