/*
* Entry point - start the OneWire messaging server,
* listening on a socket.
*/
int main (int argc, char **argv)
{
ServerReturnCode returnCode = SERVER_ERR_GENERAL_FAILURE;
UInt16 oneWireServerPort;
setDebugPrintsOn();
setProgressPrintsOn();
if (argc == 2)
{
oneWireServerPort = atoi (argv[1]);
printProgress ("OneWireServer listening on port %d.\n", oneWireServerPort);
returnCode = runMessagingServer (oneWireServerPort);
if (returnCode == SERVER_EXIT_NORMALLY)
{
printProgress ("OneWireServer exiting normally.\n");
}
else
{
printProgress ("OneWireServer exiting with returnCode %d.\n", returnCode);
}
}
else
{
printProgress ("Usage: %s portnumber\ne.g. %s 5234\n", argv[0], argv[0]);
}
return returnCode;
}
/**
* Initializes the SMTP communications by sending the EHLO
* If EHLO errors out, it will try the HELO command.
*
* Params
* sd - Socket descriptor
* domain - Your domain name.
*
* Return
* - ERROR
* - SUCCESS
*/
int
smtpInit(dsocket *sd, const char *domain)
{
int retval;
printProgress("Init connection...");
retval = init(sd);
if (retval == ERROR) {
return retval;
}
printProgress("Greeting the SMTP server...");
retval = ehlo(sd, domain);
if (retval == ERROR) {
/*
* Per RFC, if ehlo error's out, you can
* ignore the error, RSET and try a
* regular helo.
*/
rset(sd);
retval = helo(sd, domain);
}
return retval;
}
void ConsoleUpdater::onProgressChange(const ProgressInfo& info)
{
bool progressPrinted = false;
switch (info.type)
{
case ProgressInfo::FileDownload:
if( info.mirrorDisplayName.empty() )
break;
// Download progress
if (!_d->info.file.toString().empty()
&& info.file.toString() != _d->info.file.toString() )
{
// New file, finish the current download
_d->info.progressFraction = 1.0f;
_d->progressDone = false;
progressPrinted = true;
printProgress();
// Add a line break when a new file starts
Logger::warning( fmt::format( "\nDownloading from Mirror {}: {}", info.mirrorDisplayName, info.file.toString() ) );
}
else if (_d->info.file.toString().empty())
{
// First file
Logger::warning( fmt::format( " Downloading from Mirror {}: {}", info.mirrorDisplayName, info.file.toString() ) );
}
_d->info = info;
// Print the new info
if( !progressPrinted )
printProgress();
// Add a new line if we're done here
if( info.progressFraction >= 1 && !_d->progressDone)
{
_d->progressDone = true;
Logger::warning( "\n" );
}
break;
case ProgressInfo::FileOperation:
_d->info = info;
// Print the new info
printProgress();
// Add a new line if we're done here
if (info.progressFraction >= 1)
{
Logger::warning( "\n");
}
break;
default: break;
};
}
bool QInstallPage::writeQString2File( const QString& the_string,
const QString& fname ){
QFile* the_file = new QFile( fname );
if ( ! the_file->open( QIODevice::WriteOnly ) ){
printProgress( (QString)"Error opening file " + fname + " for writing \n" );
printProgress( (QString)"Check that it exists or could be created ..." );
return false;
}
QTextStream the_stream;
the_stream.setDevice( the_file );
the_stream << the_string;
the_file->close();
return true;
}
void XMLerLoadUrlThread::run()
{
QNetworkRequest request(url);
QNetworkReply* rep = mNetworkManager->get(request);
connect(rep, SIGNAL(downloadProgress(qint64, qint64)), this, SLOT(printProgress(qint64, qint64)));
disconnect(rep, SIGNAL(downloadProgress(qint64, qint64)));
}
int calcMD5(int file, int size, char* fname){
unsigned char c[MD5_DIGEST_LENGTH];
MD5_CTX mdContext;
int delay = 0, bytes, i, written = 0;
unsigned char data[DATA_BUF_SIZE];
MD5_Init(&mdContext);
while((bytes = read(file, data, DATA_BUF_SIZE)) != 0){
written+=bytes;
if(++delay > DELAY_LENGTH) {
printProgress(MD5_TAG, written, size);
delay = 0;
}
MD5_Update(&mdContext, data, bytes);
}
MD5_Final(c, &mdContext);
printf("\n%s: ", MD5_TAG);
for(i=0; i < MD5_DIGEST_LENGTH; i++) printf("%02x",c[i]);
printf("\n");
lseek(file, 0, SEEK_SET); //return to beginning of file
//write to file
char final[256] = MD5_TAG;
strcat(final, fname);
strcat (final, ".txt");
FILE *fp = fopen(final, "w");
if(fp){
for(i=0; i < MD5_DIGEST_LENGTH; i++) fprintf(fp, "%02x",c[i]);
fprintf(fp, "\t%s", fname);
}
fclose(fp);
return 0;
}
int RecursiveSolver::guess(int index) {
printProgress(count, _field);
bool succes = false;
for (int option : options[index]) {
if (_field.get(index) >= option) { // We have tried this slot before
continue;
}
if (_field.fit(index, option)) {
_field.set(index, option);
succes = true;
break;
}
}
map<int, vector<int>>::iterator it;
it = options.find(index);
if (succes) {
if (_field.countEmpty(true) > 0) {
// Find the the next empty slot in the vector
//guess(std::next(it)->first);
return RETURN_NEXT;
} else {
return RETURN_EXIT;
}
} else {
_field.set(index, 0);
// Find the the previous tried slot in the vector
//guess(std::prev(it)->first);
return RETURN_PREV;
}
}
/**
* Sends the QUIT\r\n signal to the smtp server.
*
* Params
* sd - Socket Descriptor
*
* Return
* - ERROR
* - SUCCESS
*/
int
smtpQuit(dsocket *sd)
{
int retval=0;
printProgress("Sending QUIT...");
retval = quit(sd);
dsbDestroy(errorstr);
return retval;
}
int
smtpInitAfterTLS(dsocket *sd, const char *domain)
{
int retval;
printProgress("Greeting the SMTP server...");
retval = ehlo(sd, domain);
return retval;
}
/**
* Takes a timer structure and a pointer to the progress array.
* it checks if the time since given structure was initiated has passed 500 ms
* if so it passed the progress structure to the printprogress function
* @param timer
* @param progress
*/
void checkTimer(timeval &timer,int *progress){
timeval time2;
gettimeofday(&time2, NULL);
long millis = (timer.tv_sec * 1000) + (timer.tv_usec / 1000);
long millis2 = (time2.tv_sec * 1000) + (time2.tv_usec / 1000);
long timeElapsed = millis2 - millis;
if(timeElapsed>=500){
printProgress(progress);
resetTimer(timer);
}
}
void checkTimer(SYSTEMTIME &timer,int *progress){
SYSTEMTIME time2;
GetSystemTime(&time2);
long millis = (timer.wHour*3600000)+(timer.wMinute*60000)+(timer.wSecond * 1000) + timer.wMilliseconds;
long millis2 = (time2.wHour*3600000)+(time2.wMinute*60000)+(time2.wSecond * 1000) + time2.wMilliseconds;
float timeElapsed = millis2-millis;
if(timeElapsed>=500){
printProgress(progress);
resetTimer(timer);
}
}
QString QInstallPage::readFile2QString( const QString& fname,
const QString& err ){
QFile* the_file = new QFile( fname );
if ( ! the_file->open( QIODevice::ReadOnly ) ){
printProgress( err );
return QString::null;
}
QTextStream the_stream;
the_stream.setDevice( the_file );
QString the_string = the_stream.readAll();
// the_stream.unsetDevice();
the_file->close();
return the_string;
}
void ClassifierApplication::showNextSubStep(int subStep)
{
mutex->lock();
mSubStep = subStep;
int progress = 0;
if (mSubStepCount != 0)
progress = int(10 * mSubStep / mSubStepCount);
if (mCurrentSubProgress < progress)
{
mCurrentSubProgress = progress;
printProgress();
}
mutex->unlock();
}
int FrameCapture::qt_metacall(QMetaObject::Call _c, int _id, void **_a)
{
_id = QObject::qt_metacall(_c, _id, _a);
if (_id < 0)
return _id;
if (_c == QMetaObject::InvokeMetaMethod) {
switch (_id) {
case 0: finished(); break;
case 1: printProgress((*reinterpret_cast< int(*)>(_a[1]))); break;
case 2: saveResult((*reinterpret_cast< bool(*)>(_a[1]))); break;
default: ;
}
_id -= 3;
}
return _id;
}
Launcher::Launcher(int numImages, int numThreads, QString workerCommand, QStringList args) : runningProcs(0),
timer(this),workCmd(workerCommand),procCount(1),workArgs(args)
{
if(numThreads > numImages)
numThreads = numImages;// more threads than images are useless!
int iPerThread = numImages / numThreads; //we roud down here as we use ints
for(int i = 0; i < (numThreads - 1); i++){
startProcess(i*iPerThread, iPerThread);
}
startProcess((numThreads -1)*iPerThread, numImages - (numThreads -1)*iPerThread);
connect(&timer,SIGNAL(timeout()),this,SLOT(printProgress()));
timer.setInterval(100);
timer.start();
}
void Scene::render()
{
vec2 pixel;
Ray r;
Color c;
printProgressHeader();
int count = 0;
while (getSample(&pixel)) {
r = cam->generateRay(pixel);
c = rt->trace(r, scene->getMaxDepth());
film->put(pixel, c);
count++;
printProgress(count);
}
cout << endl;
film->writeToFile(outputPath);
}
/* genera tutte le chiavi wpa possibili per ssid-series-macAddr specificati */
int generateKeys(unsigned long int ssid, unsigned long int series, unsigned char *macAddr)
{
int i;
for(serial = userOptions.startSerial; serial < userOptions.endSerial; serial++) /* per ogni serial... */
{
if(cycle % PRINT_RATE == 0)
{
printProgress();
}
sprintf(seriesXserial, "%05dX%07d", series, serial); /* crea la stringa serie-X-seriale */
/* calcola l'hash SHA256(fixedPadding + serie-X-seriale + MAC) */
sha256_starts(shaCtx);
sha256_update(shaCtx, fixedPadding, sizeof(fixedPadding));
sha256_update(shaCtx, seriesXserial, SERIESXSERIAL_SIZE);
sha256_update(shaCtx, macAddr, MAC_SIZE);
sha256_finish(shaCtx, hash);
/* converte l'hash in caratteri ASCII */
for(i = 0; i < WPA_SIZE; i++) wpa[i] = charset[hash[i]];
if(userOptions.opMode == FINDKEY) /* stiamo cercando una chiave particolare */
{
if(isWpaCorrect() == TRUE)
{
return KEYFOUND;
}
}
else if(userOptions.opMode == GENFILE) /* stiamo generando il dizionario */
{
if(writeWpaToBuffer() == FAILURE)
{
lastErr = FILE_ERR;
return FAILURE;
}
}
cycle++;
}
return SUCCESS;
}
Message* Parser::parseMessage(uint64_t& reference, uint64_t& match) {
char test = '\0';
if (!binaryData.get(test)) return NULL;
binaryData.get(test);
uint32_t size = test - '\0';
binaryData.read(buffer, size);
printProgress(size + 2);
switch (*buffer) {
case 'R':
return buildSD(buffer);
break;
case 'A':
case 'F':
return buildAO(buffer, reference);
break;
case 'E':
return buildOE(buffer, reference, match);
break;
case 'C':
return buildOEWP(buffer, reference, match);
break;
case 'D':
return buildOD(buffer, reference);
break;
case 'U':
return buildOR(buffer, reference);
break;
case 'P':
case 'Q':
return buildT(buffer, match);
break;
case 'B':
return buildBT(buffer, match);
break;
default: {
//cout << "skipping non-relevant message, type: " << *buffer << endl;
return new Message('\0');
}
}
}
/**
* Let's the SMTP server know it's the end of the data stream.
*
* Params
* sd - Socket descriptor
*
* Return
* - ERROR
* - SUCCESS
*/
int
smtpEndData(dsocket *sd)
{
int retval=ERROR;
dstrbuf *rbuf = DSB_NEW;
printProgress("Ending Data...");
if (writeResponse(sd, "\r\n.\r\n") != ERROR) {
retval = readResponse(sd, rbuf);
if (retval != 250) {
if (retval != ERROR) {
smtpSetErr(rbuf->str);
retval = ERROR;
}
}
} else {
smtpSetErr("Lost Connection with SMTP server: smtpEndData()");
retval = ERROR;
}
dsbDestroy(rbuf);
return retval;
}
int
smtpStartTls(dsocket *sd)
{
int retval=SUCCESS;
#ifdef HAVE_LIBSSL
dstrbuf *sb=DSB_NEW;
printProgress("Starting TLS Communications...");
if (writeResponse(sd, "STARTTLS\r\n") < 0) {
smtpSetErr("Lost connection to SMTP Server");
retval = ERROR;
goto end;
}
#ifdef DEBUG_SMTP
printf("--> STARTTLS\n");
fflush(stdout);
#endif
retval = readResponse(sd, sb);
if (retval != 220) {
smtpSetErr(sb->str);
retval = ERROR;
}
#ifdef DEBUG_SMTP
printf("<-- %s\n", sb->str);
fflush(stdout);
#endif
end:
dsbDestroy(sb);
#else
sd = sd;
#endif
return retval;
}
int VCS_SOLVE::vcs_setMolesLinProg()
{
size_t ik, irxn;
double test = -1.0E-10;
if (DEBUG_MODE_ENABLED && m_debug_print_lvl >= 2) {
plogf(" --- call setInitialMoles\n");
}
double dg_rt;
int idir;
double nu;
double delta_xi, dxi_min = 1.0e10;
bool redo = true;
int retn;
int iter = 0;
bool abundancesOK = true;
bool usedZeroedSpecies;
vector_fp sm(m_numElemConstraints*m_numElemConstraints, 0.0);
vector_fp ss(m_numElemConstraints, 0.0);
vector_fp sa(m_numElemConstraints, 0.0);
vector_fp wx(m_numElemConstraints, 0.0);
vector_fp aw(m_numSpeciesTot, 0.0);
for (ik = 0; ik < m_numSpeciesTot; ik++) {
if (m_speciesUnknownType[ik] != VCS_SPECIES_INTERFACIALVOLTAGE) {
m_molNumSpecies_old[ik] = max(0.0, m_molNumSpecies_old[ik]);
}
}
if (DEBUG_MODE_ENABLED && m_debug_print_lvl >= 2) {
printProgress(m_speciesName, m_molNumSpecies_old, m_SSfeSpecies);
}
while (redo) {
if (!vcs_elabcheck(0)) {
if (DEBUG_MODE_ENABLED && m_debug_print_lvl >= 2) {
plogf(" --- seMolesLinProg Mole numbers failing element abundances\n");
plogf(" --- seMolesLinProg Call vcs_elcorr to attempt fix\n");
}
retn = vcs_elcorr(&sm[0], &wx[0]);
if (retn >= 2) {
abundancesOK = false;
} else {
abundancesOK = true;
}
} else {
abundancesOK = true;
}
/*
* Now find the optimized basis that spans the stoichiometric
* coefficient matrix, based on the current composition, m_molNumSpecies_old[]
* We also calculate sc[][], the reaction matrix.
*/
retn = vcs_basopt(false, &aw[0], &sa[0], &sm[0], &ss[0],
test, &usedZeroedSpecies);
if (retn != VCS_SUCCESS) {
return retn;
}
if (DEBUG_MODE_ENABLED && m_debug_print_lvl >= 2) {
plogf("iteration %d\n", iter);
}
redo = false;
iter++;
if (iter > 15) {
break;
}
// loop over all reactions
for (irxn = 0; irxn < m_numRxnTot; irxn++) {
// dg_rt is the Delta_G / RT value for the reaction
ik = m_numComponents + irxn;
dg_rt = m_SSfeSpecies[ik];
dxi_min = 1.0e10;
const double* sc_irxn = m_stoichCoeffRxnMatrix.ptrColumn(irxn);
for (size_t jcomp = 0; jcomp < m_numElemConstraints; jcomp++) {
dg_rt += m_SSfeSpecies[jcomp] * sc_irxn[jcomp];
}
// fwd or rev direction.
// idir > 0 implies increasing the current species
// idir < 0 implies decreasing the current species
idir = (dg_rt < 0.0 ? 1 : -1);
if (idir < 0) {
dxi_min = m_molNumSpecies_old[ik];
}
for (size_t jcomp = 0; jcomp < m_numComponents; jcomp++) {
nu = sc_irxn[jcomp];
// set max change in progress variable by
// non-negativity requirement
if (nu*idir < 0) {
delta_xi = fabs(m_molNumSpecies_old[jcomp]/nu);
// if a component has nearly zero moles, redo
// with a new set of components
if (!redo && delta_xi < 1.0e-10 && (m_molNumSpecies_old[ik] >= 1.0E-10)) {
if (DEBUG_MODE_ENABLED && m_debug_print_lvl >= 2) {
plogf(" --- Component too small: %s\n", m_speciesName[jcomp]);
}
redo = true;
}
dxi_min = std::min(dxi_min, delta_xi);
}
}
// step the composition by dxi_min, check against zero, since
// we are zeroing components and species on every step.
// Redo the iteration, if a component went from positive to zero on this step.
double dsLocal = idir*dxi_min;
m_molNumSpecies_old[ik] += dsLocal;
m_molNumSpecies_old[ik] = max(0.0, m_molNumSpecies_old[ik]);
for (size_t jcomp = 0; jcomp < m_numComponents; jcomp++) {
bool full = false;
if (m_molNumSpecies_old[jcomp] > 1.0E-15) {
full = true;
}
m_molNumSpecies_old[jcomp] += sc_irxn[jcomp] * dsLocal;
m_molNumSpecies_old[jcomp] = max(0.0, m_molNumSpecies_old[jcomp]);
if (full && m_molNumSpecies_old[jcomp] < 1.0E-60) {
redo = true;
}
}
}
if (DEBUG_MODE_ENABLED && m_debug_print_lvl >= 2) {
printProgress(m_speciesName, m_molNumSpecies_old, m_SSfeSpecies);
}
}
if (DEBUG_MODE_ENABLED && m_debug_print_lvl == 1) {
printProgress(m_speciesName, m_molNumSpecies_old, m_SSfeSpecies);
plogf(" --- setInitialMoles end\n");
}
retn = 0;
if (!abundancesOK) {
retn = -1;
} else if (iter > 15) {
retn = 1;
}
return retn;
}
int uncompress(FILE *input, FILE *output) {
printProgress(1,0.00);
return 0;
}
void getXsecExtended(const TString mc_input, int debugMode=0, bool useFEWZ=true, int fineGrid=0)
{
// check whether it is a calculation
if (mc_input.Contains("_DebugRun_")) {
std::cout << "getXsec: _DebugRun_ detected. Terminating the script\n";
return;
}
if (debugMode==1) std::cout << "\n\n\tDEBUG MODE is ON\n\n";
if (debugMode==-1) std::cout << "\n\n\tPLOT ONLY MODE is ON\n\n";
std::cout << "DYTools::analysisTag=" << DYTools::analysisTag << "\n";
if (DYTools::study2D && fineGrid) {
std::cout << "fineGrid=1 is allowed only for study2D=0\n";
return;
}
// normal calculation
gBenchmark->Start("getXsec");
//--------------------------------------------------------------------------------------------------------------
// Settings
//==============================================================================================================
//Bool_t doSave = false; // save plots?
TString format = "png"; // output file format
MCInputFileMgr_t inpMgr;
TString fineGridStr;
if (fineGrid==1) fineGridStr="fineGrid_";
else if (fineGrid==2) fineGridStr="summer2011Grid_";
else if (fineGrid==3) fineGridStr="summer2011specGrid_";
Double_t massLow = DYTools::massBinLimits[0];
Double_t massHigh = DYTools::massBinLimits[DYTools::nMassBins];
// fine grid: 0, 1, 2, ..., (fineGrid_1GeVstop-1), fineGrid_1GeVstop, fineGrid_1GeVstop+fineGridLargerStep, fineGrid_1GeVstop+2*fineGridLargerStep, ..., 1500
//
double fineGrid_1GeVstop=200.;
double fineGrid_LargerStep=20.;
int locMassBinCount=DYTools::nMassBins;
double *massRangeEdges=NULL;
if (!fineGrid) {
massRangeEdges=new double[locMassBinCount+1];
for (int i=0; i<=DYTools::nMassBins; ++i) {
massRangeEdges[i]=DYTools::massBinLimits[i];
}
}
else if (fineGrid==1) {
// 1GeV grid
locMassBinCount=int(fineGrid_1GeVstop-massLow+1e-3);
std::cout << "1GeV grid size=" << locMassBinCount << "\n";
// fineGrid_LargerStep
double upperRange= (massHigh-fineGrid_1GeVstop);
double upperCount= upperRange/fineGrid_LargerStep + 1e-3;
if (upperCount - trunc(upperCount) > 1e-3) {
std::cout << "(upperCount -1e-3)=" << (upperCount -1e-3) << "\n";
std::cout << "should be integer value\n";
return;
}
locMassBinCount += int(upperCount);
std::cout << "mass grid[" << locMassBinCount << "]\n";
massRangeEdges=new double[locMassBinCount+1];
double m=massLow, dm=1;
int count=0;
while (m<=massHigh) {
massRangeEdges[count]=m;
if (1) {
if (m<massHigh) std::cout << "count=" << count << ", massRange=" << m << " .. " << (m+dm) << "\n";
else std::cout << "last edge=" << m << "\n";
}
count++;
m+=dm;
if (m==fineGrid_1GeVstop) dm=fineGrid_LargerStep;
}
}
else if (fineGrid==2) {
const int nMassBinTh=518;
Double_t mxl = 14.0;
locMassBinCount=nMassBinTh;
massRangeEdges=new double[nMassBinTh+1];
for(int iTh=0; iTh<=nMassBinTh; iTh++){
// mass limits
if ( iTh >= 0 && iTh < 11 ) {mxl += 1.0;}
else if( iTh >= 11 && iTh < 18 ) {mxl += 5.0;}
else if( iTh >= 18 && iTh < 118 ) {mxl += 1.0;}
else if( iTh >= 118 && iTh < 340 ) {mxl += 2.0;}
else if( iTh >= 340 && iTh < nMassBinTh) {mxl += 5.0; }
else if( iTh == nMassBinTh) {mxl = 1500; }
massRangeEdges[iTh]=mxl;
}
}
else if (fineGrid==3) {
const int nMassBinTh=518;
Double_t mxl = 14.0;
locMassBinCount=nMassBinTh;
massRangeEdges=new double[nMassBinTh+1];
int iTh_new=0, tmpCounter=0;
for(int iTh=0; iTh<=nMassBinTh; iTh++, iTh_new++){
// mass limits
if ( iTh >= 0 && iTh < 11 ) {mxl += 1.0;}
else if( iTh >= 11 && iTh < 18 ) {mxl += 5.0;}
else if( iTh >= 18 && iTh < 118 ) {mxl += 1.0;}
else if( iTh >= 118 && iTh < 340 ) {
if (iTh>=139) {
std::cout << "iTh=" << iTh << ", current mxl=" << mxl << " +2\n";
if (iTh==139) tmpCounter=10;
tmpCounter--;
if (tmpCounter>0) iTh_new--;
else if (tmpCounter==0) {
tmpCounter=10;
std::cout << "iTh=" << iTh << ", iTh_new=" << iTh_new << ", current mxl=" << mxl << " +10\n";
}
}
mxl += 2.0;
}
else if( iTh >= 340 && iTh < nMassBinTh) {
std::cout << "iTh=" << iTh << ", current mxl=" << mxl << " +5\n";
if (iTh<342) iTh_new--;
else {
if ((iTh-342)%4>0) iTh_new--;
else std::cout << "iTh=" << iTh << ", iTh_new=" << iTh_new << ", current mxl=" << mxl << " +10\n";
}
mxl += 5.0;
}
else if( iTh == nMassBinTh) {mxl = 1500; }
massRangeEdges[iTh_new]=mxl;
}
massRangeEdges[iTh_new-2]=1500.;
std::cout << "iTh_new=" << iTh_new << "\n";
locMassBinCount=iTh_new-2;
}
TVectorD massGrid(locMassBinCount+1);
for (int i=0; i<=locMassBinCount; ++i) massGrid[i]=massRangeEdges[i];
TH1F hMassIdx("h_massIdx","h_massIdx",locMassBinCount-1,massRangeEdges);
//delete massRangeEdges;
if (0) {
printHisto(&hMassIdx);
if (0) {
for (int i=0; i<int(massHigh); ++i) {
double m=i+0.5;
std::cout << "i=" << i << ", m=" << m << ", idx=" << (hMassIdx.FindBin(m)-1) << "\n";
}
}
return;
}
//std::cout << "massHigh=" << massHigh << "\n";
//std::cout << "locMassBinCount=" << locMassBinCount << "\n";
if (!inpMgr.Load(mc_input)) {
return;
}
//--------------------------------------------------------------------------------------------------------------
// Main code
//==============================================================================================================
//
// Set up histograms
//
//vector<TH1D*> hZMassv;
Double_t nZv = 0;
TMatrixD nEvents (locMassBinCount,DYTools::nYBinsMax); // number of weigthed events
TMatrixD nEventsDET (locMassBinCount,DYTools::nYBinsMax); // number of weighted events in the detector acceptance
TMatrixD nEventsDETrecoPostIdx (locMassBinCount,DYTools::nYBinsMax); // number of weigthed events
TMatrixD w2Events (locMassBinCount,DYTools::nYBinsMax);
TMatrixD w2EventsDET (locMassBinCount,DYTools::nYBinsMax);
TMatrixD w2EventsDETrecoPostIdx (locMassBinCount,DYTools::nYBinsMax);
Double_t nZpeak=0, w2Zpeak=0;
double nZpeakDET=0, w2ZpeakDET=0;
double nZpeakDETrecoPostIdx=0, w2ZpeakDETrecoPostIdx=0;
nEvents = 0;
w2Events = 0;
nEventsDET = 0;
w2EventsDET = 0;
nEventsDETrecoPostIdx = 0;
w2EventsDETrecoPostIdx = 0;
//char hname[100];
//for(UInt_t ifile = 0; ifile<fnamev.size(); ifile++) {
// sprintf(hname,"hZMass_%i",ifile); hZMassv.push_back(new TH1F(hname,"",500,0,500)); hZMassv[ifile]->Sumw2();
//}
//
// Read weights from a file
//
const bool useFewzWeights = useFEWZ;
const bool cutZPT100 = true;
FEWZ_t fewz(useFewzWeights,cutZPT100);
if (useFewzWeights && !fewz.isInitialized()) {
std::cout << "failed to prepare FEWZ correction\n";
throw 2;
}
//
// Access samples and fill histograms
//
TFile *infile=0;
TTree *eventTree=0;
// Data structures to store info from TTrees
mithep::TGenInfo *gen = new mithep::TGenInfo();
// loop over samples
double lumi0=0;
if (debugMode!=-1) {
for(UInt_t ifile=0; ifile<inpMgr.fileNames().size(); ifile++) {
// Read input file
cout << "Processing " << inpMgr.fileName(ifile) << "..." << endl;
infile = new TFile(inpMgr.fileName(ifile));
assert(infile);
// Get the TTrees
eventTree = (TTree*)infile->Get("Events"); assert(eventTree);
// Find weight for events for this file
// The first file in the list comes with weight 1,
// all subsequent ones are normalized to xsection and luminosity
double lumi = eventTree->GetEntries()/inpMgr.xsec(ifile);
if (ifile==0) lumi0=lumi;
double scale = lumi0/lumi;
std::cout << " -> sample weight is " << scale << endl;
// Set branch address to structures that will store the info
eventTree->SetBranchAddress("Gen",&gen);
TBranch *genBr = eventTree->GetBranch("Gen");
// loop over events
nZv += scale * eventTree->GetEntries();
for(UInt_t ientry=0; ientry<eventTree->GetEntries(); ientry++) {
if (debugMode && (ientry>100000)) break;
genBr->GetEntry(ientry);
if (ientry%1000000==0) printProgress("ientry=",ientry,eventTree->GetEntriesFast());
double massPreFsr = gen->vmass; // pre-FSR
double yPreFsr = gen->vy; // pre-FSR
double massPostFsr = gen->mass; // post-FSR
double yPostFsr = gen->y; // post-FSR
if ((massPreFsr < massLow) || (massPreFsr > massHigh)) continue;
if ((fabs(yPreFsr) < DYTools::yRangeMin) ||
(fabs(yPreFsr) > DYTools::yRangeMax)) continue;
int ibinMassPreFsr=-1, ibinYPreFsr=-1;
int ibinMassPostFsr=-1, ibinYPostFsr=-1;
if (!fineGrid) {
ibinMassPreFsr = DYTools::findMassBin(massPreFsr);
ibinMassPostFsr= DYTools::findMassBin(massPostFsr);
ibinYPreFsr = DYTools::findAbsYBin(ibinMassPreFsr, yPreFsr);
ibinYPostFsr= DYTools::findAbsYBin(ibinMassPostFsr, yPostFsr);
}
else {
ibinMassPreFsr=hMassIdx.FindBin(massPreFsr)-1;
ibinMassPostFsr=hMassIdx.FindBin(massPostFsr)-1;
ibinYPreFsr=0;
ibinYPostFsr=0;
//printf("massPreFsr=%8.4lf, idx=%3d; massPostFsr=%8.4lf, idx=%3d\n", massPreFsr,ibinMassPreFsr, massPostFsr,ibinMassPostFsr);
}
// We are only interested in the events, reconstructed with
// good mass and rapidity
if (ibinMassPreFsr==-1 ||
ibinMassPreFsr>=locMassBinCount ||
ibinYPreFsr==-1) {
printf(".. skipping mass=%6.4lf, y=%6.4lf. ibinMass=%d, ibinY=%d\n",massPreFsr,yPreFsr,ibinMassPreFsr,ibinYPreFsr);
continue;
}
// Find FEWZ-powheg reweighting factor
// that depends on pre-FSR Z/gamma* rapidity, pt, and mass
double fewz_weight = 1.0;
if(useFewzWeights) {
fewz_weight=fewz.getWeight(gen->vmass,gen->vpt,gen->vy);
}
//std::cout << "weight=scale*gen->weight*fewz: " << scale << " * " << gen->weight << " * " << fewz_weight << "\n";
double fullWeight = scale * gen->weight * fewz_weight;
nEvents(ibinMassPreFsr,ibinYPreFsr) += fullWeight;
w2Events(ibinMassPreFsr,ibinYPreFsr) += fullWeight*fullWeight;
// Pre-FSR cross section
if( DYTools::goodEtPair(gen->vpt_1, gen->vpt_2) &&
DYTools::goodEtaPair(gen->veta_1, gen->veta_2) ) {
nEventsDET(ibinMassPreFsr,ibinYPreFsr) += fullWeight;
w2EventsDET(ibinMassPreFsr,ibinYPreFsr) += fullWeight*fullWeight;
}
// Post-FSR cross section
if( (ibinMassPostFsr!=-1) && (ibinYPostFsr!=-1) &&
DYTools::goodEtPair(gen->pt_1, gen->pt_2) &&
DYTools::goodEtaPair(gen->eta_1, gen->eta_2) ) {
nEventsDETrecoPostIdx(ibinMassPostFsr,ibinYPostFsr) += fullWeight;
w2EventsDETrecoPostIdx(ibinMassPostFsr,ibinYPostFsr) += fullWeight*fullWeight;
}
}
delete infile;
infile=0, eventTree=0;
}
delete gen;
// Determine Z-peak event count
for (int i=0; i<locMassBinCount; i++) {
int isZpeak=0;
// bin idx is (i+1)
if ((hMassIdx.GetBinLowEdge(i+1)>=60-1e-3)
&& (hMassIdx.GetBinLowEdge(i+1+1)<=120+1e-3)) isZpeak=1;
if (isZpeak) {
int yiMax=(fineGrid) ? 1:DYTools::nYBins[i];
for (int yi=0; yi<yiMax; ++yi) {
nZpeak += nEvents(i,yi);
w2Zpeak += w2Events(i,yi);
nZpeakDET += nEventsDET(i,yi);
w2ZpeakDET += w2EventsDET(i,yi);
nZpeakDETrecoPostIdx += nEventsDETrecoPostIdx(i,yi);
w2ZpeakDETrecoPostIdx += w2EventsDETrecoPostIdx(i,yi);
}
}
}
std::cout << "\n";
std::cout << "nZpeak=" << nZpeak << ", w2Zpeak=" << w2Zpeak << "\n";
std::cout << "nZpeakDET=" << nZpeakDET << ", w2ZpeakDET=" << w2ZpeakDET << "\n";
std::cout << "nZpeakDETrecoPostIdx=" << nZpeakDETrecoPostIdx << ", w2ZpeakDETrecoPostIdx=" << w2ZpeakDETrecoPostIdx << "\n";
std::cout << "\n";
if (nZpeak==0) {
std::cout << "no events in the Z-peak region\n";
return ;
}
} // if (debugMode!=-1)
// Containers of the normalized event counts
TMatrixD nEventsNorm (locMassBinCount,DYTools::nYBinsMax); // number of weigthed events, normalized to Z-peak
TMatrixD nEventsDETNorm (locMassBinCount,DYTools::nYBinsMax); // number of weighted events in the detector acceptance, normalized to Z-peak
TMatrixD nEventsDETrecoPostIdxNorm (locMassBinCount,DYTools::nYBinsMax); // number of weighted events in the detector acceptance, normalized to Z-peak
TMatrixD nEventsNormErr (locMassBinCount,DYTools::nYBinsMax);
TMatrixD nEventsDETNormErr (locMassBinCount,DYTools::nYBinsMax);
TMatrixD nEventsDETrecoPostIdxNormErr (locMassBinCount,DYTools::nYBinsMax);
TMatrixD nEventsErr (locMassBinCount,DYTools::nYBinsMax);
TMatrixD nEventsDETErr (locMassBinCount,DYTools::nYBinsMax);
TMatrixD nEventsDETrecoPostIdxErr (locMassBinCount,DYTools::nYBinsMax);
nEventsNorm=0;
nEventsDETNorm=0;
nEventsDETrecoPostIdxNorm=0;
nEventsNormErr=0;
nEventsDETNormErr=0;
nEventsDETrecoPostIdxNormErr=0;
nEventsErr=0;
nEventsDETErr=0;
if (debugMode!=-1) {
for(int i=0; i<locMassBinCount; i++) {
int yiMax=(fineGrid) ? 1:DYTools::nYBins[i];
for (int j=0; j<yiMax; j++) {
nEventsErr(i,j)=sqrt(w2Events(i,j));
nEventsDETErr(i,j)=sqrt(w2EventsDET(i,j));
nEventsDETrecoPostIdxErr(i,j)=sqrt(w2EventsDETrecoPostIdx(i,j));
nEventsNorm(i,j) = nEvents(i,j)/nZpeak;
nEventsNormErr(i,j) =
getErrorOnRatio(nEvents(i,j),nEventsErr(i,j),
nZpeak, sqrt(w2Zpeak));
nEventsDETNorm(i,j) = nEventsDET(i,j)/nZpeakDET;
nEventsDETNormErr(i,j) =
getErrorOnRatio(nEventsDET(i,j),nEventsDETErr(i,j),
nZpeakDET, sqrt(w2ZpeakDET));
nEventsDETrecoPostIdxNorm(i,j) = nEventsDETrecoPostIdx(i,j)/nZpeakDETrecoPostIdx;
nEventsDETrecoPostIdxNormErr(i,j) =
getErrorOnRatio(nEventsDETrecoPostIdx(i,j),nEventsDETrecoPostIdxErr(i,j),
nZpeakDETrecoPostIdx, sqrt(w2ZpeakDETrecoPostIdx));
}
}
}
TString outFile= TString("../root_files/xSecThExt_");
//outFile.Append("2MCfiles_");
if (!useFewzWeights) outFile.Append("noFEWZ_");
if (fineGridStr.Length()) outFile.Append(fineGridStr);
if (debugMode==1) outFile.Append("debug_");
outFile.Append( DYTools::analysisTag + TString("_tmp.root") );
TVectorD rapidityGrid(massGrid.GetNoElements()-1);
rapidityGrid=1;
if (debugMode!=-1) {
TFile thFile(outFile,"recreate");
massGrid.Write("massBinEdges");
if (fineGrid) rapidityGrid.Write("rapidityBinCount");
nEvents.Write("nGenEvents");
nEventsErr.Write("nGenEventsErr");
nEventsDET.Write("nGenEventsDET");
nEventsDETErr.Write("nGenEventsDETErr");
nEventsDETrecoPostIdx.Write("nGenEventsDETrecoPostIdx");
nEventsDETrecoPostIdxErr.Write("nGenEventsDETRecoPostIdxErr");
nEventsNorm.Write("nGenEventsNorm");
nEventsNormErr.Write("nGenEventsNormErr");
nEventsDETNorm.Write("nGenEventsDETNorm");
nEventsDETNormErr.Write("nGenEventsDETNormErr");
nEventsDETrecoPostIdxNorm.Write("nGenEventsDETrecoPostIdxNorm");
nEventsDETrecoPostIdxNormErr.Write("nGenEventsDETrecoPostIdxNormErr");
TVectorD zPeakInfo(6);
zPeakInfo(0)=nZpeak; zPeakInfo(1)=sqrt(w2Zpeak);
zPeakInfo(2)=nZpeakDET; zPeakInfo(3)=sqrt(w2ZpeakDET);
zPeakInfo(4)=nZpeakDETrecoPostIdx; zPeakInfo(5)=sqrt(w2ZpeakDETrecoPostIdx);
zPeakInfo.Write("zPeakCountAndErr");
thFile.Close();
std::cout << "file <" << outFile << "> created\n";
}
else {
TFile thFile(outFile);
nEvents.Read("nGenEvents");
nEventsErr.Read("nGenEventsErr");
nEventsDET.Read("nGenEventsDET");
nEventsDETErr.Read("nGenEventsDETErr");
nEventsDETrecoPostIdx.Read("nGenEventsDETrecoPostIdx");
nEventsDETrecoPostIdxErr.Read("nGenEventsDETRecoPostIdxErr");
nEventsNorm.Read("nGenEventsNorm");
nEventsNormErr.Read("nGenEventsNormErr");
nEventsDETNorm.Read("nGenEventsDETNorm");
nEventsDETNormErr.Read("nGenEventsDETNormErr");
nEventsDETrecoPostIdxNorm.Read("nGenEventsDETrecoPostIdxNorm");
nEventsDETrecoPostIdxNormErr.Read("nGenEventsDETrecoPostIdxNormErr");
TVectorD zPeakInfo(6);
zPeakInfo.Read("zPeakCountAndErr");
thFile.Close();
nZpeak=zPeakInfo[0]; w2Zpeak=SQR(zPeakInfo[1]);
nZpeakDET=zPeakInfo[2]; w2ZpeakDET=SQR(zPeakInfo[3]);
nZpeakDETrecoPostIdx=zPeakInfo[4]; w2ZpeakDETrecoPostIdx=SQR(zPeakInfo[5]);
std::cout << "file <" << outFile << "> loaded\n";
}
//--------------------------------------------------------------------------------------------------------------
// Make plots
//==============================================================================================================
CPlot::sOutDir="plots" + DYTools::analysisTag;
TString fileNamePlots=outFile;
fileNamePlots.ReplaceAll("_tmp.root","_plots_tmp.root");
TFile *filePlots=new TFile(fileNamePlots,"recreate");
if (!filePlots) {
std::cout << "failed to create file <" << fileNamePlots << ">\n";
throw 2;
}
// string buffers
//char ylabel[50]; // y-axis label
if (DYTools::study2D) {
TString c2Dname="canvXsectTh_2D";
if (useFewzWeights) c2Dname.Append("_FEWZ");
TCanvas *c2D = MakeCanvas(c2Dname,c2Dname,600,600+300*DYTools::study2D);
std::vector<TH1F*> hXsecV;
std::vector<CPlot*> cpV;
hXsecV.reserve(DYTools::nMassBins);
cpV.reserve(DYTools::nMassBins);
for (int iM=0; iM<DYTools::nMassBins; ++iM) {
double massMin=DYTools::massBinLimits[iM];
double massMax=DYTools::massBinLimits[iM+1];
CPlot *cp=new CPlot(Form("cpMass%2.0lf_%2.0lf",massMin,massMax),
"","|Y|","counts");
cpV.push_back(cp);
hXsecV.push_back( plotXsec2D("xsec",iM,nEvents,nEventsErr,cp,kBlack,1) );
}
c2D->Divide(2,3);
for (int ipad=1; ipad<=6; ++ipad) {
cpV[ipad]->Draw(c2D,false,"png",ipad);
}
c2D->Update();
SaveCanvas(c2D,c2Dname);
}
{
TString canvName=TString("canvXsectTh_") + fineGridStr + TString("1D");
if (useFewzWeights) canvName.Append("_FEWZ");
TCanvas *c1D = MakeCanvas(canvName,canvName,600,600);
CPlot *cp=new CPlot("cplot_1D","","M_{ee} (GeV)","counts");
TH1F *hXsec= plotXsec1D("xsec1D",nEvents,nEventsErr,cp,kBlue, fineGrid);
hXsec->SetDirectory(0);
cp->SetLogx();
cp->Draw(c1D,false,"png");
c1D->Update();
SaveCanvas(c1D,canvName);
}
{
TString canvName=TString("canvXsectThNorm_") + fineGridStr + TString("1D");
if (useFewzWeights) canvName.Append("_FEWZ");
TCanvas *c1D = MakeCanvas(canvName,canvName,600,600);
CPlot *cp=new CPlot("cplotNorm_1D","","M_{ee} (GeV)","normalized counts");
TH1F *hXsec= plotXsec1D("xsec1D",nEventsNorm,nEventsNormErr,cp,kBlue, fineGrid);
hXsec->SetDirectory(0);
cp->SetLogx();
cp->Draw(c1D,false,"png");
c1D->Update();
SaveCanvas(c1D,canvName);
}
/*
// Z mass
sprintf(ylabel,"a.u. / %.1f GeV/c^{2}",hZMassv[0]->GetBinWidth(1));
CPlot plotZMass1("zmass1","","m(Z) [GeV/c^{2}]",ylabel);
for(UInt_t i=0; i<fnamev.size(); i++) {
plotZMass1.AddHist1D(hZMassv[i],labelv[i],"hist",colorv[i],linev[i]);
}
plotZMass1.SetLogy();
plotZMass1.Draw(c);
SaveCanvas(c, "zmass1");
PlotMatrixVariousBinning(accv, "acceptance", "LEGO2",filePlots);
filePlots->Close();
if (DYTools::study2D==0)
Plot1D(accv,accErrv,"acceptance1D","acceptance");
//delete filePlots;
*/
//--------------------------------------------------------------------------------------------------------------
// Summary print out
//==============================================================================================================
if (!fineGrid) {
const int printSystErr=0;
TMatrixD zeroErr=nEventsErr; zeroErr=0;
printYields("nGenEvents", nEvents,nEventsErr,zeroErr, printSystErr);
printYields("nGenEventsDET", nEventsDET,nEventsDETErr,zeroErr, printSystErr);
printYields("nGenEventsDETrecoPostIdx",nEventsDETrecoPostIdx,nEventsDETrecoPostIdxErr, zeroErr,printSystErr);
}
gBenchmark->Show("getXsec");
}
/*
* Main solver routine.
*/
idxint ECOS_solve(pwork* w)
{
idxint i, initcode, KKT_FACTOR_RETURN_CODE;
pfloat dtau_denom, dtauaff, dkapaff, sigma, dtau, dkap, bkap, pres_prev;
idxint exitcode = ECOS_FATAL;
#if PROFILING > 0
timer tsolve;
#endif
#if PROFILING > 1
timer tfactor, tkktsolve;
#endif
#if PROFILING > 0
/* start timer */
tic(&tsolve);
#endif
/* Initialize solver */
initcode = init(w);
if( initcode == ECOS_FATAL ){
#if PRINTLEVEL > 0
if( w->stgs->verbose ) PRINTTEXT("\nFatal error during initialization, aborting.");
#endif
return ECOS_FATAL;
}
/* MAIN INTERIOR POINT LOOP ---------------------------------------------------------------------- */
for( w->info->iter = 0; w->info->iter <= w->stgs->maxit; w->info->iter++ ){
/* Compute residuals */
computeResiduals(w);
/* Update statistics */
updateStatistics(w);
#if PRINTLEVEL > 1
/* Print info */
if( w->stgs->verbose ) printProgress(w->info);
#endif
/* SAFEGUARD: Backtrack to old iterate if the update was bad such that the primal residual PRES has
* increased by a factor of SAFEGUARD.
* If the safeguard is activated, the solver quits with the flag ECOS_NUMERICS.
*/
if( w->info->iter > 0 && w->info->pres > SAFEGUARD*pres_prev ){
#if PRINTLEVEL > 1
if( w->stgs->verbose ) PRINTTEXT("\nNUMERICAL PROBLEMS, recovering iterate %d and stopping.\n", (int)w->info->iter-1);
#endif
/* Backtrack */
for( i=0; i < w->n; i++ ){ w->x[i] -= w->info->step * w->KKT->dx2[i]; }
for( i=0; i < w->p; i++ ){ w->y[i] -= w->info->step * w->KKT->dy2[i]; }
for( i=0; i < w->m; i++ ){ w->z[i] -= w->info->step * w->KKT->dz2[i]; }
for( i=0; i < w->m; i++ ){ w->s[i] -= w->info->step * w->dsaff[i]; }
w->kap -= w->info->step * dkap;
w->tau -= w->info->step * dtau;
exitcode = ECOS_NUMERICS;
computeResiduals(w);
updateStatistics(w);
break;
}
pres_prev = w->info->pres;
/* Check termination criteria and exit if necessary */
/* Optimal? */
if( ( ( -w->cx > 0 ) || ( -w->by - w->hz > 0) ) &&
w->info->pres < w->stgs->feastol && w->info->dres < w->stgs->feastol &&
( w->info->gap < w->stgs->abstol || w->info->relgap < w->stgs->reltol ) ){
#if PRINTLEVEL > 0
if( w->stgs->verbose ) PRINTTEXT("\nOPTIMAL (within feastol=%3.1e, reltol=%3.1e, abstol=%3.1e).", w->stgs->feastol, w->stgs->reltol, w->stgs->abstol);
#endif
exitcode = ECOS_OPTIMAL;
break;
}
/* Primal infeasible? */
else if( ((w->info->pinfres != NAN) && (w->info->pinfres < w->stgs->feastol)) ||
((w->tau < w->stgs->feastol) && (w->kap < w->stgs->feastol && w->info->pinfres < w->stgs->feastol)) ){
#if PRINTLEVEL > 0
if( w->stgs->verbose ) PRINTTEXT("\nPRIMAL INFEASIBLE (within feastol=%3.1e, reltol=%3.1e, abstol=%3.1e).", w->stgs->feastol, w->stgs->reltol, w->stgs->abstol);
#endif
w->info->pinf = 1;
w->info->dinf = 0;
exitcode = ECOS_PINF;
break;
}
/* Dual infeasible? */
else if( (w->info->dinfres != NAN) && (w->info->dinfres < w->stgs->feastol) ){
#if PRINTLEVEL > 0
if( w->stgs->verbose ) PRINTTEXT("\nUNBOUNDED (within feastol=%3.1e, reltol=%3.1e, abstol=%3.1e).", w->stgs->feastol, w->stgs->reltol, w->stgs->abstol);
#endif
w->info->pinf = 0;
w->info->dinf = 1;
exitcode = ECOS_DINF;
break;
}
/* Did the line search c**k up? (zero step length) */
else if( w->info->iter > 0 && w->info->step == STEPMIN*GAMMA ){
#if PRINTLEVEL > 0
if( w->stgs->verbose ) PRINTTEXT("\nNo further progress possible (- numerics?), exiting.");
#endif
exitcode = ECOS_NUMERICS;
break;
}
/* MAXIT reached? */
else if( w->info->iter == w->stgs->maxit ){
#if PRINTLEVEL > 0
if( w->stgs->verbose ) PRINTTEXT("\nMaximum number of iterations reached, exiting.");
#endif
exitcode = ECOS_MAXIT;
break;
}
/* Compute scalings */
if( updateScalings(w->C, w->s, w->z, w->lambda) == OUTSIDE_CONE ){
#if PRINTLEVEL > 0
if( w->stgs->verbose ) PRINTTEXT("\nSlacks or multipliers leaving the positive orthant (- numerics ?), exiting.\n");
#endif
return ECOS_OUTCONE;
}
/* Update KKT matrix with scalings */
kkt_update(w->KKT->PKPt, w->KKT->PK, w->C);
#if DEBUG > 0
dumpSparseMatrix(w->KKT->PKPt,"PKPt_updated.txt");
#endif
/* factor KKT matrix */
#if PROFILING > 1
tic(&tfactor);
KKT_FACTOR_RETURN_CODE = kkt_factor(w->KKT, w->stgs->eps, w->stgs->delta, &w->info->tfactor_t1, &w->info->tfactor_t2);
w->info->tfactor += toc(&tfactor);
#else
KKT_FACTOR_RETURN_CODE = kkt_factor(w->KKT, w->stgs->eps, w->stgs->delta);
#endif
/* Solve for RHS1, which is used later also in combined direction */
#if PROFILING > 1
tic(&tkktsolve);
#endif
w->info->nitref1 = kkt_solve(w->KKT, w->A, w->G, w->KKT->RHS1, w->KKT->dx1, w->KKT->dy1, w->KKT->dz1, w->n, w->p, w->m, w->C, 0, w->stgs->nitref);
#if PROFILING > 1
w->info->tkktsolve += toc(&tkktsolve);
#endif
/* AFFINE SEARCH DIRECTION (predictor, need dsaff and dzaff only) */
RHS_affine(w);
#if PROFILING > 1
tic(&tkktsolve);
#endif
w->info->nitref2 = kkt_solve(w->KKT, w->A, w->G, w->KKT->RHS2, w->KKT->dx2, w->KKT->dy2, w->KKT->dz2, w->n, w->p, w->m, w->C, 0, w->stgs->nitref);
#if PROFILING > 1
w->info->tkktsolve += toc(&tkktsolve);
#endif
/* dtau_denom = kap/tau - (c'*x1 + by1 + h'*z1); */
dtau_denom = w->kap/w->tau - ddot(w->n, w->c, w->KKT->dx1) - ddot(w->p, w->b, w->KKT->dy1) - ddot(w->m, w->h, w->KKT->dz1);
/* dtauaff = (dt + c'*x2 + by2 + h'*z2) / dtau_denom; */
dtauaff = (w->rt - w->kap + ddot(w->n, w->c, w->KKT->dx2) + ddot(w->p, w->b, w->KKT->dy2) + ddot(w->m, w->h, w->KKT->dz2)) / dtau_denom;
/* dzaff = dz2 + dtau_aff*dz1 */
for( i=0; i<w->m; i++ ){ w->W_times_dzaff[i] = w->KKT->dz2[i] + dtauaff*w->KKT->dz1[i]; }
scale(w->W_times_dzaff, w->C, w->W_times_dzaff);
/* W\dsaff = -W*dzaff -lambda; */
for( i=0; i<w->m; i++ ){ w->dsaff_by_W[i] = -w->W_times_dzaff[i] - w->lambda[i]; }
/* dkapaff = -(bkap + kap*dtauaff)/tau; bkap = kap*tau*/
dkapaff = -w->kap - w->kap/w->tau*dtauaff;
/* Line search on W\dsaff and W*dzaff */
w->info->step_aff = lineSearch(w->lambda, w->dsaff_by_W, w->W_times_dzaff, w->tau, dtauaff, w->kap, dkapaff, w->C, w->KKT);
/* Centering parameter */
sigma = 1.0 - w->info->step_aff;
sigma = sigma*sigma*sigma;
if( sigma > SIGMAMAX ) sigma = SIGMAMAX;
if( sigma < SIGMAMIN ) sigma = SIGMAMIN;
w->info->sigma = sigma;
/* COMBINED SEARCH DIRECTION */
RHS_combined(w);
#if PROFILING > 1
tic(&tkktsolve);
#endif
w->info->nitref3 = kkt_solve(w->KKT, w->A, w->G, w->KKT->RHS2, w->KKT->dx2, w->KKT->dy2, w->KKT->dz2, w->n, w->p, w->m, w->C, 0, w->stgs->nitref);
#if PROFILING > 1
w->info->tkktsolve += toc(&tkktsolve);
#endif
/* bkap = kap*tau + dkapaff*dtauaff - sigma*info.mu; */
bkap = w->kap*w->tau + dkapaff*dtauaff - sigma*w->info->mu;
/* dtau = ((1-sigma)*rt - bkap/tau + c'*x2 + by2 + h'*z2) / dtau_denom; */
dtau = ((1-sigma)*w->rt - bkap/w->tau + ddot(w->n, w->c, w->KKT->dx2) + ddot(w->p, w->b, w->KKT->dy2) + ddot(w->m, w->h, w->KKT->dz2)) / dtau_denom;
/* dx = x2 + dtau*x1; dy = y2 + dtau*y1; dz = z2 + dtau*z1; */
for( i=0; i < w->n; i++ ){ w->KKT->dx2[i] += dtau*w->KKT->dx1[i]; }
for( i=0; i < w->p; i++ ){ w->KKT->dy2[i] += dtau*w->KKT->dy1[i]; }
for( i=0; i < w->m; i++ ){ w->KKT->dz2[i] += dtau*w->KKT->dz1[i]; }
/* ds_by_W = -(lambda \ bs + conelp_timesW(scaling,dz,dims)); */
/* note that ath this point w->dsaff_by_W holds already (lambda \ ds) */
scale(w->KKT->dz2, w->C, w->W_times_dzaff);
for( i=0; i < w->m; i++ ){ w->dsaff_by_W[i] = -(w->dsaff_by_W[i] + w->W_times_dzaff[i]); }
/* dkap = -(bkap + kap*dtau)/tau; */
dkap = -(bkap + w->kap*dtau)/w->tau;
/* Line search on combined direction */
w->info->step = lineSearch(w->lambda, w->dsaff_by_W, w->W_times_dzaff, w->tau, dtau, w->kap, dkap, w->C, w->KKT) * w->stgs->gamma;
/* ds = W*ds_by_W */
scale(w->dsaff_by_W, w->C, w->dsaff);
/* Update variables */
for( i=0; i < w->n; i++ ){ w->x[i] += w->info->step * w->KKT->dx2[i]; }
for( i=0; i < w->p; i++ ){ w->y[i] += w->info->step * w->KKT->dy2[i]; }
for( i=0; i < w->m; i++ ){ w->z[i] += w->info->step * w->KKT->dz2[i]; }
for( i=0; i < w->m; i++ ){ w->s[i] += w->info->step * w->dsaff[i]; }
w->kap += w->info->step * dkap;
w->tau += w->info->step * dtau;
}
/* scale variables back */
backscale(w);
/* stop timer */
#if PROFILING > 0
w->info->tsolve = toc(&tsolve);
#endif
#if PRINTLEVEL > 0
#if PROFILING > 0
if( w->stgs->verbose ) PRINTTEXT("\nRuntime: %f seconds.", w->info->tsetup + w->info->tsolve);
#endif
if( w->stgs->verbose ) PRINTTEXT("\n\n");
#endif
return exitcode;
}
/*!
* This is done by running
* each reaction as far forward or backward as possible, subject
* to the constraint that all mole numbers remain
* non-negative. Reactions for which \f$ \Delta \mu^0 \f$ are
* positive are run in reverse, and ones for which it is negative
* are run in the forward direction. The end result is equivalent
* to solving the linear programming problem of minimizing the
* linear Gibbs function subject to the element and
* non-negativity constraints.
*/
int VCS_SOLVE::vcs_setMolesLinProg() {
int ik, irxn;
double test = -1.0E-10;
#ifdef DEBUG_MODE
std::string pprefix(" --- seMolesLinProg ");
if (m_debug_print_lvl >= 2) {
plogf(" --- call setInitialMoles\n");
}
#endif
// m_mu are standard state chemical potentials
// Boolean on the end specifies standard chem potentials
// m_mix->getValidChemPotentials(not_mu, DATA_PTR(m_mu), true);
// -> This is already done coming into the routine.
double dg_rt;
int idir;
double nu;
double delta_xi, dxi_min = 1.0e10;
bool redo = true;
int jcomp;
int retn;
int iter = 0;
bool abundancesOK = true;
int usedZeroedSpecies;
std::vector<double> sm(m_numElemConstraints*m_numElemConstraints, 0.0);
std::vector<double> ss(m_numElemConstraints, 0.0);
std::vector<double> sa(m_numElemConstraints, 0.0);
std::vector<double> wx(m_numElemConstraints, 0.0);
std::vector<double> aw(m_numSpeciesTot, 0.0);
for (ik = 0; ik < m_numSpeciesTot; ik++) {
if (m_speciesUnknownType[ik] != VCS_SPECIES_INTERFACIALVOLTAGE) {
m_molNumSpecies_old[ik] = MAX(0.0, m_molNumSpecies_old[ik]);
}
}
#ifdef DEBUG_MODE
if (m_debug_print_lvl >= 2) {
printProgress(m_speciesName, m_molNumSpecies_old, m_SSfeSpecies);
}
#endif
while (redo) {
if (!vcs_elabcheck(0)) {
#ifdef DEBUG_MODE
if (m_debug_print_lvl >= 2) {
plogf("%s Mole numbers failing element abundances\n", pprefix.c_str());
plogf("%sCall vcs_elcorr to attempt fix\n", pprefix.c_str());
}
#endif
retn = vcs_elcorr(VCS_DATA_PTR(sm), VCS_DATA_PTR(wx));
if (retn >= 2) {
abundancesOK = false;
} else {
abundancesOK = true;
}
} else {
abundancesOK = true;
}
/*
* Now find the optimized basis that spans the stoichiometric
* coefficient matrix, based on the current composition, m_molNumSpecies_old[]
* We also calculate sc[][], the reaction matrix.
*/
retn = vcs_basopt(FALSE, VCS_DATA_PTR(aw), VCS_DATA_PTR(sa),
VCS_DATA_PTR(sm), VCS_DATA_PTR(ss),
test, &usedZeroedSpecies);
if (retn != VCS_SUCCESS) return retn;
#ifdef DEBUG_MODE
if (m_debug_print_lvl >= 2) {
plogf("iteration %d\n", iter);
}
#endif
redo = false;
iter++;
if (iter > 15) break;
// loop over all reactions
for (irxn = 0; irxn < m_numRxnTot; irxn++) {
// dg_rt is the Delta_G / RT value for the reaction
ik = m_numComponents + irxn;
dg_rt = m_SSfeSpecies[ik];
dxi_min = 1.0e10;
const double *sc_irxn = m_stoichCoeffRxnMatrix[irxn];
for (jcomp = 0; jcomp < m_numElemConstraints; jcomp++) {
dg_rt += m_SSfeSpecies[jcomp] * sc_irxn[jcomp];
}
// fwd or rev direction.
// idir > 0 implies increasing the current species
// idir < 0 implies decreasing the current species
idir = (dg_rt < 0.0 ? 1 : -1);
if (idir < 0) {
dxi_min = m_molNumSpecies_old[ik];
}
for (jcomp = 0; jcomp < m_numComponents; jcomp++) {
nu = sc_irxn[jcomp];
// set max change in progress variable by
// non-negativity requirement
if (nu*idir < 0) {
delta_xi = fabs(m_molNumSpecies_old[jcomp]/nu);
// if a component has nearly zero moles, redo
// with a new set of components
if (!redo) {
if (delta_xi < 1.0e-10 && (m_molNumSpecies_old[ik] >= 1.0E-10)) {
#ifdef DEBUG_MODE
if (m_debug_print_lvl >= 2) {
plogf(" --- Component too small: %s\n", m_speciesName[jcomp].c_str());
}
#endif
redo = true;
}
}
if (delta_xi < dxi_min) dxi_min = delta_xi;
}
}
// step the composition by dxi_min, check against zero, since
// we are zeroing components and species on every step.
// Redo the iteration, if a component went from positive to zero on this step.
double dsLocal = idir*dxi_min;
m_molNumSpecies_old[ik] += dsLocal;
m_molNumSpecies_old[ik] = MAX(0.0, m_molNumSpecies_old[ik]);
for (jcomp = 0; jcomp < m_numComponents; jcomp++) {
bool full = false;
if (m_molNumSpecies_old[jcomp] > 1.0E-15) {
full = true;
}
m_molNumSpecies_old[jcomp] += sc_irxn[jcomp] * dsLocal;
m_molNumSpecies_old[jcomp] = MAX(0.0, m_molNumSpecies_old[jcomp]);
if (full) {
if (m_molNumSpecies_old[jcomp] < 1.0E-60) {
redo = true;
}
}
}
}
// set the moles of the phase objects to match
// updateMixMoles();
// Update the phase objects with the contents of the m_molNumSpecies_old vector
// vcs_updateVP(0);
#ifdef DEBUG_MODE
if (m_debug_print_lvl >= 2) {
printProgress(m_speciesName, m_molNumSpecies_old, m_SSfeSpecies);
}
#endif
}
#ifdef DEBUG_MODE
if (m_debug_print_lvl == 1) {
printProgress(m_speciesName, m_molNumSpecies_old, m_SSfeSpecies);
plogf(" --- setInitialMoles end\n");
}
#endif
retn = 0;
if (!abundancesOK) {
retn = -1;
} else if (iter > 15) {
retn = 1;
}
return retn;
}
//*--------------------------------------------------------------------------*//
//* MAIN MAIN *//
//*--------------------------------------------------------------------------*//
int main(int argc, char* argv[])
{
// Initialise random number generator
srandom(time(NULL));
clock_t t0 = clock();
// Print header
printHeader();
// Read options
Options uo = parseCommandLine(argc,argv);
if(!uo.noHybrid)
{
if(uo.funcGroupVec[AROM] && uo.funcGroupVec[LIPO])
{
uo.funcGroupVec[HYBL] = true;
}
if(uo.funcGroupVec[HDON] && uo.funcGroupVec[HACC])
{
uo.funcGroupVec[HYBH] = true;
}
}
std::cerr << uo.print() << std::endl;
if (uo.version)
{
printHeader();
exit(0);
}
if (uo.help)
{
printUsage();
exit(0);
}
// Db file and pharmacophore out are mandatory elements
if (uo.dbInpFile.empty())
{
mainErr("Missing database file. This is a required option (-d).");
}
if (uo.pharmOutFile.empty() && uo.molOutFile.empty() && uo.scoreOutFile.empty())
{
mainErr("No output file defined. So there is actually no use to compute anything at all.");
}
if ((uo.pharmOutFile.empty() && uo.scoreOutFile.empty()) && !uo.molOutFile.empty())
{
mainErr("No file defined to write pharmacophore information.");
}
if (uo.refInpFile.empty() && uo.pharmOutFile.empty() && uo.molOutFile.empty() && !uo.scoreOutFile.empty())
{
mainErr("Only score file requested when no reference is given. Unable to generate this output.");
}
// Reference variables
Pharmacophore refPharm;
refPharm.clear();
std::string refId;
double refVolume(0.0);
int refSize(0);
int exclSize(0);
// Database variables
std::vector<Result*> resList;
Pharmacophore dbPharm;
std::string dbId;
double dbVolume(0.0);
int dbSize(0);
//----------------------------------------------------------------------------
//...(A).. Process the reference
//----------------------------------------------------------------------------
if (!uo.refInpFile.empty())
{
//-------------------------------------------------------
//...(1).. get reference pharmacophore
//-------------------------------------------------------
if (uo.refInpType == UNKNOWN)
{
std::string ext(getExt(uo.refInpFile));
if (ext == ".phar")
{
uo.refInpType = PHAR;
}
else
{
uo.refInpType = MOL;
}
}
if (uo.refInpType == MOL)
{
OpenBabel::OBMol m;
OpenBabel::OBConversion* reader = new OpenBabel::OBConversion();
reader->SetInFormat(reader->FormatFromExt(uo.refInpFile.c_str()));
if (!reader->Read(&m, uo.refInpStream))
{
mainErr("Unable to read reference molecule");
}
calcPharm(&m, &refPharm, uo);
refId = m.GetTitle();
delete reader;
reader = NULL;
}
else if (uo.refInpType == PHAR)
{
PharmacophoreReader* reader = new PharmacophoreReader();
refPharm = reader->read(uo.refInpStream, refId);
if (refPharm.empty())
{
mainErr("Error reading reference pharmacophore");
}
delete reader;
reader = NULL;
}
else
{
mainErr("Unknown format of reference molecule.");
}
//-------------------------------------------------------
//...(2).. process reference pharmacophore
//-------------------------------------------------------
if (uo.merge)
{
pharMerger.merge(refPharm);
}
refSize = refPharm.size();
for (unsigned int i(0); i < refSize; ++i)
{
if (refPharm[i].func == EXCL)
{
// extract overlap with exclusion spheres
for (unsigned int j(0); j < refPharm.size(); ++j)
{
if (refPharm[j].func != EXCL)
{
refVolume -= VolumeOverlap(refPharm[i], refPharm[j], !uo.noNormal);
}
}
exclSize++;
}
else
{
// add point self-overlap
refVolume += VolumeOverlap(refPharm[i], refPharm[i], !uo.noNormal);
}
}
if(!uo.isQuiet)
{
std::cerr << "Reference pharmacophore " << refId << std::endl;
std::cerr << " number of points: " << refSize - exclSize << std::endl;
std::cerr << " number of exclusion spheres: " << exclSize << std::endl;
std::cerr << " totalvolume: " << refVolume << std::endl;
}
}
//----------------------------------------------------------------------------
//...(B).. Process the database file
//----------------------------------------------------------------------------
// DB files
if (uo.dbInpType == UNKNOWN)
{
std::string ext(getExt(uo.dbInpFile));
if (ext==".phar")
{
uo.dbInpType = PHAR;
}
else
{
uo.dbInpType = MOL;
}
}
// local storage of the rotation matrix
SiMath::Matrix rotMat(3,3,0.0);
unsigned int molCount(0);
OpenBabel::OBConversion* molReader = NULL;
PharmacophoreReader* pharmReader = NULL;
if (uo.dbInpType == PHAR)
{
pharmReader = new PharmacophoreReader();
}
else if (uo.dbInpType == MOL)
{
molReader = new OpenBabel::OBConversion();
molReader->SetInFormat(molReader->FormatFromExt(uo.dbInpFile.c_str()));
molReader->SetInStream(uo.dbInpStream);
}
else
{
mainErr("Unknown format of db file.");
}
bool done(false);
OpenBabel::OBMol m;
while (!done)
{
dbPharm.clear();
m.Clear();
if (uo.dbInpType == MOL)
{
if (!molReader->Read(&m))
{
done = true;
break;
}
else
{
calcPharm(&m, &dbPharm, uo);
dbId = m.GetTitle();
}
}
else
{
if (uo.dbInpStream->eof())
{
done = true;
break;
}
else
{
dbPharm = pharmReader->read(uo.dbInpStream, dbId);
}
}
if (dbPharm.empty())
{
continue;
}
++molCount;
if (!uo.isQuiet )
{
if ((molCount % 10) == 0)
{
std::cerr << "." << std::flush;
}
if ((molCount % 500) == 0)
{
std::cerr << molCount << std::endl << std::flush;
}
}
if (uo.merge)
{
pharMerger.merge(dbPharm);
}
if (uo.refInpFile.empty())
{
if (!(uo.isQuiet))
{
printProgress(molCount);
}
if( !uo.pharmOutFile.empty())
{
uo.pharmOutWriter->write(dbPharm, uo.pharmOutStream, dbId);
}
continue;
}
//-------------------------------------------------------
//...(1).. Alignment
//-------------------------------------------------------
dbSize = dbPharm.size();
dbVolume = 0.0;
for (unsigned int i(0); i < dbSize; ++i)
{
if (dbPharm[i].func == EXCL)
{
continue;
}
dbVolume += VolumeOverlap(dbPharm[i], dbPharm[i], !uo.noNormal);
}
// Create a result structure
Result res;
res.refId = refId;
res.refVolume = refVolume;
res.dbId = dbId;
res.dbVolume = dbVolume;
res.overlapVolume = 0.0;
res.exclVolume = 0.0;
res.resMol = m;
res.resPharSize = 0;
if (uo.scoreOnly)
{
FunctionMapping funcMap(&refPharm, &dbPharm, uo.epsilon);
PharmacophoreMap fMap = funcMap.getNextMap();
double volBest(-9999.999);
// loop over all reference points
while (!fMap.empty())
{
double newVol(0.0);
double exclVol(0.0);
for (PharmacophoreMap::iterator itP = fMap.begin(); itP != fMap.end(); ++itP)
{
if ((itP->first)->func == EXCL)
{
exclVol += VolumeOverlap((itP->first), (itP->second), !uo.noNormal);
}
else if (((itP->first)->func == (itP->second)->func ) ||
(((itP->first)->func == HYBH ||
(itP->first)->func == HDON ||
(itP->first)->func == HACC)
&& ((itP->second)->func == HDON ||
(itP->second)->func == HACC ||
(itP->second)->func == HYBH))
|| (((itP->first)->func == HYBL ||
(itP->first)->func == AROM ||
(itP->first)->func == LIPO)
&& ((itP->second)->func == AROM ||
(itP->second)->func == LIPO ||
(itP->second)->func == HYBL)))
{
newVol += VolumeOverlap((itP->first),(itP->second), !uo.noNormal);
}
}
if ((newVol - exclVol) > volBest)
{
res.resPhar.clear();
res.resPharSize = 0;
for (PharmacophoreMap::iterator itP = fMap.begin(); itP != fMap.end(); ++itP)
{
// add point to resulting pharmacophore
PharmacophorePoint p(itP->second);
(res.resPhar).push_back(p);
++res.resPharSize;
}
res.overlapVolume = newVol;
res.exclVolume = exclVol;
volBest = newVol - exclVol;
}
// get the next map
fMap.clear();
fMap = funcMap.getNextMap();
}
}
else
{
FunctionMapping funcMap(&refPharm, &dbPharm, uo.epsilon);
PharmacophoreMap fMap = funcMap.getNextMap();
PharmacophoreMap bestMap;
// default solution
SolutionInfo best;
best.volume = -999.9;
// rotor is set to no rotation
best.rotor.resize(4);
best.rotor = 0.0;
best.rotor[0] = 1.0;
double bestScore = -1000;
int mapSize(fMap.size());
int maxSize = mapSize - 3;
while (!fMap.empty())
{
int msize = fMap.size();
// add the exclusion spheres to the alignment procedure
if (uo.withExclusion)
{
for (unsigned int i(0); i < refSize ; ++i)
{
if (refPharm[i].func != EXCL)
{
continue;
}
for (unsigned int j(0); j < dbSize; ++j)
{
if (dbPharm[j].func == EXCL)
{
continue;
}
fMap.insert(std::make_pair(&(refPharm[i]), &(dbPharm[j])));
}
}
}
// Only align if the expected score has any chance of being larger
// than best score so far
if ((msize > maxSize)
&& (((double) msize / (refSize - exclSize + dbSize - msize)) > bestScore))
{
Alignment align(fMap);
SolutionInfo r = align.align(!uo.noNormal);
if (best.volume < r.volume)
{
best = r;
bestScore = best.volume / (refVolume + dbVolume - best.volume);
bestMap = fMap;
mapSize = msize;
}
}
else
{
// Level of mapping site to low
break;
}
if (bestScore > 0.98)
{
break;
}
// Get the next map
fMap.clear();
fMap = funcMap.getNextMap();
}
// Transform the complete pharmacophore and the molecule towards the
// best alignment
rotMat = quat2Rotation(best.rotor);
positionPharmacophore(dbPharm, rotMat, best);
positionMolecule(&res.resMol, rotMat, best);
// Update result
res.info = best;
// Compute overlap volume between exlusion spheres and pharmacophore
// points
for (int i(0); i < refSize; ++i)
{
if (refPharm[i].func != EXCL)
{
continue;
}
for (int j(0); j < dbSize; ++j)
{
res.exclVolume += VolumeOverlap(refPharm[i], dbPharm[j], !uo.noNormal);
}
}
// make copy of the best map and compute the volume overlap
for (PharmacophoreMap::iterator itP = bestMap.begin(); itP != bestMap.end(); ++itP)
{
if(((itP->first)->func == EXCL) || ((itP->second)->func == EXCL))
{
continue;
}
// compute overlap
res.overlapVolume += VolumeOverlap(itP->first, itP->second, !uo.noNormal);
// add point to resulting pharmacophore
PharmacophorePoint p(itP->second);
(res.resPhar).push_back(p);
++res.resPharSize;
}
}
// update scores
res.info.volume = res.overlapVolume - res.exclVolume;
if (res.info.volume > 0.0)
{
res.tanimoto = res.info.volume / (res.refVolume + res.dbVolume - res.info.volume);
res.tversky_ref = res.info.volume / res.refVolume;
res.tversky_db = res.info.volume / res.dbVolume;
}
switch (uo.rankby)
{
case TANIMOTO:
res.rankbyScore = res.tanimoto;
break;
case TVERSKY_REF:
res.rankbyScore = res.tversky_ref;
break;
case TVERSKY_DB:
res.rankbyScore = res.tversky_db;
break;
}
//-------------------------------------------------------
//...(5).. Generate output
//-------------------------------------------------------
if (uo.cutOff != 0.0)
{
if (res.rankbyScore < uo.cutOff)
{
continue;
}
}
if (uo.best != 0)
{
addBest(res, uo, resList);
}
else
{
if (!uo.molOutFile.empty())
{
logOut(&res, uo);
}
if (!uo.pharmOutFile.empty())
{
logPharmacophores(&res, uo);
}
if (!uo.scoreOutFile.empty())
{
logScores(&res, uo);
}
}
}
if (molReader)
{
delete molReader;
molReader = NULL;
}
if (pharmReader)
{
delete pharmReader;
pharmReader = NULL;
}
//----------------------------------------------------------------------------
//...(C).. Process best list (if defined)
//----------------------------------------------------------------------------
if (uo.best != 0)
{
std::vector<Result*>::iterator itR;
for (itR = resList.begin(); itR != resList.end(); ++itR)
{
Result* res(*itR);
if (!uo.molOutFile.empty())
{
logOut(res, uo);
}
if (!uo.pharmOutFile.empty())
{
logPharmacophores(res, uo);
}
if (!uo.scoreOutFile.empty())
{
logScores(res, uo);
}
delete res;
}
}
// done processing database
if (!uo.isQuiet)
{
if (uo.refInpFile.empty())
{
std::cerr << std::endl;
std::cerr << "Processed " << molCount << " molecules";
double tt = (double)(clock() - t0 )/CLOCKS_PER_SEC;
std::cerr << " in " << tt << " seconds (";
std::cerr << molCount/tt << " molecules per second)." << std::endl;
}
else
{
std::cerr << std::endl;
std::cerr << "Processed " << molCount << " molecules" << std::endl;
double tt = (double)(clock() - t0 )/CLOCKS_PER_SEC;
std::cerr << molCount << " alignments in " << tt << " seconds (";
std::cerr << molCount/tt << " alignments per second)." << std::endl;
}
}
exit(0);
}
/******************************************************************************
* Main function!
******************************************************************************/
int main(int argc, char **argv) {
int res;
char *file = NULL;
micronucleus *my_device = NULL;
// parse arguments
int run = 0;
int file_type = FILE_TYPE_INTEL_HEX;
int arg_pointer = 1;
char* usage = "usage: micronucleus [--run] [--dump-progress] [--type intel-hex|raw] [--no-ansi] [--timeout integer] filename";
progress_step = 0;
progress_total_steps = 5; // steps: waiting, connecting, parsing, erasing, writing, (running)?
dump_progress = 0;
timeout = 0; // no timeout by default
//#if defined(WIN)
// use_ansi = 0;
//#else
use_ansi = 1;
//#endif
while (arg_pointer < argc) {
if (strcmp(argv[arg_pointer], "--run") == 0) {
run = 1;
progress_total_steps += 1;
} else if (strcmp(argv[arg_pointer], "--type") == 0) {
arg_pointer += 1;
if (strcmp(argv[arg_pointer], "intel-hex") == 0) {
file_type = FILE_TYPE_INTEL_HEX;
} else if (strcmp(argv[arg_pointer], "raw") == 0) {
file_type = FILE_TYPE_RAW;
} else {
printf("Unknown File Type specified with --type option");
return EXIT_FAILURE;
}
} else if (strcmp(argv[arg_pointer], "--help") == 0 || strcmp(argv[arg_pointer], "-h") == 0) {
puts(usage);
puts("");
puts(" --type [intel-hex, raw]: Set upload file type to either intel hex or raw");
puts(" bytes (intel hex is default)");
puts(" --dump-progress: Output progress data in computer-friendly form");
puts(" for driving GUIs");
puts(" --run: Ask bootloader to run the program when finished");
puts(" uploading provided program");
//#ifndef WIN
puts(" --no-ansi: Don't use ANSI in terminal output");
//#endif
puts(" --timeout [integer]: Timeout after waiting specified number of seconds");
puts(" filename: Path to intel hex or raw data file to upload,");
puts(" or \"-\" to read from stdin");
return EXIT_SUCCESS;
} else if (strcmp(argv[arg_pointer], "--dump-progress") == 0) {
dump_progress = 1;
} else if (strcmp(argv[arg_pointer], "--no-ansi") == 0) {
use_ansi = 0;
} else if (strcmp(argv[arg_pointer], "--timeout") == 0) {
arg_pointer += 1;
if (sscanf(argv[arg_pointer], "%d", &timeout) != 1) {
printf("Did not understand --timeout value\n");
return EXIT_FAILURE;
}
} else {
file = argv[arg_pointer];
}
arg_pointer += 1;
}
if (argc < 2) {
puts(usage);
return EXIT_FAILURE;
}
setProgressData("waiting", 1);
if (dump_progress) printProgress(0.5);
printf("> Please plug in the device ... \n");
printf("> Press CTRL+C to terminate the program.\n");
time_t start_time, current_time;
time(&start_time);
while (my_device == NULL) {
delay(100);
my_device = micronucleus_connect();
time(¤t_time);
if (timeout && start_time + timeout < current_time) {
break;
}
}
if (my_device == NULL) {
printf("> Device search timed out\n");
return EXIT_FAILURE;
}
printf("> Device is found!\n");
// wait for CONNECT_WAIT milliseconds with progress output
float wait = 0.0f;
setProgressData("connecting", 2);
while (wait < CONNECT_WAIT) {
printProgress((wait / ((float) CONNECT_WAIT)) * 0.9f);
wait += 50.0f;
delay(50);
}
//my_device = micronucleus_connect();
printProgress(1.0);
// if (my_device->page_size == 64) {
// printf("> Device looks like ATtiny85!\n");
// } else if (my_device->page_size == 32) {
// printf("> Device looks like ATtiny45!\n");
// } else {
// printf("> Unsupported device!\n");
// return EXIT_FAILURE;
// }
printf("> Available space for user application: %d bytes\n", my_device->flash_size);
printf("> Suggested sleep time between sending pages: %ums\n", my_device->write_sleep);
printf("> Whole page count: %d\n", my_device->pages);
printf("> Erase function sleep duration: %dms\n", my_device->erase_sleep);
setProgressData("parsing", 3);
printProgress(0.0);
memset(dataBuffer, 0xFF, sizeof(dataBuffer));
int startAddress = 1, endAddress = 0;
if (file_type == FILE_TYPE_INTEL_HEX) {
if (parseIntelHex(file, dataBuffer, &startAddress, &endAddress)) {
printf("> Error loading or parsing hex file.\n");
return EXIT_FAILURE;
}
} else if (file_type == FILE_TYPE_RAW) {
if (parseRaw(file, dataBuffer, &startAddress, &endAddress)) {
printf("> Error loading raw file.\n");
return EXIT_FAILURE;
}
}
printProgress(1.0);
if (startAddress >= endAddress) {
printf("> No data in input file, exiting.\n");
return EXIT_FAILURE;
}
if (endAddress > my_device->flash_size) {
printf("> Program file is %d bytes too big for the bootloader!\n", endAddress - my_device->flash_size);
return EXIT_FAILURE;
}
setProgressData("erasing", 4);
printf("> Erasing the memory ...\n");
res = micronucleus_eraseFlash(my_device, printProgress);
if (res == 1) { // erase disconnection bug workaround
printf(">> Eep! Connection to device lost during erase! Not to worry\n");
printf(">> This happens on some computers - reconnecting...\n");
my_device = NULL;
delay(CONNECT_WAIT);
int deciseconds_till_reconnect_notice = 50; // notice after 5 seconds
while (my_device == NULL) {
delay(100);
my_device = micronucleus_connect();
deciseconds_till_reconnect_notice -= 1;
if (deciseconds_till_reconnect_notice == 0) {
printf(">> (!) Automatic reconnection not working. Unplug and reconnect\n");
printf(" device usb connector, or reset it some other way to continue.\n");
}
}
printf(">> Reconnected! Continuing upload sequence...\n");
} else if (res != 0) {
printf(">> Abort mission! %d error has occured ...\n", res);
printf(">> Please unplug the device and restart the program.\n");
return EXIT_FAILURE;
}
printProgress(1.0);
printf("> Starting to upload ...\n");
setProgressData("writing", 5);
res = micronucleus_writeFlash(my_device, endAddress, dataBuffer, printProgress);
if (res != 0) {
printf(">> Abort mission! An error has occured ...\n");
printf(">> Please unplug the device and restart the program.\n");
return EXIT_FAILURE;
}
if (run) {
printf("> Starting the user app ...\n");
setProgressData("running", 6);
printProgress(0.0);
res = micronucleus_startApp(my_device);
if (res != 0) {
printf(">> Abort mission! An error has occured ...\n");
printf(">> Please unplug the device and restart the program. \n");
return EXIT_FAILURE;
}
printProgress(1.0);
}
printf(">> Micronucleus done. Thank you!\n");
return EXIT_SUCCESS;
}
void ProgressBar::finish() {
done = toDo;
printProgress();
clear();
}
//---------------------------------------------------------------------
// ファイルの読み込みチェック(Win32APIバージョン)
//---------------------------------------------------------------------
bool readCheckOne(const kjm::_tstring& fname, DWORD bytesPerSector, bool fastMode) {
bool result = true;
_tcout << _T("残り(") << (--g_totalCount) << _T(") ") << fname << std::endl;
DWORD openFlag = FILE_ATTRIBUTE_NORMAL | FILE_FLAG_SEQUENTIAL_SCAN | (fastMode ? 0 : FILE_FLAG_NO_BUFFERING);
HANDLE hFile = CreateFile(fname.c_str(), GENERIC_READ, 0, NULL, OPEN_EXISTING, openFlag, NULL);
if (hFile != INVALID_HANDLE_VALUE) {
// ファイルアクセスのバイト数をセクタサイズの整数倍に合わせる
// バッファ アドレスをメモリ上でのディスクのセクタ境界に調整する
char* buffer = new char[bytesPerSector * 2];
char* p = (char *) ((DWORD) (buffer + bytesPerSector - 1) & ~(bytesPerSector - 1));
__int64 li1 = kjm::file::getFileSize(hFile);
__int64 li2 = 0;
DWORD lastPrintTime = 0;
DWORD dwStart = GetTickCount();
while (true) {
DWORD bytesRead;
if (ReadFile(hFile, p, bytesPerSector, &bytesRead, NULL) == FALSE) {
DWORD dwError = GetLastError();
_tcerr << _T("[ng] read error ") << dwError << _T(": ") << kjm::util::formatMessageBySystem(dwError) << std::endl;
result = false;
break;
}
li2 += bytesRead;
if ((GetTickCount() - lastPrintTime) > 500) {
lastPrintTime = GetTickCount();
// 500ms毎に進捗を出力する
printProgress(li2, li1, lastPrintTime, dwStart);
_tcout << _T("\r");
}
if (bytesRead != bytesPerSector) {
lastPrintTime = GetTickCount();
// 最後の結果出力
printProgress(li2, li1, lastPrintTime, dwStart);
_tcout << _T(" ... [ok]\n");
break;
}
}
delete[] buffer;
CloseHandle(hFile);
} else {
DWORD dwError = GetLastError();
_tcerr << _T("[ng] open error ") << dwError << _T(": ") << kjm::util::formatMessageBySystem(dwError) << std::endl;
if (dwError == ERROR_SHARING_VIOLATION || dwError == ERROR_ACCESS_DENIED) {
// 共有違反のときは、処理を継続させます。
} else {
result = false;
}
}
return result;
}
/*
* Entry point
*/
int main (int argc, char **argv)
{
Bool success = false;
UInt16 remainingCapacity;
pid_t hwServerPID;
setDebugPrintsOnToFile ("robooneremainingcapacitysync.log");
setProgressPrintsOn();
printProgress ("Synchronising remaining battery capacity values...\n");
/* Spawn a child that will become the Hardware server. */
hwServerPID = fork();
if (hwServerPID == 0)
{
/* Start Hardware Server process on a given port */
static char *argv1[] = {HARDWARE_SERVER_EXE, HARDWARE_SERVER_PORT_STRING, PNULL};
execv (HARDWARE_SERVER_EXE, argv1);
printDebug ("!!! Couldn't launch %s, err: %s. !!!\n", HARDWARE_SERVER_EXE, strerror (errno));
}
else
{
if (hwServerPID < 0)
{
printDebug ("!!! Couldn't fork to launch %s, err: %s. !!!\n", HARDWARE_SERVER_EXE, strerror (errno));
}
else
{ /* Parent process */
/* Wait for the server to start */
usleep (HARDWARE_SERVER_START_DELAY_PI_US);
/* Now setup the Hardware Server, batteries
* only on this occasion. This will restore
* the remaining battery capacity from
* non-volatile storage if it is out of date,
* which would be the case at power-on. */
success = startHardwareServer (true);
if (success)
{
/* Now do a remaining capacity reading to complete the sync back to
* non-volatile storage in case we are about to power off */
if (hardwareServerSendReceive (HARDWARE_READ_RIO_REMAINING_CAPACITY, PNULL, 0, &remainingCapacity))
{
printProgress ("Rio battery has %d mAh remaining.\n", remainingCapacity);
}
if (hardwareServerSendReceive (HARDWARE_READ_O1_REMAINING_CAPACITY, PNULL, 0, &remainingCapacity))
{
printProgress ("O1 battery has %d mAh remaining.\n", remainingCapacity);
}
if (hardwareServerSendReceive (HARDWARE_READ_O2_REMAINING_CAPACITY, PNULL, 0, &remainingCapacity))
{
printProgress ("O2 battery has %d mAh remaining.\n", remainingCapacity);
}
if (hardwareServerSendReceive (HARDWARE_READ_O3_REMAINING_CAPACITY, PNULL, 0, &remainingCapacity))
{
printProgress ("O3 battery has %d mAh remaining.\n", remainingCapacity);
}
}
/* Shut the Hardware Server down gracefully */
stopHardwareServer();
waitpid (hwServerPID, 0, 0); /* wait for Hardware Server process to exit */
}
}
setDebugPrintsOff();
if (success)
{
printProgress ("Synchronisation complete.\n");
}
else
{
printProgress ("\nSynchronisation failed!\n");
exit (-1);
}
return success;
}