bool autotrace(const V3DPluginArgList & input, V3DPluginArgList & output,V3DPluginCallback2 &callback)
{
cout<<"Welcome to MOST tracing"<<endl;
unsigned int c=1;
int InitThreshold = 20;
seed_size_all = 20;
int slipsize=20;
if (input.size()>=2)
{
vector<char*> paras = (*(vector<char*> *)(input.at(1).p));
cout<<paras.size()<<endl;
if(paras.size() >= 1) c = atoi(paras.at(0));
if(paras.size() >= 2) InitThreshold = atoi(paras.at(1));
if(paras.size() >= 3) seed_size_all = atoi(paras.at(2));
if(paras.size() >= 4) slipsize = atoi(paras.at(3));
}
char * inimg_file = ((vector<char*> *)(input.at(0).p))->at(0);
cout<<"ch = "<<c<<endl;
cout<<"threshold = "<<InitThreshold<<endl;
cout<<"inimg_file = "<<inimg_file<<endl;
cout<<"seedsize = "<<seed_size_all<<endl;
cout<<"slipsize = "<<slipsize<<endl;
Image4DSimple *subject = callback.loadImage(inimg_file);
if(!subject || !subject->valid())
{
v3d_msg("Fail to load the input image.",0);
if (subject) {delete subject; subject=0;}
return false;
}
if( c < 1 || c > subject->getCDim())
{
v3d_msg("Invalid channel input.",0);
if (subject) {delete subject; subject=0;}
return false;
}
V3DLONG N = subject->getXDim();
V3DLONG M = subject->getYDim();
V3DLONG P = subject->getZDim();
V3DLONG pagesz = N*M*P;
int datatype = subject->getDatatype();
unsigned char *data1d = subject->getRawDataAtChannel(c-1);
unsigned char *output_image=0;
switch (datatype)
{
case V3D_UINT8:
try {output_image = new unsigned char [pagesz];}
catch(...) {v3d_msg("cannot allocate memory for output_image.",0); return false;}
for(V3DLONG i = 0; i<pagesz; i++)
output_image[i] = data1d[i];
break;
default: v3d_msg("Invalid data type. Do nothing.",0); return false;
}
MOSTImage img;
img.setData( (unsigned char*)output_image, subject->getXDim(),subject->getYDim(),subject->getZDim(),subject->getCDim(),subject->getDatatype());
QString swcfile = QString(inimg_file) + "_MOST.swc";
LandmarkList seedList;
QTime qtime_seed;
qtime_seed.start();
if(1)
{
for(int i =1;i<=N;i+=20)
img.auto_detect_seedx(seedList,i,InitThreshold,seed_size_all);
}
if(1)
{
for(int i =1;i<=M;i+=20)
img.auto_detect_seedy(seedList,i,InitThreshold,seed_size_all);
}
if(1)
{
for(int i =1;i<=P;i+=20)
img.auto_detect_seedz(seedList,i,InitThreshold,seed_size_all);
}
qDebug(" cost time seed = %g sec", qtime_seed.elapsed()*0.001);
static long init_flag = 0;
for(init_flag = 0;init_flag<subject->getTotalUnitNumberPerChannel();init_flag++)
{
visited.push_back(false);
}
// converte the formate
NeuronTree vt;
QTime qtime;
qtime.start();
vt = img.trace_seed_list(seedList, visited,InitThreshold,1.0,1.0,1.0,swcfile,slipsize,0);
qDebug(" cost time totol= %g sec", qtime.elapsed()*0.001);
v3d_msg(QString("\nNow you can drag and drop the generated swc fle [%1] into Vaa3D.").arg(swcfile),0);
if (subject) {delete subject; subject=0;}
return true;
}
bool findedgeimg(V3DPluginCallback2 &callback, const V3DPluginArgList & input, V3DPluginArgList & output)
{
cout<<"Welcome to Label edge of a mask image"<<endl;
if (output.size() != 1) return false;
int method_code = 0;
if (input.size()>=2)
{
vector<char*> paras = (*(vector<char*> *)(input.at(1).p));
if(paras.size() >= 1) method_code = atoi(paras.at(0));
}
char * inimg_file = ((vector<char*> *)(input.at(0).p))->at(0);
char * outimg_file = ((vector<char*> *)(output.at(0).p))->at(0);
cout<<"method_code = "<<method_code<<endl;
cout<<"inimg_file = "<<inimg_file<<endl;
cout<<"outimg_file = "<<outimg_file<<endl;
Image4DSimple *image = callback.loadImage(inimg_file);
if (!image || !image->valid())
{
cerr<<"load image "<<inimg_file<<" error!"<<endl;
return false;
}
V3DLONG szx=image->getXDim(),
szy=image->getYDim(),
szz=image->getZDim(),
szc=image->getCDim();
V3DLONG N = image->getTotalUnitNumber();
//create the output buffer
unsigned char *outputData = 0;
try
{
outputData = new unsigned char [N];
for (V3DLONG tmpi=0; tmpi<N; ++tmpi) outputData[tmpi] = 0; //preset to be all 0
}
catch (...)
{
v3d_msg("Fail to allocate memory.");
if (outputData) {
delete []outputData;
outputData=0;
}
return false;
}
Image4DSimple outputImage;
outputImage.setData((unsigned char*)outputData, szx, szy, szz, szc, V3D_UINT8);
Image4DProxy<Image4DSimple> outputIProxy(&outputImage);
//now do computation
{
bool bset255 = (method_code==0) ? false : true;
Image4DProxy<Image4DSimple> p(image);
Image4DProxy_foreach(p, ix, iy, iz, ic)
{
double v = p.value_at(ix, iy, iz, ic);
V3DLONG cx, cy, cz;
bool bb=false;
for (cz = iz-1; cz<iz+2; ++cz)
{
for (cy = iy-1; cy<iy+2; ++cy)
{
for (cx = ix-1; cx<ix+2; ++cx)
{
if (!p.is_inner(cx, cy, cz, ic))
continue;
if (v!=p.value_at(cx, cy, cz, ic))
{
*outputIProxy.at(ix, iy, iz, ic) = (bset255) ? 255 : v;
bb = true;
break;
}
}
if (bb) break;
}
if (bb) break;
}
//note that all value had been preset as 0, thus no need to set as the background color in case not an edge point
}
}
void set_dialog(V3DPluginCallback2 &v3d, QWidget *parent)
{
int x_begin;
int x_end;
int x_distance;
int y_begin;
int y_end;
int y_distance;
int z_begin;
int z_end;
int z_distance;
int pruning_flag;
int c;
QString swcfile;
int sslip;
x_flag = 0;
y_flag = 0;
z_flag = 0;
pruning_flag = 0;
v3dhandle curwin = v3d.currentImageWindow();
if (!curwin)
{
v3d_msg("You don't have any image open in the main window.");
return;
}
Image4DSimple* img = v3d.getImage(curwin);
if (!img || !img->valid())
return;
AdaTDialog dialog;
dialog.endx->setMaximum(img->getXDim()); dialog.endx->setMinimum(1); dialog.endx->setValue(img->getXDim());
dialog.endy->setMaximum(img->getYDim()); dialog.endy->setMinimum(1); dialog.endy->setValue(img->getYDim());
dialog.endz->setMaximum(img->getZDim()); dialog.endz->setMinimum(1); dialog.endz->setValue(img->getZDim());
dialog.ds->setText(QString(img->getFileName()) + "_MOST.swc");
dialog.channel->setMaximum(img->getCDim()); dialog.channel->setMinimum(1);dialog.channel->setValue(1);
if (dialog.exec()!=QDialog::Accepted)
return;
else
{
InitThreshold = dialog.threshould_value->value();
res_x_all = dialog.resx->value();
res_y_all = dialog.resy->value();
res_z_all = dialog.resz->value();
seed_size_all = dialog.size->value();
sslip = dialog.slipsize->value();
swcfile = dialog.ds->text();
c = dialog.channel->value();
QFile file(swcfile);
if (!file.open(QIODevice::WriteOnly|QIODevice::Text))
{
v3d_msg("Cannot create the swc file to write, please try it again! ");
return;
}
if(dialog.x_select->isChecked())
{
x_flag =1;
x_begin = dialog.beginx->value();
x_end = dialog.endx->value();
x_distance = dialog.distancex->value();
}
if(dialog.y_select->isChecked())
{
y_flag =1;
y_begin = dialog.beginy->value();
y_end = dialog.endy->value();
y_distance = dialog.distancey->value();
}
if(dialog.z_select->isChecked())
{
z_flag =1;
z_begin = dialog.beginz->value();
z_end = dialog.endz->value();
z_distance = dialog.distancez->value();
}
// v3d.open3DWindow(curwin);
if(dialog.pruning->isChecked())
{
pruning_flag =1;
}
startVesselTracing(v3d,x_flag,y_flag,z_flag,x_begin,x_end,x_distance,y_begin,y_end,y_distance,z_begin,z_end,z_distance,swcfile,sslip,pruning_flag,c);
}
return;
}
void ThreadedTracer::run(){
qDebug()<<"loadScan input: "<<latestString;
//QString latestString = getFileString();
// latestString =QString("/data/mat/BRL/DATA_FOR_GROUP/testDataForZhi/ZSeries-06092016-1407-8470/ZSeries-06092016-1407-8470_Cycle00001_Ch1_000001.ome.tif");
// bool isAdaptive = 1;
// int methodChoice = 1;
//LandmarkList inputRootList;
QString fString;
fString = QString("Cycle%1").arg(tileNumber,5,10,QLatin1Char('0'));
qDebug()<<tileNumber;
QList<LandmarkList> newTipsList;
LandmarkList newTargetList;
QFileInfo imageFileInfo = QFileInfo(latestString);
if (imageFileInfo.isReadable()){
Image4DSimple * pNewImage = cb->loadImage(latestString.toLatin1().data());
QDir imageDir = imageFileInfo.dir();
QStringList filterList;
filterList.append(QString("*").append(fString).append("_Ch").append(channel).append("*.tif"));
qDebug()<<"filterlist.first()"<<filterList.first();
imageDir.setNameFilters(filterList);
QStringList fileList = imageDir.entryList();
//use this to id the number of images in the stack (in one channel?!)
V3DLONG x = pNewImage->getXDim();
V3DLONG y = pNewImage->getYDim();
V3DLONG nFrames = fileList.length();
V3DLONG tunits = x*y*nFrames;
unsigned short int * total1dData = new unsigned short int [tunits];
unsigned short int * total1dData_mip= new unsigned short int [x*y];
for(V3DLONG i =0 ; i < x*y; i++)
total1dData_mip[i] = 0;
V3DLONG totalImageIndex = 0;
double p_vmax=0;
qDebug()<<"nFrames = "<<nFrames;
for (int f=0; f<nFrames; f++){
qDebug()<<fileList[f];
Image4DSimple * pNewImage = cb->loadImage(imageDir.absoluteFilePath(fileList[f]).toLatin1().data());
if (pNewImage->valid()){
unsigned short int * data1d = 0;
data1d = new unsigned short int [x*y];
data1d = (unsigned short int*)pNewImage->getRawData();
for (V3DLONG i = 0; i< (x*y); i++)
{
total1dData[totalImageIndex]= data1d[i];
if(data1d[i] > p_vmax) p_vmax = data1d[i];
if(total1dData_mip[i] < data1d[i]) total1dData_mip[i] = data1d[i];
totalImageIndex++;
}
if(data1d) {delete []data1d; data1d = 0;}
}else{
qDebug()<<imageDir.absoluteFilePath(fileList[f])<<" failed!";
}
}
Image4DSimple* total4DImage = new Image4DSimple;
total4DImage->setData((unsigned char*)total1dData, x, y, nFrames, 1, V3D_UINT16);
Image4DSimple* total4DImage_mip = new Image4DSimple;
total4DImage_mip->setData((unsigned char*)total1dData_mip, x, y, 1, 1, V3D_UINT16);
QString swcString = saveDirString;
swcString.append("/x_").append(QString::number((int)tileLocation.x)).append("_y_").append(QString::number((int)tileLocation.y)).append("_").append(imageFileInfo.fileName()).append(fString).append(".swc");
QString scanDataFileString = saveDirString;
scanDataFileString.append("/").append("scanData.txt");
qDebug()<<scanDataFileString;
QFile saveTextFile;
saveTextFile.setFileName(scanDataFileString);// add currentScanFile
if (!saveTextFile.isOpen()){
if (!saveTextFile.open(QIODevice::Text|QIODevice::Append )){
qDebug()<<"unable to save file!";
return;} }
QTextStream outputStream;
outputStream.setDevice(&saveTextFile);
total4DImage->setOriginX(tileLocation.x);
total4DImage->setOriginY(tileLocation.y);
qDebug()<<total4DImage->getOriginX();
outputStream<< (int) total4DImage->getOriginX()<<" "<< (int) total4DImage->getOriginY()<<" "<<swcString<<" "<< (int) x<<" "<< (int) y<<" "<<"\n";
saveTextFile.close();
V3DLONG mysz[4];
mysz[0] = total4DImage->getXDim();
mysz[1] = total4DImage->getYDim();
mysz[2] = total4DImage->getZDim();
mysz[3] = total4DImage->getCDim();
tileLocation.ev_pc1 = (double) total4DImage->getXDim();
tileLocation.ev_pc2 = (double) total4DImage->getYDim();
QString imageSaveString = saveDirString;
// add bit of code to image green - red channels. This will require an additional argument or another signal/slot combination to monitor the value of a combobox in the GUI...
// add button to do || nT on mXtls
//convert to 8bit image using 8 shiftnbits
unsigned char * total1dData_8bit = 0;
try
{
total1dData_8bit = new unsigned char [tunits];
}
catch (...)
{
v3d_msg("Fail to allocate memory in total1dData_8bit.\n");
return;
}
double dn = pow(2.0, double(5));
for (V3DLONG i=0;i<tunits;i++)
{
double tmp = (double)(total1dData[i]) / dn;
if (tmp>255) total1dData_8bit[i] = 255;
else
total1dData_8bit[i] = (unsigned char)(tmp);
}
total4DImage->setData((unsigned char*)total1dData_8bit, x, y, nFrames, 1, V3D_UINT8);
imageSaveString.append("/x_").append(QString::number((int)tileLocation.x)).append("_y_").append(QString::number((int)tileLocation.y)).append("_").append(imageFileInfo.fileName()).append(imageFileInfo.fileName()).append(fString).append(".v3draw");
simple_saveimage_wrapper(*cb, imageSaveString.toLatin1().data(),(unsigned char *)total1dData_8bit, mysz, V3D_UINT8);
qDebug()<<"=== immediately before tracing =====";
//-------------
V3DPluginArgItem arg;
V3DPluginArgList input;
V3DPluginArgList output;
QString full_plugin_name;
QString func_name;
arg.type = "random";std::vector<char*> arg_input;
std:: string fileName_Qstring(imageSaveString.toStdString());char* fileName_string = new char[fileName_Qstring.length() + 1]; strcpy(fileName_string, fileName_Qstring.c_str());
arg_input.push_back(fileName_string);
arg.p = (void *) & arg_input; input<< arg;
char* char_swcout = new char[swcString.length() + 1];strcpy(char_swcout, swcString.toStdString().c_str());
arg.type = "random";std::vector<char*> arg_output;arg_output.push_back(char_swcout); arg.p = (void *) & arg_output; output<< arg;
arg.type = "random";
std::vector<char*> arg_para;
arg_para.push_back("1");
arg_para.push_back("1");
full_plugin_name = "neuTube";
func_name = "neutube_trace";
arg.p = (void *) & arg_para; input << arg;
if(!cb->callPluginFunc(full_plugin_name,func_name,input,output))
{
qDebug()<<("Can not find the tracing plugin!\n");
return;
}
emit done();
}else{
qDebug()<<"invalid image";
}
}
