//091212 RZC
void neuron_branch_tip_count(V3DLONG &n_branch, V3DLONG &n_tip, const V_NeuronSWC & in_swc)
{
// map swc's index --> vector's index & in/out link
Link_Map link_map = get_link_map(in_swc);
//qDebug("link_map created.");
n_branch = 0;
n_tip = 0;
V3DLONG n_path=0, n_single=0; //for test
Link_Map_Iter it;
for (it=link_map.begin(); it!=link_map.end(); it++)
{
// const V_NeuronSWC_unit & cur_node = in_swc.row.at(i);
// Node_Link & nodelink = link_map[V3DLONG(cur_node.n)];
Node_Link & nodelink = (*it).second;
if(nodelink.nlink == 0) n_single++;
if (nodelink.nlink == 1)
n_tip ++;
if (nodelink.nlink == 2) n_path++;// path point
if (nodelink.nlink >= 3)
{
n_branch ++;
//qDebug("branch #%d (%g %g %g) %d", V3DLONG(cur_node.n),cur_node.x,cur_node.y,cur_node.z, nodelink.nlink);
}
}
qDebug("cojoc: all:%d/link:%d/0:%d/1:%d/2:%d/3+:%d",in_swc.row.size(),link_map.size(),n_single,n_tip,n_path,n_branch);
}
//091212 RZC
void neuron_branch_tip_count(V3DLONG &n_branch, V3DLONG &n_tip, const V_NeuronSWC & in_swc)
{
// map swc's index --> vector's index & in/out link
Link_Map link_map = get_link_map(in_swc);
//qDebug("link_map created.");
n_branch = 0;
n_tip = 0;
Link_Map_Iter it;
for (it=link_map.begin(); it!=link_map.end(); it++)
{
// const V_NeuronSWC_unit & cur_node = in_swc.row.at(i);
// Node_Link & nodelink = link_map[V3DLONG(cur_node.n)];
Node_Link & nodelink = (*it).second;
if (nodelink.nlink == 1)
n_tip ++;
//if (nodelink.nlink == 2) // path point
if (nodelink.nlink >= 3)
{
n_branch ++;
//qDebug("branch #%d (%g %g %g) %d", V3DLONG(cur_node.n),cur_node.x,cur_node.y,cur_node.z, nodelink.nlink);
}
}
}
static const struct link_map* link_map_entry_for_library(const char* library)
{
for (const struct link_map* map = get_link_map(); map != NULL; map = map->l_next)
{
if (map->l_name && strcmp(basename(map->l_name), basename(library)) == 0)
{
return map;
}
}
fprintf(stderr, "failed to locate link-map-entry for library %s\n", library);
return NULL;
}
//091212 RZC
vector <V_NeuronSWC> decompose_V_NeuronSWC(V_NeuronSWC & in_swc)
{
// map swc's index --> vector's index & in/out link
Link_Map link_map = get_link_map(in_swc);
qDebug("link_map is created.");
vector <V_NeuronSWC> out_swc_segs;
out_swc_segs.clear();
// nchild as processed counter
for (V3DLONG i=0; i<in_swc.row.size(); i++)
{
V_NeuronSWC_unit & cur_node = in_swc.row[i];
Node_Link & nodelink = link_map[V3DLONG(cur_node.n)];
cur_node.nchild = nodelink.nlink;
//qDebug("#%d nlink = %d, in %d, out %d", V3DLONG(cur_node.n), nodelink.nlink, nodelink.in_link.size(), nodelink.out_link.size());
}
for (;;)
{
// check is all nodes processed
V3DLONG n_removed = 0;
for (V3DLONG i=0; i<in_swc.row.size(); i++)
{
V_NeuronSWC_unit & cur_node = in_swc.row[i];
if (cur_node.nchild <=0) // is removed node ////// count down to 0
n_removed ++;
}
if (n_removed >= in_swc.row.size())
{
//qDebug("split_V_NeuronSWC_segs is done.");
break; //over, all nodes have been labeled to remove
}
// find a tip/out-branch/pure-out point as start point
V3DLONG istart = -1;
V3DLONG n_left = 0;
V3DLONG i_left = -1;
for (V3DLONG i=0; i<in_swc.row.size(); i++)
{
V_NeuronSWC_unit & cur_node = in_swc.row[i];
Node_Link & nodelink = link_map[V3DLONG(cur_node.n)];
if (cur_node.nchild <=0)
continue; //skip removed point
n_left++; //left valid point
i_left = i;
if ((nodelink.nlink ==1 && nodelink.in_link.size()==0) // tip point (include single point)
|| (nodelink.nlink >2 && nodelink.out_link.size() >0) // out-branch point
|| (nodelink.nlink ==2 && nodelink.in_link.size()==0)) // pure-out point
{
istart = i;
if (0)
qDebug("start from #%d", V3DLONG(cur_node.n));
break; //find a start point
}
}
if (istart <0) //not find a start point
{
if (n_left)
{
qDebug("split_V_NeuronSWC_segs cann't find start point (left %d points)", n_left);
istart = i_left;
}
else
{
qDebug("split_V_NeuronSWC_segs finished.");
break;
}
}
// extract a simple segment
V_NeuronSWC new_seg;
new_seg.clear();
//qDebug("decompose_V_NeuronSWC_segs: segment from node #%d", j);
V3DLONG inext = istart;
for (V3DLONG n=1; inext>=0; n++)
{
V_NeuronSWC_unit & cur_node = in_swc.row[inext];
Node_Link & nodelink = link_map[V3DLONG(cur_node.n)];
//qDebug(" link #%d", V3DLONG(cur_node.n));
V_NeuronSWC_unit new_node = cur_node;
new_node.n = n;
new_node.parent = n+1; // link order as original order
new_seg.row.push_back(new_node);
if(cur_node.parent <0) // root point ////////////////////////////
{
//qDebug("decompose_V_NeuronSWC_segs: segment end at root #%d", V3DLONG(cur_node.n));
cur_node.nchild --;
break; //over, a simple segment
}
else if (n>1 && nodelink.nlink >2) // branch point (in link_map) ///////////
{
//qDebug("decompose_V_NeuronSWC_segs: segment end at branch #%d", V3DLONG(cur_node.n));
cur_node.nchild --;
break; //over, a simple segment
}
else if (n>1 && inext==istart) // i_left point (a loop) ///////////
{
//qDebug("decompose_V_NeuronSWC_segs: segment end at branch #%d", V3DLONG(cur_node.n));
cur_node.nchild --;
break; //over, a simple segment
}
else //(nodelink.nlink==2) // path node ///////////////////////////////////////////////
{
//qDebug("decompose_V_NeuronSWC_segs: node #%d", j);
V3DLONG parent = cur_node.parent;
inext = link_map[parent].i; //// next point in seg
cur_node.nchild = -1; // label to remove
}
}
if (new_seg.row.size()>0)//>=2)//? single point
{
new_seg.row[new_seg.row.size()-1].parent = -1; // set segment end
char buf[10];
new_seg.name = sprintf(buf,"%d", out_swc_segs.size()+1);
new_seg.b_linegraph=true; //donot forget to do this //####################
out_swc_segs.push_back(new_seg);
}
}
return out_swc_segs;
}
V_NeuronSWC segmentPruning(V_NeuronSWC in_swc)
{
// map swc's index --> vector's index & in/out link
// code from function of "decompose_V_NeuronSWC" by RZC
// construct link map,
Link_Map link_map = get_link_map(in_swc);
/*qDebug*/("link_map is created.");
vector <V_NeuronSWC> out_swc_segs;
out_swc_segs.clear();
// nchild as processed counter
for (V3DLONG i=0; i<in_swc.row.size(); i++)
{
V_NeuronSWC_unit & cur_node = in_swc.row[i];
Node_Link & nodelink = link_map[V3DLONG(cur_node.n)];
cur_node.nchild = nodelink.nlink;
//qDebug("#%d nlink = %d, in %d, out %d", V3DLONG(cur_node.n), nodelink.nlink, nodelink.in_link.size(), nodelink.out_link.size());
}
for (;;)
{
// check is all nodes processed
V3DLONG n_removed = 0;
for (V3DLONG i=0; i<in_swc.row.size(); i++)
{
V_NeuronSWC_unit & cur_node = in_swc.row[i];
if (cur_node.nchild <=0) // is removed node ////// count down to 0
n_removed ++;
}
if (n_removed >= in_swc.row.size())
{
//qDebug("split_V_NeuronSWC_segs is done.");
break; //over, all nodes have been labeled to remove
}
// find a tip/out-branch/pure-out point as start point
V3DLONG istart = -1;
V3DLONG n_left = 0;
V3DLONG i_left = -1;
for (V3DLONG i=0; i<in_swc.row.size(); i++)
{
V_NeuronSWC_unit & cur_node = in_swc.row[i];
Node_Link & nodelink = link_map[V3DLONG(cur_node.n)];
if (cur_node.nchild <=0)
continue; //skip removed point
n_left++; //left valid point
i_left = i;
if ((nodelink.nlink ==1 && nodelink.in_link.size()==0) // tip point (include single point)
|| (nodelink.nlink >2 && nodelink.out_link.size() >0) // out-branch point
|| (nodelink.nlink ==2 && nodelink.in_link.size()==0)) // pure-out point
{
istart = i;
qDebug("start from #%d", V3DLONG(cur_node.n));
break; //find a start point
}
}
if (istart <0) //not find a start point
{
if (n_left)
{
qDebug("split_V_NeuronSWC_segs cann't find start point (left %d points)", n_left);
istart = i_left;
}
else
{
qDebug("split_V_NeuronSWC_segs finished.");
break;
}
}
// extract a simple segment
V_NeuronSWC new_seg;
new_seg.clear();
//qDebug("decompose_V_NeuronSWC_segs: segment from node #%d", j);
float segLen = 0;
bool isTip = false;
V3DLONG inext = istart;
for (V3DLONG n=1; inext>=0; n++)
{
V_NeuronSWC_unit & cur_node = in_swc.row[inext];
Node_Link & nodelink = link_map[V3DLONG(cur_node.n)];
//qDebug(" link #%d", V3DLONG(cur_node.n));
V_NeuronSWC_unit new_node = cur_node;
new_node.n = n;
new_node.parent = n+1; // link order as original order
new_seg.row.push_back(new_node);
if (nodelink.nlink ==1 && nodelink.in_link.size()==0)
{ // tip point
isTip = true;
cur_node.nchild --;
break;
}
if(cur_node.parent < 0 ) // root point ////////////////////////////
{
//qDebug("decompose_V_NeuronSWC_segs: segment end at root #%d", V3DLONG(cur_node.n));
cur_node.nchild --;
break; //over, a simple segment
}
else if (n>1 && nodelink.nlink >2) // branch point (in link_map) ///////////
{
//qDebug("decompose_V_NeuronSWC_segs: segment end at branch #%d", V3DLONG(cur_node.n));
cur_node.nchild --;
break; //over, a simple segment
}
else if (n>1 && inext==istart) // i_left point (a loop) ///////////
{
//qDebug("decompose_V_NeuronSWC_segs: segment end at branch #%d", V3DLONG(cur_node.n));
cur_node.nchild --;
break; //over, a simple segment
}
else //(nodelink.nlink==2) // path node ///////////////////////////////////////////////
{
//qDebug("decompose_V_NeuronSWC_segs: node #%d", j);
V3DLONG parent = cur_node.parent;
inext = link_map[parent].i; //// next point in seg
cur_node.nchild = -1; // label to remove
}
}
if ( isTip )
{ // measure length
segLen = 0;
float preX = new_seg.row.at(0).x;
float preY = new_seg.row.at(0).y;
float preZ = new_seg.row.at(0).z;
for (int i = 1; i < new_seg.row.size(); i++ )
{
float curX = new_seg.row.at(i).x;
float curY = new_seg.row.at(i).y;
float curZ = new_seg.row.at(i).z;
segLen += sqrt( (preX - curX)*(preX - curX) + (preY - curY)*(preY - curY) +(preZ - curZ)*(preZ - curZ) );
}
// compare the length and radius of parent branch point
if ( segLen < 2 * in_swc.row[istart].r )
{
continue;
}
}
if (new_seg.row.size()>0 )//>=2)//? single point
{
new_seg.row[new_seg.row.size()-1].parent = -1; // set segment end
char buf[10];
new_seg.name = sprintf(buf,"%d", out_swc_segs.size()+1);
new_seg.b_linegraph=true; //donot forget to do this //####################
out_swc_segs.push_back(new_seg);
}
}
// merge the segments
V_NeuronSWC_list swcList;
swcList.seg = out_swc_segs;
V_NeuronSWC out_swc = merge_V_NeuronSWC_list (swcList);
return out_swc;
}
