void SetNeuronDisplayColor::do1clickcolor(V3DPluginCallback2 &callback, QWidget *parent)
{
//select the window to operate
QList <V3dR_MainWindow *> allWindowList = callback.getListAll3DViewers();
QList <V3dR_MainWindow *> selectWindowList;
V3dR_MainWindow * v3dwin;
QList<NeuronTree> * ntTreeList;
int winid;
qDebug("search for 3D windows");
for (V3DLONG i=0;i<allWindowList.size();i++)
{
ntTreeList = callback.getHandleNeuronTrees_Any3DViewer(allWindowList[i]);
if(ntTreeList->size()>0)
selectWindowList.append(allWindowList[i]);
}
qDebug("match and select 3D windows");
if(selectWindowList.size()<1){
v3d_msg("Cannot find 3D view with SWC file. Please load the SWC files you want to color in the 3D view");
return;
}else if(selectWindowList.size()>1){
//pop up a window to select
QStringList items;
for(int i=0; i<selectWindowList.size(); i++){
items.append(callback.getImageName(selectWindowList[i]));
}
bool ok;
QString selectitem = QInputDialog::getItem(parent, QString::fromUtf8("1-click neuron color"), QString::fromUtf8("Select A Window to Operate"), items, 0, false, &ok);
if(!ok) return;
for(int i=0; i<selectWindowList.size(); i++){
if(selectitem==callback.getImageName(selectWindowList[i]))
{
winid=i;
break;
}
}
}else{
winid=0;
}
v3dwin = selectWindowList[winid];
//load neuron tree
ntTreeList=callback.getHandleNeuronTrees_Any3DViewer(v3dwin);
for(int i=0; i<ntTreeList->size(); i++){
NeuronTree* p = (NeuronTree*)&(ntTreeList->at(i));
int k=i%8;
p->color.r=R_table[k];
p->color.g=G_table[k];
p->color.b=B_table[k];
p->color.a=255;
}
qDebug("Done Setting Color");
callback.update_3DViewer(v3dwin);
}
void border_tips::dosearch(V3DPluginCallback2 &callback, QWidget *parent)
{
//select the window to operate
QList <V3dR_MainWindow *> allWindowList = callback.getListAll3DViewers();
QList <V3dR_MainWindow *> selectWindowList;
V3dR_MainWindow * v3dwin;
QList<NeuronTree> * ntTreeList;
int winid;
qDebug("search for 3D windows");
for (V3DLONG i=0;i<allWindowList.size();i++)
{
ntTreeList = callback.getHandleNeuronTrees_Any3DViewer(allWindowList[i]);
if(ntTreeList->size()>0)
selectWindowList.append(allWindowList[i]);
}
qDebug("match and select 3D windows");
if(selectWindowList.size()<1){
v3d_msg("Cannot find 3D view with SWC file. Please load the SWC file you want to identify border tips on.");
return;
}else if(selectWindowList.size()>1){
//pop up a window to select
QStringList items;
for(int i=0; i<selectWindowList.size(); i++){
items.append(callback.getImageName(selectWindowList[i]));
}
bool ok;
QString selectitem = QInputDialog::getItem(parent, QString::fromUtf8("Neuron Stitcher"), QString::fromUtf8("Select A Window to Operate"), items, 0, false, &ok);
if(!ok) return;
for(int i=0; i<selectWindowList.size(); i++){
if(selectitem==callback.getImageName(selectWindowList[i]))
{
winid=i;
break;
}
}
}else{
winid=0;
}
v3dwin = selectWindowList[winid];
neuron_tipspicker_dialog * myDialog = NULL;
myDialog = new neuron_tipspicker_dialog(&callback, v3dwin);
myDialog->show();
}
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 autotrace(V3DPluginCallback2 &callback, QWidget *parent)
{
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;
}
//Mc_Stack *stack = NVInterface::makeStack(p4DImage);
unsigned char* data1d = p4DImage->getRawData();
V3DLONG N = p4DImage->getXDim();
V3DLONG M = p4DImage->getYDim();
V3DLONG P = p4DImage->getZDim();
V3DLONG sc = p4DImage->getCDim();
int in_sz[3];
in_sz[0] = N;
in_sz[1] = M;
in_sz[2] = P;
bool ok1;
int c;
if(sc==1)
{
c=1;
ok1=true;
}
else
{
c = QInputDialog::getInteger(parent, "Channel",
"Enter channel NO:",
1, 1, sc, 1, &ok1);
}
if(!ok1)
return;
IM = new ImageOperation;
Tracer = new OpenSnakeTracer;
// IM->ImRead(callback.getImageName(curwin).toStdString().c_str());
IM->Imcreate(data1d,in_sz);
//preprocessing
std::cout<<"Compute Gradient Vector Flow..."<<std::endl;
IM->computeGVF(1000,5,0);
std::cout<<"Compute Vesselness (CPU)..."<<std::endl;
IM->ComputeGVFVesselness();
std::cout<<"Detect Seed Points..."<<std::endl;
IM->SeedDetection(IM->v_threshold,0,0);
std::cout<<"Adjust Seed Points..."<<std::endl;
IM->SeedAdjustment(10);
std::cout<<"Preprocessing Finished..."<<std::endl;
IM->ImComputeInitBackgroundModel(IM->v_threshold);
IM->ImComputeInitForegroundModel();
//tracing
std::cout<<"--------------Tracing--------------"<<std::endl;
IM->ImRefresh_LabelImage();
Tracer->SetImage(IM);
Tracer->use_multi_threads = true;
Tracer->Init();
Tracer->tracing_thread->stopped = false;
float alpha = 0;
int iter_num = 50;
int ITER = 5;
int pt_distance = 2;
float beta = 0.05;
float kappa = 1;
float gamma = 1;
float stretchingRatio = 3;
int collision_dist = 1;
int minimum_length = 5;
bool automatic_merging = true;
int max_angle = 99;
bool freeze_body = true;
int s_force = 1;
int tracing_model = 0;
int coding_method = 0;
float sigma_ratio = 1;
int border = 0;
Tracer->setParas(pt_distance,gamma,stretchingRatio,minimum_length,collision_dist,5,5,automatic_merging,max_angle,
freeze_body,s_force,tracing_model,false,coding_method,sigma_ratio,border);
IM->SetCodingMethod(0);
Tracer->Open_Curve_Snake_Tracing();
Tracer->RemoveSeeds();
//tracing finished
while( IM->SeedPt.GetSize() != IM->visit_label.sum() )
{
Tracer->Open_Curve_Snake_Tracing();
Tracer->RemoveSeeds();
}
std::cout<<std::endl;
std::cout<<"--------------Processing Finished--------------"<<std::endl;
QString fileName = callback.getImageName(curwin) + "_snake.swc";
QFile swc_file(fileName);
PointList3D wrote_pt, All_Pt;
if (swc_file.open(QFile::WriteOnly | QFile::Truncate))
{
QTextStream *out_txt;
out_txt = new QTextStream(&swc_file);
vnl_vector<int> *snake_visit_label;
snake_visit_label = new vnl_vector<int>(Tracer->SnakeList.NSnakes);
snake_visit_label->fill(0);
int *point_id;
point_id = new int[1];
point_id[0] = 1;
All_Pt.RemoveAllPts();
std::vector<int> *branch_label;
branch_label = new std::vector<int>[1];
for( int i = 0; i < Tracer->SnakeList.NSnakes; i++ )
{
if( snake_visit_label[0](i) == 1 )
continue;
if( Tracer->SnakeList.valid_list[i] == 0 )
continue;
wrote_pt.RemoveAllPts();
int snake_id = i;
findBranch_Raw( snake_id, -1, Tracer->SnakeList.Snakes[i].Cu.GetFirstPt(), snake_visit_label, point_id, out_txt, &wrote_pt, &All_Pt, branch_label );
}
}
v3d_msg(QString("Now you can drag and drop the generated swc fle [%1] into Vaa3D.").arg(fileName));
return;
}
void GVFplugin::domenu(const QString &menu_name, V3DPluginCallback2 &callback, QWidget *parent)
{
if (menu_name == tr("Gradient vector flow based Segmentation"))
{
// the GVF function wants a pointer to a Vol3DSimple, which I haven't seen before.
// this code below generates it (take from plugin_FL_cellseg)
// check what's up with the current window: is there a valid image pointer?
v3dhandle curwin = callback.currentImageWindow();
if (!curwin)
{
v3d_msg("Please open an image.");
return;
}
Image4DSimple* subject = callback.getImage(curwin);
QString m_InputFileName = callback.getImageName(curwin);
if (!subject)
{
QMessageBox::information(0, "", QObject::tr("No image is open."));
return;
}
if (subject->getDatatype()!=V3D_UINT8)
{
QMessageBox::information(0, "", QObject::tr("This demo program only supports 8-bit data. Your current image data type is not supported."));
return;
}
V3DLONG sz0 = subject->getXDim();
V3DLONG sz1 = subject->getYDim();
V3DLONG sz2 = subject->getZDim();
V3DLONG sz3 = subject->getCDim();
Image4DProxy<Image4DSimple> pSub(subject);
V3DLONG channelsz = sz0*sz1*sz2;
float *pLabel = 0;
unsigned char *pData = 0;
gvfsegPara segpara; // set these fields one at a time:
segpara.diffusionIteration= 5;
segpara.fusionThreshold = 10;
segpara.minRegion = 10;
segpara.sigma = 3; // doesn't seem to be used in the actual function?
//input parameters
bool ok1;
int c=1;
if (sz3>1) //only need to ask if more than one channel
{
c = QInputDialog::getInteger(parent, "Channel",
"Choose channel for segmentation:",
1, 1, sz3, 1, &ok1);
c = c-1; //channels are indexed to 0 in Image4DSimple->getRawDataAtChannel
if (!ok1)
return;
}
// read in parameters
segpara.diffusionIteration = QInputDialog::getInteger(parent, "Diffusion Iterations",
"Choose Number of Diffusion Iterations:",
5, 1, 10, 1, &ok1);
if (!ok1)
return;
segpara.fusionThreshold = QInputDialog::getInteger(parent, "Fusion Threshold",
"Choose Fusion Threshold :",
2, 1, 10, 1, &ok1);
if (!ok1)
return;
segpara.minRegion= QInputDialog::getInteger(parent, "Minimum Region",
"Choose Minimum Region Size (voxels):",
10, 1, 1000, 1, &ok1);
if (!ok1)
return;
// allocate memory for the images
Vol3DSimple <unsigned char> * tmp_inimg = 0;
Vol3DSimple <USHORTINT16> * tmp_outimg = 0;
try
{
tmp_inimg = new Vol3DSimple <unsigned char> (sz0, sz1, sz2);
tmp_outimg = new Vol3DSimple <USHORTINT16> (sz0, sz1, sz2);
}
catch (...)
{
v3d_msg("Unable to allocate memory for processing.");
if (tmp_inimg) {delete tmp_inimg; tmp_inimg=0;}
if (tmp_outimg) {delete tmp_outimg; tmp_outimg=0;}
return;
}
//copy image data into our new memory
memcpy((void *)tmp_inimg->getData1dHandle(), (void *)subject->getRawDataAtChannel(c), sz0*sz1*sz2);
//now do computation
//bool b_res = gvfCellSeg(img3d, outimg3d, segpara);
bool b_res = gvfCellSeg(tmp_inimg, tmp_outimg, segpara);
// clear out temporary space
if (tmp_inimg) {delete tmp_inimg; tmp_inimg=0;}
if (!b_res)
{
v3d_msg("image segmentation using gvfCellSeg() failed \n");
}
else
{ // now display the results
// parameters for the new image data
V3DLONG new_sz0 = tmp_outimg->sz0();
V3DLONG new_sz1 = tmp_outimg->sz1();
V3DLONG new_sz2 = tmp_outimg->sz2();
V3DLONG new_sz3 = 1;
V3DLONG tunits = new_sz0*new_sz1*new_sz2*new_sz3;
//
USHORTINT16 * outvol1d = new USHORTINT16 [tunits];
// USHORTINT16 * tmpImg_d1d = (USHORTINT16 *)(tmp_outimg->getData1dHandle());
memcpy((void *)outvol1d, (void *)tmp_outimg->getData1dHandle(), tunits*sizeof(USHORTINT16));
if (tmp_outimg) {delete tmp_outimg; tmp_outimg=0;} //free the space immediately for better use of memory
Image4DSimple p4DImage;
p4DImage.setData((unsigned char*)outvol1d, sz0, sz1, sz2, 1, V3D_UINT16);
v3dhandle newwin = callback.newImageWindow();
callback.setImage(newwin, &p4DImage);
callback.setImageName(newwin, QString("Segmented Image"));
callback.updateImageWindow(newwin);
}
return;
}
else
{
v3d_msg(tr("A plugin for cell segmentation using Gradient Vector Flow. "
"Developed based on the source code developed by Tianming Liu, Fuhui Long, and Hanchuan Peng (2010-2014)"));
}
}
void neuron_render_ESWC_features::docolor(V3DPluginCallback2 &callback, QWidget *parent)
{
//select the window to operate
QList <V3dR_MainWindow *> allWindowList = callback.getListAll3DViewers();
QList <V3dR_MainWindow *> selectWindowList;
V3dR_MainWindow * v3dwin;
QList<NeuronTree> * ntTreeList;
int winid;
qDebug("search for 3D windows");
for (V3DLONG i=0;i<allWindowList.size();i++)
{
ntTreeList = callback.getHandleNeuronTrees_Any3DViewer(allWindowList[i]);
if(ntTreeList->size()>0){
qDebug()<<"cojoc:";
for(V3DLONG j=0; j<ntTreeList->size(); j++){
if(ntTreeList->at(j).listNeuron.at(0).fea_val.size()>0){
selectWindowList.append(allWindowList[i]);
break;
}
}
qDebug()<<"cojoc:";
qDebug()<<ntTreeList->at(0).listNeuron.at(0).fea_val.size();
}
}
qDebug("match and select 3D windows");
if(selectWindowList.size()<1){
v3d_msg("Cannot find 3D view with eligible ESWC file. Please load the ESWC files with features you want to display 3D view");
return;
}else if(selectWindowList.size()>1){
//pop up a window to select
QStringList items;
for(int i=0; i<selectWindowList.size(); i++){
items.append(callback.getImageName(selectWindowList[i]));
}
bool ok;
QString selectitem = QInputDialog::getItem(parent, QString::fromUtf8("Color Render ESWC"), QString::fromUtf8("Select A Window to Operate"), items, 0, false, &ok);
if(!ok) return;
for(int i=0; i<selectWindowList.size(); i++){
if(selectitem==callback.getImageName(selectWindowList[i]))
{
winid=i;
break;
}
}
}else{
winid=0;
}
v3dwin = selectWindowList[winid];
V3DLONG nid=0;
ntTreeList = callback.getHandleNeuronTrees_Any3DViewer(v3dwin);
QList<V3DLONG> selectNeuronList;
for(V3DLONG j=0; j<ntTreeList->size(); j++){
if(ntTreeList->at(j).listNeuron.at(0).fea_val.size()>0){
selectNeuronList.append(j);
}
}
if(selectNeuronList.size()>1){
//pop up a window to select
QStringList items;
for(int i=0; i<selectNeuronList.size(); i++){
items.append(QString::number(i+1)+": "+ntTreeList->at(selectNeuronList.at(i)).file);
}
bool ok;
QString selectitem = QInputDialog::getItem(parent, QString::fromUtf8("Color Render ESWC"), QString::fromUtf8("Select A Neuron to Color"), items, 0, false, &ok);
if(!ok) return;
for(int i=0; i<selectNeuronList.size(); i++){
if(selectitem==items.at(i))
{
nid==selectNeuronList.at(i);
break;
}
}
}else{
nid=selectNeuronList.at(0);
}
color_render_ESWC_dialog * myDialog = NULL;
myDialog = new color_render_ESWC_dialog(&callback, v3dwin, nid);
myDialog->show();
}
void bwlabelimg(V3DPluginCallback2 &callback, QWidget *parent, int method_code)
{
v3dhandle curwin = callback.currentImageWindow();
if (!curwin)
{
v3d_msg("You don't have any image open in the main window.");
return;
}
if (method_code!=3 && method_code!=2)
{
v3d_msg("Invalid BWLabel method code. You should never see this message. Report this bug to the developer");
return;
}
LabelImgObjectParaDialog dialog(callback, parent);
if (!dialog.image)
return;
if (dialog.exec()!=QDialog::Accepted)
return;
V3DLONG ch = dialog.ch;
V3DLONG th_idx = dialog.th_idx;
double tt = dialog.thresh;
V3DLONG volsz_thres = (dialog.b_filtersmallobjs) ? dialog.volsz : 0; //the threshold to filter out small objects
int start_t = clock(); // record time
Image4DSimple* subject = callback.getImage(curwin);
QString m_InputFileName = callback.getImageName(curwin);
if (!subject)
{
QMessageBox::information(0, title, QObject::tr("No image is open."));
return;
}
if (subject->getDatatype()!=V3D_UINT8)
{
QMessageBox::information(0, title, QObject::tr("This demo program only supports 8-bit data. Your current image data type is not supported."));
return;
}
if (th_idx==0 || th_idx==1)
{
double mm, vv;
mean_and_std(subject->getRawDataAtChannel(ch), subject->getTotalUnitNumberPerChannel(), mm, vv);
tt = (th_idx == 0) ? mm : mm+vv;
v3d_msg(QString("in fast image object labeling: ch=%1 mean=%2 std=%2").arg(ch).arg(mm).arg(vv), 0);
}
Image4DProxy<Image4DSimple> pSub(subject);
V3DLONG sz0 = subject->getXDim();
V3DLONG sz1 = subject->getYDim();
V3DLONG sz2 = subject->getZDim();
V3DLONG sz3 = subject->getCDim();
//----------------------------------------------------------------------------------------------------------------------------------
V3DLONG channelsz = sz0*sz1*sz2;
unsigned short int *pLabel = 0;
unsigned char *pData = 0;
try
{
pLabel = new unsigned short int [channelsz];
pData = new unsigned char [channelsz];
}
catch (...)
{
v3d_msg("Fail to allocate memory in Fast Object Labeling Plugin.");
if (pLabel) {delete []pLabel; pLabel=0;}
if (pData) {delete []pData; pData=0;}
return;
}
unsigned char * pSubtmp = pSub.begin();
for(V3DLONG i = 0; i < channelsz; i++)
{
pData[i] = (pSubtmp[i]<=tt) ? 0 : 1;
}
// dist transform
V3DLONG sz_data[4]; sz_data[0]=sz0; sz_data[1]=sz1; sz_data[2]=sz2; sz_data[3]=1;
V3DLONG nobjs=0;
if (method_code==3)
{
V3DLONG nh_code=26; //6,18,or 26
nobjs = findConnectedComponent(pData, sz_data, 3, nh_code, pLabel);
}
else if (method_code==2)
{
V3DLONG nh_code=8; //4 or 8
nobjs = findConnectedComponent(pData, sz_data, 2, nh_code, pLabel);
}
else
{
v3d_msg("Invalid BWLabelN method code. You should never see this message. Report this bug to the developer");
return;
}
if (pData) {delete []pData; pData=0;}
if (volsz_thres>0) //filter out small objects
{
try {
float * hh = new float [nobjs];
float * mapval = new float [nobjs];
V3DLONG j;
for (j=0;j<nobjs;j++) {hh[j]=0; mapval[j]=j;} //of course, 0 also map to 0!
for (j=0;j<channelsz;j++)
{
//pLabel[j]--; //it seems Fuhui's data is 1-based, so subtract 1. Is this correct?
hh[pLabel[j]]++;
}
V3DLONG k=0;
for (j=1;j<nobjs;j++) //start from 1 as it is the background!
{
if (hh[j]<volsz_thres)
{
mapval[j]=0; //if less than a thres, then map to 0, which is background
}
else
{
printf("Obj [%ld] = [%ld]\n", V3DLONG(j), V3DLONG(hh[j]));
k++;
mapval[j] = k; //otherwise map to a continous label-value
}
}
for (j=0;j<channelsz;j++)
pLabel[j] = mapval[pLabel[j]];
if (hh) {delete []hh; hh=0;}
if (mapval) {delete []mapval; mapval=0;}
}
catch (...) {
v3d_msg("Unable to allocate memory to filter small objects. Thus skip it.");
}
}
//----------------------------------------------------------------------------------------------------------------------------------
int end_t = clock();
printf("time eclapse %d s for labeling objects!\n", (end_t-start_t)/1000000);
Image4DSimple p4DImage;
p4DImage.setData((unsigned char*)pLabel, sz0, sz1, sz2, 1, V3D_UINT16);
v3dhandle newwin = callback.newImageWindow();
callback.setImage(newwin, &p4DImage);
callback.setImageName(newwin, QString("Object-Labeled Image"));
callback.updateImageWindow(newwin);
}
void FL_cellseg(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* subject = callback.getImage(curwin);
QString m_InputFileName = callback.getImageName(curwin);
if (!subject)
{
QMessageBox::information(0, title, QObject::tr("No image is open."));
return;
}
if (subject->getDatatype()!=V3D_UINT8)
{
QMessageBox::information(0, title, QObject::tr("This demo program only supports 8-bit data. Your current image data type is not supported."));
return;
}
V3DLONG sz0 = subject->getXDim();
V3DLONG sz1 = subject->getYDim();
V3DLONG sz2 = subject->getZDim();
V3DLONG sz3 = subject->getCDim();
Image4DProxy<Image4DSimple> pSub(subject);
//----------------------------------------------------------------------------------------------------------------------------------
V3DLONG channelsz = sz0*sz1*sz2;
float *pLabel = 0;
unsigned char *pData = 0;
//get the segmentation parameters
segParameter segpara;
dialog_watershed_para *p_mydlg=0;
if (!p_mydlg) p_mydlg = new dialog_watershed_para(&segpara, subject);
int res = p_mydlg->exec();
if (res!=QDialog::Accepted)
return;
else
p_mydlg->fetchData(&segpara);
if (p_mydlg) {delete p_mydlg; p_mydlg=0;}
// now allocate memory and do computation
int start_t = clock();
Vol3DSimple <unsigned char> * tmp_inimg = 0;
Vol3DSimple <USHORTINT16> * tmp_outimg = 0;
try
{
tmp_inimg = new Vol3DSimple <unsigned char> (sz0, sz1, sz2);
tmp_outimg = new Vol3DSimple <USHORTINT16> (sz0, sz1, sz2);
}
catch (...)
{
v3d_msg("Unable to allocate memory for processing. Do nothing.");
if (tmp_inimg) {delete tmp_inimg; tmp_inimg=0;}
if (tmp_outimg) {delete tmp_outimg; tmp_outimg=0;}
return;
}
//do computation
memcpy((void *)tmp_inimg->getData1dHandle(), (void *)subject->getRawDataAtChannel(segpara.channelNo), sz0*sz1*sz2);
bool b_res = FL_cellseg(tmp_inimg, tmp_outimg, segpara);
if (tmp_inimg) {delete tmp_inimg; tmp_inimg=0;} //free the space immediately for better use of memory
if (!b_res)
{
v3d_msg("Fail to do the cell segmentation using FL_cellseg().\n");
}
else
{
V3DLONG new_sz0 = tmp_outimg->sz0();
V3DLONG new_sz1 = tmp_outimg->sz1();
V3DLONG new_sz2 = tmp_outimg->sz2();
V3DLONG new_sz3 = 1;
V3DLONG tunits = new_sz0*new_sz1*new_sz2*new_sz3;
USHORTINT16 * outvol1d = new USHORTINT16 [tunits];
USHORTINT16 * tmpImg_d1d = (USHORTINT16 *)(tmp_outimg->getData1dHandle());
memcpy((void *)outvol1d, (void *)tmp_outimg->getData1dHandle(), tunits*sizeof(USHORTINT16));
if (tmp_outimg) {delete tmp_outimg; tmp_outimg=0;} //free the space immediately for better use of memory
Image4DSimple p4DImage;
p4DImage.setData((unsigned char*)outvol1d, sz0, sz1, sz2, 1, V3D_UINT16);
v3dhandle newwin = callback.newImageWindow();
callback.setImage(newwin, &p4DImage);
callback.setImageName(newwin, QString("Segmented Image"));
callback.updateImageWindow(newwin);
}
//----------------------------------------------------------------------------------------------------------------------------------
int end_t = clock();
printf("time eclapse %d s for labeling objects!\n", (end_t-start_t)/1000000);
}
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;
}
