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; }