double
SortedDistanceComparator::compareStructures(
const SortedDistanceComparisonData & dist1,
const SortedDistanceComparisonData & dist2) const
{
typedef StridedIndexAdapter< size_t> IndexAdapter;
const size_t numSpecies = dist1.species.size();
if(numSpecies != dist2.species.size())
return std::numeric_limits< double>::max(); // Species mismatch
std::set< std::string> speciesCheck(dist1.species.begin(),
dist1.species.end());
std::set< std::string>::const_iterator it;
BOOST_FOREACH(const std::string & species2, dist2.species)
{
it = speciesCheck.find(species2);
if(it == speciesCheck.end())
return std::numeric_limits< double>::max(); // Species mismatch
else
speciesCheck.erase(it);
}
if(!speciesCheck.empty())
return std::numeric_limits< double>::max(); // Species mismatch
// Set up the adapters
const unsigned int leastCommonMultiple = math::leastCommonMultiple(
dist1.numAtoms, dist2.numAtoms);
IndexAdapter adapt1(leastCommonMultiple / dist1.numAtoms);
IndexAdapter adapt2(leastCommonMultiple / dist2.numAtoms);
spl::math::RunningStats stats;
common::AtomSpeciesId::Value specI, specJ;
for(size_t i = 0; i < numSpecies; ++i)
{
specI = dist1.species[i];
// Do others
const SortedDistanceComparisonData::DistancesMap & distMapI1 =
dist1.speciesDistancesMap(specI);
const SortedDistanceComparisonData::DistancesMap & distMapI2 =
dist2.speciesDistancesMap(specI);
for(size_t j = i; j < numSpecies; ++j)
{
specJ = dist1.species[j];
calcProperties(stats, *distMapI1(specJ), adapt1, *distMapI2(specJ),
adapt2);
}
}
return stats.rms();
}
static void AllocationGenerateScriptMips(RsContext con, RsAllocation va) {
Context *rsc = static_cast<Context *>(con);
Allocation *texAlloc = static_cast<Allocation *>(va);
uint32_t numFaces = texAlloc->getType()->getDimFaces() ? 6 : 1;
for (uint32_t face = 0; face < numFaces; face ++) {
Adapter2D adapt(rsc, texAlloc);
Adapter2D adapt2(rsc, texAlloc);
adapt.setFace(face);
adapt2.setFace(face);
for (uint32_t lod=0; lod < (texAlloc->getType()->getLODCount() -1); lod++) {
adapt.setLOD(lod);
adapt2.setLOD(lod + 1);
mip(adapt2, adapt);
}
}
}
double SortedDistanceComparator::compareStructures(
const SortedDistanceComparisonData & dist1,
const SortedDistanceComparisonData & dist2) const
{
typedef ::std::vector<double> DistancesVec;
typedef StridedIndexAdapter<size_t> IndexAdapter;
const size_t numSpecies = dist1.species.size();
if(numSpecies != dist2.species.size())
{
// Species mismatch!
return ::std::numeric_limits<double>::max();
}
// Set up the adapters
const unsigned int leastCommonMultiple = math::leastCommonMultiple(dist1.numAtoms, dist2.numAtoms);
IndexAdapter adapt1(leastCommonMultiple / dist1.numAtoms);
IndexAdapter adapt2(leastCommonMultiple / dist2.numAtoms);
double max = ::std::numeric_limits<double>::min();
double sqSum = 0.0;
unsigned int totalCompared = 0;
common::AtomSpeciesId::Value specI, specJ;
for(size_t i = 0; i < numSpecies - 1; ++i)
{
specI = dist1.species[i];
// Do others
const SortedDistanceComparisonData::DistancesMap & distMapI1 = dist1.speciesDistancesMap(specI);
const SortedDistanceComparisonData::DistancesMap & distMapI2 = dist2.speciesDistancesMap(specI);
for(size_t j = i; j < numSpecies; ++j)
{
specJ = dist1.species[j];
calcProperties(*distMapI1(specJ), adapt1, *distMapI2(specJ), adapt2, sqSum, max, totalCompared);
}
}
return sqrt(sqSum / totalCompared);
//return max;
}
int main(int argc, char *argv[])
{
b_po::variables_map vmgeneral;
parsecommandlineExtract(argc, argv, vmgeneral);
ralab::findmf::apps::Params aparam;
analysisParameters(aparam,vmgeneral);
int res = 0;
boost::filesystem::path p1,p2;
{
// LOG(INFO) << "i::::" << i << std::endl;
p1 = ralab::findmf::createOutputs(aparam.infile,"");
p2 = ralab::findmf::createOutputs(aparam.infile,"filtered");
if( !boost::filesystem::exists(aparam.infile) )
{
return -1;
}
ralab::findmf::datastruct::MSFileInfoPtr sip;
try{
ralab::findmf::SwathPropertiesReader swathPropReader(aparam.infile);
sip = swathPropReader.getSwathInfo();
} catch(std::exception & e){
std::cerr << "infile : " << aparam.infile << std::endl;
std::cerr << "can't open file: " << e.what() << std::endl;
return 0;
}
double ppm = aparam.ppm;
pwiz::msdata::MSDataPtr msdataptr = pwiz::msdata::MSDataPtr(new pwiz::msdata::MSDataFile(aparam.infile));
ralab::findmf::LCMSImageReader sm(msdataptr, sip, ppm, aparam.rt2sum_ );
ralab::findmf::datastruct::LCMSImage mp;
sm.getMap( 0 , aparam.minmass, aparam.maxmass, mp);
// LOG(INFO) << " " << mp.getMZsize() << " " << mp.getRTsize();
ralab::findmf::datastruct::LCMSImage mp2( mp );
{
ralab::findmf::LCMSImageFilterGauss imgf;
// imgf.filterMap( mp2.getImageMap().getMap() , aparam.mzpixelwidth , aparam.rtpixelwidth, aparam.mzscale, aparam.rtscale);
imgf.filter( mp2.getImageMap().getMap() , aparam.mzpixelwidth , aparam.rtpixelwidth, aparam.mzscale, aparam.rtscale);
mp2.getImageMap().updateImageRange();
std::cout << mp2.getImageMap().getImageMin() << std::endl;
//imgf.filterMap();
}
// feature finding
ralab::findmf::FeatureFinderLocalMax ff;
ff.findFeature( mp2.getImageMap().getMap() , aparam.minintensity );
ralab::findmf::datastruct::FeaturesMap map;
map.setMapDescription(mp2.getMapDescription());
ralab::findmf::ComputeFeatureStatistics cfs;
cfs.extractFeatures(map,mp2.getImageMap().getMap(),ff.getLabels());
//this writes the accessor....
cfs.writeFeatures(aparam.outdir , p1.stem().string() );
ralab::FeaturesMapPrinter fp;
fp.writeFeatures(aparam.outdir , p1.stem().string(), map);
ralab::MultiArrayVisSegments<int> mavL( ff.getLabels() );
//write filtered data into mzML file
//TODO check why this isn't working
sm.write( p2.string() , mp2 );
if(1){
QApplication app(argc, argv);
ralab::TwoPaneledImageWidget tpi;
ralab::MultiArrayVisLog<float> adapt2( mp2.getImageMap().getMap() );
ralab::MultiArrayVisAsinh<float> adapt1( mp2.getImageMap().getMap() );
ralab::MultiArrayVisLog<float> adapt0( mp.getImageMap().getMap() );
tpi.setTopMap(&mavL);
//tpi.setBottomMap(&adapt0);
tpi.setBottomMap(&adapt0);
tpi.show();
res = app.exec();
}
}
return res;
}