mirror of
https://gitlab.ethz.ch/gfattori/glocalize.git
synced 2026-05-04 06:04:33 +02:00
Working version of gLocalize software installed at the CNAO.
This extends the embedded function in gOTS code with: - manual volume masking - visualization tools - no memory issues.
This commit is contained in:
Giovanni Fattori
Executable
+380
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#include "gLocalize.h"
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#include <qeventloop.h>
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#include <qapplication.h>
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gLocalize::gLocalize(){
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abortSignal=false;
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}
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void gLocalize::localize(vtkImageData* vol,
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int march_tresh,
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double thrDown_D,
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double thrUp_D,
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double thr_HAUSD,
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double thr_S,
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QList <bool> selectedFilters){
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abortSignal=false;
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int i=0;
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int progress=0;
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//variabili
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vtkSmartPointer<vtkImageData> fixOutput = vtkSmartPointer<vtkImageData>::New();
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vtkSmartPointer<vtkPolyDataConnectivityFilter> filter = vtkSmartPointer<vtkPolyDataConnectivityFilter>::New();
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vtkSmartPointer<vtkMarchingCubes> marchingcubes = vtkSmartPointer<vtkMarchingCubes>::New() ;
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vtkSmartPointer<vtkWindowedSincPolyDataFilter> smoother = vtkSmartPointer<vtkWindowedSincPolyDataFilter>::New();
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vtkSmartPointer<vtkImageData> fixed = vtkSmartPointer<vtkImageData> :: New();
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marchingcubes->SetInput(vol);
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//The algorithm starts with a marching cube at a given intensity level threshold
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marchingcubes->SetValue(0,march_tresh); // Surface #0, iso-value=1
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marchingcubes->SetComputeNormals(0);
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if (marchingcubes.GetPointer()->GetNumberOfInputConnections(0)==0)
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{return;
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//EMIT FAIL QUALCOSA
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//return -1;
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}
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marchingcubes->Update();
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std::cout<< "inizio run" <<std::endl;
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QString item= item.number(marchingcubes->GetNumberOfContours());
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if(item.toInt()<=0){
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throw("CRITICAL: No surfaces found with given treshold");
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QList <surf> dummylist;
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// emit sendrenderMarkerList (dummylist);
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}
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// Smoothing filter and normals calculation on marching cubes output data
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smoother->SetInput(marchingcubes->GetOutput());
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smoother->SetNumberOfIterations(20);
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smoother->NormalizeCoordinatesOn();
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smoother->SetPassBand(0.01);
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smoother->BoundarySmoothingOn();
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smoother->Update();
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vtkSmartPointer<vtkPolyDataNormals> normals=vtkSmartPointer<vtkPolyDataNormals>::New();
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normals->SetInput(smoother->GetOutput());
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vtkSmartPointer<vtkActor> normalact=vtkSmartPointer<vtkActor>::New();
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vtkSmartPointer<vtkPolyDataMapper> normalmap=vtkSmartPointer<vtkPolyDataMapper>::New();
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normalmap->SetInput( normals->GetOutput());
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normalact->SetMapper(normalmap);
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// Start of marker recognitioning procedure
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filter->AddInput(normals->GetOutput());
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filter->SetExtractionModeToAllRegions();
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filter->SetColorRegions(0);
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filter->Update();
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QString regionnumber = regionnumber.number(filter->GetNumberOfExtractedRegions());
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filter->SetExtractionModeToSpecifiedRegions();
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filter->Update();
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//Some data allocation:
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//surflist: list of surfaces where the recognized marker are added
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//tempsurf: one surface used as temporary variable during geometrical filtering
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QList <surf> surflist;
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surflist.clear();
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surf tempsurf;
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//Double check on number of surface in ConnectivityFilter output
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if(regionnumber.toInt()==0){
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std::cout<<"ok"<<std::endl;
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throw("CRITICAL: No surfaces in ConnectivityFilter output");
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QList <surf> dummylist;
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// emit sendrenderMarkerList (dummylist);
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};
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if(regionnumber.toInt()>3000){
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cout<<"ho trovato troppe superfici: "<<regionnumber.toInt()<<endl;
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};
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int ok;
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cout<<regionnumber.toDouble()<<endl;
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//progress bar initialization
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//emit recognitionProgress (regionnumber.toInt(),0);
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int OKd=0;
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int OKh=0;
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int OKs=0;
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for(double idouble=0;idouble<regionnumber.toDouble() ;idouble++)
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{
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QApplication::processEvents();
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progress++;
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emit localizationProgress( (double)progress/(double)regionnumber.toDouble() * 100 );
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if(abortSignal==true){
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abortSignal=false;
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emit localizationAborted();
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return;
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}
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//flag need for good filtering driving
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ok=1;
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//Add one surface at once and check for geometrical constraints
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filter->AddSpecifiedRegion(idouble);
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filter->Update();
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// Filter on bounding box diagonal lenght
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if(selectedFilters.at(0))
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if(ok==1) {
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tempsurf.lenght=filter->GetOutput()->GetLength();
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if(tempsurf.lenght<thrDown_D || tempsurf.lenght>thrUp_D )
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ok=0;
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}
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//Hausdorf reads from tempsurf the bounding box center and use it as reference center
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if(selectedFilters.at(1))
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if(ok==1) {
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OKd++;
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filter->GetOutput()->GetCenter(tempsurf.center);
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tempsurf.hausdorff=hausdorff(filter,tempsurf);
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if(tempsurf.hausdorff> (thr_HAUSD) )
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ok=0;
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}
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// Filter based on sides difference
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if(selectedFilters.at(2))
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if(ok==1) {
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OKh++;
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filter->GetOutput()->GetBounds(tempsurf.bounds);
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tempsurf.confronto_lati=lati(tempsurf.bounds);
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if(tempsurf.confronto_lati>thr_S)
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ok=0;
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}
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//if all filters are verified, add a surface index and append it to the surflist
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if(ok==1) {
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OKs++;
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tempsurf.sorting=idouble; //indexing
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surflist.append(tempsurf);
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}
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// MANDATORY filter cleaning
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filter->DeleteSpecifiedRegion(idouble);
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}
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cout<<"Nsurfaces"<<regionnumber.toInt() <<endl;
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cout<<"OKD "<< OKd<<" OKH "<<OKh<<" OKS "<<OKs<<endl;
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// marker center calculation
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// final_list: surf list returned through emit
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// tmp_p: surf used as temporary variable
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QList<surf> final_list;
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surf tmp_p;
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if(surflist.count()!=0){
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for(i=0;i<surflist.count();i++){
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tmp_p=surflist.at(i);
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filter->AddSpecifiedRegion(surflist.at(i).sorting);
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filter->Update();
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//Centroid calculation needs mesh vertex
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vtkSmartPointer<vtkExtractEdges> edge_extractor =vtkSmartPointer<vtkExtractEdges>::New();
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edge_extractor->RemoveAllInputs();
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edge_extractor->SetInput(filter->GetOutput());
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edge_extractor->Update();
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vtkSmartPointer<vtkPolyData> tmp = vtkSmartPointer<vtkPolyData>::New();
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tmp=edge_extractor->GetOutput();
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tmp->Update();
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tmp->BuildCells();
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tmp->BuildLinks();
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QList <point> punti;
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point ptemp;
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for (int id=0;id< (int) tmp->GetNumberOfPoints();id++){
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ptemp.x=tmp->GetPoint(id)[0];
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ptemp.y=tmp->GetPoint(id)[1];
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ptemp.z=tmp->GetPoint(id)[2];
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/*cout<<filter->GetOutput()->GetPoint(id)[0]<<" "<<filter->GetOutput()->GetPoint(id)[1]<<" "<<filter->GetOutput()->GetPoint(id)[2]<<endl;*/
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punti.append(ptemp);
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};
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//Call centroid calculation
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tmp_p.centroid=centroid(punti);
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punti.clear();
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// MANDATORY filter cleaning
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filter->DeleteSpecifiedRegion(surflist.at(i).sorting);
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final_list.append(tmp_p);
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};
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};
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for(int ii=0;ii<final_list.size();ii++)
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{
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std::cout<<1000*final_list.at(ii).centroid.x<<
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" "<<1000*final_list.at(ii).centroid.y<<
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" "<<1000*final_list.at(ii).centroid.z<<std::endl;
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}
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emit localizationEnd(final_list);
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}
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//
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//
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///**
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// * Centroid calculation of a given points cloud
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// */
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point gLocalize::centroid(QList< point > punti)
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{
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int i;
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point centroide;
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centroide.x=0,centroide.y=0,centroide.z=0;
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for ( i=0;i<punti.size();i++){
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centroide.x+=punti.at(i).x/1000;
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centroide.y+=punti.at(i).y/1000;
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centroide.z+=punti.at(i).z/1000;
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};
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centroide.x=centroide.x/punti.size();
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centroide.y=centroide.y/punti.size();
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centroide.z=centroide.z/punti.size();
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return centroide;
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}
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//
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//
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///**
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// * performs bounding box side difference and return the larger one
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// */
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double gLocalize::lati(double p[6])
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{
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double x=p[1]-p[0];double y=p[3]-p[2];double z=p[5]-p[4];
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double d1=(x-y); double d2=(x-z); double d3=(y-z);
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if(d1<0) d1=d1*-1;if(d2<0) d2=d2*-1;if(d3<0) d3=d3*-1;
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if(d1>d2 && d1>d3) return d1;
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if(d2>d1 && d2>d3) return d2;
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if(d3>d2 && d3>d1) return d3;
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return 9999;
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}
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int gLocalize::get_byteorder()
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{
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union {
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long l;
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char c[4];
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} test;
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test.l = 1;
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if( test.c[3] && !test.c[2] && !test.c[1] && !test.c[0] )
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return ORDER_BIGENDIAN;
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if( !test.c[3] && !test.c[2] && !test.c[1] && test.c[0] )
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return ORDER_LITTLEENDIAN;
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return ORDER_UNKNOWN;
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}
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/**
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* Implementation of the Hausdorff distance from a reference 1 cm diameter sphere
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*/
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double gLocalize::hausdorff(vtkPolyDataConnectivityFilter* filter, surf tempsurf)
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{
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vtkSmartPointer<vtkSphereSource> source_sphere = vtkSmartPointer<vtkSphereSource>::New();
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source_sphere->SetCenter(tempsurf.center[0],tempsurf.center[1],tempsurf.center[2]);
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source_sphere->SetRadius(5.0);
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source_sphere->Update();
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vtkSmartPointer<vtkPolyData> sphere = source_sphere->GetOutput();
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sphere->Update();
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sphere->BuildCells();
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vtkSmartPointer<vtkExtractEdges> edge_extractor =vtkSmartPointer<vtkExtractEdges>::New();
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edge_extractor->RemoveAllInputs();
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edge_extractor->SetInput(filter->GetOutput());
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edge_extractor->Update();
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vtkSmartPointer<vtkPolyData> tmp = vtkSmartPointer<vtkPolyData>::New();
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tmp=edge_extractor->GetOutput();
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tmp->Update();
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tmp->BuildCells();
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tmp->BuildLinks();
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QList <point> punti_sup;
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point ptemp;
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for (int id=0;id< (int) tmp->GetNumberOfPoints();id++){
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ptemp.x=tmp->GetPoint(id)[0];
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ptemp.y=tmp->GetPoint(id)[1];
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ptemp.z=tmp->GetPoint(id)[2];
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/*cout<<filter->GetOutput()->GetPoint(id)[0]<<" "<<filter->GetOutput()->GetPoint(id)[1]<<" "<<filter->GetOutput()->GetPoint(id)[2]<<endl;*/
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punti_sup.append(ptemp);
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};
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QList <point> punti_sphere;
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for (int id=0;id< (int) sphere->GetNumberOfPoints();id++){
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ptemp.x=sphere->GetPoint(id)[0];
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ptemp.y=sphere->GetPoint(id)[1];
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ptemp.z=sphere->GetPoint(id)[2];
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/*cout<<filter->GetOutput()->GetPoint(id)[0]<<" "<<filter->GetOutput()->GetPoint(id)[1]<<" "<<filter->GetOutput()->GetPoint(id)[2]<<endl;*/
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punti_sphere.append(ptemp);
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};
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int nr_source_points = punti_sup.count();
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int nr_target_points = punti_sphere.count();
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double summax = 0;
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double summin = 0;
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double maxmin = -1e9;
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double maxmax = -1e9;
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for(int i=0; i < nr_source_points; i++) {
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double smallest = 1e9;
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double largest = 0;
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double x1 = punti_sup.at(i).x;
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double y1 = punti_sup.at(i).y;
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double z1 = punti_sup.at(i).z;
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for(int j=0; j < nr_target_points; j++) {
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double x2 = punti_sphere.at(j).x;
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double y2 = punti_sphere.at(j).y;
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double z2 = punti_sphere.at(j).z;
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double dx = x1 - x2;
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double dy = y1 - y2;
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double dz = z1 - z2;
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double dist = dx * dx + dy * dy + dz*dz;
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if (dist < smallest) smallest = dist;
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if (dist > largest) largest = dist;
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}
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summin += smallest;
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summax += largest;
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if (smallest > maxmin) maxmin = smallest; // so this is max min
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if (largest > maxmax) maxmax = largest; // and this is max max
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}
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punti_sphere.clear();
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punti_sup.clear();
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return maxmin; // Hausdorff distance
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}
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