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;
}
ZSwcTree* ZNeuronTracer::trace(Stack *stack, bool doResampleAfterTracing)
{
startProgress();
ZSwcTree *tree = NULL;
//Extract seeds
//First mask
std::cout << "Binarizing ..." << std::endl;
/* <bw> allocated */
Stack *bw = binarize(stack);
C_Stack::translate(bw, GREY, 1);
advanceProgress(0.05);
std::cout << "Removing noise ..." << std::endl;
/* <mask> allocated */
Stack *mask = bwsolid(bw);
advanceProgress(0.05);
/* <bw> freed */
C_Stack::kill(bw);
//Thin line mask
/* <mask2> allocated */
Stack *mask2 = NULL;
if (m_enhancingMask) {
std::cout << "Enhancing thin branches ..." << std::endl;
mask2 = enhanceLine(stack);
advanceProgress(0.05);
}
if (mask2 != NULL) {
std::cout << "Making mask for thin branches ..." << std::endl;
ZStackBinarizer binarizer;
binarizer.setMethod(ZStackBinarizer::BM_LOCMAX);
binarizer.setRetryCount(5);
binarizer.setMinObjectSize(27);
if (binarizer.binarize(mask2) == false) {
std::cout << "Thresholding failed" << std::endl;
C_Stack::kill(mask2);
mask2 = NULL;
}
}
/* <mask2> freed */
if (mask2 != NULL) {
C_Stack::translate(mask2, GREY, 1);
Stack_Or(mask, mask2, mask);
C_Stack::kill(mask2);
mask2 = NULL;
}
advanceProgress(0.05);
//Trace each seed
std::cout << "Extracting seed points ..." << std::endl;
/* <seedPointArray> allocated */
Geo3d_Scalar_Field *seedPointArray = extractSeed(mask);
m_mask = mask;
advanceProgress(0.05);
std::cout << "Sorting seeds ..." << std::endl;
ZNeuronTraceSeeder seeder;
setTraceScoreThreshold(TRACING_SEED);
m_baseMask = seeder.sortSeed(seedPointArray, stack, m_traceWorkspace);
#ifdef _DEBUG_2
C_Stack::write(GET_TEST_DATA_DIR + "/test.tif", m_baseMask);
#endif
advanceProgress(0.1);
/* <seedPointArray> freed */
Kill_Geo3d_Scalar_Field(seedPointArray);
std::vector<Local_Neuroseg>& locsegArray = seeder.getSeedArray();
std::vector<double>& scoreArray = seeder.getScoreArray();
std::cout << "Tracing ..." << std::endl;
/* <chainArray> allocated */
std::vector<Locseg_Chain*> chainArray = trace(stack, locsegArray, scoreArray);
if (m_recover > 0) {
std::vector<Locseg_Chain*> newChainArray = recover(stack);
chainArray.insert(
chainArray.end(), newChainArray.begin(), newChainArray.end());
}
advanceProgress(0.1);
chainArray = screenChain(stack, chainArray);
advanceProgress(0.3);
/* <mask2> freed */
// C_Stack::kill(mask);
std::cout << "Reconstructing ..." << std::endl;
ZNeuronConstructor constructor;
constructor.setWorkspace(m_connWorkspace);
constructor.setSignal(stack);
//Create neuron structure
BOOL oldSpTest = m_connWorkspace->sp_test;
if (chainArray.size() > 1000) {
std::cout << "Too many chains: " << chainArray.size() << std::endl;
std::cout << "Turn off shortest path test" << std::endl;
m_connWorkspace->sp_test = FALSE;
}
/* free <chainArray> */
tree = constructor.reconstruct(chainArray);
m_connWorkspace->sp_test = oldSpTest;
advanceProgress(0.1);
//Post process
Swc_Tree_Remove_Zigzag(tree->data());
Swc_Tree_Tune_Branch(tree->data());
Swc_Tree_Remove_Spur(tree->data());
Swc_Tree_Merge_Close_Node(tree->data(), 0.01);
Swc_Tree_Remove_Overshoot(tree->data());
if (doResampleAfterTracing) {
ZSwcResampler resampler;
resampler.optimalDownsample(tree);
}
advanceProgress(0.1);
std::cout << "Done!" << std::endl;
endProgress();
return tree;
}