int main(int argc, char** argv) {
try {
util::ProgramOptions::init(argc, argv);
logger::LogManager::init();
pipeline::Process<ImageStackDirectoryReader> intensityReader(optionIntensities.as<std::string>());
pipeline::Process<ImageStackDirectoryReader> labelReader(optionLabels.as<std::string>());
pipeline::Value<ImageStack> intensityStack = intensityReader->getOutput();
pipeline::Value<ImageStack> labelStack = labelReader->getOutput();
if (optionExtractLabels) {
LOG_DEBUG(logger::out) << "[main] extracting labels from connected components" << std::endl;
pipeline::Process<ExtractLabels> extractLabels;
extractLabels->setInput(labelReader->getOutput());
labelStack = extractLabels->getOutput();
}
unsigned int width = labelStack->width();
unsigned int height = labelStack->height();
unsigned int depth = labelStack->size();
if (width != intensityStack->width() ||
height != intensityStack->height() ||
depth != intensityStack->size())
UTIL_THROW_EXCEPTION(
UsageError,
"intensity and label stacks have different sizes");
// create volumes from stacks
ExplicitVolume<float> intensities(*intensityStack);
ExplicitVolume<int> labels(*labelStack);
intensities.normalize();
// store them in the project file
boost::filesystem::remove(optionProjectFile.as<std::string>());
Hdf5VolumeStore volumeStore(optionProjectFile.as<std::string>());
volumeStore.saveIntensities(intensities);
volumeStore.saveLabels(labels);
} catch (boost::exception& e) {
handleException(e, std::cerr);
}
}
std::pair<int,double> LeastRecentlyUsedCache::getIntensity(int frameLow, int frameHigh, double percentile ){
std::pair<int,double> intensities( -1, 0 );
int position = 0;
for ( QLinkedList<LeastRecentlyUsedCacheEntry>::iterator iter = m_cache.begin();
iter != m_cache.end(); iter++ ){
if ( (*iter).getFrameLow() == frameLow ){
if ( (*iter).getFrameHigh() == frameHigh ){
if ( qAbs( percentile - (*iter).getPercentile() )< ERROR_MARGIN ){
intensities.first = (*iter).getLocation();
intensities.second = (*iter).getIntensity();
_refresh(position);
break;
}
}
}
position++;
}
return intensities;
}