Geo3d_Scalar_Field* ZNeuronTracer::extractSeedOriginal(const Stack *mask)
{
/* alloc <dist> */
Stack *dist = Stack_Bwdist_L_U16(mask, NULL, 0);
/* alloc <seeds> */
Stack *seeds = Stack_Local_Max(dist, NULL, STACK_LOCMAX_CENTER);
/* alloc <list> */
Voxel_List *list = Stack_To_Voxel_List(seeds);
/* alloc <pa> */
Pixel_Array *pa = Voxel_List_Sampling(dist, list);
/* free <dist> */
C_Stack::kill(dist);
/* alloc <voxel_array> */
Voxel_P *voxel_array = Voxel_List_To_Array(list, 1, NULL, NULL);
//double *pa_array = (double *) pa->array;
uint16 *pa_array = (uint16 *) pa->array;
printf("%d seeds found.\n", pa->size);
/* alloc field */
Geo3d_Scalar_Field *field = Make_Geo3d_Scalar_Field(pa->size);
field->size = 0;
int i;
for (i = 0; i < pa->size; i++) {
if (IS_IN_OPEN_RANGE3(voxel_array[i]->x, voxel_array[i]->y,
voxel_array[i]->z, 0, seeds->width - 1,
0, seeds->height - 1, 0, seeds->depth - 1)) {
field->points[field->size][0] = voxel_array[i]->x;
field->points[field->size][1] = voxel_array[i]->y;
field->points[field->size][2] = voxel_array[i]->z;
field->values[field->size] = sqrt((double)pa_array[i]);
field->size++;
}
}
/* free <list> */
Kill_Voxel_List(list);
/* free <pa> */
Kill_Pixel_Array(pa);
/* free <voxel_array> */
free(voxel_array);
/* free <seeds> */
C_Stack::kill(seeds);
/* return <field> */
return field;
}
Geo3d_Scalar_Field* ZNeuronTracer::extractSeedSkel(const Stack *mask)
{
Stack *skel = Stack_Bwthin(mask, NULL);
/* alloc <dist> */
Stack *dist = Stack_Bwdist_L_U16(mask, NULL, 0);
ZStackProcessor::RemoveBranchPoint(skel, 26);
Stack *skel_proc = C_Stack::clone(skel);
Geo3d_Scalar_Field *field1 = extractLineSeed(skel_proc, dist);
C_Stack::kill(skel_proc);
for (int i = 0; i <field1->size; ++i) {
int x = field1->points[i][0];
int y = field1->points[i][1];
int z = field1->points[i][2];
Set_Stack_Pixel(skel, x, y, z, 0, 0);
}
#ifdef _DEBUG_2
C_Stack::write(GET_TEST_DATA_DIR + "/test.tif", skel);
#endif
Geo3d_Scalar_Field *field2 = extractLineSeed(skel, dist, 0);
Geo3d_Scalar_Field *field = Geo3d_Scalar_Field_Merge(field1, field2, NULL);
Kill_Geo3d_Scalar_Field(field1);
Kill_Geo3d_Scalar_Field(field2);
#ifdef _DEBUG_2
ZSwcTree tree;
tree.forceVirtualRoot();
for (int i = 0; i <field->size; ++i) {
int x = field->points[i][0];
int y = field->points[i][1];
int z = field->points[i][2];
double radius = field->values[i];
SwcTreeNode::setFirstChild(
tree.root(), SwcTreeNode::makePointer(x, y, z, radius));
}
tree.save(GET_TEST_DATA_DIR + "/test.swc");
#endif
/* free <dist> */
C_Stack::kill(dist);
C_Stack::kill(skel);
return field;
}
/*
* 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[])
{
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;
}
