void setPrefixAndRegisterAsTemp(std::string const & prefix, uint64_t const numbwt, uint64_t const numgt)
{
setPrefix(prefix, numbwt, numgt);
for ( uint64_t i = 0; i < getGT().size(); ++i )
::libmaus2::util::TempFileRemovalContainer::addTempFile(getGT()[i]);
for ( uint64_t i = 0; i < getBWT().size(); ++i )
::libmaus2::util::TempFileRemovalContainer::addTempFile(getBWT()[i]);
::libmaus2::util::TempFileRemovalContainer::addTempFile(getHWT());
::libmaus2::util::TempFileRemovalContainer::addTempFile(getHist());
::libmaus2::util::TempFileRemovalContainer::addTempFile(getSampledISA());
}
int VcfRecord::getAlleleCount(unsigned int index,
VcfSubsetSamples* sampleSubset)
{
unsigned int numAlts = getNumAlts();
if(index > numAlts)
{
// Index out of range.
// Throw an exception.
throw(std::runtime_error("VcfRecord::getAlleles called with an index that is greater than the number of alternates."));
return(-1);
}
if(myAlleleCount.size() == 0)
{
unsigned int gt = 0;
myAlleleCount.resize(numAlts+1, 0);
// Loop through the samples, counting the number of each allele.
for(int sampleNum = 0; sampleNum < getNumSamples();
sampleNum++)
{
if((sampleSubset != NULL) &&
!(sampleSubset->keep(sampleNum)))
{
// Skip this sample.
continue;
}
for(int gtNum = 0; gtNum < getNumGTs(sampleNum); gtNum++)
{
gt = getGT(sampleNum, gtNum);
if((gt < 0) || (gt > numAlts))
{
// Out of range GT, so continue to the next gt
continue;
}
// Increment the minor allele count
++myAlleleCount[gt];
}
}
}
// Alternate allele, so return the alternate.
return(myAlleleCount[index]);
}
// ######################################################################
int main(const int argc, const char **argv)
{
MYLOGVERB = LOG_INFO; // suppress debug messages
volatile int signum = 0;
catchsignals(&signum);
ModelManager manager("Test Motion Energy");
nub::ref<InputFrameSeries> ifs(new InputFrameSeries(manager));
manager.addSubComponent(ifs);
nub::ref<OutputFrameSeries> ofs(new OutputFrameSeries(manager));
manager.addSubComponent(ofs);
nub::ref<FoeDetector> fd(new FoeDetector(manager));
manager.addSubComponent(fd);
if (manager.parseCommandLine((const int)argc, (const char**)argv,
"<stimuli> <options>", 0, 9) == false)
return(1);
fd->reset(NUM_PYR_LEVEL, NUM_DIRS, NUM_SPEEDS);
std::string stimuli("Image");
if(manager.numExtraArgs() > 0)
stimuli = manager.getExtraArgAs<std::string>(0);
LINFO("Stimuli: %s", stimuli.c_str());
manager.start();
Timer timer(1000000);
timer.reset(); // reset the timer
int frame = 0;
PauseWaiter p;
uint step; step = 0;
// to get to the good part
//for(uint i = 0; i < 50; i++) //was 25
// ifs->updateNext();
// get ground truth file
std::string gtFilename
("/lab/tmpib/u/siagian/neuroscience/Data/FOE/driving_nat_Browning.txt");
std::vector<Point2D<int> > gt = getGT(gtFilename);
int ldpos = gtFilename.find_last_of('.');
std::string prefix = gtFilename.substr(0, ldpos);
// for finding ground truth
rutz::shared_ptr<XWinManaged> win;
float totalErr = 0.0;
std::vector<std::string> args;
for(uint i = 0; i < manager.numExtraArgs(); i++)
args.push_back(manager.getExtraArgAs<std::string>(i));
Image<byte> prevLum;
Image<PixRGB<byte> > prevImage;
Image<PixRGB<byte> > prevImage2;
while (1)
{
if (signum != 0)
{
LINFO("quitting because %s was caught", signame(signum));
break;
}
if (ofs->becameVoid())
{
LINFO("quitting because output stream was closed or became void");
break;
}
if (p.checkPause())
continue;
const FrameState is = ifs->updateNext();
if (is == FRAME_COMPLETE) break; // done receiving frames
Image< PixRGB<byte> > input = ifs->readRGB();
if(frame == 0)
{
uint width = input.getWidth();
uint height = input.getHeight();
win.reset(new XWinManaged(Dims(width, height), 0, 0, "GT"));
}
// empty image signifies end-of-stream
if (!input.initialized()) break;
Image<byte> lum = luminance(input);
Point2D<float> pshift(0.0,0.0);
if(step != 0)
{
// calculate planar shift using SIFT
lum = calculateShift(lum,prevLum, ofs);
}
if( manager.numExtraArgs() > 0)
lum = getImage(stimuli, args, fd, step);
// for saving videos
prevImage2 = prevImage;
prevImage = input;
if (!lum.initialized()) break; step++;
// compute the focus of expansion (FOE)
Point2D<int> foe = fd->getFoe(lum, FOE_METHOD_TEMPLATE, false);
//Point2D<int> foe = fd->getFoe(lum, FOE_METHOD_AVERAGE);
LINFO("[%d]Foe: %d %d", frame, foe.i, foe.j);
// illustration of the size of the receptive field
if(!stimuli.compare("ShowRF"))
{
uint rfI = 44;
uint rfJ = 152;
lum.setVal(rfI, rfJ, 300.0F);
drawRect(lum, Rectangle::tlbrI(144,36,159,51), byte(255));
drawRect(lum, Rectangle::tlbrI(148,40,155,47), byte(255));
drawRect(lum, Rectangle::tlbrI(rfJ-8, rfI-8, rfJ+8, rfI+8), byte(255));
drawRect(lum, Rectangle::tlbrI(rfJ-16,rfI-16,rfJ+16,rfI+16), byte(255));
}
ofs->writeGrayLayout(fd->getMTfeaturesDisplay(lum), "MT Features",
FrameInfo("motion energy output images", SRC_POS));
// write the file
if(frame >= 4)
{
float err = foe.distance(gt[frame-2]);
totalErr += err;
LINFO("Foe: %d %d: GT: %d %d --> %f --> avg: %f",
foe.i, foe.j, gt[frame-2].i, gt[frame-2].j,
err, totalErr/(frame-3));
Image<PixRGB<byte> > simg = prevImage2;
drawCross(simg, foe , PixRGB<byte>(0,255,0), 10, 2);
drawCross(simg, gt[frame-2], PixRGB<byte>(255,0,0), 10, 2);
win->drawImage(simg,0,0);
//Raster::WriteRGB(simg, sformat("%s_STnPS_%06d.ppm", prefix.c_str(), frame-2));
}
//ofs->writeGrayLayout
// (lum, "test-FOE Main", FrameInfo("foe output", SRC_POS));
const FrameState os = ofs->updateNext();
//LINFO("frame[%d]: %8.3f %8.3f", frame, pshift.i, pshift.j);
Raster::waitForKey();
if (os == FRAME_FINAL)
break;
prevLum = lum;
frame++;
}
LINFO("%d frames in %gs (%.2ffps)\n",
frame, timer.getSecs(), frame / timer.getSecs());
// stop all our ModelComponents
manager.stop();
// all done!
return 0;
}
// Spike logic is driven by TrgSpikeParams:
// {periEvtSecs, refractSecs, inarow, nS, T}.
// Corresponding states defined above.
//
void TrigSpike::run()
{
Debug() << "Trigger thread started.";
setYieldPeriod_ms( 100 );
initState();
while( !isStopped() ) {
double loopT = getTime();
bool inactive;
// -------
// Active?
// -------
inactive = ISSTATE_Done || !isGateHi();
if( inactive )
goto next_loop;
// -------------
// If gate start
// -------------
// Set gateHiT as place from which to start
// searching for edge in getEdge().
if( !imCnt.edgeCt || !niCnt.edgeCt ) {
usrFlt->reset();
double gateT = getGateHiT();
if( imQ && !imQ->mapTime2Ct( imCnt.edgeCt, gateT ) )
goto next_loop;
if( niQ && !niQ->mapTime2Ct( niCnt.edgeCt, gateT ) )
goto next_loop;
}
// --------------
// Seek next edge
// --------------
if( ISSTATE_GetEdge ) {
if( p.trgSpike.stream == "imec" ) {
if( !getEdge( imCnt, imQ, niCnt, niQ ) )
goto next_loop;
}
else {
if( !getEdge( niCnt, niQ, imCnt, imQ ) )
goto next_loop;
}
QMetaObject::invokeMethod(
gw, "blinkTrigger",
Qt::QueuedConnection );
// ---------------
// Start new files
// ---------------
imCnt.remCt = -1;
niCnt.remCt = -1;
{
int ig, it;
if( !newTrig( ig, it, false ) )
break;
setSyncWriteMode();
}
SETSTATE_Write();
}
// ----------------
// Handle this edge
// ----------------
if( ISSTATE_Write ) {
if( !writeSome( DstImec, imQ, imCnt )
|| !writeSome( DstNidq, niQ, niCnt ) ) {
break;
}
// -----
// Done?
// -----
if( imCnt.remCt <= 0 && niCnt.remCt <= 0 ) {
endTrig();
usrFlt->reset();
imCnt.edgeCt += imCnt.refracCt;
niCnt.edgeCt += niCnt.refracCt;
if( ++nS >= nCycMax )
SETSTATE_Done;
else
SETSTATE_GetEdge;
}
}
// ------
// Status
// ------
next_loop:
if( loopT - statusT > 0.25 ) {
QString sOn, sWr;
int ig, it;
getGT( ig, it );
statusOnSince( sOn, loopT, ig, it );
statusWrPerf( sWr );
Status() << sOn << sWr;
statusT = loopT;
}
// -------------------
// Moderate fetch rate
// -------------------
yield( loopT );
}
endRun();
Debug() << "Trigger thread stopped.";
emit finished();
}
