Stack *transpose_copy_uint8( Stack *s )
/* not optimized */
{ Stack *out;
int x,y,z;
if( s->kind != GREY8 )
{ error( "Only GREY8 images currently supported.\n" );
goto error;
}
out = Make_Stack( s->kind, s->height, s->width, s->depth);
for( x=0; x< (s->width); x++)
for( y=0; y< (s->height); y++)
for( z=0; z< (s->depth); z++)
*STACK_PIXEL_8( out,y,x,z,0 ) = *STACK_PIXEL_8( s,x,y,z,0 );
return out;
error:
return (NULL);
}
/*
* 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;
}
