int check_eswc_toolbox(const V3DPluginArgList & input)
{
vaa3d_neurontoolbox_paras * paras = (vaa3d_neurontoolbox_paras *)(input.at(0).p);
NeuronTree neuron = paras->nt;
QString fileOpenName = neuron.file;
vector<V3DLONG> segment_id, segment_layer;
vector<double> feature;
if (fileOpenName.endsWith(".eswc") || fileOpenName.endsWith(".ESWC"))
neuron = read_eswc(segment_id, segment_layer, feature, fileOpenName);
else {
v3d_msg("The file type you specified is not in eswc format. Please check.");
return -1;
}
int check_result = check_eswc(neuron, segment_id, segment_layer);
if (check_result==-1 || check_result==0)
{
QMessageBox msgBox;
if (check_result==-1)
msgBox.setText("Something is wrong with the eswc file.");
else
msgBox.setText("Your eswc is written in default values.");
msgBox.setInformativeText("Do you still want to overwrite it with a standard one?");
msgBox.setStandardButtons(QMessageBox::Yes | QMessageBox::Cancel);
msgBox.setDefaultButton(QMessageBox::Cancel);
if (msgBox.exec()==QMessageBox::Yes)
{
swc2eswc(neuron, segment_id, segment_layer);
export_eswc(neuron, segment_id, segment_layer, qPrintable(fileOpenName), qPrintable(fileOpenName));
v3d_msg(QString("%1 has been updated!").arg(fileOpenName));
}
else return -1;
}
else
v3d_msg("Your eswc file is in correct format!");
return 1;
}
void NEURONSEGlugin::domenu(const QString &menu_name, V3DPluginCallback &callback, QWidget *parent)
{
if (menu_name == tr("Swc segment"))
{
swc_to_segments(callback, parent,1);
}
else if (menu_name == tr("Help"))
{
v3d_msg("(version 0.11)Neuronseg Plugin 1.0 developed by Jinzhu Yang. (Peng Lab, Janelia Research Farm Campus, HHMI), save swc files according to different segments of swc file");
return;
}
}
int swc2eswc_toolbox(const V3DPluginArgList & input)
{
vaa3d_neurontoolbox_paras * paras = (vaa3d_neurontoolbox_paras *)(input.at(0).p);
NeuronTree neuron = paras->nt;
QString fileOpenName = neuron.file;
vector<V3DLONG> segment_id, segment_layer;
if (fileOpenName.endsWith(".swc") || fileOpenName.endsWith(".SWC"))
{
segment_id, segment_layer;
if (!swc2eswc(neuron,segment_id, segment_layer))
{
v3d_msg("Cannot convert swc to eswc.\n");
return -1;
}
}
else {
v3d_msg("The file type you specified is not in swc format. Please check.");
return -1;
}
QString fileDefaultName = fileOpenName;
fileDefaultName.chop(3);
fileDefaultName += QString("eswc");
//write new SWC to file
QString fileSaveName = QFileDialog::getSaveFileName(0, QObject::tr("Save File"),
fileDefaultName,
QObject::tr("Supported file (*.eswc)"
";;Extended Neuron structure (*.eswc)"
));
if (!export_eswc(neuron,segment_id,segment_layer,qPrintable(fileOpenName),qPrintable(fileSaveName)))
{
v3d_msg("fail to write the output eswc file.");
return -1;
}
return 1;
}
void combiner::is_dialog_ok_clicked()
{
//check number of files.
//close window
if (load_is_combo->count()>0)
{
load_is_dialog->close();
edit_is->setText(QString::number(load_is_combo->count())+" csv file(s) selected");
check_button();
}
else
{
v3d_msg("No files selected. Please select");
}
}
void BWLabelNPlugin::domenu(const QString &menu_name, V3DPluginCallback2 &callback, QWidget *parent)
{
if (menu_name == tr("3D"))
{
bwlabelimg(callback, parent, 3); //3 - 3D
}
else if (menu_name == tr("2D (for all individual Z-sections)"))
{
bwlabelimg(callback, parent, 2); //2 - 2D
}
else if (menu_name == tr("about"))
{
v3d_msg(QString("This plugin thresholds an image and then labels all image objects. Developed by Hanchuan Peng, by wrapping Fuhui Long's original code. (version %1)").arg(getPluginVersion()));
}
}
void neuron_tipspicker_dialog::output_markers(QString fname)
{
QFile file(fname);
if (!file.open(QIODevice::WriteOnly|QIODevice::Text)){
v3d_msg("cannot open "+ fname +" for write");
return;
}
QTextStream myfile(&file);
myfile<<"##x,y,z,radius,shape,name,comment, color_r,color_g,color_b"<<endl;
//matched candidates first
int info[4];
for(int i=0; i<mList->size(); i++){
get_marker_info(mList->at(i), info);
if(info[2]==1)
myfile<<mList->at(i).x<<","<<mList->at(i).y<<","<<mList->at(i).z<<",0,1, , ,0,255,0"<<endl;
}
file.close();
}
void MovieFrom3Dviewer(V3DPluginCallback2 & v3d, QWidget * parent)
{
v3dhandle curwin = v3d.currentImageWindow();
if (!curwin)
{
v3d_msg("You don't have any image open in the main window.");
return;
}
v3d.open3DWindow(curwin);
if (controlPanel::m_pLookPanel)
{
controlPanel::m_pLookPanel->show();
return;
}
controlPanel* p = new controlPanel(v3d, parent);
if (p) p->show();
}
void neuron_tipspicker_dialog::checkStatus()
{
if(cb_tips->count()>mList->size()){
v3d_msg("The number of markers does not match, please click Update or Reload button.");
cb_tips->setEnabled(false);
btn_accept->setEnabled(false);
btn_skip->setEnabled(false);
btn_reject->setEnabled(false);
}else if(cb_tips->count()>0){
cb_tips->setEnabled(true);
btn_accept->setEnabled(true);
btn_skip->setEnabled(true);
btn_reject->setEnabled(true);
}else{
btn_accept->setEnabled(false);
btn_skip->setEnabled(false);
btn_reject->setEnabled(false);
}
}
// build atlas
void fl_procPC_Atlas_build_atlas(atlasConfig & cfginfo)
{
apoAtlasBuilderInfo atlasbuiderinfo;
fl_func_procIO_build_atlas(atlasbuiderinfo);
apoAtlasLinkerInfoAll apoinfo;
if (atlasbuiderinfo.linkerFileName.compare("")!=0) // otherwise, you have selected cancel, no need to merge
{
// atlasbuiderinfo.linkerFileName.append("/");
fl_func_procCompute_build_atlas(atlasbuiderinfo, cfginfo, apoinfo);
// v3d_msg("Results can be found in the output folder that you've set up through adjust preference function. End of coexpression merging.");
}
else
v3d_msg("You canceled atlas building function. No results generated. End of atlas building.");
}
void fl_procPC_atlas_detect_coexpress_cells(atlasConfig & cfginfo)
{
apoAtlasCoexpressionDetect apoCoExpressInfo;
fl_func_procIO_detect_coexpress_cells(apoCoExpressInfo, cfginfo);
for (int i=0; i<apoCoExpressInfo.apoAtlasFilelist.size(); i++)
printf("%s\n", qPrintable(apoCoExpressInfo.apoAtlasFilelist.at(i)));
printf("%s\n", qPrintable(apoCoExpressInfo.coExpressionOutputFilePrefix));
if (apoCoExpressInfo.coExpressionOutputFilePrefix.compare("")!=0)
fl_func_procCompute_atlas_detect_coexpress_cells(apoCoExpressInfo, cfginfo);
// v3d_msg("The coexpression files have been generated [fl_procPC_atlas_detect_coexpress_cells() done].");
v3d_msg("End of coexpression detection.");
}
void SnapShoot3Dviewer(V3DPluginCallback2 & v3d, QWidget * parent)
{
v3dhandle curwin = v3d.currentImageWindow();
if (!curwin)
{
v3d_msg("You don't have any image opened in the main window.");
return;
}
v3d.open3DWindow(curwin);
QFileDialog d(parent);
d.setWindowTitle(QObject::tr("Choose output snapshot filename"));
d.setAcceptMode(QFileDialog::AcceptSave);
if (!d.exec()) return;
QString BMPfilename = (d.selectedFiles())[0];
if (BMPfilename.endsWith(".BMP", Qt::CaseInsensitive))
BMPfilename.resize(BMPfilename.length()-4); //by PHC
v3d.screenShot3DWindow(curwin, BMPfilename);
QMessageBox::information(0, title, QString("Snapshot was saved to: %1.BMP\n").arg(BMPfilename));
}
bool v3d_imaging(MainWindow* mainwindow, const v3d_imaging_paras & p)
{
v3d_msg(QString("Now try to do imaging or other plugin functions [%1]").arg(p.OPS), 0);
try
{
const char* filename=p.imgp->getFileName();
//v3d_msg(QString("[")+filename+"]");
XFormWidget *curw = 0;
if (filename)
{
curw = mainwindow->findMdiChild(QString(filename)); //search window using name. ZJL
//unsigned char* rawdata=p.imgp->getRawData();
//QList <V3dR_MainWindow *> winlist=mainwindow->list_3Dview_win;
//V3dR_MainWindow *curwin;
//for(int i=0;i<winlist.size();i++)
//{
// unsigned char* winrawdata=winlist.at(i)->getGLWidget()->getiDrawExternalParameter()->image4d->getRawData();
// if(rawdata==winrawdata)
// {
// curwin=winlist.at(i);
// continue;
// }
//}
if (!curw)
{
v3d_msg(QString("No window open yet (error detected in v3d_imaging() main entry point [filename={%1}]).").arg(filename));
return false;
}
}
else
{
if (p.OPS != "Load file using Vaa3D data IO manager") //only allow data IO manager to pass an empty file name parameter here
return false;
}
QDir pluginsDir = QDir(qApp->applicationDirPath());
#if defined(Q_OS_WIN)
if (pluginsDir.dirName().toLower() == "debug" || pluginsDir.dirName().toLower() == "release")
pluginsDir.cdUp();
#elif defined(Q_OS_MAC)
if (pluginsDir.dirName() == "MacOS") {
pluginsDir.cdUp();
pluginsDir.cdUp();
pluginsDir.cdUp();
}
#endif
if (p.OPS == "Vaa3D-Neuron2-APP2")
{
if (pluginsDir.cd("plugins/neuron_tracing/Vaa3D_Neuron2")==false)
{
v3d_msg("Cannot find ./plugins/neuron_tracing/Vaa3D_Neuron2 directory!");
return false;
}
}
else if (p.OPS == "Fetch Highrez Image Data from File")
{
// @FIXED by Alessandro on 2015-09-30.
// Since TeraFly is part of Vaa3D, here we can directly call TeraFly's domenu function w/o using QPluginLoader.
curw->getImageData()->setCustomStructPointer((void *)(&p)); //to pass parameters to the imaging plugin
tf::TeraFly::doaction(p.OPS);
return true;
}
else if (p.OPS == "Load file using Vaa3D data IO manager")
{
if (pluginsDir.cd("plugins/data_IO/data_IO_manager")==false)
{
v3d_msg("Cannot find ./plugins/data_IO/data_IO_manager directory!");
return false;
}
}
else
{
if (pluginsDir.cd("plugins/smartscope_controller")==false)
{
v3d_msg("Cannot find ./plugins/smartscope_controller directory!");
return false;
}
}
QStringList fileList = pluginsDir.entryList(QDir::Files);
if (fileList.size()<1)
{
v3d_msg("Cannot find any file in the ./plugins/smartscope_controller directory!");
return false;
}
QString fullpath = pluginsDir.absoluteFilePath(fileList.at(0)); //always just use the first file (assume it is the only one) found in the folder as the "correct" dll
//the real dll name should be "microimaging.dll"
QPluginLoader* loader = new QPluginLoader(fullpath);
if (!loader)
{
qDebug("ERROR in V3d_PluginLoader::searchPluginFiles the imaging module(%s)", qPrintable(fullpath));
return false;
}
v3d_msg(fullpath, 0);
V3d_PluginLoader mypluginloader(mainwindow);
if (curw)
{
//mypluginloader.runPlugin(loader, QString("about this plugin"));
curw->getImageData()->setCustomStructPointer((void *)(&p)); //to pass parameters to the imaging plugin
QTime t;
t.start();
mypluginloader.runPlugin(loader, p.OPS);
//mypluginloader.runPlugin(loader, "about");
v3d_msg(QString("** invoke time for the plugin is [%1] ms.").arg(t.elapsed()*1000), 0);
}
else //for data IO manager in which case curw is NULL
{
QTime t;
t.start();
mypluginloader.runPlugin(loader, p.datafilename); //the data IO manager is specially designed to pass the datafilename parameter in this way. 2013-12-02. by PHC. what an ugly design here!
v3d_msg(QString("** invoke time for the plugin is [%1] ms.").arg(t.elapsed()*1000), 0);
}
}
catch (...)
{
v3d_msg("Catch a problem in v3d_imaging() wrapper function.", 1);
return false;
}
return true;
}
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;
}
vector<float> calc_mean_shift_center(V3DLONG ind, int windowradius,float *data1Dc_float,
V3DLONG sz_image[],int methodcode)
{
//qDebug()<<"methodcode:"<<methodcode;
V3DLONG y_offset=sz_image[0];
V3DLONG z_offset=sz_image[0]*sz_image[1];
V3DLONG page_size=sz_image[0]*sz_image[1]*sz_image[2];
V3DLONG pos;
vector<V3DLONG> coord;
float total_x,total_y,total_z,v_color,sum_v,v_prev,x,y,z;
float center_dis=1;
vector<float> center_float(3,0);
coord=pos2xyz(ind, y_offset, z_offset);
x=(float)coord[0];y=(float)coord[1];z=(float)coord[2];
//qDebug()<<"x,y,z:"<<x<<":"<<y<<":"<<z<<"ind:"<<ind;
//find out the channel with the maximum intensity for the marker
v_prev=data1Dc_float[ind];
int channel=0;
for (int j=1;j<sz_image[3];j++)
{
if (data1Dc_float[ind+page_size*j]>v_prev)
{
v_prev=data1Dc_float[ind+page_size*j];
channel=j;
}
}
//qDebug()<<"v_Prev:"<<v_prev;
int testCount=0;
int testCount1=0;
while (center_dis>=0.5)
{
total_x=total_y=total_z=sum_v=0;
testCount=testCount1=0;
for(V3DLONG dx=MAX(x+0.5-windowradius,0); dx<=MIN(sz_image[0]-1,x+0.5+windowradius); dx++){
for(V3DLONG dy=MAX(y+0.5-windowradius,0); dy<=MIN(sz_image[1]-1,y+0.5+windowradius); dy++){
for(V3DLONG dz=MAX(z+0.5-windowradius,0); dz<=MIN(sz_image[2]-1,z+0.5+windowradius); dz++){
pos=xyz2pos(dx,dy,dz,y_offset,z_offset);
double tmp=(dx-x)*(dx-x)+(dy-y)*(dy-y)
+(dz-z)*(dz-z);
double distance=sqrt(tmp);
if (distance>windowradius) continue;
v_color=data1Dc_float[pos+page_size*channel];
total_x=v_color*(float)dx+total_x;
total_y=v_color*(float)dy+total_y;
total_z=v_color*(float)dz+total_z;
sum_v=sum_v+v_color;
testCount++;
if(v_color>100)
testCount1++;
}
}
}
//qDebug()<<"windowradius:"<<windowradius;
//qDebug()<<"total xyz:"<<total_x<<":"<<total_y<<":"<<total_z<<":"<<sum_v<<":"<<sum_v/testCount<<":"<<testCount<<":"<<testCount1;
center_float[0]=total_x/sum_v;
center_float[1]=total_y/sum_v;
center_float[2]=total_z/sum_v;
if (total_x<1e-5||total_y<1e-5||total_z<1e-5) //a very dark marker.
{
v3d_msg("Sphere surrounding the marker is zero. Mean-shift cannot happen. Marker location will not move",0);
center_float[0]=x;
center_float[1]=y;
center_float[2]=z;
return center_float;
}
V3DLONG prev_ind=xyz2pos((int)(x+0.5),(int)(y+0.5),(int)(z+0.5),y_offset,z_offset);
V3DLONG tmp_ind=xyz2pos((int)(center_float[0]+0.5),(int)(center_float[1]+0.5),(int)(center_float[2]+0.5),
y_offset,z_offset);
if (methodcode==2)
{
if (data1Dc_float[tmp_ind+channel*page_size]<data1Dc_float[prev_ind+channel*page_size]&& windowradius>=2) // && windowradius>2)
{
//qDebug()<<methodcode<<" window too large"<<windowradius;
windowradius--;
center_dis=1;
continue;
}
}
float tmp_1=(center_float[0]-x)*(center_float[0]-x)+(center_float[1]-y)*(center_float[1]-y)
+(center_float[2]-z)*(center_float[2]-z);
center_dis=sqrt(tmp_1);
//qDebug()<<"new_center:"<<center_float[0]<<":"<<center_float[1]<<":"<<center_float[2]<<" intensity:"<<data1Dc_float[tmp_ind+channel*page_size];
//qDebug()<<"center distance:"<<center_dis;
x=center_float[0]; y=center_float[1]; z=center_float[2];
}
return center_float;
}
vector<float> mean_shift_fun::ray_shoot_center(V3DLONG ind,int bg_thr,int j)
{
V3DLONG y_offset=sz_image[0];
V3DLONG z_offset=sz_image[0]*sz_image[1];
V3DLONG pos,pos_prev;
vector<V3DLONG> coord;
float dir_vec[48][3]={{0.6667,0.6667,0.3333},{0.2852,0.6886,0.6667},{0.6886,0.2852,0.6667},
{0.2826,0.2826,0.9167},{-0.6667,0.6667,0.3333},{-0.6886,0.2852,0.6667},
{-0.2852,0.6886,0.6667},{-0.2826,0.2826,0.9167},{-0.6667,-0.6667,0.3333},
{-0.2852,-0.6886,0.6667},{-0.6886,-0.2852,0.6667},{-0.2826,-0.2826,0.9167},
{0.6667,-0.6667,0.3333},{0.6886,-0.2852,0.6667},{0.2852,-0.6886,0.6667},
{0.2826,-0.2826,0.9167},{0.9428,0.0000,-0.3333},{0.9239,0.3827,0.0000},
{0.9239,-0.3827,0.0000},{0.9428,0.0000,0.3333},{0.0000,0.9428,-0.3333},
{-0.3827,0.9239,0.0000},{0.3827,0.9239,0.0000},{0.0000,0.9428,0.3333},
{-0.9428,0.0000,-0.3333},{-0.9239,-0.3827,0.0000},{-0.9239,0.3827,0.0000},
{-0.9428,0.0000,0.3333},{0.0000,-0.9428,-0.3333},{0.3827,-0.9239,0.0000},
{-0.3827,-0.9239,0.0000},{0.0000,-0.9428,0.3333},{0.2826,0.2826,-0.9167},
{0.2852,0.6886,-0.6667},{0.6886,0.2852,-0.6667},{0.6667,0.6667,-0.3333},
{-0.2826,0.2826,-0.9167},{-0.6886,0.2852,-0.6667},{-0.2852,0.6886,-0.6667},
{-0.6667,0.6667,-0.3333},{-0.2826,-0.2826,-0.9167},{-0.2852,-0.6886,-0.6667},
{-0.6886,-0.2852,-0.6667},{-0.6667,-0.6667,-0.3333},{0.2826,-0.2826,-0.9167},
{0.6886,-0.2852,-0.6667},{0.2852,-0.6886,-0.6667},{0.6667,-0.6667,-0.3333}};
int dir_vec_size=48;
vector<float> center_float(3,0);
vector<float> intensity_vec;
float v_prev,v_new,x,y,z,x_new,y_new,z_new,sum_x,sum_y,sum_z,x_prev,y_prev,z_prev,dx_sum,dy_sum,dz_sum;
float center_dis=1;
float bound[48][3];
coord=pos2xyz(ind, y_offset, z_offset);
x=(float)coord[0];y=(float)coord[1];z=(float)coord[2];
//qDebug()<<"x,y,z:"<<x<<":"<<y<<":"<<z;
dx_sum=dy_sum=dz_sum=0;
for (int k=0;k<dir_vec_size;k++)
{
dx_sum=dx_sum+ABS(dir_vec[k][0]);
dy_sum=dy_sum+ABS(dir_vec[k][1]);
dz_sum=dz_sum+ABS(dir_vec[k][2]);
}
//find out the channel with the maximum intensity for the marker
v_prev=data1Dc_float[ind];
int channel=0;
for (int j=1;j<sz_image[3];j++)
{
if (data1Dc_float[ind+page_size*j]>v_prev)
{
v_prev=data1Dc_float[ind+page_size*j];
channel=j;
}
}
// QString myfile="record.txt";
// FILE * fp1 = fopen(myfile.toLatin1(), "wt");
// fprintf(fp1, "j=: %ld\n",j);
// fprintf(fp1,"##dir_vect,x,y,z,intensity\n");
float converge_dis=0.5;
while (center_dis>converge_dis)
{
sum_x=sum_y=sum_z=0;
for (int i=0;i<dir_vec_size;i++)
{
//qDebug()<<"new round";
intensity_vec.clear();
intensity_vec.push_back(v_prev);
float dx=dir_vec[i][0];
float dy=dir_vec[i][1];
float dz=dir_vec[i][2];
//qDebug()<<"dx,dy,dz:"<<dx<<":"<<dy<<":"<<dz;
pos_prev=ind;
x_prev=x;
y_prev=y;
z_prev=z;
v_new=v_prev;
while (v_new>bg_thr)
{
x_new=x_prev+dx;
if (x_new<0 || x_new>sz_image[0]-1)
{
y_new=y_prev+dy;
z_new=z_prev+dz;
//qDebug()<<"x touches edge";
break;
}
y_new=y_prev+dy;
if (y_new<0 || y_new>sz_image[1]-1)
{
z_new=z_prev+dz;
//qDebug()<<"y touches edge";
break;
}
z_new=z_prev+dz;
if (z_new<0 || z_new>sz_image[2]-1)
{
//qDebug()<<"z touches edge";
break;
}
pos=xyz2pos(x_new+0.5,y_new+0.5,z_new+0.5,y_offset,z_offset); //float to int
v_new=data1Dc_float[pos+channel*page_size];
x_prev=x_new;
y_prev=y_new;
z_prev=z_new;
if (pos==pos_prev) continue;
pos_prev=pos;
intensity_vec.push_back(v_new);
//qDebug()<<"dir i:"<<i<<" x,y,z:"<<x_prev<<":"<<y_prev<<":"<<":"<<z_prev<<":"<<"intensity:"<<v_new;
//fprintf(fp1,"%1d %5.3f %5.3f %5.3f %4.1f \n",i,x_prev,y_prev,z_prev,v_new);
}
//qDebug()<<"intensity_vec size:"<<intensity_vec.size();
//fprintf(fp1,"___________intensity_vec_size: %1d\n",intensity_vec.size());
if (intensity_vec.size()>4)
{
int id;
bool reverse=false;
for (id=2;id<intensity_vec.size()-2;id++)
{
if ((intensity_vec[id]<intensity_vec[id-1])&&(intensity_vec[id]<=intensity_vec[id-2]-9)
&&intensity_vec[id]<intensity_vec[id+1]&&intensity_vec[id]<=intensity_vec[id+2]-9)
{
//qDebug()<<"reversed order: "<<id;
bound[i][0]=x+id*dx;
bound[i][1]=y+id*dy;
bound[i][2]=z+id*dz;
sum_x=sum_x+ABS(dx)*bound[i][0];
sum_y=sum_y+ABS(dy)*bound[i][1];
sum_z=sum_z+ABS(dz)*bound[i][2];
reverse=true;
//fprintf(fp1,"reverse order %1d\n",id);
break;
}
}
if (!reverse)
{
bound[i][0]=x_new-dx;
bound[i][1]=y_new-dy;
bound[i][2]=z_new-dz;
sum_x=sum_x+ABS(dx)*(x_new-dx);
sum_y=sum_y+ABS(dy)*(y_new-dy);
sum_z=sum_z+ABS(dz)*(z_new-dz);
}
}
else
{
bound[i][0]=x_new-dx;
bound[i][1]=y_new-dy;
bound[i][2]=z_new-dz;
//qDebug()<<"Out of loop";
sum_x=sum_x+ABS(dx)*(x_new-dx);
sum_y=sum_y+ABS(dy)*(y_new-dy);
sum_z=sum_z+ABS(dz)*(z_new-dz);
}
}
//qDebug()<<"bounds:"<<bound[0][0]<<":"<<bound[0][1]<<":"<<bound[0][2];
// qDebug()<<"dx_sum,y,z:"<<dx_sum<<":"<<dy_sum<<":"<<dz_sum;
// qDebug()<<"sum_x,y,z:"<<sum_x<<":"<<sum_y<<":"<<sum_z;
if (sum_x<1e-5||sum_y<1e-5||sum_z<1e-5) //a very dark marker.
{
v3d_msg("marker "+QString::number(j+1)+ " is below background threshold. Ray shoot will not move"
"the location");
center_float[0]=x;
center_float[1]=y;
center_float[2]=z;
return center_float;
}
center_float[0]=(float)sum_x/dx_sum;
center_float[1]=(float)sum_y/dy_sum;
center_float[2]=(float)sum_z/dz_sum;
float tmp_dis=(center_float[0]-x)*(center_float[0]-x)+(center_float[1]-y)*(center_float[1]-y)
+(center_float[2]-z)*(center_float[2]-z);
center_dis=sqrt(tmp_dis);
//qDebug()<<"new_center:"<<center_float[0]<<":"<<center_float[1]<<":"<<center_float[2];;
//qDebug()<<"center distance:"<<center_dis;
//fprintf(fp1,"center distance: %5.3f\n",center_dis);
x=center_float[0]; y=center_float[1]; z=center_float[2];
V3DLONG tmp_ind=xyz2pos((int)(center_float[0]+0.5),(int)(center_float[1]+0.5),(int)(center_float[2]+0.5),
y_offset,z_offset);
v_prev=data1Dc_float[tmp_ind+channel*page_size];
}
//fclose(fp1);
//return center_float;
// QString curFile = "result.swc";
// qDebug()<<"writing file";
// FILE * fp = fopen(curFile.toLatin1(), "a");
// if (!fp)
// {
// v3d_msg("Could not open the file to save the neuron.");
// }
// fprintf(fp, "#name %s\n", qPrintable(QString("no name")));
// fprintf(fp, "#comment %s\n", qPrintable(QString("no comment")));
// fprintf(fp, "##n,type,x,y,z,radius,parent\n");
// fprintf(fp, "%ld %d %5.3f %5.3f %5.3f %5.3f %ld\n",
// 1+j*49, 1, x, y, z, 1, -1);
// for (int m=0+j*49;m<j*49+dir_vec_size; m++)
// {
// fprintf(fp, "%ld %d %5.3f %5.3f %5.3f %5.3f %ld\n",
// m+2, 1, bound[m-j*49][0], bound[m-j*49][1], bound[m-j*49][2], 1, 1+j*49);
// }
// fclose(fp);
return center_float;
}
color_render_ESWC_dialog::color_render_ESWC_dialog(V3DPluginCallback2 * cb, V3dR_MainWindow* inwin, int nid)
{
v3dwin=inwin;
callback=cb;
//load neuron tree
nt=(NeuronTree*)&(callback->getHandleNeuronTrees_Any3DViewer(v3dwin)->at(nid));
feaNum=nt->listNeuron.at(0).fea_val.size();
if(feaNum<=0.1){
v3d_msg("Cannot identify feature value for the selected neuron");
return;
}
//back up type
bk_type.clear();
for(int i=0; i<nt->listNeuron.size(); i++){
bk_type.push_back(nt->listNeuron.at(i).type);
}
//create
this->setWindowTitle(nt->file);
cb_feature = new QComboBox();
for(int i=0; i<feaNum; i++)
cb_feature->addItem(QString::number(i+1));
cb_colormap= new QComboBox();
cb_colormap->addItem(QString("heatmap"));
cb_colormap->addItem(QString("rainbow"));
spin_min = new QDoubleSpinBox();
spin_max = new QDoubleSpinBox();
spin_black = new QDoubleSpinBox();
spin_white = new QDoubleSpinBox();
spin_meg = new QDoubleSpinBox();
check_black = new QCheckBox("black threshold (<=)");
check_white = new QCheckBox("white threshold (<=)");
check_meg = new QCheckBox("magenta threshold (>=)");
btn_update = new QPushButton("update");
btn_quit = new QPushButton("quit");
btn_reset = new QPushButton("reset");
connect(check_black, SIGNAL(clicked()),this,SLOT(set_black()));
connect(check_white, SIGNAL(clicked()),this,SLOT(set_white()));
connect(check_meg, SIGNAL(clicked()),this,SLOT(set_magenta()));
connect(btn_update, SIGNAL(clicked()),this,SLOT(update()));
connect(btn_quit, SIGNAL(clicked()),this,SLOT(reject()));
connect(btn_reset, SIGNAL(clicked()),this,SLOT(reset()));
connect(cb_feature, SIGNAL(currentIndexChanged(int)),this,SLOT(set_span()));
connect(cb_colormap, SIGNAL(currentIndexChanged(int)),this,SLOT(set_colormap()));
//layout
QGridLayout * gridLayout = new QGridLayout();
QLabel* label_feature = new QLabel("feature id:");
gridLayout->addWidget(label_feature,1,0,1,2);
gridLayout->addWidget(cb_feature,1,2,1,1);
QLabel* label_colormap= new QLabel("colormap:");
gridLayout->addWidget(label_colormap,2,0,1,2);
gridLayout->addWidget(cb_colormap,2,2,1,1);
QLabel* label_min = new QLabel("color bar low:");
gridLayout->addWidget(label_min,3,0,1,2);
gridLayout->addWidget(spin_min,3,2,1,1);
QLabel* label_max = new QLabel("color bar high:");
gridLayout->addWidget(label_max,4,0,1,2);
gridLayout->addWidget(spin_max,4,2,1,1);
QFrame *line_2 = new QFrame();
line_2->setFrameShape(QFrame::HLine);
line_2->setFrameShadow(QFrame::Sunken);
gridLayout->addWidget(line_2,5,0,1,3);
QLabel* label_color = new QLabel("special color");
QLabel* label_val = new QLabel("value");
gridLayout->addWidget(label_color,6,0,1,2);
gridLayout->addWidget(label_val,6,2,1,1);
gridLayout->addWidget(check_black,7,0,1,2);
gridLayout->addWidget(spin_black,7,2,1,1);
gridLayout->addWidget(check_white,8,0,1,2);
gridLayout->addWidget(spin_white,8,2,1,1);
gridLayout->addWidget(check_meg,9,0,1,2);
gridLayout->addWidget(spin_meg,9,2,1,1);
QFrame *line_3 = new QFrame();
line_3->setFrameShape(QFrame::HLine);
line_3->setFrameShadow(QFrame::Sunken);
gridLayout->addWidget(line_3,13,0,1,3);
gridLayout->addWidget(btn_update,14,2,1,1);
gridLayout->addWidget(btn_reset,15,2,1,1);
gridLayout->addWidget(btn_quit,16,2,1,1);
setLayout(gridLayout);
set_black();
set_white();
set_magenta();
set_span();
set_colormap();
}
void lookPanel::_slot_sync_onetime()
{
v3dhandleList win_list = m_v3d.getImageWindowList();
int i1 = combo_master->currentIndex();
int i2 = combo_slave->currentIndex();
if (i1==i2)
{
v3d_msg("You have selected the same image. You need to specify and sync two different images. Try again!");
return;
}
if (i1 < win_list.size() &&
i2 < win_list.size() &&
i1 < win_list_past.size() &&
i2 < win_list_past.size())
{
QString current1 = m_v3d.getImageName(win_list[i1]);
QString current2 = m_v3d.getImageName(win_list[i2]);
QString past1 = m_v3d.getImageName(win_list_past[i1]);
QString past2 = m_v3d.getImageName(win_list_past[i2]);
if (current1==past1 && current2==past2)
{
if (win_list[i1] && win_list[i2])//ensure the 3d viewer window is open; if not, then open it
{
m_v3d.open3DWindow(win_list[i1]);
View3DControl *view_master = m_v3d.getView3DControl(win_list[i1]);
m_v3d.open3DWindow(win_list[i2]);
View3DControl *view_slave = m_v3d.getView3DControl(win_list[i2]);
if (view_master && view_slave)
{
view_master->absoluteRotPose();
int xRot = view_master->xRot();
int yRot = view_master->yRot();
int zRot = view_master->zRot();
int xShift = view_master->xShift();
int yShift = view_master->yShift();
int zShift = view_master->zShift();
int zoom = view_master->zoom();
if (check_rotation->isChecked())
{
view_slave->resetRotation();
view_slave->doAbsoluteRot(xRot,yRot,zRot);
}
if (check_shift->isChecked())
{
view_slave->setXShift(xShift);
view_slave->setYShift(yShift);
view_slave->setZShift(zShift);
}
if (check_zoom->isChecked())
view_slave->setZoom(zoom);
}
}
}
else
{
v3d_msg(warning_msg);
QStringList items;
for (int i=0; i<win_list.size(); i++)
items << m_v3d.getImageName(win_list[i]);
combo_master->clear(); combo_master->addItems(items);
combo_slave->clear(); combo_slave->addItems(items);
win_list_past = win_list;
return;
}
}
else
{
v3d_msg(warning_msg);
QStringList items;
for (int i=0; i<win_list.size(); i++)
items << m_v3d.getImageName(win_list[i]);
combo_master->clear(); combo_master->addItems(items);
combo_slave->clear(); combo_slave->addItems(items);
win_list_past = win_list;
return;
}
return;
}
void Image4DSimple::loadImage(const char* filename, bool b_useMyLib)
{
cleanExistData(); // note that this variable must be initialized as NULL.
strcpy(imgSrcFile, filename);
V3DLONG * tmp_sz = 0; // note that this variable must be initialized as NULL.
int tmp_datatype = 0;
int pixelnbits=1; //100817
const char * curFileSuffix = getSuffix(imgSrcFile);
printf("The current input file has the suffix [%s]\n", curFileSuffix);
if (curFileSuffix && (strcasecmp(curFileSuffix, "tif")==0 || strcasecmp(curFileSuffix, "tiff")==0 ||
strcasecmp(curFileSuffix, "lsm")==0) ) //read tiff/lsm stacks
{
printf("Image4DSimple::loadImage loading filename=[%s]\n", filename);
#if defined _WIN32
{
v3d_msg("(Win32) Now try to use LIBTIFF (slightly revised by PHC) to read the TIFF/LSM...\n",0);
if (strcasecmp(curFileSuffix, "tif")==0 || strcasecmp(curFileSuffix, "tiff")==0)
{
if (loadTif2Stack(imgSrcFile, data1d, tmp_sz, tmp_datatype))
{
v3d_msg("Error happens in TIF file reading (using libtiff). \n", false);
b_error=1;
}
}
else //if ( strcasecmp(curFileSuffix, "lsm")==0 ) //read lsm stacks
{
if (loadLsm2Stack(imgSrcFile, data1d, tmp_sz, tmp_datatype))
{
v3d_msg("Error happens in LSM file reading (using libtiff, slightly revised by PHC). \n", false);
b_error=1;
}
}
}
#else
if (b_useMyLib)
{
v3d_msg("Now try to use MYLIB to read the TIFF/LSM again...\n",0);
if (loadTif2StackMylib(imgSrcFile, data1d, tmp_sz, tmp_datatype, pixelnbits))
{
v3d_msg("Error happens in TIF/LSM file reading (using MYLIB). Stop. \n", false);
b_error=1;
return;
}
else
b_error=0; //when succeed then reset b_error
}
else
{
v3d_msg("Now try to use LIBTIFF (slightly revised by PHC) to read the TIFF/LSM...\n",0);
if (strcasecmp(curFileSuffix, "tif")==0 || strcasecmp(curFileSuffix, "tiff")==0)
{
if (loadTif2Stack(imgSrcFile, data1d, tmp_sz, tmp_datatype))
{
v3d_msg("Error happens in TIF file reading (using libtiff). \n", false);
b_error=1;
}
}
else //if ( strcasecmp(curFileSuffix, "lsm")==0 ) //read lsm stacks
{
if (loadLsm2Stack(imgSrcFile, data1d, tmp_sz, tmp_datatype))
{
v3d_msg("Error happens in LSM file reading (using libtiff, slightly revised by PHC). \n", false);
b_error=1;
}
}
}
printf("Image4DSimple::loadImage finished\n");
#endif
}
else if (curFileSuffix && (strcasecmp(curFileSuffix, "nrrd")==0 || strcasecmp(curFileSuffix, "nhdr")==0)) //read nrrd stacks
{
printf("Image4DSimple::loadImage loading filename=[%s]\n", filename);
float pxinfo[4];
float spaceorigin[3];
if (!read_nrrd_with_pxinfo(imgSrcFile, data1d, tmp_sz, tmp_datatype, pxinfo, spaceorigin))
{
v3d_msg("Error happens in NRRD file reading. Stop. \n", false);
b_error=1;
return;
}
else
{ //copy the pixel size and origin info when the nrrd read is successful
//note that pixinfo[3] is reserved for future extension to include the temporal sampling rate. It is not used right now.
rez_x = pxinfo[0];
rez_y = pxinfo[1];
rez_z = pxinfo[2];
origin_x = spaceorigin[0];
origin_y = spaceorigin[1];
origin_z = spaceorigin[2];
}
}
else if ( curFileSuffix && strcasecmp(curFileSuffix, "mrc")==0 ) //read mrc stacks
{
if (loadMRC2Stack(imgSrcFile, data1d, tmp_sz, tmp_datatype))
{
v3d_msg("Error happens in MRC file reading. Stop. \n", false);
b_error=1;
return;
}
}
#ifdef _ALLOW_WORKMODE_MENU_
//else if ( curFileSuffix && ImageLoader::hasPbdExtension(QString(filename)) ) // read v3dpbd - pack-bit-difference encoding for sparse stacks
else if ( curFileSuffix && strcasecmp(curFileSuffix, "v3dpbd")==0 ) // read v3dpbd - pack-bit-difference encoding for sparse stacks
{
v3d_msg("start to try v3dpbd", 0);
ImageLoaderBasic imageLoader;
if (! imageLoader.loadRaw2StackPBD(imgSrcFile, this, false) == 0) {
v3d_msg("Error happens in v3dpbd file reading. Stop. \n", false);
b_error=1;
return;
}
// The following few lines are to avoid disturbing the existing code below
tmp_datatype=this->getDatatype();
tmp_sz=new V3DLONG[4];
tmp_sz[0]=this->getXDim();
tmp_sz[1]=this->getYDim();
tmp_sz[2]=this->getZDim();
tmp_sz[3]=this->getCDim();
this->setFileName(filename); // PHC added 20121213 to fix a bug in the PDB reading.
}
#endif
else //then assume it is Hanchuan's Vaa3D RAW format
{
v3d_msg("The data does not have supported image file suffix, -- now this program assumes it is Vaa3D's RAW format and tries to load it... \n", false);
if (loadRaw2Stack(imgSrcFile, data1d, tmp_sz, tmp_datatype))
{
printf("The data doesn't look like a correct 4-byte-size Vaa3D's RAW file. Try 2-byte-raw. \n");
if (loadRaw2Stack_2byte(imgSrcFile, data1d, tmp_sz, tmp_datatype))
{
v3d_msg("Error happens in reading 4-byte-size and 2-byte-size Vaa3D's RAW file. Stop. \n", false);
b_error=1;
return;
}
}
}
//080302: now convert any 16 bit or float data to the range of 0-255 (i.e. 8bit)
switch (tmp_datatype)
{
case 1:
datatype = V3D_UINT8;
break;
case 2: //080824
//convert_data_to_8bit((void *&)data1d, tmp_sz, tmp_datatype);
//datatype = UINT8; //UINT16;
datatype = V3D_UINT16;
break;
case 4:
//convert_data_to_8bit((void *&)data1d, tmp_sz, tmp_datatype);
datatype = V3D_FLOAT32; //FLOAT32;
break;
default:
v3d_msg("The data type is not UINT8, UINT16 or FLOAT32. Something wrong with the program, -- should NOT display this message at all. Check your program. \n");
if (tmp_sz) {delete []tmp_sz; tmp_sz=0;}
return;
}
sz0 = tmp_sz[0];
sz1 = tmp_sz[1];
sz2 = tmp_sz[2];
sz3 = tmp_sz[3]; //no longer merge the 3rd and 4th dimensions
/* clean all workspace variables */
if (tmp_sz) {delete []tmp_sz; tmp_sz=0;}
return;
}
void ImageTip::Compute_DFS()
{
static int nDx[] = {-1,0,1,-1,0,1,-1,0,1};
static int nDy[] = {-1,-1,-1,0,0,0,1,1,1};
static int nDz[] = {-1,0,1};
V3DLONG x = 0;
V3DLONG y = 0;
V3DLONG z = 0;
V3DLONG count = 0;
V3DLONG i = 0;
V3DLONG j = 0;
V3DLONG k = 0;
V3DLONG l = 0;
deque<DPoint_t> dfs;
V3DLONG temp_l = 0;
V3DLONG index_nei = 0;
DPoint_t point;
point.m_x = m_sptSeed.m_x + 1;
point.m_y = m_sptSeed.m_y + 1;
point.m_z = m_sptSeed.m_z + 1;
point.m_l = 0;
dfs.push_back(point);
try //m_piDFS indicates the distance values
{
m_piDFS = new float [totallen];
}
catch (...)
{
v3d_msg("Fail to allocate memory in Distance Transform.", 0);
if (m_piDFS) {delete []m_piDFS; m_piDFS=0;}
return;
}
memset(m_piDFS, NONVISITED, totallen * sizeof(float));
V3DLONG m_pagesz = realszx*realszy;
m_piDFS[point.m_z * m_pagesz + point.m_y * realszx + point.m_x] = 0; //the distance to the starting pt is 0 (of course!)
while(!dfs.empty())
{
point = dfs.front();
dfs.pop_front();
i = point.m_z;
j = point.m_y;
k = point.m_x;
l = point.m_l;
// 26
count = 0; //to indicate the direction type
for(int m = 0; m < 3; m++)
{
for(int n = 0; n < 9; n++)
{
z = i + nDz[m];
y = j + nDy[n];
x = k + nDx[n];
++count;
index_nei = z * m_pagesz + y * realszx + x;
if (m_ppsImgData[index_nei] != BACKGROUND)
{
switch(count)
{
// 6 faces
case 5:
case 11:
case 13:
case 15:
case 17:
case 23:
temp_l = l + 1;
if(m_piDFS[index_nei] != NONVISITED)
{
if(temp_l < m_piDFS[index_nei])
{
//printf("temp=%d m_pidfs=%d\n",temp_l,m_piDFS[index_nei]);
m_piDFS[index_nei] = temp_l;
point.m_x = x;
point.m_y = y;
point.m_z = z;
point.m_l = temp_l;
dfs.push_back(point);
}
}
else //set initial value
{
// printf("tem=%d",temp_l);
m_piDFS[index_nei] = temp_l;
point.m_x = x;
point.m_y = y;
point.m_z = z;
point.m_l = temp_l;
dfs.push_back(point);
}
break;
// 12 edges
case 2:
case 4:
case 6:
case 8:
case 10:
case 12:
case 16:
case 18:
case 20:
case 22:
case 24:
case 26:
temp_l = l + sqrt(2.0);
if(m_piDFS[index_nei] != NONVISITED)
{
if(temp_l < m_piDFS[index_nei])
{
m_piDFS[index_nei] = temp_l;
point.m_x = x;
point.m_y = y;
point.m_z = z;
point.m_l = temp_l;
dfs.push_back(point);
}
}
else //set initial value
{
m_piDFS[index_nei] = temp_l;
point.m_x = x;
point.m_y = y;
point.m_z = z;
point.m_l = temp_l;
dfs.push_back(point);
}
break;
// 8 vertexes
case 1:
case 3:
case 7:
case 9:
case 19:
case 21:
case 25:
case 27:
temp_l = l + sqrt(3.0);
if(m_piDFS[index_nei] != NONVISITED)
{
if(temp_l < m_piDFS[index_nei])
{
m_piDFS[index_nei] = temp_l;
point.m_x = x;
point.m_y = y;
point.m_z = z;
point.m_l = temp_l;
dfs.push_back(point);
}
}
else //set initial value
{
m_piDFS[index_nei] = temp_l;
point.m_x = x;
point.m_y = y;
point.m_z = z;
point.m_l = temp_l;
dfs.push_back(point);
}
break;
default:
break;
}
}
}
}
}
return;
}
void lookPanel::_slot_syncAuto()
{
v3dhandleList win_list = m_v3d.getImageWindowList();
bool b_filelistchanged = (win_list.size()==win_list_past.size()) ? false : true;
if (!b_filelistchanged)
{
for (int i=0; i<win_list.size(); i++)
{
if (win_list.at(i) != win_list_past.at(i))
{
b_filelistchanged = true;
break;
}
}
}
if (b_filelistchanged)
{
v3d_msg(warning_msg);
QStringList items;
for (int i=0; i<win_list.size(); i++)
items << m_v3d.getImageName(win_list[i]);
combo_master->clear(); combo_master->addItems(items);
combo_slave->clear(); combo_slave->addItems(items);
win_list_past = win_list;
return;
}
//only execute the sync if the file list has not changed
int i_master = combo_master->currentIndex();
int i_slave = combo_slave->currentIndex();
if (i_master==i_slave)
{
v3d_msg("You have selected the same image. You need to specify and sync two different images. Try again!");
resetSyncAutoState();
QStringList items;
for (int i=0; i<win_list.size(); i++)
items << m_v3d.getImageName(win_list[i]);
if (combo_master)
{
combo_master->clear(); combo_master->addItems(items);
combo_master->setEnabled(true);
}
if (combo_slave)
{
combo_slave->clear(); combo_slave->addItems(items);
combo_slave->setEnabled(true);
}
return;
}
b_autoON = !b_autoON; // a simple bi-state switch
if (b_autoON)
{
syncAuto->setText("Stop Sync (real time)");
xRot_past = -1;
yRot_past = -1;
zRot_past = -1;
xShift_past = -1;
yShift_past = -1;
zShift_past = -1;
zoom_past = -1;
if (!(view_master = m_v3d.getView3DControl(win_list[i_master])))
{
m_v3d.open3DWindow(win_list[i_master]);
view_master = m_v3d.getView3DControl(win_list[i_master]);
}
if (!(view_slave = m_v3d.getView3DControl(win_list[i_slave])))
{
m_v3d.open3DWindow(win_list[i_slave]);
view_slave = m_v3d.getView3DControl(win_list[i_slave]);
}
combo_master->setEnabled( false );
combo_slave->setEnabled( false );
long interval = 0.2 * 1000;
m_pTimer->start(interval);
}
else
{
resetSyncAutoState();
return;
}
return;
}
bool join_two_V_NeuronSWC(V_NeuronSWC & destination_swc, V_NeuronSWC & subject_swc)
{
if (subject_swc.nrows()<=0) {
qDebug("subject_swc is empty in join_two_V_NeuronSWC()");
return false;
}
if (destination_swc.nrows()<=0) {
destination_swc = subject_swc;
return true;
}
//step 0: to simplify the des neuron, to make the joining simpler
if (!simplify_V_NeuronSWC_nodeindex(destination_swc))
{
qDebug("inconsistent destination neuron structure found in join_two_V_NeuronSWC()");
return false; //some error happens
}
//first just concatenate records
V_NeuronSWC_unit v, vp;
V3DLONG i=0, j=0;
V3DLONG nr_des = destination_swc.nrows();
for (i=0; i<subject_swc.nrows(); i++)
{
v = subject_swc.row.at(i);
v.n += nr_des;
if (v.parent>=0) v.parent += nr_des;
destination_swc.append(v);
}
nr_des = destination_swc.nrows();
//then produce the adjacency matrix
vector<V_NeuronSWC_coord> unpos = destination_swc.unique_ncoord();
V3DLONG N = unpos.size();
map <V3DLONG, V3DLONG> nid_row_lut;
for (i=0; i<nr_des; i++) {
nid_row_lut[destination_swc.row.at(i).n] = i;
}
map <V3DLONG, V3DLONG> row_unid_lut;
for (i=0; i<nr_des; i++)
{
V_NeuronSWC_coord c = destination_swc.row.at(i).get_coord();
V3DLONG ic = value_in_vector(unpos, c);
if (ic<0)
{
v3d_msg("Indexing error! Check data in join_two_V_NeuronSWC.");
return false;
}
row_unid_lut[i] = ic;
}
vector < vector <V3DLONG> > adjm;
vector <V3DLONG> plist;
for (i=0; i<N; i++) adjm.push_back(plist); //initialize as empty
vector < vector <float> > adjm_radius;
vector <float> tmpr;
for (i=0; i<N; i++) adjm_radius.push_back(tmpr); //initialize as empty
vector < vector <float> > adjm_type;
vector <float> tmpt;
for (i=0; i<N; i++) adjm_type.push_back(tmpt); //initialize as empty
for (i=0; i<nr_des; i++)
{
v = destination_swc.row.at(i);
V3DLONG iv = row_unid_lut[i];
if (v.parent>=0)
{
vp = destination_swc.row.at(nid_row_lut[v.parent]);
V3DLONG ip = row_unid_lut[nid_row_lut[v.parent]];
adjm.at(iv).push_back(ip); //add it anyway, will find unique one later. Indeed even unnecessary to find the unique ones, because the repeated record will merge automatically
adjm_radius.at(iv).push_back(float(v.r));
adjm_type.at(iv).push_back(float(v.type));
//need to record neuron edge type and radius as well later
}
else
{
//do nothing about the parent, i.e. this is a root for this record, and thus do not add to the parent list at all
//but still update type and radius
adjm_radius.at(iv).push_back(float(v.r));
adjm_type.at(iv).push_back(float(v.type));
}
}
//no need to find unique ones
//then re-produce a new swc
V_NeuronSWC newswc = destination_swc;
newswc.row.clear();
for (i=0; i<N; i++)
{
vector <V3DLONG> & cur_pa = adjm.at(i);
vector <float> & cur_r = adjm_radius.at(i);
vector <float> & cur_t = adjm_type.at(i);
V_NeuronSWC_coord & cur_coord = unpos.at(i);
if (cur_pa.size()<=0) //a root
{
v.n = i;
v.type = double(cur_t.back()); //direct use the last one, which means the later one overwrite the first one
v.x = cur_coord.x;
v.y = cur_coord.y;
v.z = cur_coord.z;
v.r = cur_r.back(); //direct use the last one, which means the later one overwrite the first one
v.parent = -1;
newswc.append(v);
}
else
{
for (j=0; j<cur_pa.size(); j++)
{
v.n = i;
v.type = double(cur_t.at(j)); //allow he later one overwrite the earlier one(s) if there are redundant records
v.x = cur_coord.x;
v.y = cur_coord.y;
v.z = cur_coord.z;
v.r = cur_r.at(j); //so I allow the later one overwrite the earlier one(s) if there are redundant records
v.parent = cur_pa.at(j);
newswc.append(v);
}
}
}
//copy the results
destination_swc = newswc;
destination_swc.b_jointed = true;
return true;
}
bool combiner::eswc_generate()
{
//qDebug()<<"in eswc generate";
//1-5 spine. 1:volume; 2:max_dis; 3:min_dis; 4:center_dis; 5:head-width
//6-7 IS. 6:volume; 2:on_dendrite
for (QMap<int,node_info>::iterator iter_map=nodegroup_map.begin();
iter_map!=nodegroup_map.end();iter_map++)
{
// qDebug()<<"key:"<<iter_map.key()<<" spine:"<<iter_map.value().spine_lut.size()<<
// " IS:"<<iter_map.value().is_lut.size();
int node_id = iter_map.key();
QVector<spineunit> spine_vec = iter_map.value().spine_lut;
QVector<isunit> is_vec = iter_map.value().is_lut;
//qDebug()<<"key:"<<iter_map.key()<<"spine:"<<spine_vec.size()<<" is:"<<is_vec.size();
//needs to first check if the node_id goes beyond the swc
//if true, then the swc and the table is not the right match
if (node_id>neuron.listNeuron.size())
{
v3d_msg("SWC and tables do not match. Please check inputs.\n");
return false;
}
//fill in the original node
if (!spine_vec.isEmpty())
{
//take out the first spine
spineunit first_spine = spine_vec.front();
neuron.listNeuron[node_id].fea_val[0] = (float)first_spine.volume;
neuron.listNeuron[node_id].fea_val[1] = (float)first_spine.max_dis;
neuron.listNeuron[node_id].fea_val[2] = (float)first_spine.min_dis;
neuron.listNeuron[node_id].fea_val[3] = (float)first_spine.center_dis;
neuron.listNeuron[node_id].fea_val[4] = (float)first_spine.head_width;
//pop out this spine
spine_vec.pop_front();
}
if (!is_vec.isEmpty())
{
isunit first_is = is_vec.front();
neuron.listNeuron[node_id].fea_val[5] = first_is.volume;
neuron.listNeuron[node_id].fea_val[6] = first_is.on_dendrite;
is_vec.pop_front();
}
//start creating new nodes
while (!(is_vec.isEmpty() && spine_vec.isEmpty()))
{
NeuronSWC S;
S.n = neuron.listNeuron.length()+1;
// qDebug()<<"~~~~~~~~~~~~~New node add:"<<S.n<<"ori node: "<<neuron.listNeuron[node_id].n
// <<" ori node parent:"<<neuron.listNeuron[node_id].parent;
S.type = neuron.listNeuron[node_id].type;
S.x = neuron.listNeuron[node_id].x;
S.y = neuron.listNeuron[node_id].y;
S.z = neuron.listNeuron[node_id].z;
S.r = neuron.listNeuron[node_id].r;
S.parent = neuron.listNeuron[node_id].parent;
S.fea_val.clear();
for (int jj=0;jj<7;jj++)
S.fea_val.push_back(-1);
if (!spine_vec.isEmpty())
{
S.fea_val[0] = (float)spine_vec.front().volume;
S.fea_val[1] = (float)spine_vec.front().max_dis;
S.fea_val[2] = (float)spine_vec.front().min_dis;
S.fea_val[3] = (float)spine_vec.front().center_dis;
S.fea_val[4] = (float)spine_vec.front().head_width;
spine_vec.pop_front();
}
if (!is_vec.isEmpty())
{
S.fea_val[5] = (float)is_vec.front().volume;
S.fea_val[6] = (float)is_vec.front().on_dendrite;
is_vec.pop_front();
}
neuron.listNeuron[node_id].parent=S.n; //change the ori node's parent to this new node
neuron.listNeuron.append(S);
}
}
QString eswc_out_name="";
if (!writeESWC_file(eswc_out_name,neuron))
return false;
//qDebug()<<"voxel_group:"<<neuron.listNeuron.size()<<"finish writing out"<<endl;
QMessageBox::information(0,"combiner plug-in","File has been succesfully saved to the specified folder.",
QMessageBox::Ok);
return true;
}
void pointcloud_atlas_builderPlugin::domenu(const QString &menu_name, V3DPluginCallback &callback, QWidget *parent)
{
atlasConfig cfginfo;
QDir curdir;
// v3d_msg(curdir.currentPath());
//
// printf("%s", curdir.currentPath().toStdString().c_str());
QString fileName = curdir.currentPath() + V3DFOLDER;
if (!loadPointCloudAtlasConfigFile(qPrintable(fileName.trimmed()), cfginfo))
{
v3d_msg("Fail to load the configuration file atlas_config.txt");
return;
}
if (menu_name == tr("Edit an existing point cloud atlas linker file"))
{
fl_procPC_Atlas_edit_atlaslinkerfile();
}
else if (menu_name == tr("Create a new point cloud atlas linker file"))
{
fl_procPC_Atlas_create_atlaslinkerfile();
}
else if (menu_name == tr("Build the atlas"))
{
fl_procPC_Atlas_build_atlas(cfginfo);
}
else if (menu_name == tr("Detect coexpressing cells"))
{
fl_procPC_atlas_detect_coexpress_cells(cfginfo);
}
// else if (menu_name == tr("Edit coexpressing cells"))
// {
// fl_procPC_atlas_edit_coexpress_cells();
// }
else if (menu_name == tr("Merge coexpressing cells"))
{
// fl_procPC_atlas_merge_coexpress_cells(callback);
fl_procPC_atlas_merge_coexpress_cells(cfginfo);
}
// else if (menu_name == tr("Display atlas"))
// {
// fl_procPC_atlas_display();
// }
else if (menu_name == tr("Adjust preference"))
{
fl_procPC_adjust_preference();
}
else if (menu_name == tr("About this plugin"))
{
QMessageBox::information(parent, "Version info", "Point cloud atlas builder v1.0. Developed by Fuhui Long .");
}
else
return;
}
bool doNeuronToolBoxPlugin(MainWindow* mainwindow, const vaa3d_neurontoolbox_paras & p)
{
v3d_msg(QString("Now try to run NeuronToolbox [%1]").arg(p.OPS), 0);
try
{
QDir pluginsDir = QDir(qApp->applicationDirPath());
#if defined(Q_OS_WIN)
if (pluginsDir.dirName().toLower() == "debug" || pluginsDir.dirName().toLower() == "release")
pluginsDir.cdUp();
#elif defined(Q_OS_MAC)
if (pluginsDir.dirName() == "MacOS") {
pluginsDir.cdUp();
pluginsDir.cdUp();
pluginsDir.cdUp();
}
#endif
if (pluginsDir.cd("plugins/neuron_toolbox")==false)
{
v3d_msg("Cannot find ./plugins/neuron_toolbox directory!");
return false;
}
QStringList fileList = pluginsDir.entryList(QDir::Files);
if (fileList.size()<1)
{
v3d_msg("Cannot find any file in the ./plugins/neuron_toolbox directory!");
return false;
}
QString fullpath = pluginsDir.absoluteFilePath(fileList.at(0)); //always just use the first file (assume it is the only one) found in the folder as the "correct" dll
QPluginLoader* loader = new QPluginLoader(fullpath);
if (!loader)
{
qDebug("unable to load neuron_toolbox plugin");
return false;
}
// v3d_msg(fullpath, 0);
// V3d_PluginLoader mypluginloader(mainwindow);
V3d_PluginLoader* mypluginloader = mainwindow->pluginLoader;
//mypluginloader.runPlugin(loader, QString("about this plugin"));
// curw->getImageData()->setCustomStructPointer((void *)(&p)); //to pass parameters to the imaging plugin
// mypluginloader.runPlugin(loader, p.OPS);
//mypluginloader.runPlugin(loader, "about");
V3DPluginArgList input;
V3DPluginArgList output;
V3DPluginArgItem arg;
arg.p = (void *)(&p);
input<<arg;
mypluginloader->callPluginFunc(fullpath, "neuron_toolbox", input, output);
// MainWindow * mainWin = qobject_cast<MainWindow*>(qApp->topLevelWidgets().at(0));
//mainwindow->pluginLoader->callPluginFunc(fullpath, "neuron_toolbox", input, output);
}
catch (...)
{
v3d_msg("NeuronToolbox has a problem", 1);
return false;
}
return true;
}
bool eswc2swc_io(const V3DPluginArgList & input, V3DPluginArgList & output)
{
cout<<"Welcome to eswc2swc_io"<<endl;
vector<char*>* inlist = (vector<char*>*)(input.at(0).p);
vector<char*>* outlist = NULL;
if(input.size() != 1)
{
printf("Please specify both input file name.\n");
return false;
}
QString fileOpenName = QString(inlist->at(0));
QString fileSaveName;
QString tmp = fileOpenName;
if (output.size()==0)
{
printf("No outputfile specified.\n");
tmp.chop(4);
fileSaveName = tmp + "swc";
}
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;
}
NeuronTree neuron;
vector<V3DLONG> segment_id, segment_layer;
vector<double> feature;
if (fileOpenName.endsWith(".eswc") || fileOpenName.endsWith(".ESWC"))
{
neuron = read_eswc(segment_id, segment_layer, feature, fileOpenName);
if (!swc2eswc(neuron,segment_id, segment_layer))
{
v3d_msg("Cannot convert eswc to swc.\n");
return false;
}
}
else {
v3d_msg("The file type you specified is not supported. Please check.");
return false;
}
int ret = QMessageBox::Yes;
if (check_eswc(neuron, segment_id, segment_layer)==-1)
{
v3d_msg("WARNING: Something is wrong with the eswc file", 0);
v3d_msg("But we still put convert it to swc format", 0);
}
QString fileDefaultName = fileOpenName;
fileDefaultName.chop(4);
fileDefaultName += QString("swc");
//write new SWC to file
if (!export_swc(neuron,qPrintable(fileSaveName)))
{
v3d_msg("fail to write the output swc file.", 0);
return false;
}
return true;
}
void lookPanel::_slot_timerupdate()
{
int i_master = combo_master->currentIndex();
int i_slave = combo_slave->currentIndex();
if (i_master==i_slave)
{
v3d_msg("Somehow you have specified the same image for both master and slave views. Do nothing!", 0);
resetSyncAutoState();
return;
}
if (!(view_master = m_v3d.getView3DControl(win_list[i_master])))
{
m_v3d.open3DWindow(win_list[i_master]);
view_master = m_v3d.getView3DControl(win_list[i_master]);
}
if (!(view_slave = m_v3d.getView3DControl(win_list[i_slave])))
{
m_v3d.open3DWindow(win_list[i_slave]);
view_slave = m_v3d.getView3DControl(win_list[i_slave]);
}
if (view_master && view_slave)
{
if (check_rotation->isChecked())
{
view_master->absoluteRotPose();
int xRot = view_master->xRot();
int yRot = view_master->yRot();
int zRot = view_master->zRot();
if (xRot!=xRot_past || yRot!=yRot_past || zRot!=zRot_past)
{
view_slave->resetRotation();
view_slave->doAbsoluteRot(xRot,yRot,zRot);
xRot_past = xRot;
yRot_past = yRot;
zRot_past = zRot;
}
}
if (check_shift->isChecked())
{
int xShift = view_master->xShift();
int yShift = view_master->yShift();
int zShift = view_master->zShift();
if (xShift!=xShift_past || yShift!=yShift_past || zShift!=zShift_past)
{
view_slave->setXShift(xShift);
view_slave->setYShift(yShift);
view_slave->setZShift(zShift);
xShift_past = xShift;
yShift_past = yShift;
zShift_past = zShift;
}
}
if (check_zoom->isChecked())
{
int zoom = view_master->zoom();
if (zoom!=zoom_past)
{
view_slave->setZoom(zoom);
zoom_past = zoom;
}
}
}
}
bool SortESWC(QList<NeuronSWC> & neurons, QList<NeuronSWC> & result, V3DLONG newrootid, double thres)
{
if (neurons.size()<1){
cout <<"sorteswc(): empty input neuron."<<endl;
return false;
}
//create a LUT, from the original id to the position in the listNeuron, different neurons with the same x,y,z & r are merged into one position
QHash<V3DLONG, V3DLONG> LUT = getUniqueLUT(neurons);
//create a new id list to give every different neuron a new id
QList<V3DLONG> idlist = ((QSet<V3DLONG>)LUT.values().toSet()).toList();
//create a child-parent table, both child and parent id refers to the index of idlist
QHash<V3DLONG, V3DLONG> cp = ChildParent(neurons,idlist,LUT);
V3DLONG siz = idlist.size();
bool** matrix = new bool*[siz];
for (V3DLONG i = 0;i<siz;i++)
{
matrix[i] = new bool[siz];
for (V3DLONG j = 0;j<siz;j++) matrix[i][j] = false;
}
//generate the adjacent matrix for undirected matrix
for (V3DLONG i = 0;i<siz;i++)
{
QList<V3DLONG> parentSet = cp.values(i); //id of the ith node's parents
for (V3DLONG j=0;j<parentSet.size();j++)
{
V3DLONG v2 = (V3DLONG) (parentSet.at(j));
if (v2==-1) continue;
matrix[i][v2] = true;
matrix[v2][i] = true;
}
}
//do a DFS for the the matrix and re-allocate ids for all the nodes
V3DLONG root = idlist.indexOf(LUT.value(1)); //default value: the first node, in case there is no root defined in the input swc
if (newrootid==VOID)
{
for (V3DLONG i=0;i<neurons.size();i++)
if (neurons.at(i).pn==-1){
root = idlist.indexOf(LUT.value(neurons.at(i).n));
break;
}
}
else{
root = idlist.indexOf(LUT.value(newrootid));
if (LUT.keys().indexOf(newrootid)==-1)
{
v3d_msg("The new root id you have chosen does not exist in the SWC file.");
return(false);
}
}
V3DLONG* neworder = new V3DLONG[siz];
int* numbered = new int[siz];
for (V3DLONG i=0;i<siz;i++) numbered[i] = 0;
V3DLONG id[] = {0};
int group[] = {1};
DFS(matrix,neworder,root,id,siz,numbered,group);
while (*id<siz)
{
V3DLONG iter;
(*group)++;
for (iter=0;iter<siz;iter++)
if (numbered[iter]==0) break;
DFS(matrix,neworder,iter,id,siz,numbered,group);
}
//find the point in non-group 1 that is nearest to group 1,
//include the nearest point as well as its neighbors into group 1, until all the nodes are connected
while((*group)>1)
{
double min = VOID;
double dist2 = 0;
int mingroup = 1;
V3DLONG m1,m2;
for (V3DLONG ii=0;ii<siz;ii++){
if (numbered[ii]==1)
for (V3DLONG jj=0;jj<siz;jj++)
if (numbered[jj]!=1)
{
dist2 = computeDist2(neurons.at(idlist.at(ii)),neurons.at(idlist.at(jj)));
if (dist2<min)
{
min = dist2;
mingroup = numbered[jj];
m1 = ii;
m2 = jj;
}
}
}
for (V3DLONG i=0;i<siz;i++)
if (numbered[i]==mingroup)
numbered[i] = 1;
if (min<=thres*thres)
{
matrix[m1][m2] = true;
matrix[m2][m1] = true;
}
(*group)--;
}
id[0] = 0;
for (int i=0;i<siz;i++)
{
numbered[i] = 0;
neworder[i]= VOID;
}
*group = 1;
V3DLONG new_root=root;
V3DLONG offset=0;
while (*id<siz)
{
V3DLONG cnt = 0;
DFS(matrix,neworder,new_root,id,siz,numbered,group);
(*group)++;
NeuronSWC S;
S.n = offset+1;
S.pn = -1;
V3DLONG oripos = idlist.at(new_root);
S.x = neurons.at(oripos).x;
S.y = neurons.at(oripos).y;
S.z = neurons.at(oripos).z;
S.r = neurons.at(oripos).r;
S.type = neurons.at(oripos).type;
S.seg_id = neurons.at(oripos).seg_id;
S.level = neurons.at(oripos).level;
S.fea_val = neurons.at(oripos).fea_val;
result.append(S);
cnt++;
for (V3DLONG ii=offset+1;ii<(*id);ii++)
{
for (V3DLONG jj=offset;jj<ii;jj++) //after DFS the id of parent must be less than child's
{
if (neworder[ii]!=VOID && neworder[jj]!=VOID && matrix[neworder[ii]][neworder[jj]] )
{
NeuronSWC S;
S.n = ii+1;
S.pn = jj+1;
V3DLONG oripos = idlist.at(neworder[ii]);
S.x = neurons.at(oripos).x;
S.y = neurons.at(oripos).y;
S.z = neurons.at(oripos).z;
S.r = neurons.at(oripos).r;
S.type = neurons.at(oripos).type;
S.seg_id = neurons.at(oripos).seg_id;
S.level = neurons.at(oripos).level;
S.fea_val = neurons.at(oripos).fea_val;
result.append(S);
cnt++;
break; //added by CHB to avoid problem caused by loops in swc, 20150313
}
}
}
for (new_root=0;new_root<siz;new_root++)
if (numbered[new_root]==0) break;
offset += cnt;
}
if ((*id)<siz) {
v3d_msg("Error!");
return false;
}
//free space by Yinan Wan 12-02-02
if (neworder) {delete []neworder; neworder=NULL;}
if (numbered) {delete []numbered; numbered=NULL;}
if (matrix){
for (V3DLONG i=0;i<siz;i++) {delete matrix[i]; matrix[i]=NULL;}
if (matrix) {delete []matrix; matrix=NULL;}
}
return(true);
};
void fl_func_procIO_import_atlas_apofolder(apoAtlasLinkerInfoAll & apoinfo)
{
// QMessageBox::information(0, "Information about import pointcloud APO files to an .atlas linker file",
// "To import a series of images to an .atlas linker file, these files should be put into the same folder and have the same size (X,Y,Z dimensions and number of color channels). <br><br>"
// "You will be first asked to specify one of these files, and you can define a string filter of their file names.<br><br>"
// "Normally these files should be aligned/registered images; but this function can also be used to produce a linker file just for screening a series of image stacks.<br><br>"
// "Note that these files must be valid .tif files (or another image file format supported in V3D).<br><br>"
// "You will be then asked to specify a file name of the output .atlas linker file.<br><br>"
// );
//first load a series of annotation files and build the record
while (1)
{
PointCloudAtlas_LinkerLoadDialog d(apoinfo); //everytime create a new dialog instance, so that apoinfo becomes longer and longer
int rescode = d.exec();
if (rescode==QDialog::Accepted)
{
d.fetchData(apoinfo);
printf("Now apoinfo has the %d classes\n", apoinfo.items.size());
break;
}
else if (rescode==QDialog::Rejected)
{
v3d_msg("The point cloud atlas linker file editing is canceled.");
return; //break;
}
else if (rescode==2) //"2" is a special code I define in dialog_pointcloudatlas_linkerload.cpp for "add another"
{
d.fetchData(apoinfo);
printf("Now apoinfo has the %d classes\n", apoinfo.items.size());
}
else
{
v3d_msg("invalid rescode returned in PointCloudAtlas_LinkerLoadDialog(). Check your program.");
break;
}
}
//now determine the output .atlas file
QString fileName = QFileDialog::getSaveFileName(0, QString("Save Atlas File (*.pc_atlas)"),
"import.pc_atlas",
QString("point cloud atlas linker file (*.pc_atlas)"));
if (fileName.isEmpty())
{
v3d_msg("No output file is selected. Do nothing.");
return;
}
//append(".pc_atlas");
//now save the record to a pointcloud atlas file
if (savePointCloudAtlasInfoListToFile(qPrintable(fileName), apoinfo))
v3d_msg(qPrintable(fileName.prepend("The point cloud atlas linker file [").append("] has been created.")));
else
v3d_msg("Fail to save the point cloud atlas file.");
}
bool join_two_V_NeuronSWC_old(V_NeuronSWC & destination_swc, V_NeuronSWC & subject_swc)
{
if (subject_swc.nrows()<=0)
{
qDebug("subject_swc is empty in join_two_V_NeuronSWC()");
return false;
}
if (destination_swc.nrows()<=0) {
destination_swc = subject_swc;
return true;
}
else
{
if (!simplify_V_NeuronSWC_nodeindex(destination_swc))
{
qDebug("inconsistent destination neuron structure found in join_two_V_NeuronSWC()");
return false; //some error happens
}
V_NeuronSWC_unit v;
V3DLONG i=0;
destination_swc.printInfo();
//one problem I don't consider now is that the nodes (3D locations) in a neuron reconstruction may duplicated. This should be simplified later too
V3DLONG n0 = destination_swc.nrows();
map <V3DLONG, V3DLONG> sub_index_map = unique_V_NeuronSWC_nodeindex(subject_swc);
V3DLONG *ipos=0;
ipos=new V3DLONG [subject_swc.nrows()];
qDebug()<<"start ==================== map "<<subject_swc.name.c_str();
for (i=0; i<subject_swc.nrows(); i++)
{
ipos[i] = destination_swc.getFirstIndexof3DPos(subject_swc.row.at(i));
if (ipos[i]>=0) qDebug("**detect an overlapping node [sub ind = %d, dest_ind=%d]",i,ipos[i]);
sub_index_map[subject_swc.row.at(i).data[0]] = (ipos[i]>=0) ? destination_swc.row.at(ipos[i]).data[0] : (sub_index_map[subject_swc.row.at(i).data[0]]+n0);
qDebug()<<"map "<<subject_swc.row.at(i).data[0]<<" to "<<sub_index_map[subject_swc.row.at(i).data[0]];
}
qDebug()<<"finish ==================== map ";
for (i=0; i<subject_swc.nrows(); i++)
{
v = subject_swc.row.at(i);
qDebug()<<i<<"before : "<<v.data[0]<<" "<<v.data[1]<<" "<<v.data[2]<<" "<<v.data[3]<<" "<<v.data[4]<<" "<<v.data[5]<<" "<<v.data[6];
v.data[0] = sub_index_map[v.data[0]];
if (ipos[i]>=0) //overlap
{
if (v.data[6]>=0) //non-root
{
if (ipos[V3DLONG(v.data[6])]<0) //if the parent overlap as well, then do no add
{
v.data[6] = sub_index_map[v.data[6]]; //if the overalp node is not a root (thus has its own parent, then inherit)
destination_swc.append(v); //in this case, still need to add this swc unit into the dest_swc
}
}
else //root
{
v.data[6] = destination_swc.row.at(ipos[i]).data[6]; //if the overlap node is a root for subject seg, then copy the parent in dest_swc
qDebug()<<"**omit one overlap node **";
//in this case, no need to add this swc unit into the dest_swc
}
}
else //if not an overlap node, should just add (but the node indexes should be updated)
{
if (v.data[6]>=0)
{
v.data[6] = sub_index_map[v.data[6]]; //if the overalp node is not a root (thus has its own parent, then inherit)
destination_swc.append(v);
}
else
{
//if the overlap node is a root for subject seg, then copy the parent in dest_swc
qDebug()<<"**copy a non-overlapping root node **";
destination_swc.append(v); //in this case, still need to add as it is not overlap
}
}
qDebug()<<i<<"after : "<<v.data[0]<<" "<<v.data[1]<<" "<<v.data[2]<<" "<<v.data[3]<<" "<<v.data[4]<<" "<<v.data[5]<<" "<<v.data[6];
}
//search for all root nodes
destination_swc.printInfo();
vector < vector<V3DLONG> > des_rootnode_overlap_info;
vector <V3DLONG> overlap_root_array;
V_NeuronSWC newswc = destination_swc;
newswc.row.clear();
for (i=0; i<destination_swc.row.size(); i++) //note that I search the entire merged destination, so that the part originally from subject will get searched again
{
v = destination_swc.row.at(i);
if (v.parent<0)
{
vector <V3DLONG> mypos = destination_swc.getAllIndexof3DPos(v, i);
if (mypos.size()>1)
{
v3d_msg("Detect a root node that has the same coordinates of more than one other neuron nodes. Your data may have error. ");
}
if (mypos.size()>0) //overlap root, remove
{
vector <V3DLONG> mypos1;
for (V3DLONG j=0; j<mypos.size(); j++)
{
if (destination_swc.row.at(mypos.at(j)).parent<0) //if it is a root
{
if (destination_swc.row.at(mypos.at(j)).n!=v.n) //then it is not a redundant row, -- maybe there is some other nodes link to this one. then do not add it to the newswc
{
destination_swc.row.at(mypos.at(j)).n = v.n;
}
}
else //the overlap one is not a root
{
if (destination_swc.row.at(mypos.at(j)).n!=v.n)
mypos1.push_back(destination_swc.row.at(mypos.at(j)).n);
//if equal, do nothing (which means remove this root-row. In this case, no node mapping is needed, but the root should be deleted
}
}
if (mypos1.size()>0)
{
overlap_root_array.push_back(v.n);
des_rootnode_overlap_info.push_back(mypos1);
//remove the current row by not copy to the new structure
qDebug()<<"remove overlap root node"<<v.n;
}
//newswc.append(v);
}
else //non-overlapping root, keep
{
newswc.append(v);
}
}
else //non_root, keep
{
newswc.append(v);
}
}
for (i=0; i<overlap_root_array.size(); i++)
qDebug()<<"overlapping root array "<<overlap_root_array.at(i);
for (i=0; i<newswc.row.size(); i++) //now merge & update
{
v = newswc.row.at(i);
V3DLONG cur_parent = V3DLONG(v.parent);
V3DLONG mytmp = value_in_vector(overlap_root_array, cur_parent);
if (mytmp>=0)
{
qDebug()<<"cur node "<<v.n<< " cur parent "<<v.parent << "new parent " << des_rootnode_overlap_info.at(mytmp).at(0);
newswc.row.at(i).parent = des_rootnode_overlap_info.at(mytmp).at(0);
for (V3DLONG j=1; j<des_rootnode_overlap_info.at(mytmp).size(); j++)
{
v.parent = des_rootnode_overlap_info.at(mytmp).at(j);
newswc.append(v); //append some new records if one root mapped to multiple other non-root nodes
}
}
}
destination_swc = newswc; //update
//save a temp swc file
FILE * fp = fopen("/Users/pengh/temp/testaaa.swc", "wt");
if (fp)
{
fprintf(fp, "#name %s\n", "test123.swc");
fprintf(fp, "#comment %s\n", "jointed neuron");
fprintf(fp, "#n,type,x,y,z,radius,parent\n");
for (i=0; i<destination_swc.row.size(); i++)
{
v = destination_swc.row.at(i);
fprintf(fp, "%ld %ld %5.3f %5.3f %5.3f %5.3f %ld\n", V3DLONG(v.data[0]), V3DLONG(v.data[1]), v.data[2], v.data[3], v.data[4], v.data[5], V3DLONG(v.data[6]));
}
fclose(fp);
}
if(ipos) {
delete []ipos;
ipos=0;
}
}
destination_swc.b_jointed = true; //091029 RZC
return true;
}
bool ImageTip::Initialize(unsigned char* data, V3DLONG sz[3]) //do padding
{
try
{
if (!data || !sz || sz[0]<=0 || sz[1]<=0 || sz[2]<=0)
{
v3d_msg("Invalid data in SetImageInfo()", 0);
return false;
}
}
catch (...)
{
v3d_msg("Invalid data in SetImageInfo()", 0);
return false;
}
m_ppsOriData1D = data;
m_szx = sz[0];
m_szy = sz[1];
m_szz = sz[2];
// add margins to x,y,z for 26 neighborhood searching
realszx = m_szx + 2;
realszy = m_szy + 2;
realszz = m_szz + 2;
totallen = realszx*realszy*realszz;
V3DLONG i,j,k;
V3DLONG pagesz = realszx*realszy;
//allocate memory and set default
m_ppsImgData = new unsigned char [totallen];
memset(m_ppsImgData, BACKGROUND, totallen);
//padding with 1 (margin)
for (k=0; k<m_szz; k++)
for (j=0; j<m_szy; j++)
for (i=0; i<m_szx; i++)
{
m_ppsImgData[(k+1)*pagesz + (j+1)*realszx + (i+1)] = m_ppsOriData1D[(k)*m_szy*m_szx + (j)*m_szx + (i)];
}
//find all boundary/surface points
for (V3DLONG k=1; k<realszz-1; k++)
for (V3DLONG j=1; j<realszy-1; j++)
for (V3DLONG i=1; i<realszx-1; i++)
{
if (m_ppsImgData[k*pagesz + j*realszx + i] != BACKGROUND)
{
for (int koff=-1; koff<=1; koff++)
for (int joff=-1; joff<=1; joff++)
for (int ioff=-1; ioff<=1; ioff++)
if (m_ppsImgData[(k+koff)*pagesz + (j+joff)*realszx + (i+ioff)] == BACKGROUND)
{
DPoint_t t;
t.m_x = i; t.m_y = j; t.m_z = k; t.m_l = -1;
m_vdfbptSurface.push_back(t);
goto Label_BoundaryPt_Found;
}
}
Label_BoundaryPt_Found:
continue;
}
//
return true;
}
