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;
}
TargetList::TargetList(QWidget *parent) :
QWidget(parent)
{
targetTable = new QTableWidget(1,3,this);
scanLocTable = new QTableWidget(1,5,this);
QLabel* targetTableLabel = new QLabel("&Targets");
QLabel* scanLocTableLabel = new QLabel("ROI locations");
QStringList ttHeaders;
ttHeaders.append("Target Number");
ttHeaders.append("x (um)");
ttHeaders.append("y (um)");
targetTable->setHorizontalHeaderLabels(ttHeaders);
QStringList sltHeaders;
sltHeaders.append("ROI Number");
sltHeaders.append("x (um)");
sltHeaders.append("y (um)");
sltHeaders.append("x width");
sltHeaders.append("y width");
scanLocTable->setHorizontalHeaderLabels(sltHeaders);
targetTableLabel->setBuddy(targetTable);
connect(targetTable,SIGNAL(cellClicked(int,int)), this, SLOT(updateScanTable(int,int)));
mainLayout = new QGridLayout;
mainLayout->addWidget(targetTableLabel,0,0);
mainLayout->addWidget(targetTable, 1,0,3,1);
mainLayout->addWidget(scanLocTableLabel,0,1);
mainLayout->addWidget(scanLocTable,1,2,3,2 );
scanLocTable->adjustSize();
targetTable->adjustSize();
setLayout(mainLayout);
qDebug()<<"constructed targettable";
qDebug()<<QString::number(scanLocTable->isVisible());
LandmarkList fakeTargetList;
LocationSimple testLoc1;
fakeTargetList.append(testLoc1);
QList<LandmarkList> fakeScanLocations;
fakeScanLocations.append(fakeTargetList);
updateTargetTable(fakeTargetList, fakeScanLocations);
}
void TargetList::updateTargetTable(LandmarkList inputTargetList, QList<LandmarkList> inputScanLocations){
qDebug()<<"updating Table";
targetList = inputTargetList;
scanLocations = inputScanLocations;
if (inputTargetList.isEmpty()){
qDebug()<<"no targets";
return;
}
targetTable->clearContents();
for (int i=0; i<inputTargetList.length(); i++){
targetTable->insertRow(i);
QTableWidgetItem *cell = targetTable->item(i,0);
if (!cell){
cell = new QTableWidgetItem;
targetTable->setItem(i,0,cell);
}
cell->setText(QString::number(i));
cell = targetTable->item(i,1);
if (!cell){
cell = new QTableWidgetItem;
targetTable->setItem(i,1,cell);
}
cell->setText(QString::number(inputTargetList.value(i).x));
cell = targetTable->item(i,2);
if (!cell){
cell = new QTableWidgetItem;
targetTable->setItem(i,2,cell);
}
cell->setText(QString::number(inputTargetList.value(i).y));
}
targetTable->setCurrentCell(0,0);
targetTable->adjustSize();
}
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;
}
bool load_data(V3DPluginCallback2 *cb,unsigned char * & image1Dc_in,LandmarkList &LList,ImagePixelType &pixeltype,
V3DLONG sz_img[4],v3dhandle &curwin)
{
V3DPluginCallback2 *callback=cb;
v3dhandleList v3dhandleList_current=callback->getImageWindowList();
QList <V3dR_MainWindow *> cur_list_3dviewer = callback->getListAll3DViewers();
LandmarkList LList_in;
if (v3dhandleList_current.size()==0){
v3d_msg("Please open image and select markers");
return false;
}
else if (v3dhandleList_current.size()==1) //One window open
{
//get markers and check markers
LList_in.clear();
LList_in = callback->getLandmark(v3dhandleList_current[0]);
if (LList_in.size()==0)
{
v3d_msg("Please load markers");
return false;
}
curwin=v3dhandleList_current[0];
}
else if (v3dhandleList_current.size()>1)
{
QStringList items;
int i;
for (i=0; i<v3dhandleList_current.size(); i++)
items << callback->getImageName(v3dhandleList_current[i]);
for (i=0; i<cur_list_3dviewer.count(); i++)
{
QString curname = callback->getImageName(cur_list_3dviewer[i]).remove("3D View [").remove("]");
bool b_found=false;
for (int j=0; j<v3dhandleList_current.size(); j++)
if (curname==callback->getImageName(v3dhandleList_current[j]))
{
b_found=true;
break;
}
if (!b_found)
items << callback->getImageName(cur_list_3dviewer[i]);
}
//qDebug()<<"Number of items:"<<items.size();
QDialog *mydialog=new QDialog;
QComboBox *combo=new QComboBox;
combo->insertItems(0,items);
QLabel *label_win=new QLabel;
label_win->setText("You have multiple windows open, please select one image:");
QGridLayout *layout= new QGridLayout;
layout->addWidget(label_win,0,0,1,1);
layout->addWidget(combo,1,0,4,1);
QPushButton *button_d_ok=new QPushButton("Ok");
button_d_ok->setFixedWidth(100);
QPushButton *button_d_cancel=new QPushButton("Cancel");
button_d_cancel->setFixedWidth(100);
QHBoxLayout *box=new QHBoxLayout;
box->addWidget(button_d_ok,Qt::AlignCenter);
box->addWidget(button_d_cancel,Qt::AlignCenter);
layout->addLayout(box,5,0,1,1);
QDialog::connect(button_d_ok,SIGNAL(clicked()),mydialog,SLOT(accept()));
QDialog::connect(button_d_cancel,SIGNAL(clicked()),mydialog,SLOT(reject()));
mydialog->setLayout(layout);
mydialog->exec();
if (mydialog->result()==QDialog::Accepted)
{
int tmp=combo->currentIndex();
curwin=v3dhandleList_current[tmp];
}
else
{
v3d_msg("You have not selected a window");
return false;
}
//get markers and check markers
LList_in.clear();
LList_in = callback->getLandmark(curwin);
if (LList_in.size()==0)
{
v3d_msg("Please load markers");
return false;
}
}
//Get the image info
Image4DSimple* p4DImage = callback->getImage(curwin);
if (!p4DImage){
QMessageBox::information(0, "", "The image pointer is invalid. Ensure your data is valid and try again!");
return false;
}
sz_img[0]=p4DImage->getXDim();
sz_img[1]=p4DImage->getYDim();
sz_img[2]=p4DImage->getZDim();
sz_img[3]=p4DImage->getCDim();
if (sz_img[3]>3){
sz_img[3]=3;
QMessageBox::information(0,"","More than 3 channels were loaded."
"The first 3 channel will be applied for analysis.");
}
V3DLONG size_tmp=sz_img[0]*sz_img[1]*sz_img[2]*sz_img[3];
pixeltype = p4DImage->getDatatype();
image1Dc_in=memory_allocate_uchar1D(size_tmp);
unsigned char * ptmp=p4DImage->getRawData();
memcpy(image1Dc_in,ptmp,size_tmp*pixeltype);
LList.clear();
for(int i=0; i<LList_in.size(); i++){
LList.append(LList_in.at(i));
LList[i].color.r=196;
LList[i].color.g=LList[i].color.b=0;
}
return true;
}
//return a list of predictions ? Or a mask image?
// Also need numbers of cells, and centers of cells
//work on local maxima
//use different preprocessing, feature extraction etc.
//1d_dimension is ROIDImension + 1
//Note: be aware of the order x, y, z are passed to submethods.
unsigned char* CellClassifier::annotateAnImage(V3DPluginCallback &callback, v3dhandle win, Image4DSimple* image, int ch, int grid, int dimension_1d)
{
std::vector <LocationSimple> detectedPos;
LandmarkList markerList;
long sx=image->sz0, sy=image->sz1, sz=image->sz2;
long pagesz=sx*sy;
long channelsz=sx*sy*sz;
//smoothed and get local maxima
//sensitive gaussian filtering radius
// ??????? use distance transform image???????
int Wx = dimension_1d, Wy = dimension_1d, Wz = dimension_1d;
unsigned char * filtered = gaussianfiltering(image->getRawData(), sx, sy, sz, Wx, Wy, Wz);
unsigned char * flag_lm = check_localMaxima_ker(filtered, sx, sy, sz, 0);
//unsigned char * flag_lm = check_localMaxima(callback, image, ch); //062110
unsigned char *results = new unsigned char [channelsz]; //prediction results.
if (!results)
{
printf("Fail to allocate memory.\n");
return NULL;
}
unsigned char *clearFlag = new unsigned char [channelsz]; //prediction results.
if (!clearFlag)
{
printf("Fail to allocate memory.\n");
return NULL;
}
//get model from file
//string modelfile = "test_svm_model.txt";
struct svm_model * pmodel = pclassifier->loadSVMModel();
int r = dimension_1d/2;
int prediction;
int total = 0, cellcount = 0;
//use (a somehow more restrict) template matching for adding some candidates.
bool candidateflag = false;
long cubesize = dimension_1d*dimension_1d*dimension_1d;
double sigmax = (dimension_1d-1)/4.0, sigmay = (dimension_1d-1)/4.0, sigmaz = (dimension_1d-1)/4.0;
double *g_1d = genGaussianKernel1D(dimension_1d, dimension_1d, dimension_1d, sigmax, sigmay, sigmaz);
double curcoeff;
//double coeff_th = 0.66; //will use average coeff of positive ones from training!!!!
//init results
for(long iz = 0; iz < sz; iz++)
{
long offsetk = iz*sx*sy;
for(long iy = 0; iy < sy; iy++)
{
long offsetj = iy*sx;
for(long ix = 0; ix < sx; ix++)
{
long idx = offsetk + offsetj + ix;
results[idx] = 0;
clearFlag[idx] = 1; //will be cleared later
}
}
}
//start search
int denied = 0;
for(long iz = r; iz < sz-r; iz++)
{
long offsetk = iz*sx*sy;
for(long iy = r; iy < sy-r; iy++)
{
long offsetj = iy*sx;
for(long ix = r; ix < sx-r; ix++)
{
long idx = offsetk + offsetj + ix;
//debug:
//if(ix == 61 && iy==39 && iz==17) cout << "the missed one is here!!" << (int) flag_lm[idx] << endl;
//if(ix == 63 && iy ==43 && iz ==16) cout << "the valley one (#3) is here!!" << (int) flag_lm[idx] << endl;;
//if(ix == 65 && iy ==43 && iz ==14) cout << "the valley start point is here!!" << (int) flag_lm[idx] << endl;;
if(flag_lm[idx] == 255 && clearFlag[idx] == 1 ) //only work on local maxima (and not cleared)
{
//classify to see if it is a center
prediction = classifyAVoxel(image, ch, iz, iy, ix, dimension_1d, pmodel);
if(prediction == 0)
denied ++;
candidateflag = false;
if (prediction == 1 || candidateflag)
{
//cellcount ++;
//results[idx] = 255;
//
double ncx, ncy, ncz;
unsigned char * currentCube =getACube(image, ch, iz, iy, ix, dimension_1d, dimension_1d*dimension_1d, pagesz, channelsz); //fixed a bug 060210
curcoeff = coeff(currentCube, g_1d, cubesize);
//debug
if(ix == 65 && iy ==43 && iz ==14)
std::cout << "coeff at valley:" << curcoeff << std::endl ;
delete[] currentCube;
//if(curcoeff < 0.45)
//{
// std::cout << "coeff too low for (" << ix << " " << iy << " " << iz << ") " << " coef: " << curcoeff << endl;
// continue;
//}
//converge toward center of mass,
//move the center using highest score (either matching or classifier).
/*
getMatchingCenter(image, ix, iy, iz, r, ch, ncx, ncy, ncz, flag_lm);
double nncx, nncy, nncz;
//getMassCenter(image, ncx, ncy, ncz, r, ch, nncx, nncy, nncz, flag_lm);
getMassCenter(filtered, sx,sy,sz, ncx, ncy, ncz, r, ch, nncx, nncy, nncz, flag_lm);
int newx = (int) (nncx+0.5), newy = (int) (nncy+0.5), newz = (int) (nncz+0.5); //rounding
*/
getMassCenter(filtered, sx,sy,sz, ix, iy, iz, r, ch, ncx, ncy, ncz, flag_lm);
int newx = (int) (ncx+0.5), newy = (int) (ncy+0.5), newz = (int) (ncz+0.5); //rounding
//make a final decision if, after moving, there is a close neighbor identified already on the new spot
if (nearACenter(newx, newy, newz, results, r, sx, sy, sz))
{
// std::cout << "#" << cellcount << ", there's 1 nearby. Skip. " ;
continue;
}
long foundidx = newz*sx*sy + newy*sx + newx;
//check if move to a lm , possible for valley area between cells.
//why this made the debug image has 20 down to 9 cells!!
/*if ( flag_lm[foundidx] == 0)
{
std::cout << "non-lm. Skip. " ;
continue;
}*/
//else: a cell is found, set that to 255
results[foundidx] = 255;
//remove foreground around that center from image: based on radius? reestimate based on std?
//int testt=0; for(int lll =0; lll < channelsz; lll++) if (flag_lm[lll] ==255) testt ++;
//cout << "postive flags: " << testt << endl;
//will not consider its neighbors in the future.
clearSurrounding(image, ch, newx, newy, newz, r, clearFlag);
//testt=0; for(int lll =0; lll < channelsz; lll++) if (flag_lm[lll] ==255) testt ++;
//cout << "postive flags after: " << testt << endl;
//increase cell counter by 1.
LocationSimple pp(newx, newy, newz);
detectedPos.push_back(pp);
LocationSimple marker(newx +1, newy +1, newz +1); //convert back to 1-base
marker.radius = r;
markerList.push_back(marker);
cellcount ++;
}
}//end local maxima
}//end ix
}//end iy
}//end iz
std::cout << "total number of cells:" << cellcount << std::endl;
char buf[30];
itoa(cellcount, buf, 10);
string resstring = "total cells:";
resstring.append(buf);
QMessageBox::information(0, "debug", QString(resstring.c_str()));
std::cout << "total denied local maximum:" << denied << std::endl;
svm_destroy_model(pmodel);
/* //results only
Image4DSimple p4DImage;
p4DImage.setData(results, sx, sy, sz, 1, image->datatype);
v3dhandle newwin = callback.newImageWindow();
callback.setImage(newwin, &p4DImage);
callback.setImageName(newwin, "prediction results image");
callback.updateImageWindow(newwin);
*/
//v3d does not allow me to use the same image data in a different (new) window?
//I need to make a copy of the data first?
unsigned char *newimage1d = new unsigned char [channelsz];
if(!newimage1d)
{
std::cout << "not enough memory to create result window";
return results;
}
unsigned char* image1d = image->getRawData();
for(long n = 0; n < channelsz; n++)
newimage1d[n] = image1d[ch*channelsz + n];
//show resulting cell markers in a new window
Image4DSimple newImage;
newImage.setData(newimage1d, sx, sy, sz, 1, image->datatype);
v3dhandle newwin = callback.newImageWindow();
callback.setImage(newwin, &newImage);
callback.setImageName(newwin, "cell_counted");
callback.updateImageWindow(newwin);
callback.setLandmark(newwin, markerList);
//de-alloc
//should I close svm file here???
if(filtered) { std::cout << "clean up memory for filtered image." << endl; delete[] filtered; }
if(flag_lm) { std::cout << "clean up memory for local maximum." << endl; delete[] flag_lm; }
if(clearFlag) { std::cout << "clean up memory for flags." << endl; delete[] clearFlag; }
return results;
}
//void startVesselTracing ( V3DPluginCallback2 &v3d, QWidget *parent )
void startVesselTracing(V3DPluginCallback2 &v3d,int xflag,int yflag,int zflag,int xbegin, int xend,int xdis,int ybegin,int yend,int ydis,int zbegin,int zend,int zdis,QString swcfile,int slipsize,int pruning_flag,int c)
{
v3dhandle curwin = v3d.currentImageWindow();
if (!curwin)
{
v3d_msg("You don't have any image open in the main window.");
return;
}
//ensure the 3d viewer window is open; if not, then open it
// v3d.open3DWindow(curwin);
// get land mark list
LandmarkList seedList = v3d.getLandmark(curwin);
Image4DSimple* oldimg = v3d.getImage(curwin);
unsigned char* data1d = oldimg->getRawDataAtChannel(c-1);
ImagePixelType pixeltype = oldimg->getDatatype();
V3DLONG pagesz = oldimg->getTotalUnitNumberPerChannel();
unsigned char *output_image=0;
switch (pixeltype)
{
case V3D_UINT8:
try {output_image = new unsigned char [pagesz];}
catch(...) {v3d_msg("cannot allocate memory for output_image."); return;}
for(V3DLONG i = 0; i<pagesz; i++)
output_image[i] = data1d[i];
break;
default: v3d_msg("Invalid data type. Do nothing."); return;
}
V3DLONG in_sz[4];
in_sz[0] = oldimg->getXDim(); in_sz[1] = oldimg->getYDim(); in_sz[2] = oldimg->getZDim();in_sz[3] = 1;
// simple_saveimage_wrapper(v3d, "temp.v3draw", (unsigned char *)output_image, in_sz, pixeltype);
MOSTImage img;
// set data
img.setData( (unsigned char*)output_image, oldimg->getXDim(),oldimg->getYDim(),oldimg->getZDim(),oldimg->getCDim(),oldimg->getDatatype());
if ( seedList.isEmpty() )
{
QTime qtime_seed;
qtime_seed.start();
//img.auto_detect_seedz(seedList,img.getZDim()/2);
if(xflag)
{
for(int i =xbegin;i<=xend;i+=xdis)
img.auto_detect_seedx(seedList,i,InitThreshold,seed_size_all);
// img.auto_detect_seedx(seedList,xend);
}
if(yflag)
{
for(int i =ybegin;i<=yend;i+=ydis)
img.auto_detect_seedy(seedList,i,InitThreshold,seed_size_all);
// img.auto_detect_seedy(seedList,yend);
}
if(zflag)
{
for(int i =zbegin;i<=zend;i+=zdis)
img.auto_detect_seedz(seedList,i,InitThreshold,seed_size_all);
//img.auto_detect_seedz(seedList,zend);
}
qDebug(" cost time seed = %g sec", qtime_seed.elapsed()*0.001);
}
// clear visited, only excute once
static long init_flag = 0;
/* if ( init_flag <= 0 )
{
visited.fill( false, oldimg->getTotalUnitNumber());
init_flag ++;
}*/
for(init_flag = 0;init_flag<oldimg->getTotalUnitNumber();init_flag++)
{
visited.push_back(false);
}
// converte the formate
NeuronTree vt;
QTime qtime;
qtime.start();
vt = img.trace_seed_list(seedList, visited,InitThreshold,res_x_all,res_y_all,res_z_all,swcfile,slipsize,pruning_flag);
qDebug(" cost time totol= %g sec", qtime.elapsed()*0.001);
v3d_msg(QString("Now you can drag and drop the generated swc fle [%1] into Vaa3D.").arg(swcfile),1);
// NeuronTree vt_old = v3d.getSWC(curwin);
// visualization
// v3d.setLandmark(curwin, seedList);
// v3d.setSWC(curwin,vt);
// v3d.pushObjectIn3DWindow(curwin);
// v3d.updateImageWindow(curwin);
//img.~MOSTImage();
}
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;
}
