int main(void)
{
//set outputs
DDRB=0xff; //all out for now
PORTB=0b000; //all output low
//make sure heater is OFF and the slot is not held down
heater(0);
//set inputs
DDRA=0x00; //all in
PORTA=0b011; //no pull-up for the trimmer
//setup interupt for counting time
TCCR1A=(1<<WGM12); //clear counter on compare match
TCCR1B=(1<<CS11)|(1<CS10); //1MHZ/64=15.625kHz
OCR1A=15625; //compare match at 1Hz
TIMSK1=(1<<OCIE1A); //interupt on compare match a
//setup adc for trimmer
ADMUX=(1<<MUX1); //set PA2 for adc
ADCSRB=(1<<ADLAR); //set for reading of highest bits
ADCSRA=(1<<ADEN)|(1<<ADSC)|(1<<ADATE); //start free run mode
//setup SPI slave
DDRA|=(1<<5);
USICR = (1<<USIWM0)|(1<<USICS1)|(1<<USIOIE);
USISR = (1<<USICNT0);
sei();//enable interrupt
//end of setup
while(1) //be stuck forever.
{
if(!slot()) //hold the toast down
{
time=trimmer(); //set timer according to knob
heater(1);
debug(1);
hold(1);
while(button()); //wait for user input
heater(0);
hold(0);
debug(0);
while(!button()); //wait untill button is released
}
}
}
void GroomingTreeProducer::ProduceTree()
{
TFile OutputFile (outFileName.c_str(), "RECREATE");
Float_t mass_PFjet, mass_Filtered_PFjet, mass_Pruned_PFjet, mass_Pruned_PFjet_subtracted, mass_Trimmed_PFjet, pt_PFjet, mass_GENjet, mass_Filtered_GENjet, mass_Pruned_GENjet, mass_Trimmed_GENjet, pt_GENjet, mass_PFjet_subtracted, mass_soft_drop;
Int_t nPU;
TTree *PF_tree = new TTree("PF", "PF");
TTree *GEN_tree = new TTree("GEN", "GEN");
PF_tree -> Branch("mass_PFjet",&mass_PFjet,"mass_PFjet/F");
PF_tree -> Branch("mass_PFjet_subtracted",&mass_PFjet_subtracted,"mass_PFjet_subtracted/F");
PF_tree -> Branch("pt_PFjet",&pt_PFjet,"pt_PFjet/F");
PF_tree -> Branch("mass_Pruned_PFjet",&mass_Pruned_PFjet,"mass_Pruned_PFjet/F");
PF_tree -> Branch("mass_Pruned_PFjet_subtracted",&mass_Pruned_PFjet_subtracted,"mass_Pruned_PFjet_subtracted/F");
PF_tree -> Branch("mass_Trimmed_PFjet",&mass_Trimmed_PFjet,"mass_Trimmed_PFjet/F");
PF_tree -> Branch("mass_Filtered_PFjet",&mass_Filtered_PFjet,"mass_Filtered_PFjet/F");
PF_tree -> Branch("mass_soft_drop",&mass_soft_drop,"mass_soft_drop/F");
PF_tree -> Branch("nPU",&nPU,"nPU/I");
GEN_tree -> Branch("mass_GENjet",&mass_GENjet,"mass_GENjet/F");
GEN_tree -> Branch("pt_GENjet",&pt_GENjet,"pt_GENjet/F");
GEN_tree -> Branch("mass_Pruned_GENjet",&mass_Pruned_GENjet,"mass_Pruned_GENjet/F");
GEN_tree -> Branch("mass_Trimmed_GENjet",&mass_Trimmed_GENjet,"mass_Trimmed_GENjet/F");
GEN_tree -> Branch("mass_Filtered_GENjet",&mass_Filtered_GENjet,"mass_Filtered_GENjet/F");
GEN_tree -> Branch("nPU",&nPU,"nPU/I");
for (unsigned int jj = 0; jj < inputFileNames.size(); jj++)
{
TFile* fIn = TFile::Open((prefixSamples + inputFileNames.at(jj)).c_str());
TTree* tree = (TTree*) fIn->Get("Events");
TClonesArray *PF = new TClonesArray("baconhep::TPFPart");
TClonesArray *Gen = new TClonesArray("baconhep::TGenParticle");
TEventInfo *ev_Info = new TEventInfo();
tree -> SetBranchAddress("PFPart", &PF);
tree -> SetBranchAddress("GenParticle", &Gen);
tree -> SetBranchAddress("Info",&ev_Info);
for(int i0 =0; i0 <tree -> GetEntriesFast(); i0++)
{
//1, event loop
tree -> GetEntry(i0);
bool leptonic = false;
std::vector<fastjet::PseudoJet> PFparticles;
std::vector<fastjet::PseudoJet> GENparticles;
nPU = ev_Info -> nPU;
for( int i1 = 0; i1 < PF -> GetEntriesFast(); i1++)
{
//2,entries loop,fill the vector particles with PF particles
baconhep::TPFPart *PFTmp = (baconhep::TPFPart*)((*PF)[i1]);
double Px=PFTmp->pt*cos(PFTmp->phi);
double Py= PFTmp->pt*sin(PFTmp->phi);
double theta = 2*atan(exp(-PFTmp->eta)); //eta = -ln(tan(theta/2))
double Pz = PFTmp->pt/tan(theta);
double E = PFTmp->e;
fastjet::PseudoJet tmp_psjet(Px, Py, Pz, E);
PFparticles.push_back(tmp_psjet);
}
//loop over genparticles
for( int i3 = 0; i3 < Gen -> GetEntriesFast(); i3++)
{
baconhep::TGenParticle *GenParticleTmp = (baconhep::TGenParticle*)((*Gen)[i3]);
double Px=GenParticleTmp->pt*cos(GenParticleTmp->phi);
double Py= GenParticleTmp->pt*sin(GenParticleTmp->phi);
double theta = 2*atan(exp(-GenParticleTmp->eta)); //eta = -ln(tan(theta/2))
double Pz = GenParticleTmp->pt/tan(theta);
double Genmass = GenParticleTmp -> mass;
double E = sqrt(Px*Px + Py*Py + Pz*Pz + Genmass*Genmass);
fastjet::PseudoJet tmp_genpsjet(Px, Py, Pz, E);
// cout << "Number "<< i3 << "|status " << GenParticleTmp -> status << "| pdgId " << GenParticleTmp -> pdgId << "| parent " << GenParticleTmp -> parent << endl;
//check if W decays leptonically
if (fabs(GenParticleTmp -> pdgId) == 11 || fabs(GenParticleTmp -> pdgId) == 13 || fabs(GenParticleTmp -> pdgId) == 15)
{
if ( fabs(((baconhep::TGenParticle*)((*Gen)[GenParticleTmp -> parent])) -> pdgId) == 24) leptonic = true;
}
if ((GenParticleTmp -> status) == 1 && fabs(GenParticleTmp -> pdgId)!=12 && fabs(GenParticleTmp -> pdgId)!=14 && fabs(GenParticleTmp -> pdgId)!=16 ) GENparticles.push_back(tmp_genpsjet);//taking particles only with status == 1 and filtering neutrinos
}
if (leptonic) continue;//use only leptonically decays of W
fastjet::AreaDefinition area_def(active_area_explicit_ghosts,GhostedAreaSpec(SelectorAbsRapMax(4.0)));
fastjet::ClusterSequenceArea clust_seq_PF(PFparticles, jet_def, area_def);
fastjet::ClusterSequenceArea clust_seq_GEN(GENparticles, jet_def, area_def);
std::vector<fastjet::PseudoJet> PF_jets_basic = sorted_by_pt(clust_seq_PF.inclusive_jets(300.0));
std::vector<fastjet::PseudoJet> GEN_jets_basic = sorted_by_pt(clust_seq_GEN.inclusive_jets(300.0));
fastjet::Selector rho_range = SelectorAbsRapMax(4.0);
JetMedianBackgroundEstimator bge_rho (rho_range, clust_seq_PF);
JetMedianBackgroundEstimator bge_rhom(rho_range, clust_seq_PF);
BackgroundJetPtMDensity m_density;
bge_rhom.set_jet_density_class(&m_density);
contrib::SafeAreaSubtractor *area_subtractor = new contrib::SafeAreaSubtractor(&bge_rho, &bge_rhom);
double RCut= 0.5;
Pruner pruner(jet_def, 0.1,RCut);
Filter trimmer(jet_def_filtering ,SelectorPtFractionMin(0.05) );
Filter filter(jet_def_filtering , SelectorNHardest(3) );
contrib::SoftDrop softdrop(2., 0.1, 1.0);
trimmer.set_subtractor(area_subtractor);
filter.set_subtractor(area_subtractor);
softdrop.set_subtractor(area_subtractor);
PseudoJet pruned_jet, pruned_jet_subtracted, trimmed_jet, filtered_jet, subtracted_jet, soft_drop_jet;
for (unsigned j =0; j < PF_jets_basic.size();++j)
{
subtracted_jet = (PseudoJet) (*area_subtractor)(PF_jets_basic.at(j));
trimmed_jet = (PseudoJet) trimmer.result(PF_jets_basic.at(j));
filtered_jet = (PseudoJet) filter.result(PF_jets_basic.at(j));
soft_drop_jet= (PseudoJet) softdrop.result(PF_jets_basic.at(j));
pruned_jet = pruner(PF_jets_basic.at(j));
pruned_jet_subtracted = pruner(subtracted_jet);
mass_PFjet = PF_jets_basic.at(j).m();
mass_PFjet_subtracted = subtracted_jet.m();
pt_PFjet = PF_jets_basic.at(j).pt();
mass_Pruned_PFjet = pruned_jet.m();
mass_Pruned_PFjet_subtracted = pruned_jet_subtracted.m();
mass_Filtered_PFjet = filtered_jet.m();
mass_Trimmed_PFjet = trimmed_jet.m();
mass_soft_drop = soft_drop_jet.m();
PF_tree -> Fill();
}
for (unsigned j =0; j < GEN_jets_basic.size();++j)
{
pruned_jet = pruner(GEN_jets_basic.at(j));
trimmed_jet = (PseudoJet) trimmer.result(GEN_jets_basic.at(j));
filtered_jet = (PseudoJet) filter.result(GEN_jets_basic.at(j));
mass_GENjet = GEN_jets_basic.at(j).m();
pt_GENjet = GEN_jets_basic.at(j).pt();
mass_Pruned_GENjet = pruned_jet.m();
mass_Filtered_GENjet = filtered_jet.m();
mass_Trimmed_GENjet = trimmed_jet.m();
GEN_tree -> Fill();
}
PF_jets_basic.clear();
GEN_jets_basic.clear();
}//end of event loop
}
OutputFile.cd();
GEN_tree -> Write();
PF_tree -> Write();
}
unsigned long int fq_stream_trimmer(UT_string *fq_fn, int pipe_fd, UT_string *out_prefix, int no_pre, int len_pre, unsigned long int *comp_cnt, unsigned long int *org, char split, int fmt_fasta) {
UT_string *new_head_data;
utstring_new(new_head_data);
UT_string *head_data;
utstring_new(head_data);
UT_string *seq_data;
utstring_new(seq_data);
UT_string *extra_data;
utstring_new(extra_data);
UT_string *qual_data;
utstring_new(qual_data);
unsigned long int cnt = 0;
char *start = NULL;
char *end = NULL;
char *suffix = NULL;
FILE *fq_file = NULL;
FILE *pipe_in = fdopen(pipe_fd, "w");
if (!(utstring_len(fq_fn))) {
fclose(pipe_in);
return(0);
}
// Try to open the fastq file
if (!(fq_file = gzopen(utstring_body(fq_fn), "r"))) {
utstring_printf(fq_fn, ".gz");
if (!(fq_file = gzopen(utstring_body(fq_fn), "r"))) {
fclose(pipe_in);
return(0);
}
}
int x = 0;
char head_char = '@';
if (fmt_fasta) {
head_char = '>';
}
while (ss_gzget_utstring(fq_file, head_data)) {
ss_gzget_utstring(fq_file, seq_data);
ss_gzget_utstring(fq_file, extra_data);
ss_gzget_utstring(fq_file, qual_data);
if (!split || ((suffix = strchr(utstring_body(head_data), '/')) && (suffix[1] == split))) {
(*org)++;
if ((x = trimmer(utstring_body(qual_data))) >= min_len) { // Keep at least some of read
// Reject read if complexity is too low
if ((entropy_cutoff < 0.0) || (entropy_calc(utstring_body(seq_data), x) >= entropy_cutoff)) {
// Truncate sequence
ss_trim_utstring(seq_data, x);
ss_strcat_utstring(seq_data, "\n");
if (!fmt_fasta) {
ss_trim_utstring(qual_data, x);
ss_strcat_utstring(qual_data, "\n");
}
// Fixup the read name
utstring_clear(new_head_data);
end = strchr(utstring_body(head_data), ':');
if (no_pre) {
if ((start = strchr(utstring_body(head_data), '|'))) {
start++;
} else {
if (colorspace_flag) {
start = utstring_body(head_data) + 4;
} else {
start = utstring_body(head_data) + 1;
}
}
*end = '\0';
} else {
start = utstring_body(out_prefix);
}
end++;
if (colorspace_flag) {
if (len_pre) {
utstring_printf(new_head_data, "%c%.2s+%u|%s:%s",head_char,utstring_body(head_data)+1,x,start,end);
} else {
utstring_printf(new_head_data, "%c%.2s+%s:%s",head_char,utstring_body(head_data)+1,start,end);
}
} else {
if (len_pre) {
utstring_printf(new_head_data, "%c%u|%s:%s",head_char,x,start,end);
} else {
utstring_printf(new_head_data, "%c%s:%s",head_char,start,end);
}
}
fputs(utstring_body(new_head_data), pipe_in);
fputs(utstring_body(seq_data), pipe_in);
if (!fmt_fasta) {
fputs(utstring_body(extra_data), pipe_in);
fputs(utstring_body(qual_data), pipe_in);
}
cnt++;
} else {
// rejected by entropy filter
// Send along placeholder read to be discarded, keeping read1 and read2 in sync
// Empty fastq header is a read to be rejected by consumer threads
(*comp_cnt)++;
fputs("\n", pipe_in);
}
} else {
// rejected by minimum length cutoff
// Send along placeholder read to be discarded, keeping read1 and read2 in sync
// Empty fastq header is a read to be rejected by consumer threads
fputs("\n", pipe_in);
}
}
}
fclose(pipe_in);
gzclose(fq_file);
utstring_free(new_head_data);
utstring_free(head_data);
utstring_free(seq_data);
utstring_free(extra_data);
utstring_free(qual_data);
return(cnt);
}