bool V_NeuronSWC_list::reverse()
{
int oldnseg = seg.size();
bool res = false;
//must first decompose to simple segments
{
seg = merge_V_NeuronSWC_list(*this).decompose();
}
for (int i=0; i<seg.size(); i++)
{
res = reverse_V_NeuronSWC_inplace(seg[i]);
if (!res) break;
}
// keep old segment number
if (oldnseg==1)
{
merge();
}
return res;
}
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;
}
void V_NeuronSWC_list::merge()
{
V_NeuronSWC new_seg = merge_V_NeuronSWC_list(*this);
clear();
append(new_seg);
}
void swc_to_segments(V3DPluginCallback &callback, QWidget *parent, int method_code)
{
NeuronTree neuron;
QString filename;
QStringList filenames;
///////////////////////////////////////////////////////
if (method_code ==1)
{
filenames = QFileDialog::getOpenFileNames(0, 0,"","Supported file (*.swc)" ";;Neuron structure(*.swc)",0,0);
if(filenames.isEmpty())
{
v3d_msg("You don't have any SWC file open in the main window.");
return;
}
NeuronSWC *p_cur=0;
QDir dir;
for (V3DLONG i = 0; i < filenames.size();i++)//////re-search the bounding box
{
filename = filenames[i];
QString swcname = QFileInfo(filename).fileName();
QString curFilePath = QFileInfo(filename).path();
qDebug()<<"filenames"<<"name"<<"path"<<filename<<swcname<<curFilePath;
dir=QFileInfo(filename).dir();
QString dirname= swcname + "_seg";
dir.mkdir(dirname);
if (filename.size()>0)
{
neuron = readSWC_file(filename);
//V3DLONG seg_id, nodeinseg_id;
QList <NeuronSWC> listNeuron;
QString file= neuron.file;
//QList<NeuronSWC> & qlist = neuron.listNeuron;
V_NeuronSWC_list NeuronList = NeuronTree__2__V_NeuronSWC_list(&neuron);
V_NeuronSWC seg = merge_V_NeuronSWC_list(NeuronList);
seg.name = NeuronList.name;
seg.file = NeuronList.file;
QString swcfile;
for(int n =0; n < NeuronList.seg.size(); n++)
{
NeuronTree SS;
QList <NeuronSWC> listNeuron;
QHash <int, int> hashNeuron;
listNeuron.clear();
hashNeuron.clear();
for (V3DLONG i=0;i< NeuronList.seg.at(n).row.size();i++)
{
NeuronSWC v;
v.n = NeuronList.seg.at(n).row.at(i).data[0];
v.type = NeuronList.seg.at(n).row.at(i).data[1];
v.x = NeuronList.seg.at(n).row.at(i).data[2];
v.y = NeuronList.seg.at(n).row.at(i).data[3];
v.z = NeuronList.seg.at(n).row.at(i).data[4];
v.r = NeuronList.seg.at(n).row.at(i).data[5];
v.pn = NeuronList.seg.at(n).row.at(i).data[6];
v.seg_id = seg.row.at(n).seg_id;
v.nodeinseg_id = seg.row.at(n).nodeinseg_id;
listNeuron.append(v);
hashNeuron.insert(v.n, listNeuron.size()-1);
}
SS.n = -1;
SS.color = XYZW(seg.color_uc[0],seg.color_uc[1],seg.color_uc[2],seg.color_uc[3]);
SS.on = true;
SS.listNeuron = listNeuron;
SS.hashNeuron = hashNeuron;
SS.name = seg.name.c_str();
SS.file = seg.file.c_str();
swcfile.sprintf("%d",n);
QString curImageName1 = curFilePath +"/"+swcname + "_seg" +"/" + swcname + swcfile +".swc";
qDebug()<<"curImage"<<curImageName1;
writeSWC_file(curImageName1,SS);
//printf("NeuronListsize=%ld qlistsize=%ld num=%ld\n",a,qlist.size(),num);
//printf("name=%ls fila=%ls n=%ld\n",name,file,n);
}
}
else
{
v3d_msg("You don't have any SWC file open in the main window.");
return;
}
}
}
}
