Stack_Tile* Read_Stack_Tile(const char *filePath)
{
#ifdef HAVE_LIBXML2
Stack_Document *stack_doc = Xml_Read_Stack_Document(filePath);
Stack *stack = NULL;
Stack_Tile *tile = NULL;
if (stack_doc != NULL) {
stack = Import_Stack_Document(stack_doc);
if (stack != NULL) {
tile = Make_Stack_Tile(stack, stack_doc->offset);
}
Kill_Stack_Document(stack_doc);
}
return tile;
#else
TZ_ERROR(ERROR_NA_FUNC);
return NULL;
#endif
}
int main(int argc, char *argv[])
{
if (Show_Version(argc, argv, "1.0") == 1) {
return 0;
}
static char *Spec[] = {
"[-R<string> -T<string> -M<string>] -D<string> [-minlen <double>]",
"[-root <double> <double> <double>] [-trans <double> <double> <double>]",
"[-rtlist <string>] [-sup_root] [-dist <double>]",
"[-C<string>] [-I<string>] [-z <double>] -o <string> [-b] [-res <string>]",
"[-screen] [-sp] [-intp] [-sl] [-rb] [-rz] [-rs] [-ct] [-al <double>]",
"[-screenz <double>] [-force_merge <double>] [-ct_break <double>]",
"[-jumpz <double>] [-single_break]",
NULL};
Print_Arguments(argc, argv);
Process_Arguments(argc, argv, Spec, 1);
char *dir = Get_String_Arg("-D");
Stack_Document *stack_doc = NULL;
if (Is_Arg_Matched("-I")) {
if (!fexist(Get_String_Arg("-I"))) {
PRINT_EXCEPTION("File does not exist", "");
fprintf(stderr, "%s cannot be found.\n", Get_String_Arg("-I"));
return 1;
}
if (fhasext(Get_String_Arg("-I"), "xml")) {
stack_doc = Xml_Read_Stack_Document(Get_String_Arg("-I"));
}
}
/* Get number of chains */
int chain_number2 = dir_fnum_p(dir, "^chain.*\\.tb");
if (chain_number2 == 0) {
printf("No tube found.\n");
printf("Quit reconstruction.\n");
return 1;
}
int i;
int *chain_map = iarray_malloc(chain_number2);
int chain_number;
Locseg_Chain **chain_array =
Dir_Locseg_Chain_Nd(dir, "chain.*\\.tb", &chain_number, chain_map);
if (Is_Arg_Matched("-screenz")) {
Locseg_Chain_Array_Screen_Z(chain_array, chain_number,
Get_Double_Arg("-screenz"));
}
if (Is_Arg_Matched("-single_break")) {
int i;
for (i = 0; i < chain_number; i++) {
if (Locseg_Chain_Length(chain_array[i]) == 1) {
/* break the segment into two parts */
Locseg_Chain_Break_Node(chain_array[i], 0, 0.5);
}
}
}
if (Is_Arg_Matched("-ct_break")) {
int tmp_chain_number;
Locseg_Chain **tmp_chain_array =
Locseg_Chain_Array_Break_Jump(chain_array, chain_number,
Get_Double_Arg("-ct_break"), &tmp_chain_number);
kill_locseg_chain_array(chain_array, chain_number);
chain_array = tmp_chain_array;
chain_number = tmp_chain_number;
}
Connection_Test_Workspace *ctw = New_Connection_Test_Workspace();
if (Is_Arg_Matched("-res")) {
FILE *fp = fopen(Get_String_Arg("-res"), "r");
if (fp != NULL) {
if (darray_fscanf(fp, ctw->resolution, 3) != 3) {
fprintf(stderr, "Failed to load %s\n", Get_String_Arg("-res"));
ctw->resolution[0] = 1.0;
ctw->resolution[1] = 1.0;
ctw->resolution[2] = 1.0;
} else {
ctw->unit = 'u';
}
fclose(fp);
} else {
fprintf(stderr, "Failed to load %s. The file may not exist.\n",
Get_String_Arg("-res"));
}
} else if (stack_doc != NULL) {
ctw->resolution[0] = stack_doc->resolution[0];
ctw->resolution[1] = stack_doc->resolution[1];
ctw->resolution[2] = stack_doc->resolution[2];
}
if (Is_Arg_Matched("-force_merge")) {
Connection_Test_Workspace *ws = New_Connection_Test_Workspace();
ws->dist_thre = Get_Double_Arg("-force_merge");
ws->interpolate = FALSE;
ws->resolution[2] = ctw->resolution[2] / ctw->resolution[0];
for (i = 0; i < chain_number; i++) {
//Locseg_Chain_Correct_Ends(chain_array[i]);
}
Locseg_Chain_Array_Force_Merge(chain_array, chain_number, ws);
Kill_Connection_Test_Workspace(ws);
}
chain_number2 = 0;
Neuron_Component *chain_array2;
GUARDED_MALLOC_ARRAY(chain_array2, chain_number, Neuron_Component);
for (i = 0; i < chain_number; i++) {
if (Locseg_Chain_Is_Empty(chain_array[i]) == FALSE) {
chain_map[chain_number2] = chain_map[i];
Set_Neuron_Component(chain_array2+(chain_number2++),
NEUROCOMP_TYPE_LOCSEG_CHAIN, chain_array[i]);
} else {
printf("chain_%d is empty.\n", chain_map[i]);
}
}
/*
Dir_Locseg_Chain_Nc(dir, "^chain.*\\.tb", &chain_number2, chain_map);
*/
Stack *signal = NULL;
//Stack *canvas = NULL;
if (Is_Arg_Matched("-I")) {
signal = Read_Stack_U(Get_String_Arg("-I"));
//canvas = Translate_Stack(signal, COLOR, 0);
} else {
if (Is_Arg_Matched("-screen")) {
perror("The -screen option requires -I option to be supplied.\n");
return 1;
}
}
/* Minimal tube length. */
double minlen = 25.0;
if (Is_Arg_Matched("-minlen")) {
minlen = Get_Double_Arg("-minlen");
}
chain_number = 0;
//int i;
if (signal != NULL) {
ctw->mask = Make_Stack(GREY, signal->width, signal->height, signal->depth);
One_Stack(ctw->mask);
}
FILE *result_file = fopen(full_path(dir, Get_String_Arg("-o")), "w");
double z_scale = 1.0;
if (Is_Arg_Matched("-z")) {
z_scale = Get_Double_Arg("-z");
}
/* Array to store corrected chains */
Neuron_Component *chain_array_c = Make_Neuron_Component_Array(chain_number2);
int screen = 0;
double average_intensity = 0.0;
if (Is_Arg_Matched("-screen")) {
int good_chain_number = 0;
int bad_chain_number = 0;
for (i = 0; i < chain_number2; i++) {
Locseg_Chain *chain = NEUROCOMP_LOCSEG_CHAIN(chain_array2 + i);
average_intensity += Locseg_Chain_Average_Score(chain, signal, z_scale,
STACK_FIT_MEAN_SIGNAL);
if ((Locseg_Chain_Geolen(chain) > 55) ||
(Locseg_Chain_Average_Score(chain, signal, z_scale,
STACK_FIT_CORRCOEF) > 0.6)) {
good_chain_number++;
} else {
bad_chain_number++;
}
}
printf("good %d bad %d\n", good_chain_number, bad_chain_number);
if (good_chain_number + bad_chain_number > 50) {
if (bad_chain_number > good_chain_number) {
screen = 1;
}
} else {
screen = 3;
/*
if (bad_chain_number > good_chain_number * 2) {
screen = 2;
}
*/
}
}
average_intensity /= chain_number2;
/* build chain map */
for (i = 0; i < chain_number2; i++) {
Locseg_Chain *chain = NEUROCOMP_LOCSEG_CHAIN(chain_array2 + i);
BOOL good = FALSE;
switch (screen) {
case 1:
case 2:
if ((Locseg_Chain_Geolen(chain) > 100) ||
(Locseg_Chain_Average_Score(chain, signal, z_scale,
STACK_FIT_CORRCOEF)
> 0.6)) {
good = TRUE;
} else {
if (Locseg_Chain_Geolen(chain) < 100) {
if ((Locseg_Chain_Average_Score(chain, signal, z_scale,
STACK_FIT_CORRCOEF) > 0.5) ||
(Locseg_Chain_Average_Score(chain, signal, z_scale,
STACK_FIT_MEAN_SIGNAL) >
average_intensity)) {
good = TRUE;
}
}
}
break;
case 3:
if ((Locseg_Chain_Average_Score(chain, signal, z_scale,
STACK_FIT_CORRCOEF) > 0.50) ||
(Locseg_Chain_Average_Score(chain, signal, z_scale,
STACK_FIT_MEAN_SIGNAL) >
average_intensity)) {
good = TRUE;
}
break;
default:
good = TRUE;
}
if (good == TRUE) {
if (Locseg_Chain_Geolen(chain) < minlen) {
good = FALSE;
}
}
if (good == TRUE) {
Locseg_Chain *tmpchain = chain;
if (signal != NULL) {
//Locseg_Chain_Trace_Np(signal, 1.0, tmpchain, tw);
Locseg_Chain_Erase(chain, ctw->mask, 1.0);
}
fprintf(result_file, "%d %d\n", chain_number, chain_map[i]);
chain_map[chain_number] = chain_map[i];
if (z_scale != 1.0) {
Locseg_Chain_Scale_Z(chain, z_scale);
}
Set_Neuron_Component(chain_array_c + chain_number,
NEUROCOMP_TYPE_LOCSEG_CHAIN, tmpchain);
chain_number++;
} else {
#ifdef _DEBUG_
printf("chain%d is excluded.\n", i);
/*
char tmpfile[500];
sprintf(tmpfile, "../data/diadem_c1/bad_chain/chain%d.tb", i);
Write_Locseg_Chain(tmpfile, chain);
*/
#endif
}
}
z_scale = 1.0;
fprintf(result_file, "#\n");
//Int_Arraylist *hit_spots = Int_Arraylist_New(0, chain_number);
/* reconstruct neuron */
if (Is_Arg_Matched("-res")) {
FILE *fp = fopen(Get_String_Arg("-res"), "r");
if (fp != NULL) {
if (darray_fscanf(fp, ctw->resolution, 3) != 3) {
fprintf(stderr, "Failed to load %s\n", Get_String_Arg("-res"));
ctw->resolution[0] = 1.0;
ctw->resolution[1] = 1.0;
ctw->resolution[2] = 1.0;
} else {
ctw->unit = 'u';
}
fclose(fp);
} else {
fprintf(stderr, "Failed to load %s. The file may not exist.\n",
Get_String_Arg("-res"));
}
} else if (stack_doc != NULL) {
ctw->resolution[0] = stack_doc->resolution[0];
ctw->resolution[1] = stack_doc->resolution[1];
ctw->resolution[2] = stack_doc->resolution[2];
}
if (!Is_Arg_Matched("-sp")) {
ctw->sp_test = FALSE;
if (ctw->sp_test == FALSE) {
ctw->dist_thre = NEUROSEG_DEFAULT_H / 2.0;
}
} else {
ctw->dist_thre = NEUROSEG_DEFAULT_H * 1.5;
}
if (Is_Arg_Matched("-dist")) {
ctw->dist_thre = Get_Double_Arg("-dist");
}
if (!Is_Arg_Matched("-intp")) {
ctw->interpolate = FALSE;
}
//ctw->dist_thre = 100.0;
double *tube_offset = NULL;
if (Is_Arg_Matched("-trans")) {
tube_offset = darray_malloc(3);
tube_offset[0] = Get_Double_Arg("-trans", 1);
tube_offset[1] = Get_Double_Arg("-trans", 2);
tube_offset[2] = Get_Double_Arg("-trans", 3);
} else {
if (stack_doc != NULL) {
tube_offset = darray_malloc(3);
tube_offset[0] = stack_doc->offset[0];
tube_offset[1] = stack_doc->offset[1];
tube_offset[2] = stack_doc->offset[2];
}
}
Neuron_Structure *ns = New_Neuron_Structure();
ns->comp = chain_array_c;
ns->graph = New_Graph();
ns->graph->nvertex = chain_number;
if (Is_Arg_Matched("-rtlist")) {
int m, n;
double *d = darray_load_matrix(Get_String_Arg("-rtlist"), NULL, &m, &n);
if (n > 0) {
coordinate_3d_t *roots = GUARDED_MALLOC_ARRAY(roots, n, coordinate_3d_t);
int i;
for (i = 0; i < n; i++) {
if (Is_Arg_Matched("-trans")) {
roots[i][0] = d[i*3] - tube_offset[0];
roots[i][1] = d[i*3 + 1] - tube_offset[1];
roots[i][2] = d[i*3 + 2] - tube_offset[2];
} else {
roots[i][0] = d[i*3];
roots[i][1] = d[i*3 + 1];
roots[i][2] = d[i*3 + 2];
}
}
Neuron_Structure_Break_Root(ns, roots, n);
Neuron_Structure_Load_Root(ns, roots, n);
}
}
Locseg_Chain_Comp_Neurostruct_W(ns, signal, z_scale, ctw);
if (tube_offset != NULL) {
for (i = 0; i < chain_number; i++) {
Locseg_Chain_Translate(NEUROCOMP_LOCSEG_CHAIN(chain_array_c + i),
tube_offset);
}
}
/*
Neuron_Structure *ns = Locseg_Chain_Comp_Neurostruct(chain_array,
chain_number,
signal, z_scale, ctw);
*/
FILE *tube_fp = fopen(full_path(dir, "tube.swc"), "w");
int start_id = 1;
for (i = 0; i < chain_number; i++) {
int node_type = i % 10;
int n = Locseg_Chain_Swc_Fprint_T(tube_fp,
NEUROCOMP_LOCSEG_CHAIN(chain_array_c + i),
node_type, start_id,
-1, DL_FORWARD, 1.0, NULL);
start_id += n;
}
fclose(tube_fp);
//Neuron_Structure_To_Swc_File(ns, full_path(dir, "tube.swc"));
/*
Graph *testgraph = New_Graph(0, 0, FALSE);
Int_Arraylist *cidx = Make_Int_Arraylist(0, 2);
Int_Arraylist *sidx = Make_Int_Arraylist(0, 2);
Locseg_Chain_Network_Simlify(&net, testgraph, cidx, sidx);
*/
/* Find branch points */
//Locseg_Chain *branches = Locseg_Chain_Network_Find_Branch(ns);
//Graph *graph = Locseg_Chain_Graph(chain_array, chain_number, hit_spots);
//Graph *graph = ns->graph;
if (Is_Arg_Matched("-sup_root")) {
if (Is_Arg_Matched("-rtlist")) {
int m, n;
double *d = darray_load_matrix(Get_String_Arg("-rtlist"), NULL, &m, &n);
if (n > 0) {
coordinate_3d_t *roots =
GUARDED_MALLOC_ARRAY(roots, n, coordinate_3d_t);
int i;
for (i = 0; i < n; i++) {
roots[i][0] = d[i*3];
roots[i][1] = d[i*3 + 1];
roots[i][2] = d[i*3 + 2];
/*
if (tube_offset != NULL) {
roots[i][0] += tube_offset[0];
roots[i][1] += tube_offset[1];
roots[i][2] += tube_offset[2];
}
*/
}
neuron_structure_suppress(ns, roots, n);
free(roots);
}
}
}
Process_Neuron_Structure(ns);
Print_Neuron_Structure(ns);
#ifdef _DEBUG_
for (i = 0; i < NEURON_STRUCTURE_LINK_NUMBER(ns); i++) {
printf("chain_%d (%d) -- chain_%d (%d) ",
chain_map[ns->graph->edges[i][0]],
ns->graph->edges[i][0],
chain_map[ns->graph->edges[i][1]],
ns->graph->edges[i][1]);
Print_Neurocomp_Conn(ns->conn + i);
}
#endif
if (Is_Arg_Matched("-ct")) {
Neuron_Structure_Crossover_Test(ns,
ctw->resolution[0] / ctw->resolution[2]);
}
if (Is_Arg_Matched("-al")) {
Neuron_Structure_Adjust_Link(ns, Get_Double_Arg("-al"));
}
Neuron_Structure_To_Tree(ns);
Neuron_Structure_Remove_Negative_Conn(ns);
#ifdef _DEBUG_
printf("\nTree:\n");
for (i = 0; i < NEURON_STRUCTURE_LINK_NUMBER(ns); i++) {
printf("chain_%d (%d) -- chain_%d (%d) ",
chain_map[ns->graph->edges[i][0]],
ns->graph->edges[i][0],
chain_map[ns->graph->edges[i][1]],
ns->graph->edges[i][1]);
Print_Neurocomp_Conn(ns->conn + i);
}
#endif
/*
printf("\ncross over changed: \n");
Print_Neuron_Structure(ns);
*/
#ifdef _DEBUG_2
ns->graph->nedge = 0;
Neuron_Structure_To_Swc_File(ns, "../data/test.swc");
return 1;
#endif
//Print_Neuron_Structure(ns);
Neuron_Structure* ns2= NULL;
if (Is_Arg_Matched("-intp")) {
ns2 = Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
} else {
ns2 = Neuron_Structure_Locseg_Chain_To_Circle(ns);
}
/*
Neuron_Structure* ns2=
Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
*/
Graph_To_Dot_File(ns2->graph, full_path(dir, "graph_d.dot"));
//Neuron_Structure_Main_Graph(ns2);
Neuron_Structure_To_Tree(ns2);
double root[3];
if (Is_Arg_Matched("-root")) {
root[0] = Get_Double_Arg("-root", 1);
root[1] = Get_Double_Arg("-root", 2);
root[2] = Get_Double_Arg("-root", 3);
}
Swc_Tree *tree = NULL;
if (Is_Arg_Matched("-root")) {
/*
int root_index = Neuron_Structure_Find_Root_Circle(ns2, root);
Graph_Workspace *gw2 = New_Graph_Workspace();
Graph_Clean_Root(ns2->graph, root_index, gw2);
Neuron_Structure_To_Swc_File_Circle_Z(ns2, full_path(dir, "graph_d.swc"),
z_scale, root);
*/
tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, z_scale, root);
if (Swc_Tree_Node_Is_Virtual(tree->root) == TRUE) {
tree->root->first_child->next_sibling = NULL;
}
Swc_Tree_Clean_Root(tree);
} else {
/*
Neuron_Structure_To_Swc_File_Circle_Z(ns2, full_path(dir, "graph_d.swc"),
z_scale, NULL);
*/
tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, z_scale, NULL);
}
ns->graph->nedge = 0;
//Neuron_Structure_To_Swc_File(ns, full_path(dir, "tube.swc"));
if (Is_Arg_Matched("-rb")) {
//Swc_Tree_Tune_Branch(tree);
Swc_Tree_Tune_Fork(tree);
}
if (Is_Arg_Matched("-sl")) {
Swc_Tree_Leaf_Shrink(tree);
}
if (Is_Arg_Matched("-rz")) {
Swc_Tree_Remove_Zigzag(tree);
}
if (Is_Arg_Matched("-rs")) {
Swc_Tree_Remove_Spur(tree);
}
Swc_Tree_Resort_Id(tree);
Write_Swc_Tree(full_path(dir, "graph_d.swc"), tree);
if (Is_Arg_Matched("-rtlist")) {
int m, n;
double *d = darray_load_matrix(Get_String_Arg("-rtlist"), NULL, &m, &n);
if (n > 0) {
coordinate_3d_t *roots = GUARDED_MALLOC_ARRAY(roots, n, coordinate_3d_t);
int i;
for (i = 0; i < n; i++) {
roots[i][0] = d[i*3];
roots[i][1] = d[i*3 + 1];
roots[i][2] = d[i*3 + 2];
/*
if (tube_offset != NULL) {
roots[i][0] += tube_offset[0];
roots[i][1] += tube_offset[1];
roots[i][2] += tube_offset[2];
}
*/
Swc_Tree *subtree = Swc_Tree_Pull_R(tree, roots[i]);
char filename[MAX_PATH_LENGTH];
if (subtree->root != NULL) {
//Swc_Tree_Clean_Root(subtree);
Swc_Tree_Clean_Root(subtree);
Swc_Tree_Node_Set_Pos(subtree->root, roots[i]);
if (Is_Arg_Matched("-jumpz")) {
//swc_tree_remove_zjump(subtree, Get_Double_Arg("-jumpz"));
}
Swc_Tree_Resort_Id(subtree);
sprintf(filename, "graph%d.swc", i + 1);
Write_Swc_Tree(full_path(dir, filename), subtree);
}
}
}
}
printf("%d chains\n", chain_number);
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;
}
