Trace_Record* Trace_Record_Fread_V(Trace_Record *tr, FILE *stream,
double version)
{
if (version == 0.0) {
ASSERT(stream != NULL, "Invalid file pointer");
if (feof(stream)) {
return NULL;
}
Bitmask_t mask = ZERO_BIT_MASK;
if (fread(&mask, sizeof(Bitmask_t), 1, stream) != 1) {
return NULL;
}
BOOL is_local_alloc = FALSE;
if (tr == NULL) {
if (mask == ZERO_BIT_MASK) {
return NULL;
} else {
tr = New_Trace_Record();
is_local_alloc = TRUE;
}
}
tr->mask = mask;
if (mask != ZERO_BIT_MASK) {
if (fread(BYTE_ARRAY(tr) + sizeof(Bitmask_t),
sizeof(Trace_Record) - sizeof(Bitmask_t) -
sizeof(tr->fix_point), 1, stream) != 1) {
if (is_local_alloc == TRUE) {
Delete_Trace_Record(tr);
}
tr = NULL;
}
}
} else if (version == 1.0) {
tr = Trace_Record_Fread(tr, stream);
} else if (version == 2.0) {
tr = Trace_Record_Fread(tr, stream);
if (tr != NULL) {
int fix_point;
fread(&fix_point, sizeof(fix_point), 1, stream);
tr->fix_point = fix_point;
}
} else if (version == 3.0) {
tr = Trace_Record_Fread(tr, stream);
if (tr != NULL) {
fread(&(tr->fix_point), sizeof(tr->fix_point), 1, stream);
}
} else {
TZ_ERROR(ERROR_IO_FORMAT);
}
return tr;
}
Trace_Record* Copy_Trace_Record(Trace_Record *tr)
{
if (tr == NULL) {
return NULL;
}
Trace_Record *newtr = New_Trace_Record();
Trace_Record_Copy(newtr, tr);
return newtr;
}
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;
}
Trace_Record* Trace_Record_Fread(Trace_Record *tr, FILE *stream)
{
ASSERT(stream != NULL, "Invalid file pointer");
if (feof(stream)) {
return NULL;
}
Bitmask_t mask = ZERO_BIT_MASK;
if (fread(&mask, sizeof(Bitmask_t), 1, stream) != 1) {
return NULL;
}
BOOL is_local_alloc = FALSE;
if (tr == NULL) {
if (mask == ZERO_BIT_MASK) {
return NULL;
} else {
tr = New_Trace_Record();
is_local_alloc = TRUE;
}
}
tr->mask = mask;
if (mask != ZERO_BIT_MASK) {
/*
if (fread(((void *) tr) + sizeof(Bitmask_t),
sizeof(Trace_Record) - sizeof(Bitmask_t), 1, stream) != 1) {
if (is_local_alloc == TRUE) {
Delete_Trace_Record(tr);
}
tr = NULL;
}
*/
Stack_Fit_Score_Fread(&(tr->fs), stream);
fread(&(tr->hit_region), sizeof(tr->hit_region), 1, stream);
fread(&(tr->index), sizeof(tr->index), 1, stream);
fread(&(tr->refit), sizeof(tr->refit), 1, stream);
fread(tr->fit_height, sizeof(tr->fit_height[0]), 2, stream);
fread(&(tr->direction), sizeof(tr->direction), 1, stream);
}
return tr;
}
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;
}
