ZSwcPath ZNeuronTracer::trace(double x, double y, double z)
{
if (m_traceWorkspace->trace_mask == NULL) {
m_traceWorkspace->trace_mask =
C_Stack::make(GREY, C_Stack::width(m_stack), C_Stack::height(m_stack),
C_Stack::depth(m_stack));
Zero_Stack(m_traceWorkspace->trace_mask);
}
double pos[3];
pos[0] = x;
pos[1] = y;
pos[2] = z;
Local_Neuroseg *locseg = New_Local_Neuroseg();
Set_Neuroseg(&(locseg->seg), 3.0, 0.0, 11.0, TZ_PI_4, 0.0, 0.0, 0.0, 1.0);
Set_Neuroseg_Position(locseg, pos, NEUROSEG_CENTER);
Locseg_Fit_Workspace *ws =
(Locseg_Fit_Workspace*) m_traceWorkspace->fit_workspace;
Local_Neuroseg_Optimize_W(locseg, m_stack, 1.0, 1, ws);
Trace_Record *tr = New_Trace_Record();
tr->mask = ZERO_BIT_MASK;
Trace_Record_Set_Fix_Point(tr, 0.0);
Trace_Record_Set_Direction(tr, DL_BOTHDIR);
Locseg_Node *p = Make_Locseg_Node(locseg, tr);
Locseg_Chain *locseg_chain = Make_Locseg_Chain(p);
Trace_Workspace_Set_Trace_Status(m_traceWorkspace, TRACE_NORMAL,
TRACE_NORMAL);
Trace_Locseg(m_stack, 1.0, locseg_chain, m_traceWorkspace);
Locseg_Chain_Remove_Overlap_Ends(locseg_chain);
Locseg_Chain_Remove_Turn_Ends(locseg_chain, 1.0);
int n;
Geo3d_Circle *circles =
Locseg_Chain_To_Geo3d_Circle_Array(locseg_chain, NULL, &n);
ZSwcPath path;
for (int i = 0; i < n; ++i) {
Swc_Tree_Node *tn = SwcTreeNode::makePointer(circles[i].center[0],
circles[i].center[1], circles[i].center[2], circles[i].radius);
if (!path.empty()) {
SwcTreeNode::setParent(tn, path.back());
}
path.push_back(tn);
}
return path;
}
Local_Neuroseg* Local_R2_Rect_To_Local_Neuroseg(const Local_R2_Rect *rseg,
Local_Neuroseg *locseg)
{
if (locseg == NULL) {
locseg = New_Local_Neuroseg();
}
locseg->seg.theta = -TZ_PI_2;
locseg->seg.psi = rseg->transform.theta;
locseg->seg.h = rseg->transform.h;
locseg->pos[0] = rseg->transform.x;
locseg->pos[1] = rseg->transform.y;
locseg->pos[2] = rseg->base.z;
locseg->seg.r1 = rseg->transform.r;
locseg->seg.scale = 1.0;
return locseg;
}
ZSwcPath ZNeuronTracer::trace(double x, double y, double z)
{
setTraceScoreThreshold(TRACING_INTERACTIVE);
if (m_traceWorkspace->trace_mask == NULL) {
m_traceWorkspace->trace_mask =
C_Stack::make(GREY, getStack()->width(), getStack()->height(),
getStack()->depth());
Zero_Stack(m_traceWorkspace->trace_mask);
}
Stack *stackData = getIntensityData();
ZIntPoint stackOffset = getStack()->getOffset();
double pos[3];
pos[0] = x - stackOffset.getX();
pos[1] = y - stackOffset.getY();
pos[2] = z - stackOffset.getZ();
/* alloc <locseg> */
Local_Neuroseg *locseg = New_Local_Neuroseg();
Set_Neuroseg(&(locseg->seg), 3.0, 0.0, 11.0, TZ_PI_4, 0.0, 0.0, 0.0, 1.0);
Set_Neuroseg_Position(locseg, pos, NEUROSEG_CENTER);
Locseg_Fit_Workspace *ws =
(Locseg_Fit_Workspace*) m_traceWorkspace->fit_workspace;
Local_Neuroseg_Optimize_W(locseg, stackData, 1.0, 1, ws);
Trace_Record *tr = New_Trace_Record();
tr->mask = ZERO_BIT_MASK;
Trace_Record_Set_Fix_Point(tr, 0.0);
Trace_Record_Set_Direction(tr, DL_BOTHDIR);
/* consume <locseg> */
Locseg_Node *p = Make_Locseg_Node(locseg, tr);
/* alloc <locseg_chain> */
Locseg_Chain *locseg_chain = Make_Locseg_Chain(p);
Trace_Workspace_Set_Trace_Status(m_traceWorkspace, TRACE_NORMAL,
TRACE_NORMAL);
Trace_Locseg(stackData, 1.0, locseg_chain, m_traceWorkspace);
Locseg_Chain_Remove_Overlap_Ends(locseg_chain);
Locseg_Chain_Remove_Turn_Ends(locseg_chain, 1.0);
int n;
/* alloc <circles> */
Geo3d_Circle *circles =
Locseg_Chain_To_Geo3d_Circle_Array(locseg_chain, NULL, &n);
/* free <locseg_chain> */
Kill_Locseg_Chain(locseg_chain);
ZSwcPath path;
if (n > 0) {
// bool hit = false;
int start = 0;
int end = n;
if (Trace_Workspace_Mask_Value(m_traceWorkspace, circles[0].center) > 0) {
for (int i = 1; i < n; ++i) {
start = i - 1;
if (Trace_Workspace_Mask_Value(m_traceWorkspace, circles[i].center) == 0) {
break;
}
}
}
if (n > 1) {
if (Trace_Workspace_Mask_Value(m_traceWorkspace, circles[n - 1].center) > 0) {
for (int i = n - 2; i >= 0; --i) {
end = i + 2;
if (Trace_Workspace_Mask_Value(m_traceWorkspace, circles[i].center) == 0) {
break;
}
}
}
}
for (int i = start; i < end; ++i) {
Swc_Tree_Node *tn = SwcTreeNode::makePointer(circles[i].center[0],
circles[i].center[1], circles[i].center[2], circles[i].radius);
if (!path.empty()) {
SwcTreeNode::setParent(tn, path.back());
}
SwcTreeNode::translate(tn, stackOffset);
path.push_back(tn);
}
}
/* free <circles> */
if (circles != NULL) {
free(circles);
}
return path;
}
int main()
{
#if 0
char *filepath = "../data/fly_neuron_n2/graph_d.swc";
Neuron_Structure *ns = Neuron_Structure_From_Swc_File(filepath);
Neuron_Component_Arraylist *comp_array =
Neuron_Structure_Branch_Point(ns);
filepath = "../data/fly_neuron_n2.tif";
Stack *stack = Read_Stack(filepath);
Translate_Stack(stack, COLOR, 1);
int i;
Stack_Draw_Workspace *ws = New_Stack_Draw_Workspace();
for (i = 0; i < comp_array->length; i++) {
Neuron_Component_Draw_Stack(comp_array->array + i, stack, ws);
}
Kill_Stack_Draw_Workspace(ws);
Write_Stack("../data/test.tif", stack);
#endif
#if 0
Stack *stack = NULL;
Locseg_Chain *chain1 = Read_Locseg_Chain("../data/fly_neuron_n3/chain0.tb");
Locseg_Chain *chain2 = Read_Locseg_Chain("../data/fly_neuron_n3/chain10.tb");
Connection_Test_Workspace *ws = New_Connection_Test_Workspace();
Connection_Test_Workspace_Read_Resolution(ws, "../data/fly_neuron_n1.res");
Neurocomp_Conn conn;
conn.mode = NEUROCOMP_CONN_HL;
Locseg_Chain_Connection_Test(chain1, chain2, stack, 1.0, &conn, ws);
Print_Neurocomp_Conn(&conn);
#endif
#if 0
Locseg_Chain **chain = (Locseg_Chain**) malloc(sizeof(Locseg_Chain*) * 3);
chain[0] = Read_Locseg_Chain("../data/mouse_single_org/chain4.tb");
chain[1] = Read_Locseg_Chain("../data/mouse_single_org/chain19.tb");
chain[2] = Read_Locseg_Chain("../data/mouse_single_org/chain64.tb");
Stack *signal = Read_Stack("../data/mouse_single_org.tif");
Connection_Test_Workspace *ctw = New_Connection_Test_Workspace();
FILE *fp = fopen("../data/mouse_single_org.res", "r");
darray_fscanf(fp, ctw->resolution, 3);
Neuron_Component *chain_array = Make_Neuron_Component_Array(3);
int i;
for (i = 0; i < 3; i++) {
Set_Neuron_Component(chain_array + i,
NEUROCOMP_TYPE_LOCSEG_CHAIN, chain[i]);
}
Neuron_Structure *ns = Locseg_Chain_Comp_Neurostruct(chain_array,
3, signal, 1.0, ctw);
Graph *graph = ns->graph;
Process_Neuron_Structure(ns);
Print_Neuron_Structure(ns);
Neuron_Structure_Crossover_Test(ns, 0.5375);
printf("\ncross over changed: \n");
Print_Neuron_Structure(ns);
#endif
#if 0
Neuron_Structure *ns = Make_Neuron_Structure(5);
Set_Neuron_Component(ns->comp, NEUROCOMP_TYPE_GEO3D_CIRCLE,
New_Geo3d_Circle());
Set_Neuron_Component(ns->comp + 1, NEUROCOMP_TYPE_GEO3D_CIRCLE,
New_Geo3d_Circle());
Set_Neuron_Component(ns->comp + 2, NEUROCOMP_TYPE_GEO3D_CIRCLE,
New_Geo3d_Circle());
Set_Neuron_Component(ns->comp + 3, NEUROCOMP_TYPE_GEO3D_CIRCLE,
New_Geo3d_Circle());
Set_Neuron_Component(ns->comp + 4, NEUROCOMP_TYPE_GEO3D_CIRCLE,
New_Geo3d_Circle());
NEUROCOMP_GEO3D_CIRCLE(ns->comp)->radius = 1.5;
NEUROCOMP_GEO3D_CIRCLE(ns->comp + 1)->radius = 2.5;
NEUROCOMP_GEO3D_CIRCLE(ns->comp + 2)->radius = 3.5;
NEUROCOMP_GEO3D_CIRCLE(ns->comp + 3)->radius = 4.5;
NEUROCOMP_GEO3D_CIRCLE(ns->comp + 4)->radius = 5.5;
ns->graph = Make_Graph(5, 4, 0);
//Graph_Add_Edge(ns->graph, 0, 1);
Graph_Add_Edge(ns->graph, 1, 3);
Graph_Add_Edge(ns->graph, 1, 4);
Graph_Add_Edge(ns->graph, 0, 2);
Graph_Set_Directed(ns->graph, TRUE);
Print_Graph(ns->graph);
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns, 1.0, NULL);
Print_Swc_Tree(tree);
Swc_Tree_To_Dot_File(tree, "../data/test2.dot");
#endif
#if 0
int n;
Neuron_Component *chain_array = Dir_Locseg_Chain_Nc("../data/fly_neuron_n22",
"^chain.*\\.tb",
&n, NULL);
Neuron_Structure *ns =
Locseg_Chain_Comp_Neurostruct(chain_array, n, NULL, 1.0, NULL);
Process_Neuron_Structure(ns);
Neuron_Structure* ns2=
Neuron_Structure_Locseg_Chain_To_Circle(ns);
Neuron_Structure_To_Tree(ns2);
Graph_To_Dot_File(ns2->graph, "../data/test.dot");
Swc_Tree *tree =
Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, NULL);
Swc_Tree_Remove_Zigzag(tree);
//Swc_Tree_Tune_Fork(tree);
//Print_Swc_Tree(tree);
Write_Swc_Tree("../data/test.swc", tree);
#endif
#if 0
Graph *graph = Neuron_Structure_Import_Xml_Graph("../data/mouse_single_org/trueconn2.xml");
Graph_Normalize_Edge(graph);
Graph_Remove_Duplicated_Edge(graph);
Graph *graph2 = Neuron_Structure_Import_Xml_Graph("../data/mouse_single_org/conn.xml");
Graph_Normalize_Edge(graph2);
Graph_Remove_Duplicated_Edge(graph2);
Graph_Workspace *gw = New_Graph_Workspace();
int n = Graph_Edge_Count(graph, graph2->edges, graph2->nedge, gw);
printf("fp: %d\n", graph2->nedge - n);
printf("tp: %d\n", n);
printf("fn: %d\n", graph->nedge - n);
double p = (double) n / graph2->nedge;
double r = (double) n / graph->nedge;
printf("precision: %g\n", p);
printf("recall: %g\n", r);
printf("F-measure: %g\n", 2.0 * (p * r) / (p + r));
#endif
#if 0
Neuron_Structure *ns = Make_Neuron_Structure(2);
Local_Neuroseg *locseg = New_Local_Neuroseg();
Locseg_Chain *chain1 = New_Locseg_Chain();
Locseg_Chain_Add(chain1, locseg, NULL, DL_TAIL);
Set_Neuron_Component(ns->comp, NEUROCOMP_TYPE_LOCSEG_CHAIN, chain1);
Locseg_Chain *chain2 = New_Locseg_Chain();
locseg = New_Local_Neuroseg();
double bottom[3] = {10, 10, 5};
double top[3] = {5, 5, 5};
Local_Neuroseg_Set_Bottom_Top(locseg, bottom, top);
Locseg_Chain_Add(chain2, locseg, NULL, DL_TAIL);
Set_Neuron_Component(ns->comp + 1, NEUROCOMP_TYPE_LOCSEG_CHAIN, chain2);
Neurocomp_Conn *conn = New_Neurocomp_Conn();
Connection_Test_Workspace *ctw = New_Connection_Test_Workspace();
Locseg_Chain_Connection_Test(chain2, chain1, NULL, 1.0, conn, ctw);
Neuron_Structure_Add_Conn(ns, 1, 0, conn);
Print_Neuron_Structure(ns);
Neuron_Structure *ns2 =
Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
Neuron_Structure_To_Swc_File(ns2, "../data/test.swc");
#endif
#if 0
int n;
Locseg_Chain **chain_array = Dir_Locseg_Chain_Nd("../data/diadem_a1_part3",
"^chain.*\\.tb", &n, NULL);
/*
Locseg_Chain **chain_array =
Locseg_Chain_Import_List("../data/diadem_a1_part2/good_tube.txt", &n);
*/
//n = 100;
/*
Locseg_Chain **chain_array =
(Locseg_Chain**) malloc(sizeof(Locseg_Chain*) * 2);
n = 2;
chain_array[0] = Read_Locseg_Chain("../data/diadem_a1_part2/chain58.tb");
chain_array[1] = Read_Locseg_Chain("../data/diadem_a1_part2/chain154.tb");
*/
Stack *stack = Read_Stack("../data/diadem_a1_part3.tif");
Stack *mask = Make_Stack(GREY, stack->width, stack->height, stack->depth);
Zero_Stack(mask);
Sp_Grow_Workspace *sgw = New_Sp_Grow_Workspace();
sgw->size = Stack_Voxel_Number(stack);
sgw->resolution[0] = 0.0375 * 2.0;
sgw->resolution[1] = 0.0375 * 2.0;
sgw->resolution[2] = 0.33;
Sp_Grow_Workspace_Set_Mask(sgw, mask->array);
sgw->wf = Stack_Voxel_Weight_S;
Stack_Sp_Grow_Infer_Parameter(sgw, stack);
Neuron_Structure *ns =
Locseg_Chain_Sp_Grow_Reconstruct(chain_array, n, stack, 1.0, sgw);
Print_Neuron_Structure(ns);
Graph_To_Dot_File(ns->graph, "../data/test.dot");
//Neuron_Structure_To_Swc_File(ns, "../data/test.swc");
Neuron_Structure *ns2 =
Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
//double root[3] = {31, 430, 0};
double root[3] = {1221, 449, 8.5};
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, root);
Swc_Tree_Clean_Root(tree);
Swc_Tree_Resort_Id(tree);
Write_Swc_Tree("../data/test.swc", tree);
#endif
#if 0
int n;
Locseg_Chain **chain_array = Dir_Locseg_Chain_Nd("../data/diadem_e1",
"^chain.*\\.tb", &n, NULL);
//n = 100;
/*
Locseg_Chain **chain_array =
(Locseg_Chain**) malloc(sizeof(Locseg_Chain*) * 2);
n = 2;
chain_array[0] = Read_Locseg_Chain("../data/diadem_a1_part2/chain58.tb");
chain_array[1] = Read_Locseg_Chain("../data/diadem_a1_part2/chain154.tb");
*/
Stack *stack = Read_Stack("../data/diadem_e1.tif");
Stack *mask = Make_Stack(GREY, stack->width, stack->height, stack->depth);
Zero_Stack(mask);
Sp_Grow_Workspace *sgw = New_Sp_Grow_Workspace();
sgw->size = Stack_Voxel_Number(stack);
sgw->resolution[0] = 0.3296485;
sgw->resolution[1] = 0.3296485;
sgw->resolution[2] = 1.0;
Sp_Grow_Workspace_Set_Mask(sgw, mask->array);
sgw->wf = Stack_Voxel_Weight_S;
Stack_Sp_Grow_Infer_Parameter(sgw, stack);
Neuron_Structure *ns =
Locseg_Chain_Sp_Grow_Reconstruct(chain_array, n, stack, 1.0, sgw);
Print_Neuron_Structure(ns);
//Neuron_Structure_To_Swc_File(ns, "../data/test.swc");
Neuron_Structure *ns2 =
Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
Graph_To_Dot_File(ns2->graph, "../data/test.dot");
double root[3] = {31, 430, 0};
//double root[3] = {4882, 1797, 19};
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, root);
//Swc_Tree_Clean_Root(tree);
Swc_Tree_Resort_Id(tree);
Write_Swc_Tree("../data/test2.swc", tree);
#endif
#if 0
int n;
Locseg_Chain **chain_array =
Dir_Locseg_Chain_Nd("../data/benchmark/stack_graph/fork", "^chain.*\\.tb",
&n, NULL);
Stack *stack = Read_Stack("../data/benchmark/stack_graph/fork/fork.tif");
Stack *mask = Make_Stack(GREY, stack->width, stack->height, stack->depth);
Zero_Stack(mask);
Sp_Grow_Workspace *sgw = New_Sp_Grow_Workspace();
sgw->size = Stack_Voxel_Number(stack);
Sp_Grow_Workspace_Set_Mask(sgw, mask->array);
sgw->wf = Stack_Voxel_Weight_S;
Stack_Sp_Grow_Infer_Parameter(sgw, stack);
Neuron_Structure *ns =
Locseg_Chain_Sp_Grow_Reconstruct(chain_array, n, stack, 1.0, sgw);
Neuron_Structure *ns2 =
Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, NULL);
//Swc_Tree_Clean_Root(tree);
Swc_Tree_Resort_Id(tree);
Write_Swc_Tree("../data/test.swc", tree);
#endif
#if 0
int n = 3;
Locseg_Chain **chain_array =
(Locseg_Chain**) malloc(sizeof(Locseg_Chain) * n);
chain_array[0] = Read_Locseg_Chain("/Users/zhaot/Work/neurolabi/data/benchmark/stack_graph/fork/chain0.tb");
chain_array[1] = Read_Locseg_Chain("/Users/zhaot/Work/neurolabi/data/benchmark/stack_graph/fork/chain1.tb");
chain_array[2] = New_Locseg_Chain();
printf("%d\n", Locseg_Chain_Is_Empty(chain_array[2]));
Stack *stack = Read_Stack("../data/benchmark/stack_graph/fork/fork.tif");
Stack *mask = Make_Stack(GREY, stack->width, stack->height, stack->depth);
Zero_Stack(mask);
Sp_Grow_Workspace *sgw = New_Sp_Grow_Workspace();
sgw->size = Stack_Voxel_Number(stack);
Sp_Grow_Workspace_Set_Mask(sgw, mask->array);
sgw->wf = Stack_Voxel_Weight_S;
Stack_Sp_Grow_Infer_Parameter(sgw, stack);
Neuron_Structure *ns =
Locseg_Chain_Sp_Grow_Reconstruct(chain_array, n, stack, 1.0, sgw);
Neuron_Structure *ns2 =
Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, NULL);
//Swc_Tree_Clean_Root(tree);
Swc_Tree_Remove_Zigzag(tree);
Swc_Tree_Resort_Id(tree);
Write_Swc_Tree("../data/test2.swc", tree);
#endif
#if 0
Neuron_Structure *ns = New_Neuron_Structure();
ns->graph = New_Graph();
Graph_Add_Edge(ns->graph, 0, 1);
Graph_Add_Edge(ns->graph, 0, 2);
Graph_Add_Edge(ns->graph, 2, 3);
Graph_Add_Edge(ns->graph, 2, 4);
Graph_Add_Edge(ns->graph, 4, 5);
Graph_Add_Edge(ns->graph, 5, 6);
ns->conn = (Neurocomp_Conn*) malloc(sizeof(Neurocomp_Conn) * ns->graph->nedge);
ns->conn[0].info[0] = 0;
ns->conn[0].info[1] = 0;
ns->conn[0].cost = 0.0;
ns->conn[0].mode = NEUROCOMP_CONN_LINK;
ns->conn[1].info[0] = 1;
ns->conn[1].info[1] = 1;
ns->conn[1].cost = 0.0;
ns->conn[1].mode = NEUROCOMP_CONN_LINK;
ns->conn[2].info[0] = 0;
ns->conn[2].info[1] = 0;
ns->conn[2].cost = 0.0;
ns->conn[2].mode = NEUROCOMP_CONN_LINK;
ns->conn[3].info[0] = 1;
ns->conn[3].info[1] = 0;
ns->conn[3].cost = 1.0;
ns->conn[3].mode = NEUROCOMP_CONN_HL;
ns->conn[4].info[0] = 0;
ns->conn[4].info[1] = 1;
ns->conn[4].cost = 0.0;
ns->conn[4].mode = NEUROCOMP_CONN_LINK;
ns->conn[5].info[0] = 1;
ns->conn[5].info[1] = 1;
ns->conn[5].cost = 1.0;
ns->conn[5].mode = NEUROCOMP_CONN_LINK;
Neuron_Structure_Merge_Locseg_Chain(ns);
#endif
#if 0
Neuron_Structure *ns = New_Neuron_Structure();
ns->graph = New_Graph();
ns->comp = Dir_Locseg_Chain_Nc("../data/diadem_e3", "^chain.*\\.tb",
&(ns->graph->nvertex), NULL);
Graph_Add_Edge(ns->graph, 0, 1);
Graph_Add_Edge(ns->graph, 0, 2);
Graph_Add_Edge(ns->graph, 2, 3);
Graph_Add_Edge(ns->graph, 3, 4);
Graph_Add_Edge(ns->graph, 4, 5);
ns->conn = (Neurocomp_Conn*) malloc(sizeof(Neurocomp_Conn) * ns->graph->nedge);
ns->conn[0].info[0] = 0;
ns->conn[0].info[1] = 0;
ns->conn[0].cost = 0.0;
ns->conn[0].mode = NEUROCOMP_CONN_LINK;
ns->conn[1].info[0] = 0;
ns->conn[1].info[1] = 0;
ns->conn[1].cost = 0.0;
ns->conn[1].mode = NEUROCOMP_CONN_LINK;
ns->conn[2].info[0] = 0;
ns->conn[2].info[1] = 0;
ns->conn[2].cost = 1.0;
ns->conn[2].mode = NEUROCOMP_CONN_LINK;
ns->conn[3].info[0] = 0;
ns->conn[3].info[1] = 0;
ns->conn[3].cost = 2.0;
ns->conn[3].mode = NEUROCOMP_CONN_LINK;
ns->conn[4].info[0] = 0;
ns->conn[4].info[1] = 0;
ns->conn[4].cost = 0.0;
ns->conn[4].mode = NEUROCOMP_CONN_LINK;
int i;
for (i = 0; i < ns->graph->nvertex; i++) {
printf("%d ", Locseg_Chain_Length(NEUROCOMP_LOCSEG_CHAIN(ns->comp+i)));
}
printf("\n");
Neuron_Structure_Merge_Locseg_Chain(ns);
for (i = 0; i < ns->graph->nvertex; i++) {
printf("%d ", Locseg_Chain_Length(NEUROCOMP_LOCSEG_CHAIN(ns->comp+i)));
}
printf("\n");
#endif
#if 0
int n;
Locseg_Chain **chain_array = Dir_Locseg_Chain_Nd("../data/diadem_e1",
"^chain.*\\.tb", &n, NULL);
Stack *stack = Read_Stack("../data/diadem_e1.tif");
Stack *mask = Make_Stack(GREY, stack->width, stack->height, stack->depth);
Zero_Stack(mask);
Sp_Grow_Workspace *sgw = New_Sp_Grow_Workspace();
sgw->size = Stack_Voxel_Number(stack);
sgw->resolution[0] = 0.3296485;
sgw->resolution[1] = 0.3296485;
sgw->resolution[2] = 1.0;
Sp_Grow_Workspace_Set_Mask(sgw, mask->array);
sgw->wf = Stack_Voxel_Weight_S;
Stack_Sp_Grow_Infer_Parameter(sgw, stack);
Neuron_Structure *ns =
Locseg_Chain_Sp_Grow_Reconstruct(chain_array, n, stack, 1.0, sgw);
Neuron_Structure_Merge_Locseg_Chain(ns);
int i;
char filepath[100];
for (i = 0; i < ns->graph->nvertex; i++) {
Locseg_Chain_Regularize(NEUROCOMP_LOCSEG_CHAIN(ns->comp+i));
if (Locseg_Chain_Is_Empty(NEUROCOMP_LOCSEG_CHAIN(ns->comp+i)) == FALSE) {
sprintf(filepath, "../data/tmp/chain%d.tb", i);
Write_Locseg_Chain(filepath, NEUROCOMP_LOCSEG_CHAIN(ns->comp+i));
}
}
#endif
#if 0
Stack *stack = Read_Stack("../data/benchmark/fork2/fork2.tif");
Neuron_Structure *ns = New_Neuron_Structure();
ns->graph = New_Graph();
ns->comp = Dir_Locseg_Chain_Nc("../data/benchmark/fork2/tubes",
"^chain.*\\.tb", &(ns->graph->nvertex), NULL);
coordinate_3d_t roots[3];
roots[0][0] = 51;
roots[0][1] = 23;
roots[0][2] = 60;
roots[1][0] = 51;
roots[1][1] = 23;
roots[1][2] = 40;
roots[2][0] = 25;
roots[2][1] = 76;
roots[2][2] = 60;
Neuron_Structure_Break_Root(ns, roots, 3);
Neuron_Structure_Load_Root(ns, roots, 3);
Connection_Test_Workspace *ctw = New_Connection_Test_Workspace();
ctw->dist_thre = 100.0;
ctw->sp_test = FALSE;
Locseg_Chain_Comp_Neurostruct_W(ns, stack, 1.0, ctw);
Process_Neuron_Structure(ns);
Neuron_Structure_To_Tree(ns);
/*
Neuron_Structure_Remove_Conn(ns, 0, 2);
Neuron_Structure_Remove_Conn(ns, 2, 0);
*/
Neuron_Structure_Remove_Negative_Conn(ns);
Neuron_Structure* ns2= NULL;
ns2 = Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
Neuron_Structure_To_Tree(ns2);
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, NULL);
Swc_Tree_Resort_Id(tree);
Write_Swc_Tree("../data/test3.swc", tree);
#endif
#if 1
Stack *stack = NULL;
Locseg_Chain *chain1 = Read_Locseg_Chain("../data/benchmark/diadem/diadem_e1/chain22.tb");
Locseg_Chain *chain2 = Read_Locseg_Chain("../data/benchmark/diadem/diadem_e1/chain0.tb");
Connection_Test_Workspace *ws = New_Connection_Test_Workspace();
Connection_Test_Workspace_Read_Resolution(ws, "../data/diadem_e3.res");
Neurocomp_Conn conn;
conn.mode = NEUROCOMP_CONN_HL;
Locseg_Chain_Connection_Test(chain1, chain2, stack, 1.0, &conn, ws);
Print_Neurocomp_Conn(&conn);
#endif
return 0;
}
