bool IVSCC_smoothing_swc::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
if (func_name == tr("smooth_swc"))
{
cout<<"Welcome to resample_swc"<<endl;
vector<char*>* inlist = (vector<char*>*)(input.at(0).p);
vector<char*>* outlist = NULL;
vector<char*>* paralist = NULL;
if(input.size() != 2)
{
printf("Please specify both input file and step length parameter.\n");
return false;
}
paralist = (vector<char*>*)(input.at(1).p);
if (paralist->size()!=1)
{
printf("Please specify only two parameters.\n");
return false;
}
double length = atof(paralist->at(0));
QString fileOpenName = QString(inlist->at(0));
QString fileSaveName;
if (output.size()==0)
{
printf("No outputfile specified.\n");
fileSaveName = fileOpenName + QString("_Z_T%1.swc").arg(length);
}
else if (output.size()==1)
{
outlist = (vector<char*>*)(output.at(0).p);
fileSaveName = QString(outlist->at(0));
}
else
{
printf("You have specified more than 1 output file.\n");
return false;
}
vector<MyMarker*> inswc;
if (fileOpenName.toUpper().endsWith(".SWC") || fileOpenName.toUpper().endsWith(".ESWC"))
inswc = readSWC_file(fileOpenName.toStdString());
unsigned char* inimg1d = 0;
vector<HierarchySegment*> topo_segs;
swc2topo_segs(inswc, topo_segs, 1, inimg1d, 0, 0, 0);
cout<<"Smooth the final curve"<<endl;
for(int i = 0; i < topo_segs.size(); i++)
{
HierarchySegment * seg = topo_segs[i];
MyMarker * leaf_marker = seg->leaf_marker;
MyMarker * root_marker = seg->root_marker;
vector<MyMarker*> seg_markers;
MyMarker * p = leaf_marker;
while(p != root_marker)
{
seg_markers.push_back(p);
p = p->parent;
}
seg_markers.push_back(root_marker);
smooth_curve_Z(seg_markers, length);
// smooth_curve_XY(seg_markers, length);
}
inswc.clear();
topo_segs2swc(topo_segs, inswc, 0);
saveSWC_file(fileSaveName.toStdString(), inswc);
for(int i = 0; i < inswc.size(); i++) delete inswc[i];
return true;
}
else if (func_name == tr("help"))
{
v3d_msg("To be implemented.");
}
else return false;
return true;
}
bool consensus_swc_func(const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 &callback)
{
if(input.size()==0 || output.size() != 1) return false;
char * paras = NULL;
//parsing input
vector<char *> * inlist = (vector<char*> *)(input.at(0).p);
if (inlist->size()==0)
{
cerr<<"You must specify input linker or swc files"<<endl;
return false;
}
//parsing output
vector<char *> * outlist = (vector<char*> *)(output.at(0).p);
if (outlist->size()>1)
{
cerr << "You cannot specify more than 1 output files"<<endl;
return false;
}
//parsing parameters
int method_code = 1; //adj matrix
int cluster_distance_threshold = 5; // ignore nodes that far away for clustering
if (input.size()==2)
{
vector<char*> * paras = (vector<char*> *)(input.at(1).p);
if (paras->size() >= 1)
{
method_code = atoi(paras->at(0));
cout<<"method_code = "<<method_code<<endl;
if (paras->size() == 2) {
cluster_distance_threshold = atoi(paras->at(1));
cout<<"clustering distance threshold = "<<cluster_distance_threshold<<endl;
}
}
else
{
cerr<<"Too many parameters"<<endl;
return false;
}
}
vector<NeuronTree> nt_list;
QStringList nameList;
QString qs_linker;
char * dfile_result = NULL;
V3DLONG neuronNum = 0;
for (int i=0; i<inlist->size(); i++)
{
qs_linker = QString(inlist->at(i));
if (qs_linker.toUpper().endsWith(".ANO"))
{
cout<<"(0). reading a linker file."<<endl;
P_ObjectFileType linker_object;
if (!loadAnoFile(qs_linker,linker_object))
{
fprintf(stderr,"Error in reading the linker file.\n");
return 1;
}
nameList = linker_object.swc_file_list;
neuronNum += nameList.size();
for (V3DLONG i=0; i<neuronNum; i++)
{
NeuronTree tmp = readSWC_file(nameList.at(i));
nt_list.push_back(tmp);
}
}
else if (qs_linker.toUpper().endsWith(".SWC"))
{
cout<<"(0). reading an swc file"<<endl;
NeuronTree tmp = readSWC_file(qs_linker);
nt_list.push_back(tmp);
neuronNum++;
if (outlist->size()==0)
{
cerr<<"You must specify outfile name if you input a list of swcs"<<endl;
return false;
}
}
}
QString outfileName;
if (outlist->size()==0)
outfileName = qs_linker + "_consensus.swc";
else
outfileName = QString(outlist->at(0));
QList<NeuronSWC> merge_result;
if (!consensus_skeleton(nt_list, merge_result, method_code,cluster_distance_threshold, callback))
{
cerr<<"error in consensus_skeleton"<<endl;
return false;
}
export_listNeuron_2swc(merge_result,qPrintable(outfileName));
printf("\t %s has been generated successfully, size:%d.\n",qPrintable(outfileName), merge_result.size());
return true;
}
bool standardize::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
vector<char*> infiles, inparas, outfiles;
if(input.size() >= 1) infiles = *((vector<char*> *)input.at(0).p);
if(input.size() >= 2) inparas = *((vector<char*> *)input.at(1).p);
if(output.size() >= 1) outfiles = *((vector<char*> *)output.at(0).p);
if (func_name == tr("standardize"))
{
cout<<"This is standardize_swc plugin"<<endl;
if(infiles.size() <2)
{
cerr<<"Need both the reference swc file ( to seed the soma) and the input swc file."<<endl;
cerr<<"You can use the input swc file as the reference swc file, if no particular soma location is required." <<endl;
return false;
}
QString ref_swc_file = infiles[0];
QString inputswc_file = infiles[1];
if(inputswc_file.isEmpty() || ref_swc_file.isEmpty())
{
cerr<<"please check both input swc files"<<endl;
return false;
}
if (inparas.size() <1)
{
printf("Please specify two parameters - 1)the gap size for bridging during the sorting step; 2) the type to be assgined.\n");
return false;
}
double dis_th = atof(inparas.at(0));
int type = -1;//use the old type
if (inparas.size() ==2)
type = atof(inparas.at(1));
double sort_th = dis_th ; //the parameter in sort_neuron_swc plugin, specifying the length threshold to bridge the gap
QString outswc_file = outfiles[0];
cout<<"ref_swc_file = "<<ref_swc_file.toStdString().c_str()<<endl;
cout<<"inswc_file = "<<inputswc_file.toStdString().c_str()<<endl;
cout<<"gap threshold = "<<dis_th<<endl;
cout<<"outswc_file = "<<outswc_file.toStdString().c_str()<<endl;
cout<<"new type code = "<<type<<endl;
NeuronTree nt_input = readSWC_file(inputswc_file);
// cout<<" Standardize: 1) resample"<<endl;
// NeuronTree nt_input_rs = resample(nt_input, dis_th);
NeuronTree nt_ref = readSWC_file(ref_swc_file);
double soma_x, soma_y, soma_z, soma_r;
for (V3DLONG i = 0; i < nt_ref.listNeuron.size(); i++)
{
if(nt_ref.listNeuron[i].pn<0)
{
soma_x = nt_ref.listNeuron.at(i).x;
soma_y = nt_ref.listNeuron.at(i).y;
soma_z = nt_ref.listNeuron.at(i).z;
soma_r = nt_ref.listNeuron.at(i).r;
break;
}
}
V3DLONG neuronNum = nt_input.listNeuron.size();
QVector<QVector<V3DLONG> > children_list = QVector< QVector<V3DLONG> >(neuronNum, QVector<V3DLONG>() );
for (V3DLONG i = 0; i < neuronNum; i++)
{
V3DLONG parent = nt_input.listNeuron[i].pn;
if (parent < 0)
continue;
children_list[nt_input.hashNeuron.value(parent)].push_back(i);
}
double Dist = INT_MAX;
double Dist_inrange = INT_MAX;
V3DLONG soma_ID = -1;
V3DLONG dist_ID = -1;
int child_num = 0;
cout<<" standardize: 1) matching soma roots"<<endl;
// set the distance threshold to searching for matching soma node
QList<NeuronSWC> list_neurons = nt_input.listNeuron;
double search_distance_th = soma_r * 5 ;// choose the bigger value between soma_r*5 and search_distance_th*5
if (search_distance_th < sort_th *5)
{
search_distance_th = sort_th *5;
}
for (V3DLONG i=0;i<list_neurons.size();i++)
{
NeuronSWC curr = list_neurons.at(i);
double nodedist = sqrt(pow2(curr.x - soma_x) + pow2(curr.y - soma_y) + pow2(curr.z - soma_z));
if(nodedist <= search_distance_th && curr.pn <0)
{
soma_ID = curr.n;
child_num = 1;
break;
}
if(nodedist <= search_distance_th && children_list[i].size() > child_num)
{
soma_ID = curr.n;
child_num = children_list[i].size();
Dist_inrange = nodedist;
}
if(nodedist <= search_distance_th && children_list[i].size() == child_num && nodedist < Dist_inrange)
{
soma_ID = curr.n;
Dist_inrange = nodedist;
}
if(nodedist < Dist)
{
dist_ID = curr.n;
Dist = nodedist;
}
}
if(child_num < 1 || soma_ID == -1) soma_ID = dist_ID;
cout<<" Standardize: 2) sort"<<endl;
QList<NeuronSWC> result;
if (!SortSWC(nt_input.listNeuron, result ,soma_ID, sort_th))
{
v3d_msg("fail to call swc sorting function.",0);
return false;
}
cout<<" Standardize: 3) only keep the first tree(identified by the soma from the reference."<<endl;
//skip the first root
for (V3DLONG i = 1;i<result.size();i++)
{
if (result[i].pn == -1)
{//remove other trees, only keep the first one
cout<< "remove "<<result.size()-i<<" nodes"<<endl;
result.erase(result.begin()+i, result.end());
}
}
cout<<" Standardize: 4) reset type for soma and neurites"<<endl;
//1-soma
//2-axon
//3-dendrite
//4-apical dendrite
export_list2file_retype(result,outswc_file,0,type);
}
else if (func_name == tr("help"))
{
cout << "This super-plugin is used to post-processing auto reconstructions for comparisons. "<<endl;
cout << "It will identify the soma for each input reconstruction " <<endl;
cout << "based on the reference SWC file, and sort SWC nodes based on the soma root while bridging" <<endl;
cout << "all disconneted components when the gap is less then the specified gap_threshold. The search range "<<endl;
cout << "for the matching soma is 5*soma_radius." <<endl;
cout << "Usage : <vaa3d> -x standardize -f standardize -i <reference_swc_file> <inswc_file> -o <outswc_file> -p <gap_threshold> <new_neurite_type> "<<endl;
}
else
return false;
return true;
}