void KSegmentor3D::Update2D()
{
this->integrateUserInput();
this->CreateLLs(LL2D);
ptrCurrImage = static_cast<unsigned short*>(imageVol->GetScalarPointer());
ptrCurrLabel = static_cast<unsigned short*>(labelVol->GetScalarPointer());
ptrIntegral_Image = static_cast<double*>(this->U_Integral_image->GetScalarPointer());
size_t sz = mdims[0]*mdims[1];
if( cache_phi.size() != (size_t)sz )
cache_phi.resize(sz);
if( save_count_per_slice.size() != mdims[2] ) {
save_count_per_slice=std::vector<int>(mdims[2],0);
}
double* phiSlice = new double[ mdims[0]*mdims[1] ];
double* imgSlice = new double[ mdims[0]*mdims[1] ];
double* maskSlice = new double[ mdims[0]*mdims[1] ];
double* U_I_slice = new double[ mdims[0]*mdims[1] ];
double* labelSlice = new double[ mdims[0]*mdims[1] ];
unsigned int element3D;
long elemNum=0;
long maskThresh=0.5*labelRange[1];
double maxU = -1e99; double minU = 1e99;
for (int j=0; j<=mdims[1]-1; j++) {
for (int i=0; i<=mdims[0]-1; i++) {
// indexing definition: ptr[k*mdims[1]*mdims[0] +j*mdims[0]+i];
element3D=this->currSlice*mdims[1]*mdims[0] +j*mdims[0]+i;
imgSlice[elemNum] = (double) ptrCurrImage[element3D];
maskSlice[elemNum] = (double) ( maskThresh < ptrCurrLabel[element3D] );
U_I_slice[elemNum] = (double) ptrIntegral_Image[element3D];
if ( maxU < U_I_slice[elemNum] ) { //PKDebug
maxU = U_I_slice[elemNum]; //cout << "maxU = " << maxU << endl;
} else if ( minU > U_I_slice[elemNum] ) { //PKDebug
minU = U_I_slice[elemNum]; //cout << "minU = " << minU << endl;
}
elemNum++;
}
}
cout << "minU = " << maxU << ", " << "maxU = " << maxU << endl;
std::vector<long> dimsSlice(5);
dimsSlice[0] = mdims[0];
dimsSlice[1] = mdims[1];
dimsSlice[2] = 1;
dimsSlice[3] = dimsSlice[0]*dimsSlice[1];
dimsSlice[4] = dimsSlice[0]*dimsSlice[1]*dimsSlice[2];
ls_mask2phi3c(maskSlice,phiSlice,labelSlice,&(dimsSlice[0]),
LL2D.Lz,LL2D.Ln1,LL2D.Ln2,LL2D.Lp1,LL2D.Lp2);
cout << "prevslice=" << prevSlice << ", " << "currslice= " << currSlice << endl;
if( (prevSlice == this->currSlice) ) {
cout << "\033[01;32m\033]"
<< "using cached phi " << "\033[00m\033]" << endl;
std::memcpy( &(phiSlice[0]),&(cache_phi[0]),sizeof(double)*mdims[0]*mdims[1] );
} else {
cout << "\033[01;42m\033]"
<< "first time on slice! " << "\033[00m\033]" << endl;
}
prevSlice=currSlice;
interactive_rbchanvese(imgSlice,phiSlice,U_I_slice,labelSlice,&(dimsSlice[0]),
LL2D.Lz,LL2D.Ln1,LL2D.Lp1,LL2D.Ln2,LL2D.Lp2,LL2D.Lin2out,LL2D.Lout2in,
iter,rad,lambda*0.5,display);
//threshold phi to find segmentation label, assign it to appropriate range of label!
elemNum=0;
cv::Mat tmp(mdims[1],mdims[0],CV_64FC1);
cv::Mat tmpI(mdims[1],mdims[0],CV_64FC1);
for (int j=0; j<=mdims[1]-1; j++) {
for (int i=0; i<=mdims[0]-1; i++) {
double phi_val = phiSlice[elemNum];
double phi_out = (-phi_val + 3.0) / 6.0 ;/*6*/; // shift and scale from [-3,3] to [0,1]
element3D=this->currSlice*mdims[1]*mdims[0] +j*mdims[0]+i;
unsigned short value_IK= ( (unsigned short) 0 >= phi_val )*labelRange[1]; // IK: if phi=0, make label 0, else it's 1
unsigned short value_PK= ( (unsigned short) ( ( (phi_out > 0.95)
+ (phi_out > 0.8) + (phi_out > 0.65)
+ (phi_out > 0.5) ) * labelRange[1] / 4.0 ) );
ptrCurrLabel[element3D] = value_IK;
tmp.at<double>(j,i) = (phi_val<=0.0)*255.0f;
tmpI.at<double>(j,i) = (imgSlice[elemNum]);
//labelSlice[elemNum] = (double) value_IK;
//if( (value_PK == 0) && !( 0 == value_IK ) ) {
if(value_IK != value_PK){
//cout << "IK!=PK; IK = " << value_IK << ", PK = " << value_PK << endl;
//cout << "crap, extraneous loss of levelset! " << endl; assert(0);
}
elemNum++;
}
}
bool bSavePNG = true;
if( bSavePNG ) {
std::stringstream ss,ssI;
ss << "label_slice_" << THREE_DIGITS(currSlice) << "_"
<< THREE_DIGITS(save_count_per_slice[currSlice]) << "_"
<< FIVE_DIGITS(num_actuated_voxels) << ".png";
ssI<< "image_slice_" << THREE_DIGITS(currSlice) << ".png";
static std::vector<cv::Mat> chans(3); static cv::Mat tmpPng;
cv::flip( tmp.clone(), tmp, 0 ); double dmin,dmax; cv::minMaxLoc(tmp,&dmin,&dmax);
cout << "min_label=" << dmin << ", max_label=" << dmax << "; ";
for(int c=0;c<3;c++){ tmp.convertTo(chans[c],CV_8UC1); }
cv::merge(chans,tmpPng);
cout << "write to " << ss.str() << " result: " << cv::imwrite(ss.str(),tmpPng) << endl;
cv::flip( tmpI.clone(), tmpI, 0 ); cv::minMaxLoc(tmpI,&dmin,&dmax);
cout << "min_image=" << dmin << ", max_image=" << dmax << "; ";
for(int c=0;c<3;c++){ tmpI.convertTo(chans[c],CV_8UC1); }
cv::merge(chans,tmpPng);
cout << "write to " << ssI.str() << " result: " << cv::imwrite(ssI.str(),tmpPng) << endl;
save_count_per_slice[currSlice] += 1;
//saveMatToPNG( tmp, ss.str() );
}
cout << string("update2D in ") + string(__FILE__) + ": Lz size: " << LL2D.Lz->length << endl;
// store cached \phi level set func
std::memcpy( &(cache_phi[0]),&(phiSlice[0]),sizeof(double)*sz );
delete [] imgSlice;
delete [] labelSlice;
delete [] maskSlice;
delete [] phiSlice;
delete [] U_I_slice;
m_UpdateVector.clear();
m_CoordinatesVector.clear();
}
int main(int argc, char** argv)
{
string path=string(argv[0]);
unsigned int loc=path.rfind("/");
string basepath= loc == string::npos ? "./" : path.substr(0,loc+1);
basepath= osgDB::getRealPath (basepath);
// use an ArgumentParser object to manage the program arguments.
osg::ArgumentParser arguments(&argc,argv);
arguments.getApplicationUsage()->setApplicationName(arguments.getApplicationName());
arguments.getApplicationUsage()->setCommandLineUsage(arguments.getApplicationName()+" [options] filename ...");
bool pbufferOnly = !arguments.read("--show");
unsigned int width=512;
unsigned int height=512;
arguments.read("--pbuffer-only",width,height);
int _tileColumns=0;
int _tileRows=0;
osg::BoundingBox totalbb;
double lat=0,lon=0;
arguments.read("-lat",lat);
arguments.read("-lon",lon);
bool untex= arguments.read("-untex");
string ext;
bool nogfx= arguments.read("-nogfx",ext);
std::vector<picture_cell> cells;
FILE *fp=fopen(argv[1],"r");
if(!fp) {
fprintf(stderr,"Can't open %s\n",argv[1]);
exit(-1);
}
int cnt=0;
while(!feof(fp)) {
char fname[1024];
float minx,maxx,miny,maxy,minz,maxz;
int row,col;
int res=fscanf(fp,"%f %f %f %f %f %f %d %d %s\n",&minx,&maxx,&miny,&maxy,&minz,&maxz,&col,&row,fname);
if(res != 9) {
fprintf(stderr,"Bad parse\n");
exit(-1);
}
if(cnt==0) {
totalbb=osg::BoundingBox(minx,miny,minz,maxx,maxy,maxz);
_tileColumns=col;
_tileRows=row;
} else {
picture_cell cell;
cell.bbox=osg::BoundingBox(minx,miny,minz,maxx,maxy,maxz);
cell.col=col;
cell.row=row;
if(std::string(fname) != "null")
cell.name=std::string(argv[2])+"/"+std::string(fname);
else
cell.name=std::string(fname);
cells.push_back(cell);
}
cnt++;
}
osg::Matrixd view,proj;
std::stringstream os2;
os2<< "view.mat";
std::fstream _file(os2.str().c_str(),std::ios::binary|std::ios::in);
for(int i=0; i<4; i++)
for(int j=0; j<4; j++)
_file.read(reinterpret_cast<char*>(&(view(i,j))),sizeof(double));
for(int i=0; i<4; i++)
for(int j=0; j<4; j++)
_file.read(reinterpret_cast<char*>(&(proj(i,j))),sizeof(double));
_file.close();
// std::ostringstream os;
// os <<"subtile.ppm";//<<":deflate";
vips::VImage raw;
vips::VImage raw_untex;
printf("X: %d Y: %d\n",width*_tileColumns,height*_tileRows);
raw.initdesc(width*_tileColumns,height*_tileRows,3,vips::VImage::FMTUCHAR,vips::VImage::NOCODING,vips::VImage::sRGB,1.0,1.0,0,0);
if(untex)
raw_untex.initdesc(width*_tileColumns,height*_tileRows,3,vips::VImage::FMTUCHAR,vips::VImage::NOCODING,vips::VImage::sRGB,1.0,1.0,0,0);
double vm, rss;
process_mem_usage(vm, rss);
cout << "VM: " << get_size_string(vm) << "; RSS: " << get_size_string(rss) << endl;
osg::Matrix win;
unsigned int validCount=0;
for(int i=0; i < (int)cells.size(); i++) {
if(cells[i].name != "null")
validCount++;
}
osg::Timer_t startTick = osg::Timer::instance()->tick();
formatBar("Img",startTick,0,validCount);
FILE *logfp=fopen("DItiming.txt","w");
int count=0;
for(int i=0; i < (int)cells.size(); i++)
{
osg::Timer_t loopTick = osg::Timer::instance()->tick();
if(cells[i].name == "null" )
continue;
if(nogfx) {
char tmp[1024];
{
sprintf(tmp,"mosaic/image_r%04d_c%04d_rs%04d_cs%04d.%s",cells[i].row,cells[i].col,_tileRows,_tileColumns,ext.c_str());
if(osgDB::fileExists(tmp)) {
vips::VImage tmpI(tmp);
raw.insertplace(tmpI.extract_bands(0,3),width*cells[i].col,height*(_tileRows-cells[i].row-1));
} else {
vips::VImage tmpI;
tmpI.initdesc(width,height,3,vips::VImage::FMTUCHAR,vips::VImage::NOCODING,vips::VImage::sRGB,1.0,1.0,0,0);
memset(tmpI.data(),255,width*height*3);
raw.insertplace(tmpI,width*cells[i].col,height*(_tileRows-cells[i].row-1));
fprintf(stderr,"Can't find %s\n",tmp);
}
}
if(untex) {
sprintf(tmp,"mosaic/image_r%04d_c%04d_rs%04d_cs%04d_untex.%s",cells[i].row,cells[i].col,_tileRows,_tileColumns,ext.c_str());
if(osgDB::fileExists(tmp)) {
vips::VImage tmpI(tmp);
raw_untex.insertplace(tmpI.extract_bands(0,3),width*cells[i].col,height*(_tileRows-cells[i].row-1));
} else {
vips::VImage tmpI;
tmpI.initdesc(width,height,3,vips::VImage::FMTUCHAR,vips::VImage::NOCODING,vips::VImage::sRGB,1.0,1.0,0,0);
memset(tmpI.data(),255,width*height*3);
raw.insertplace(tmpI,width*cells[i].col,height*(_tileRows-cells[i].row-1));
fprintf(stderr,"Can't find %s\n",tmp);
}
}
} else {
osgViewer::Viewer viewer(arguments);
GLenum readBuffer = GL_BACK;
WindowCaptureCallback::FramePosition position = WindowCaptureCallback::END_FRAME;
WindowCaptureCallback::Mode mode = WindowCaptureCallback::SINGLE_PBO;
osg::ref_ptr<osg::GraphicsContext> pbuffer;
{
osg::ref_ptr<osg::GraphicsContext::Traits> traits = new osg::GraphicsContext::Traits;
traits->x = 0;
traits->y = 0;
traits->width = width;
traits->height = height;
traits->red = 8;
traits->green = 8;
traits->blue = 8;
traits->alpha = 8;
traits->windowDecoration = false;
traits->pbuffer = true;
traits->doubleBuffer = true;
traits->sharedContext = 0;
pbuffer = osg::GraphicsContext::createGraphicsContext(traits.get());
//std::cout << "Buffer obj "<< pbuffer->getState()->getMaxBufferObjectPoolSize() << " tex "<< pbuffer->getState()->getMaxBufferObjectPoolSize() <<std::endl;
if (pbuffer.valid())
{
// osg::notify(osg::INFO)<<"Pixel buffer has been created successfully."<<std::endl;
}
else
{
osg::notify(osg::INFO)<<"Pixel buffer has not been created successfully."<<std::endl;
}
}
osg::ref_ptr<WindowCaptureCallback> wcc=new WindowCaptureCallback(mode, position, readBuffer);
osg::ref_ptr<osg::Camera> camera;
if (pbuffer.valid())
{ camera = new osg::Camera;
camera->setGraphicsContext(pbuffer.get());
camera->setViewport(new osg::Viewport(0,0,width,height));
GLenum buffer = pbuffer->getTraits()->doubleBuffer ? GL_BACK : GL_FRONT;
camera->setDrawBuffer(buffer);
camera->setReadBuffer(buffer);
camera->setFinalDrawCallback(wcc);
if (pbufferOnly)
{
viewer.addSlave(camera.get(), osg::Matrixd(), osg::Matrixd());
viewer.realize();
}
else
{
viewer.realize();
viewer.stopThreading();
pbuffer->realize();
viewer.addSlave(camera.get(), osg::Matrixd(), osg::Matrixd());
viewer.startThreading();
}
}
else
{
viewer.realize();
addCallbackToViewer(viewer, wcc);
}
osg::Timer_t timeEndSetup = osg::Timer::instance()->tick();
//double setupTime = osg::Timer::instance()->delta_s(loopTick, timeEndSetup);
// load the data
osg::Matrixd offsetMatrix=osg::Matrixd::scale(_tileColumns, _tileRows, 1.0)*osg::Matrixd::translate(_tileColumns-1-2*cells[i].col, _tileRows-1-2*cells[i].row, 0.0);
/* printf("\r%03d/%03d",i,(int)cells.size());
fflush(stdout);
*/ // std::cout <<"row: "<<cells[i].row << " col: "<<cells[i].col<<" tc: "<<_tileColumns << " "<<_tileRows<<" "<<"\n"<<osg::Matrix::scale(_tileColumns, _tileRows, 1.0) << "\n"<<osg::Matrix::translate(_tileColumns-1-2*cells[i].col, _tileRows-1-2*cells[i].row, 0.0) <<"\n"<<offsetMatrix<<endl;
osg::ref_ptr<osg::Node> node=osgDB::readNodeFile(cells[i].name);
osg::Timer_t timeEndLoad = osg::Timer::instance()->tick();
double loadTime = osg::Timer::instance()->delta_s(timeEndSetup, timeEndLoad);
int mem=0;
if (node.valid() )
{
viewer.setSceneData( node );
viewer.getCamera()->setProjectionMatrix(proj*offsetMatrix);
viewer.getCamera()->setViewMatrix(view);
viewer.frame();
viewer.advance();
viewer.updateTraversal();
viewer.renderingTraversals();
osg::Timer_t timeEndRender = osg::Timer::instance()->tick();
double renderTime = osg::Timer::instance()->delta_s(timeEndLoad, timeEndRender);
gpuUsage(1,mem);
fprintf(logfp,"cnt: %d load %.1fs render: %.1fs mem1: %d MB",count,loadTime,renderTime,mem);
osg::Image *img=(wcc->getContextData(pbuffer)->_imageBuffer[wcc->getContextData(pbuffer)->_currentImageIndex]);
vips::VImage tmp(img->data(),img->s(),img->t(),4,vips::VImage::FMTUCHAR);
raw.insertplace(tmp.flipver().extract_bands(0,3),width*cells[i].col,height*(_tileRows-cells[i].row-1));
if(untex) {
node->getOrCreateStateSet()->addUniform(new osg::Uniform("shaderOut",3));
viewer.setSceneData( node );
viewer.frame();
viewer.advance();
viewer.updateTraversal();
viewer.renderingTraversals();
osg::Timer_t timeEndRender2 = osg::Timer::instance()->tick();
double renderTime2 = osg::Timer::instance()->delta_s(timeEndRender, timeEndRender2);
gpuUsage(1,mem);
osg::Image *img=(wcc->getContextData(pbuffer)->_imageBuffer[wcc->getContextData(pbuffer)->_currentImageIndex]);
vips::VImage tmp(img->data(),img->s(),img->t(),4,vips::VImage::FMTUCHAR);
raw_untex.insertplace(tmp.flipver().extract_bands(0,3),width*cells[i].col,height*(_tileRows-cells[i].row-1));
fprintf(logfp," render2: %.1fs mem2: %d",renderTime2,mem);
}
} else {
std::cout << "Invalid " << cells[i].name << "\n";
}
}
formatBar("Img",startTick,++count,validCount);
osg::Timer_t timeEndLoop = osg::Timer::instance()->tick();
double loopTime = osg::Timer::instance()->delta_s(loopTick, timeEndLoop);
fprintf(logfp," loop: %.1fs\n",loopTime);
fflush(logfp);
}
formatBar("Img",startTick,validCount,validCount);
osg::Timer_t writeStart = osg::Timer::instance()->tick();
process_mem_usage(vm, rss);
cout << "VM: " << get_size_string(vm) << "; RSS: " << get_size_string(rss) << endl;
raw.write("subtile.v");
double writeTime = osg::Timer::instance()->delta_s(writeStart, osg::Timer::instance()->tick());
fprintf(logfp,"Write Time %.1fs\n",writeTime);
if(untex) {
osg::Timer_t writeStart = osg::Timer::instance()->tick();
raw_untex.write("subtile_untex.v");
double writeTime = osg::Timer::instance()->delta_s(writeStart, osg::Timer::instance()->tick());
fprintf(logfp,"Write Time 2 %.1fs\n",writeTime);
}
printf("Done\n");
fclose(logfp);
applyGeoTags("subtile.tif",osg::Vec2(lat,lon),view*proj,raw.Xsize(),raw.Ysize(),basepath);
}
