vector<V3DLONG> landMarkList2poss(LandmarkList LandmarkList_input, V3DLONG _offset_Y, V3DLONG _offest_Z)
{
vector<V3DLONG> poss_result;
V3DLONG count_landmark=LandmarkList_input.count();
for (V3DLONG idx_input=0;idx_input<count_landmark;idx_input++)
{
poss_result.push_back(landMark2pos(LandmarkList_input.at(idx_input), _offset_Y, _offest_Z));
}
return poss_result;
}
void processImage(V3DPluginCallback2 &callback, QWidget *parent)
{
v3dhandle curwin = callback.currentImageWindow();
if (!curwin)
{
v3d_msg("You don't have any image open in the main window.");
return;
}
Image4DSimple* p4DImage = callback.getImage(curwin);
QString imgname = callback.getImageName(curwin);
if (!p4DImage)
{
v3d_msg("The image pointer is invalid. Ensure your data is valid and try again!");
return;
}
int tmpx,tmpy,tmpz,x1,y1,z1;
LandmarkList listLandmarks = callback.getLandmark(curwin);
LocationSimple tmpLocation(0,0,0);
int marknum = listLandmarks.count();
if(marknum ==0)
{
v3d_msg("No markers in the current image, please double check.");
return;
}
UndirectedGraph g(marknum);
for (int i=0;i<marknum;i++)
{
tmpLocation = listLandmarks.at(i);
tmpLocation.getCoord(tmpx,tmpy,tmpz);
x1 = tmpx;
y1 = tmpy;
z1 = tmpz;
for (int j=0;j<marknum;j++)
{
EdgeQuery edgeq = edge(i, j, *&g);
if (!edgeq.second && i!=j)
{
tmpLocation = listLandmarks.at(j);
tmpLocation.getCoord(tmpx,tmpy,tmpz);
double Vedge = sqrt(double(x1-tmpx)*double(x1-tmpx) + double(y1-tmpy)*double(y1-tmpy) + double(z1-tmpz)*double(z1-tmpz));
add_edge(i, j, LastVoted(i, Weight(Vedge)), *&g);
}
}
}
// property_map<UndirectedGraph, edge_weight_t>::type weightmap = get(edge_weight, *&g);
vector < graph_traits < UndirectedGraph >::vertex_descriptor > p(num_vertices(*&g));
prim_minimum_spanning_tree(*&g, &p[0]);
NeuronTree marker_MST;
QList <NeuronSWC> listNeuron;
QHash <int, int> hashNeuron;
listNeuron.clear();
hashNeuron.clear();
for (std::size_t i = 0; i != p.size(); ++i)
{
NeuronSWC S;
tmpLocation = listLandmarks.at(i);
tmpLocation.getCoord(tmpx,tmpy,tmpz);
int pn;
if(p[i] == i)
pn = -1;
else
pn = p[i] + 1;
S.n = i+1;
S.type = 7;
S.x = tmpx;
S.y = tmpy;
S.z = tmpz;
S.r = 1;
S.pn = pn;
listNeuron.append(S);
hashNeuron.insert(S.n, listNeuron.size()-1);
}
marker_MST.n = -1;
marker_MST.on = true;
marker_MST.listNeuron = listNeuron;
marker_MST.hashNeuron = hashNeuron;
/*
double** markEdge = new double*[marknum];
for(int i = 0; i < marknum; i++)
{
markEdge[i] = new double[marknum];
}
for (int i=0;i<marknum;i++)
{
tmpLocation = listLandmarks.at(i);
tmpLocation.getCoord(tmpx,tmpy,tmpz);
x1 = tmpx;
y1 = tmpy;
z1 = tmpz;
for (int j=0;j<marknum;j++)
{
tmpLocation = listLandmarks.at(j);
tmpLocation.getCoord(tmpx,tmpy,tmpz);
markEdge[i][j] = sqrt(double(x1-tmpx)*double(x1-tmpx) + double(y1-tmpy)*double(y1-tmpy) + double(z1-tmpz)*double(z1-tmpz));
}
}
//NeutronTree structure
NeuronTree marker_MST;
QList <NeuronSWC> listNeuron;
QHash <int, int> hashNeuron;
listNeuron.clear();
hashNeuron.clear();
//set node
NeuronSWC S;
tmpLocation = listLandmarks.at(0);
tmpLocation.getCoord(tmpx,tmpy,tmpz);
S.n = 1;
S.type = 7;
S.x = tmpx;
S.y = tmpy;
S.z = tmpz;
S.r = 1;
S.pn = -1;
listNeuron.append(S);
hashNeuron.insert(S.n, listNeuron.size()-1);
int* pi = new int[marknum];
for(int i = 0; i< marknum;i++)
pi[i] = 0;
pi[0] = 1;
int indexi,indexj;
for(int loop = 0; loop<marknum;loop++)
{
double min = INF;
for(int i = 0; i<marknum; i++)
{
if (pi[i] == 1)
{
for(int j = 0;j<marknum; j++)
{
if(pi[j] == 0 && min > markEdge[i][j])
{
min = markEdge[i][j];
indexi = i;
indexj = j;
}
}
}
}
if(indexi>=0)
{
tmpLocation = listLandmarks.at(indexj);
tmpLocation.getCoord(tmpx,tmpy,tmpz);
S.n = indexj+1;
S.type = 7;
S.x = tmpx;
S.y = tmpy;
S.z = tmpz;
S.r = 1;
S.pn = indexi+1;
listNeuron.append(S);
hashNeuron.insert(S.n, listNeuron.size()-1);
}else
{
break;
}
pi[indexj] = 1;
indexi = -1;
indexj = -1;
}
marker_MST.n = -1;
marker_MST.on = true;
marker_MST.listNeuron = listNeuron;
marker_MST.hashNeuron = hashNeuron;
*/
QString outfilename = imgname + "_boost_marker.swc";
if (outfilename.startsWith("http", Qt::CaseInsensitive))
{
QFileInfo ii(outfilename);
outfilename = QDir::home().absolutePath() + "/" + ii.fileName();
}
//v3d_msg(QString("The anticipated output file is [%1]").arg(outfilename));
writeSWC_file(outfilename,marker_MST);
v3d_msg(QString("You have totally [%1] markers for the file [%2] and the computed MST has been saved to the file [%3]").arg(marknum).arg(imgname).arg(outfilename));
return;
}
void reconstruction_func(V3DPluginCallback2 &callback, QWidget *parent, input_PARA &PARA, bool bmenu)
{
unsigned char* data1d = 0;
V3DLONG N,M,P,sc,c;
V3DLONG in_sz[4];
v3dhandle curwin;
if(bmenu)
{
curwin = callback.currentImageWindow();
v3dhandle curwin = callback.currentImageWindow();
if (!curwin)
{
QMessageBox::information(0, "", "You don't have any image open in the main window.");
return;
}
Image4DSimple* p4DImage = callback.getImage(curwin);
if (!p4DImage)
{
QMessageBox::information(0, "", "The image pointer is invalid. Ensure your data is valid and try again!");
return;
}
data1d = p4DImage->getRawData();
N = p4DImage->getXDim();
M = p4DImage->getYDim();
P = p4DImage->getZDim();
sc = p4DImage->getCDim();
in_sz[0] = N;
in_sz[1] = M;
in_sz[2] = P;
in_sz[3] = sc;
PARA.inimg_file = p4DImage->getFileName();
}
else
{
int datatype = 0;
if (!simple_loadimage_wrapper(callback,PARA.inimg_file.toStdString().c_str(), data1d, in_sz, datatype))
{
fprintf (stderr, "Error happens in reading the subject file [%s]. Exit. \n",PARA.inimg_file.toStdString().c_str());
return;
}
N = in_sz[0];
M = in_sz[1];
P = in_sz[2];
sc = in_sz[3];
}
//main neuron reconstruction code
//// THIS IS WHERE THE DEVELOPERS SHOULD ADD THEIR OWN NEURON TRACING CODE
// ofstream oImgInfofile;
string sImgPath = PARA.inimg_file.toStdString();
g_sAppDir = normalizePath(parentPath(sImgPath));
// g_sImageInfoPath = g_sAppDir + g_sImageInfoName;
// g_sInputRawFilePath = g_sAppDir + g_sInputRawFileName;
QString swc_name = PARA.inimg_file + "_nctuTW.swc";
g_sOutSwcFilePath = swc_name.toStdString();
//g_sOutSwcFilePath = g_sAppDir+ g_sOutSwcFileName;
size_t nDataSize = N * M * P * sc ;
width = N;
height = M;
zSize = P;
// oImgInfofile.open(g_sImageInfoPath.data(), ios::out|ios::binary);
// if(oImgInfofile.is_open()){
// oImgInfofile << N << " " << M << " " << P << endl;
// oImgInfofile.close();
// }
imgBuf_raw = new unsigned char [nDataSize];
memcpy(imgBuf_raw, data1d, nDataSize);
// ofstream oRawFile;
// oRawFile.open(g_sInputRawFilePath.data(), ios::out|ios::binary);
// if(oRawFile.is_open()){
// oRawFile.write((char *)data1d, nDataSize);
// oRawFile.close();
// }
/*
// For debug
if(nParaState == QDialog::Accepted){
std::string sPara = "Threshold = " + toString(g_rThreshold) + "; " +
"Soma = (" + toString(g_nSomaX) + ", " + toString(g_nSomaY) + ", " + toString(g_nSomaZ) + ")";
v3d_msg(QString(sPara.c_str()));
}
*/
QDlgPara* pqDlgPara;
g_nSomaX = -1;
g_nSomaY = -1;
g_nSomaZ = -1;
int nParaState = 1;
if(bmenu) //ui
{
LandmarkList Landmark;
Landmark = callback.getLandmark(curwin);
if(Landmark.size()>0)
{
g_nSomaX = Landmark.at(0).x-1;
g_nSomaY = Landmark.at(0).y-1;
g_nSomaZ = Landmark.at(0).z-1;
}
pqDlgPara = new QDlgPara(parent);
nParaState = pqDlgPara->exec();
}
else //command line
{
QList<ImageMarker> file_inmarkers;
if(!PARA.inmarker_file.isEmpty())
{
file_inmarkers = readMarker_file(PARA.inmarker_file);
g_nSomaX = file_inmarkers.at(0).x;
g_nSomaY = file_inmarkers.at(0).y;
g_nSomaZ = file_inmarkers.at(0).z;
}
else
{
g_nSomaX = -1;
g_nSomaY = -1;
g_nSomaZ = -1;
}
g_rThreshold = PARA.threshold;
}
if(nParaState)
{
NeuronTracingMain();
v3d_msg(QString("Now you can drag and drop the generated swc fle [%1] into Vaa3D.").arg(swc_name.toStdString().c_str()),bmenu);
}
if(bmenu) delete pqDlgPara;
bmenu=true;
//Output
// NeuronTree nt;
//QString swc_name = PARA.inimg_file + "_nctuTW.swc";
// nt.name = "nctuTW";
// writeSWC_file(swc_name.toStdString().c_str(),nt);
//QString swc_name(g_sOutSwcFilePath.data());
//Output
if(!bmenu)
{
if(data1d) {delete []data1d; data1d = 0;}
}
delete [] imgBuf_raw;
return;
}
int v3dneuron_tracing(V3DPluginCallback2 &callback, QWidget *parent)
{
v3dhandleList win_list = callback.getImageWindowList();
if(win_list.size()<1)
{
QMessageBox::information(0, title, QObject::tr("No image is open."));
return -1;
}
v3dhandle curwin = callback.currentImageWindow();
LandmarkList landmarks = callback.getLandmark(curwin);
if(landmarks.empty())
{
v3d_msg("Please set a landmark!");
return 0;
}
QList <ImageMarker> imagemarks;
for(int i = 0; i < landmarks.size(); i++)
{
ImageMarker m;
LocationSimple l = landmarks.at(i);
m.x = l.x;
m.y = l.y;
m.z = l.z;
imagemarks.push_back(m);
}
system("rm -f /tmp/mymarks.marker");
system("rm -f /tmp/tmp_out*");
writeMarker_file("/tmp/mymarks.marker",imagemarks);
QString img_file = callback.getImageName(curwin);
bool ok;
QString nt_path = QInputDialog::getText(0, QObject::tr("Set path"), QObject::tr("v3dneuron_tracing path : "), QLineEdit::Normal, "~/Local/bin/v3dneuron_tracing", &ok);
//QString paras = QObject::tr("v3dneuron_tracing -s %1 -S /tmp/mymarks.marker -o /tmp/tmp_out").arg(img_file);
QString paras = QObject::tr("%1 -s \"%2\" -S /tmp/mymarks.marker -o /tmp/tmp_out").arg(nt_path).arg(img_file);
qDebug(paras.toStdString().c_str());
//QMessageBox::information(0,"",paras);
system(paras.toStdString().c_str());
NeuronTree nt = readSWC_file("/tmp/tmp_out_0.swc");
//nt.editable = false;
callback.setSWC(curwin, nt);
callback.updateImageWindow(curwin);
callback.open3DWindow(curwin);
//callback.getView3DControl(curwin)->setShowSurfObjects(2);
//TestDialog dialog(callback, parent);
//if (dialog.exec()!=QDialog::Accepted) return -1;
//dialog.update();
//int i = dialog.i;
//int c = dialog.channel;
//Image4DSimple *p4DImage = callback.getImage(win_list[i]);
//if(p4DImage->getCDim() <= c) {v3d_msg(QObject::tr("The channel isn't existed.")); return -1;}
//V3DLONG sz[3];
//sz[0] = p4DImage->getXDim();
//sz[1] = p4DImage->getYDim();
//sz[2] = p4DImage->getZDim();
//unsigned char * inimg1d = p4DImage->getRawDataAtChannel(c);
//v3dhandle newwin;
//if(QMessageBox::Yes == QMessageBox::question(0, "", QString("Do you want to use the existing windows?"), QMessageBox::Yes, QMessageBox::No))
//newwin = callback.currentImageWindow();
//else
//newwin = callback.newImageWindow();
//p4DImage->setData(inimg1d, sz[0], sz[1], sz[2], sz[3]);
//callback.setImage(newwin, p4DImage);
//callback.setImageName(newwin, QObject::tr("v3dneuron_tracing"));
//callback.updateImageWindow(newwin);
return 1;
}
