bool SAXConfigurationHandler::startElement ( const QString & namespaceURI,
const QString & localName, const QString & qName,
const QXmlAttributes & atts ) {
int idx = qName.find ( ':' );
QString prefix = "";
if ( idx > 0 ) {
prefix = qName.left ( idx );
}
ConfigurationPtr c(new DefaultConfiguration( localName,
getLocationString(), namespaceURI, prefix ));
// if processing the toplevel item simply push it, otherwise link it
// with the parent
if( d->configuration.isNull() ) {
d->configuration = c;
} else {
ConfigurationPtr parent = d->elements.top();
parent->addChild( c );
}
// process attributes
for( int i = 0; i < atts.length(); i ++ ) {
c->setAttribute( atts.localName( i ), atts.value( i ) );
}
// push currently built configuration to the stack
d->elements.push( c );
return true;
}
void InstrumentTest::testInstrument() {
debug(LOG_DEBUG, DEBUG_LOG, 0, "testInstrument() begin");
ConfigurationPtr config = Configuration::get(dbfilename);
Database database = config->database();
// create an instrument
Instrument instrument(database, "BLUBB");
// add a few components
InstrumentComponentPtr camera = InstrumentComponentPtr(
new InstrumentComponentDirect(DeviceName::Camera,
DeviceName("camera:simulator/camera"), 7, "localhost"));
instrument.add(camera);
InstrumentComponentPtr ccd = InstrumentComponentPtr(
new InstrumentComponentDerived(DeviceName::Ccd,
instrument, DeviceName::Camera, 5));
instrument.add(ccd);
// check instrument
CPPUNIT_ASSERT(instrument.name() == "BLUBB");
// has method
debug(LOG_DEBUG, DEBUG_LOG, 0, "test 'has' method");
CPPUNIT_ASSERT(instrument.has(DeviceName::Camera));
CPPUNIT_ASSERT(instrument.has(DeviceName::Ccd));
// component_type method
debug(LOG_DEBUG, DEBUG_LOG, 0, "test 'component_type' method");
CPPUNIT_ASSERT(instrument.component_type(DeviceName::Camera)
== InstrumentComponent::direct);
CPPUNIT_ASSERT(instrument.component_type(DeviceName::Ccd)
== InstrumentComponent::derived);
// devicename method
debug(LOG_DEBUG, DEBUG_LOG, 0, "test 'devicename' method");
CPPUNIT_ASSERT(instrument.devicename(DeviceName::Camera)
== DeviceName("camera:simulator/camera"));
debug(LOG_DEBUG, DEBUG_LOG, 0, "ccd device: %s",
instrument.devicename(DeviceName::Ccd).toString().c_str());
CPPUNIT_ASSERT(instrument.devicename(DeviceName::Ccd)
== DeviceName("camera:simulator/camera"));
// name method
debug(LOG_DEBUG, DEBUG_LOG, 0, "test 'name' method");
debug(LOG_DEBUG, DEBUG_LOG, 0, "name(camera) = %s",
instrument.name(DeviceName::Camera).c_str());
CPPUNIT_ASSERT(instrument.name(DeviceName::Camera)
== DeviceName("camera:simulator/camera").toString());
debug(LOG_DEBUG, DEBUG_LOG, 0, "name(ccd) = %s",
instrument.name(DeviceName::Ccd).c_str());
CPPUNIT_ASSERT(instrument.name(DeviceName::Ccd) == "camera");
// unit method
debug(LOG_DEBUG, DEBUG_LOG, 0, "test 'unit' method");
CPPUNIT_ASSERT(instrument.unit(DeviceName::Camera) == 7);
CPPUNIT_ASSERT(instrument.unit(DeviceName::Ccd) == 5);
debug(LOG_DEBUG, DEBUG_LOG, 0, "testInstrument() end");
}
BulkPipe::BulkPipe(DevicePtr device, ConfigurationPtr conf, InterfacePtr interface, EndpointPtr in, EndpointPtr out, EndpointPtr interrupt, ITokenPtr claimToken):
_device(device), _conf(conf), _interface(interface), _in(in), _out(out), _interrupt(interrupt), _claimToken(claimToken)
{
int currentConfigurationIndex = _device->GetConfiguration();
if (conf->GetIndex() != currentConfigurationIndex)
_device->SetConfiguration(conf->GetIndex());
}
void ConfigurationTest::testConfiguration() {
debug(LOG_DEBUG, DEBUG_LOG, 0, "testConfiguration() begin");
ConfigurationPtr configuration
= Configuration::get("configtest.db");
configuration->set("global", ".", "name1", "value1");
configuration->set("global", ".", "name2", "value2");
debug(LOG_DEBUG, DEBUG_LOG, 0, "testConfiguration() end");
}
void ConfigurationTest::testRemove() {
debug(LOG_DEBUG, DEBUG_LOG, 0, "testRemove() begin");
ConfigurationPtr configuration
= Configuration::get("configtest.db");
configuration->remove("global", ".", "name1");
CPPUNIT_ASSERT(configuration->get("global", ".", "name1", "value3")
== "value3");
debug(LOG_DEBUG, DEBUG_LOG, 0, "testRemove() end");
}
VectorXd operator()(const VectorXd& x) const {
m_config->SetDOFValues(toDblVec(x.topRows(m_nDof)));
OR::Vector ptWorldA, ptWorldB, nWorldA, nWorldB;
CalcWorldPoints(x, ptWorldA, ptWorldB);
return toVector3d(ptWorldA - ptWorldB);
}
//_______________________________________________________
bool ExceptionListWidget::checkException( ConfigurationPtr exception )
{
while( exception->exceptionPattern().isEmpty() || !QRegExp( exception->exceptionPattern() ).isValid() )
{
KMessageBox::error( this, i18n("Regular Expression syntax is incorrect") );
QPointer<ExceptionDialog> dialog( new ExceptionDialog( this ) );
dialog->setException( exception );
if( dialog->exec() == QDialog::Rejected )
{
delete dialog;
return false;
}
dialog->save();
delete dialog;
}
return true;
}
void InstrumentTest::testSave() {
debug(LOG_DEBUG, DEBUG_LOG, 0, "testSave() begin");
ConfigurationPtr config = Configuration::get(dbfilename);
Database database = config->database();
DeviceMapperConfigurationPtr devicemapperconfig
= DeviceMapperConfiguration::get(config);
// make sure we have an entry in the device mapper for TEST
DeviceMapperPtr devicemapper = devicemapperconfig->devicemapper();
DeviceMap mapentry(DeviceName("filterwheel:sx/0"));
mapentry.name("TEST");
mapentry.unitid(1291);
mapentry.description("test filterwheel");
devicemapper->add(mapentry);
// create an instrument
InstrumentPtr instrument(new Instrument(database, "BLUBB"));
// add a few components
InstrumentComponentPtr camera = InstrumentComponentPtr(
new InstrumentComponentDirect(DeviceName::Camera,
DeviceName("camera:simulator/camera"), 7, "localhost"));
instrument->add(camera);
InstrumentComponentPtr ccd = InstrumentComponentPtr(
new InstrumentComponentDerived(DeviceName::Ccd,
*instrument, DeviceName::Camera, 5));
instrument->add(ccd);
InstrumentComponentPtr filterwheel = InstrumentComponentPtr(
new InstrumentComponentMapped(DeviceName::Filterwheel,
database, "TEST"));
instrument->add(filterwheel);
// add the instrument to the database
InstrumentConfigurationPtr instrumentconfig
= InstrumentConfiguration::get(config);
instrumentconfig->addInstrument(instrument);
debug(LOG_DEBUG, DEBUG_LOG, 0, "testSave() end");
}
void MainWindow::SaveConfiguration()
{
try {
int selected = ui->cbConfiguration->currentIndex();
if(selected <= 0) throw std::runtime_error("You cannot save over the default configuration.");
m_server.SaveConfiguration(m_configuration,m_configList[selected - 1]);
// reload configurations for each device
Server::DeviceList devices;
m_server.GetDeviceList(&devices);
for(Server::DeviceList::iterator device = devices.begin(); device != devices.end(); ++device)
{
ConfigurationPtr config = (*device)->GetConfiguration();
if(config && config->GetName() == m_configList[selected - 1]) {
(*device)->SetConfiguration(m_server.LoadConfiguration(m_configList[selected - 1]));
}
}
QMessageBox::information(this,"","Configuration saved.");
} catch(const std::runtime_error& e) {
QMessageBox::critical(this,"Error creating configuration.",e.what());
}
}
/**
* \brief Get a list of interface association Descriptors from the device
*/
std::list<USBDescriptorPtr> Device::interfaceAssociationDescriptors(
bool videoonly) throw(USBError) {
std::list<USBDescriptorPtr> iadescriptors;
// see whether there is any additional data that could contain
// an interface association descriptor
ConfigurationPtr config = activeConfig();
if (config->extra().size() == 0) {
debug(LOG_DEBUG, DEBUG_LOG, 0, "no data for descriptors");
return iadescriptors;
}
// try to parse additional descriptors
DescriptorFactory f(*this);
std::vector<USBDescriptorPtr> list = f.descriptors(config->extra());
debug(LOG_DEBUG, DEBUG_LOG, 0, "found %d additional descriptors",
list.size());
// no check whether they are InterfaceAssociationDescriptors
std::vector<USBDescriptorPtr>::const_iterator i;
for (i = list.begin(); i != list.end(); i++) {
USBDescriptorPtr dp = *i;
if (isPtr<InterfaceAssociationDescriptor>(dp)) {
InterfaceAssociationDescriptor *iad
= getPtr<InterfaceAssociationDescriptor>(dp);
bool isvideo = iad->isVideoInterfaceCollection();
debug(LOG_DEBUG, DEBUG_LOG, 0, "isvideo = %s",
(isvideo) ? "YES" : "NO");
if ((!videoonly) || (isvideo)) {
iadescriptors.push_back(dp);
}
}
}
// return all the interface association descriptors we have found
return iadescriptors;
}
void CalcWorldPointsAndNormal(const VectorXd& x, OR::Vector& ptWorldA, OR::Vector& ptWorldB, OR::Vector& nWorldA, OR::Vector& nWorldB) const {
DblVec dofs(x.data(), x.data() + m_nDof);
OpenRAVE::Vector ptLocalA, ptLocalB;
ptLocalA.x = x(m_nDof);
ptLocalA.y = x(m_nDof + 1);
ptLocalB.x = x(m_nDof + 2);
ptLocalB.y = x(m_nDof + 3);
m_config->SetDOFValues(dofs);
ptWorldA = m_faceA.link->GetTransform() * (m_faceA.Tlf * ptLocalA);
ptWorldB = m_faceB.link->GetTransform() * (m_faceB.Tlf * ptLocalB);
nWorldA = geometry::quatRotate(geometry::quatMultiply(m_faceA.link->GetTransform().rot,m_faceA.Tlf.rot), OR::Vector(0,0,1));
nWorldB = geometry::quatRotate(geometry::quatMultiply(m_faceB.link->GetTransform().rot,m_faceB.Tlf.rot), OR::Vector(0,0,1));
}
void testSerializeToFile () {
DefaultConfigurationBuilder builder;
DefaultConfigurationSerializer serializer;
ConfigurationPtr cg;
ConfigurationPtr cb;
QString cge, cbe;
int cgl, cgc, cbl, cbc;
//construct good configuration
cg = builder.buildFromFile(
srcdir + "/tests/test_config.xml",
cge, cgl, cgc, false );
CPPUNIT_ASSERT_MESSAGE(
QString("%1 at line %2 column %3")
.arg( cge ).arg( cgl ).arg( cgc ).latin1(),
cg );
CPPUNIT_ASSERT (
cg->setAttribute ( "escaped", "<>&\"'" ) != false );
CPPUNIT_ASSERT ( serializer.serializeToFile (
builddir + "/serialized_config.xml", cg ) );
//reconstruct good configuration from new file
cb = builder.buildFromFile(
builddir + "/serialized_config.xml", cbe, cbl, cbc );
CPPUNIT_ASSERT_MESSAGE(
QString("%1 at line %2 column %3")
.arg( cbe ).arg( cbl ).arg( cbc ).latin1(),
cb );
CPPUNIT_ASSERT ( cb->getAttribute ( "escaped" ) == "<>&\"'" );
// compare both configs
CPPUNIT_ASSERT ( cg->getName () == cb->getName () );
// TODO: compare structure
}
FaceContactErrorCalculator(ConfigurationPtr config, const Face& faceA, const Face& faceB) :
m_config(config), m_faceA(faceA), m_faceB(faceB), m_nDof(m_config->GetDOF()) {}
bool SAXConfigurationHandler::characters ( const QString & ch ) {
//qDebug( "got characters: `%s'", ch.latin1() );
ConfigurationPtr c = d->elements.top();
c->setValue( c->getValue() + ch );
return true;
}
/**
* \brief Main function for the snowfocus program
*/
int main(int argc, char *argv[]) {
snowstar::CommunicatorSingleton cs(argc, argv);
std::string instrumentname;
int steps = 10;
double exposuretime = 1.0;
double temperature = std::numeric_limits<double>::quiet_NaN();
std::string binning;
std::string frame;
std::string filtername;
astro::focusing::Focusing::method_type method
= astro::focusing::Focusing::FWHM;
int c;
int longindex;
while (EOF != (c = getopt_long(argc, argv, "b:c:de:f:hi:m:r:t:",
longopts, &longindex)))
switch (c) {
case 'b':
binning = optarg;
break;
case 'c':
astro::config::Configuration::set_default(optarg);
break;
case 'd':
debuglevel = LOG_DEBUG;
break;
case 'e':
exposuretime = std::stod(optarg);
break;
case 'f':
filtername = optarg;
break;
case 'h':
usage(argv[0]);
return EXIT_SUCCESS;
case 'i':
instrumentname = optarg;
break;
case 'm':
method = astro::focusing::Focusing::string2method(optarg);
break;
case 'r':
frame = optarg;
break;
case 's':
steps = std::stoi(optarg);
break;
case 't':
temperature = std::stod(optarg);
break;
}
// the next argument is the command
if (argc <= optind) {
throw std::runtime_error("not enough arguments");
}
std::string command = argv[optind++];
debug(LOG_DEBUG, DEBUG_LOG, 0, "command: %s", command.c_str());
if (command == "help") {
usage(argv[0]);
return EXIT_SUCCESS;
}
// get the configuration
ConfigurationPtr config = Configuration::get();
// check whether we have an instrument
if (0 == instrumentname.size()) {
throw std::runtime_error("instrument name not set");
}
RemoteInstrument instrument(config->database(),
instrumentname);
// get the device names
CcdPrx ccdprx = instrument.ccd_proxy();
std::string ccdname = ccdprx->getName();
FocuserPrx focuserprx = instrument.focuser_proxy();
std::string focusername = focuserprx->getName();
debug(LOG_DEBUG, DEBUG_LOG, 0, "ccd: %s focuser: %s", ccdname.c_str(),
focusername.c_str());
// first get a connection to the server
Ice::CommunicatorPtr ic = CommunicatorSingleton::get();
astro::ServerName servername
= instrument.servername(astro::DeviceName::Ccd);
Ice::ObjectPrx base = ic->stringToProxy(
servername.connect("FocusingFactory"));
FocusingFactoryPrx focusingfactory
= FocusingFactoryPrx::checkedCast(base);
// get the focusing interface
FocusingPrx focusing = focusingfactory->get(ccdname, focusername);
debug(LOG_DEBUG, DEBUG_LOG, 0, "got a focusing proxy");
// creating a callback
Ice::ObjectPtr callback = new FocusCallbackI();
CallbackAdapter adapter(ic);
Ice::Identity ident = adapter.add(callback);
focusing->ice_getConnection()->setAdapter(adapter.adapter());
// handle the simple commands
if (command == "status") {
std::cout << "status: ";
std::cout << focusingstate2string(focusing->status());
std::cout << std::endl;
return EXIT_SUCCESS;
}
if (command == "history") {
show_history(focusing->history());
return EXIT_SUCCESS;
}
if (command == "monitor") {
std::cout << "current status: ";
std::cout << focusingstate2string(focusing->status());
std::cout << std::endl;
focusing->registerCallback(ident);
signal(SIGINT, handler);
while (!signal_received) {
sleep(1);
}
focusing->unregisterCallback(ident);
return EXIT_SUCCESS;
}
if (command == "cancel") {
focusing->cancel();
std::cout << "cancel command sent" << std::endl;
return EXIT_SUCCESS;
}
// throw exception for unknown commands
if (command != "start") {
throw std::runtime_error("unknown command");
}
// make sure temperature is set
CoolerPrx cooler;
if (instrument.has(DeviceName::Cooler)) {
cooler = instrument.cooler_proxy();
}
CoolerTask coolertask(cooler, temperature);
coolertask.wait();
// next two arguments are the interval boundaries
if ((argc - optind) < 2) {
throw std::runtime_error("missing intervale arguments");
}
int min = std::stoi(argv[optind++]);
int max = std::stoi(argv[optind++]);
debug(LOG_DEBUG, DEBUG_LOG, 0, "interval [%d,%d]", min, max);
if (min >= max) {
throw std::runtime_error("not an interval");
}
// ensure that focuser is ready
FocusState state = focusing->status();
debug(LOG_DEBUG, DEBUG_LOG, 0, "current state = %d", state);
if ((state == FocusMOVING) && (state == FocusMEASURING)) {
throw std::runtime_error("already focusing");
}
// set up the exposure
CcdTask ccdtask(ccdprx);
ccdtask.frame(frame);
ccdtask.binning(binning);
ccdtask.exposuretime(exposuretime);
// set up the focusing
focusing->setSteps(steps);
focusing->setMethod(convert(method));
// start the focusing process
debug(LOG_DEBUG, DEBUG_LOG, 0, "starting between %d and %d", min, max);
focusing->start(min, max);
debug(LOG_DEBUG, DEBUG_LOG, 0, "focusing started, status: %d",
focusing->status());
// wait for the process to complete
bool completed = false;
signal(SIGINT, handler);
do {
sleep(1);
switch (focusing->status()) {
case FocusIDLE:
case FocusMOVING:
case FocusMEASURING:
break;
case FocusFOCUSED:
case FocusFAILED:
completed = true;
break;
}
} while ((!completed) && (!signal_received));
if (completed) {
std::cout << "final focus position: " << focuserprx->current();
std::cout << std::endl;
// display the history
show_history(focusing->history());
} else {
std::cout << "focusing incomplete" << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
/**
* \brief Construct a camera from a USB Device
*
* The constructor undertakes an extensive analysis of the descriptors
* to find the video control and video streaming interfaces of the video
* function of the device. It also makes sure no kernel driver is attached
* to the device. It does not, however, claim any of the interfaces, this
* is done when the device is really used.
* \param _device an USB device to open as a UVC camera
* \param force force opening as camera even if the
* interface associaten descriptor does not
* declare itself as a video interface association
* descriptor (handles the TIS camera)
* XXX apparently the force parameter is never used, so the question should be
* asked whether we can remove it.
*/
UVCCamera::UVCCamera(Device& _device, bool /* force */) throw(USBError)
: device(_device) {
debug(LOG_DEBUG, DEBUG_LOG, 0, "create a UVC camera object");
// make sure the camera is open, this most probably will not have
// any effect
device.open();
// scan the active configuration for one that has an Interface
// association descriptor
ConfigurationPtr config = device.activeConfig();
if (config->extra().size() == 0) {
debug(LOG_ERR, DEBUG_LOG, 0, "no extra descriptors");
throw USBError("no InterfaceAssociationDescriptor");
}
// get the list of interface association descriptors
std::list<USBDescriptorPtr> iadlist
= device.interfaceAssociationDescriptors(true);
if (0 == iadlist.size()) {
throw USBError("no Video Interface Association found");
}
iadptr = *iadlist.begin();
debug(LOG_DEBUG, DEBUG_LOG, 0, "Video Interface Association found");
// get the control interface, and the list of interface descriptors
// for the control interface, and claim it
uint8_t ci = controlInterfaceNumber();
videocontrol = (*config)[ci];
debug(LOG_DEBUG, DEBUG_LOG, 0, "Control interface number: %d", ci);
videocontrol->detachKernelDriver();
// we also need to know all the video control descriptors appended
// to this InterfaceDescriptor. The VideoControlDescriptorFactory
// does that.
debug(LOG_DEBUG, DEBUG_LOG, 0, "parse the video control descriptors");
InterfaceDescriptorPtr controlinterface = (*videocontrol)[0];
VideoControlDescriptorFactory vcdf(device);
videocontroldescriptors = vcdf.descriptors(controlinterface->extra());
std::cout << videocontroldescriptors[0];
// now claim get the various interface descriptors, i.e. the
// alternate settings for an interface
int interfacecount = iad().bInterfaceCount();
debug(LOG_DEBUG, DEBUG_LOG, 0, "interfaces in association: %d",
interfacecount);
// now parse the video streaming interfaces
debug(LOG_DEBUG, DEBUG_LOG, 0, "parse streaming interface descriptors");
VideoStreamingDescriptorFactory vsf(device);
for (int vsif = controlInterfaceNumber() + 1;
vsif < controlInterfaceNumber() + iad().bInterfaceCount();
vsif++) {
debug(LOG_DEBUG, DEBUG_LOG, 0,
"analyzing video streaming interface %d", vsif);
InterfacePtr interface = (*config)[vsif];
// only alternate setting 0 contains the formats
InterfaceDescriptorPtr id = (*interface)[0];
std::string extra = id->extra();
debug(LOG_DEBUG, DEBUG_LOG, 0, "extra descriptors: %d bytes",
extra.size());
USBDescriptorPtr vsd = vsf.descriptor(extra);
debug(LOG_DEBUG, DEBUG_LOG, 0, "parse complete");
videostreaming.push_back(vsd);
}
debug(LOG_DEBUG, DEBUG_LOG, 0, "UVCCamera constructed");
}
void ConfigsParticleDecomp::gather() {
System& system = getSystemRef();
esutil::Error err(system.comm);
int nprocs = system.comm->size();
int myrank = system.comm->rank();
int localN = system.storage->getNRealParticles();
int curNumP = 0;
boost::mpi::all_reduce(*system.comm, localN, curNumP, std::plus<int>());
if(myrank==0){
// check whether the number of particles is the same during the gathering
if( curNumP != num_of_part ){
stringstream msg;
msg<<" ConfigsParticleDecomp gathers the configurations of the same system\n"
" with the same number of particles. If you need to store the systems\n"
" with different number of particles you should use something else."
" E.g `Configurations`";
err.setException( msg.str() );
}
}
ConfigurationPtr config = make_shared<Configuration> ();
for (int rank_i=0; rank_i<nprocs; rank_i++) {
map< size_t, Real3D > conf;
if (rank_i == myrank) {
CellList realCells = system.storage->getRealCells();
for(CellListIterator cit(realCells); !cit.isDone(); ++cit) {
int id = cit->id();
Real3D property = Real3D(0,0,0);
if(key=="position")
property = cit->position();
else if(key=="velocity")
property = cit->velocity();
else if(key=="unfolded"){
Real3D& pos = cit->position();
Int3D& img = cit->image();
Real3D Li = system.bc->getBoxL();
for (int i = 0; i < 3; ++i) property[i] = pos[i] + img[i] * Li[i];
}
else{
stringstream msg;
msg<<"Error. Key "<<key<<" is unknown. Use position, unfolded or"
" velocity.";
err.setException( msg.str() );
}
conf[id] = property;
}
}
boost::mpi::broadcast(*system.comm, conf, rank_i);
for (map<size_t,Real3D>::iterator itr=conf.begin(); itr != conf.end(); ++itr) {
size_t id = itr->first;
Real3D p = itr->second;
if(idToCpu[id]==myrank) config->set(id, p[0], p[1], p[2]);
}
}
pushConfig(config);
}
void Configurations::gather() {
System& system = getSystemRef();
// determine number of local particles and total particles
int myN = system.storage->getNRealParticles();
int maxN; // maximal number of particles one processor has
int totalN; // totlal number of particles all processors have
boost::mpi::all_reduce(*system.comm, myN, maxN, boost::mpi::maximum<int>());
boost::mpi::all_reduce(*system.comm, myN, totalN, std::plus<int>());
LOG4ESPP_INFO(logger, "#Partices: me = " << myN << ", max = " << maxN
<< ", totalN = " << totalN);
int* ids = new int [maxN]; // buffer for gather
Real3D* coordinates;
Real3D* velocities;
Real3D* forces;
real* radii;
if (gatherPos) coordinates = new Real3D [maxN]; // buffer for gather
if (gatherVel) velocities = new Real3D [maxN]; // buffer for gather
if (gatherForce) forces = new Real3D [maxN]; // buffer for gather
if (gatherRadius) radii = new real [maxN]; // buffer for gather
// fill the buffer with my values
CellList realCells = system.storage->getRealCells();
int i = 0;
for(CellListIterator cit(realCells); !cit.isDone(); ++cit) {
ids[i] = cit->id();
if (gatherPos) {
Real3D pos = cit->position();
Int3D img = cit->image();
if (folded)
system.bc->foldPosition(pos, img);
else
system.bc->unfoldPosition(pos, img);
coordinates[i] = pos;
}
if (gatherVel) velocities[i] = cit->velocity();
if (gatherForce) forces[i] = cit->force();
if (gatherRadius) radii[i] = cit->radius();
i++;
}
if (i != myN) {
LOG4ESPP_ERROR(logger, "mismatch for number of local particles");
}
// each proc sends its data to master process
if (system.comm->rank() == 0) {
ConfigurationPtr config = make_shared<Configuration> (); //totalN
// root process collects data from all processors and sets it
int nproc = system.comm->size();
for (int iproc = 0; iproc < nproc; iproc++) {
int nother;
if (iproc) {
int nIds, nVals; // number of received values
int tmp;
boost::mpi::request req;
boost::mpi::status stat;
LOG4ESPP_DEBUG(logger, "receive tags from " << iproc);
req = system.comm->irecv<int>(iproc, DEFAULT_TAG, ids, maxN);
system.comm->send(iproc, DEFAULT_TAG, 0);
stat = req.wait();
nIds = *stat.count<int>();
if (gatherPos) {
req = system.comm->irecv<Real3D>(iproc, DEFAULT_TAG, coordinates, maxN);
system.comm->send(iproc, DEFAULT_TAG, 0);
stat = req.wait();
nVals = *stat.count<Real3D>();
if (nVals != nIds) {
LOG4ESPP_ERROR(logger, "serious error collecting data, got " <<
nIds << " ids, but " << nVals << " coordinates");
}
}
if (gatherVel) {
req = system.comm->irecv<Real3D>(iproc, DEFAULT_TAG, velocities, maxN);
system.comm->send(iproc, DEFAULT_TAG, 0);
stat = req.wait();
nVals = *stat.count<Real3D>();
if (nVals != nIds) {
LOG4ESPP_ERROR(logger, "serious error collecting data, got " <<
nIds << " ids, but " << nVals << " velocities");
}
}
if (gatherForce) {
req = system.comm->irecv<Real3D>(iproc, DEFAULT_TAG, forces, maxN);
system.comm->send(iproc, DEFAULT_TAG, 0);
stat = req.wait();
nVals = *stat.count<Real3D>();
if (nVals != nIds) {
LOG4ESPP_ERROR(logger, "serious error collecting data, got " <<
nIds << " ids, but " << nVals << " forces");
}
}
if (gatherRadius) {
req = system.comm->irecv<real>(iproc, DEFAULT_TAG, radii, maxN);
system.comm->send(iproc, DEFAULT_TAG, 0);
stat = req.wait();
nVals = *stat.count<real>();
if (nVals != nIds) {
LOG4ESPP_ERROR(logger, "serious error collecting data, got " <<
nIds << " ids, but " << nVals << " radii");
}
}
nother = nIds;
} else {
nother = myN;
}
LOG4ESPP_INFO(logger, "add " << nother << " coordinates of proc " << iproc);
for (int i = 0; i < nother; i++) {
//LOG4ESPP_DEBUG(logger, "set coordinates of particle with id = " << index <<
// ": " << coordinates[3*i] << " " << coordinates[3*i+1] << " " << coordinates[3*i+2]);
int index = ids[i];
if (gatherPos) config->setCoordinates(index, coordinates[i]);
if (gatherVel) config->setVelocities(index, velocities[i]);
if (gatherForce) config->setForces(index, forces[i]);
if (gatherRadius) config->setRadius(index, radii[i]);
}
}
LOG4ESPP_INFO(logger, "save the latest configuration");
pushConfig(config);
} else {
LOG4ESPP_INFO(logger, "proc " << system.comm->rank() << " sends data "
<< " of " << myN << " particles");
// not master process, send data to master process
int tmp;
boost::mpi::status stat;
// wait for a signal (empty message) before sending
system.comm->irecv<int>(0, DEFAULT_TAG, tmp);
system.comm->send<int>(0, DEFAULT_TAG, ids, myN);
if (gatherPos) {
system.comm->irecv<int>(0, DEFAULT_TAG, tmp);
system.comm->send<Real3D>(0, DEFAULT_TAG, coordinates, myN);
}
if (gatherVel) {
system.comm->irecv<int>(0, DEFAULT_TAG, tmp);
system.comm->send<Real3D>(0, DEFAULT_TAG, velocities, myN);
}
if (gatherForce) {
system.comm->irecv<int>(0, DEFAULT_TAG, tmp);
system.comm->send<Real3D>(0, DEFAULT_TAG, forces, myN);
}
if (gatherRadius) {
system.comm->irecv<int>(0, DEFAULT_TAG, tmp);
system.comm->send<real>(0, DEFAULT_TAG, radii, myN);
}
}
// ToDo: remove first configuration if capacity is exhausted
// master process saves the configuration
if (gatherRadius) delete [] radii;
if (gatherForce) delete [] forces;
if (gatherVel) delete [] velocities;
if (gatherPos) delete [] coordinates;
delete [] ids;
}
python::list StaticStructF::computeArraySingleChain(int nqx, int nqy, int nqz,
real bin_factor, int chainlength) const {
//fist the system coords are saved at each CPU
System& system = getSystemRef();
esutil::Error err(system.comm);
Real3D Li = system.bc->getBoxL(); //Box size (Lx, Ly, Lz)
int nprocs = system.comm->size(); // number of CPUs
int myrank = system.comm->rank(); // current CPU's number
int num_part = 0;
ConfigurationPtr config = make_shared<Configuration > ();
// loop over all CPU-numbers - to give all CPUs all particle coords
for (int rank_i = 0; rank_i < nprocs; rank_i++) {
map< size_t, Real3D > conf;
if (rank_i == myrank) {
CellList realCells = system.storage->getRealCells();
for (CellListIterator cit(realCells); !cit.isDone(); ++cit) {
int id = cit->id();
conf[id] = cit->position();
}
}
boost::mpi::broadcast(*system.comm, conf, rank_i);
// for simplicity we will number the particles from 0
for (map<size_t, Real3D>::iterator itr = conf.begin(); itr != conf.end(); ++itr) {
size_t id = itr->first;
Real3D p = itr->second;
config->set(id, p[0], p[1], p[2]);
//config->set(num_part, p[0], p[1], p[2]);
num_part++;
}
}
cout << "particles are given to each CPU!\n";
// now all CPUs have all particle coords and num_part is the total number
// of particles
// use all CPUs
// TODO it could be a problem if n_nodes > num_part
// here starts calculation of the static structure factor
//step size for qx, qy, qz
real dqs[3];
dqs[0] = 2. * M_PIl / Li[0];
dqs[1] = 2. * M_PIl / Li[1];
dqs[2] = 2. * M_PIl / Li[2];
Real3D q;
//calculations for binning
real bin_size = bin_factor * min(dqs[0], (dqs[1], dqs[2]));
real q_sqr_max = nqx * nqx * dqs[0] * dqs[0]
+ nqy * nqy * dqs[1] * dqs[1]
+ nqz * nqz * dqs[2] * dqs[2];
real q_max = sqrt(q_sqr_max);
int num_bins = (int) ceil(q_max / bin_size);
vector<real> sq_bin;
vector<real> q_bin;
vector<int> count_bin;
sq_bin.resize(num_bins);
q_bin.resize(num_bins);
count_bin.resize(num_bins);
if (myrank == 0) {
cout << nprocs << " CPUs\n\n"
<< "bin size \t" << bin_size << "\n"
<< "q_max \t" << q_max << "\n";
}
real n_reci = 1. / num_part;
real chainlength_reci = 1. / chainlength;
real scos_local = 0; //will store cos-sum on each CPU
real ssin_local = 0; //will store sin-sum on each CPU
//will store the summation of the the single chain structure factor
real singleChain_localSum = 0;
Real3D coordP;
python::list pyli;
//calculations for parallelizing (over chains)
int num_chains;
if (num_part % chainlength == 0)
num_chains = num_part / chainlength;
else {
cout << "ERROR: chainlenght does not match total number of "
<< "particles. num_part % chainlenght is unequal 0. \n"
<< "Calculation of SingleChain_StaticStructF aborted\n";
return pyli;
}
int cpp = (int) ceil((double) num_chains / nprocs); //chains per proc
cout << "chains per proc\t" << cpp << "\n";
//loop over different q values
//starting from zero because combinations with negative components
//will give the same result in S(q). so S(q) is the same for
//the 8 vectors q=(x,y,z),(-x,y,z), (x,-y,z),(x,y,-z),(-x,-y,z),...
for (int hx = -nqx; hx <= nqx; hx++) {
for (int hy = -nqy; hy <= nqy; hy++) {
for (int hz = 0; hz <= nqz; hz++) {
//values of q-vector
q[0] = hx * dqs[0];
q[1] = hy * dqs[1];
q[2] = hz * dqs[2];
real q_abs = q.abs();
//determining the bin number
int bin_i = (int) floor(q_abs / bin_size);
q_bin[bin_i] += q_abs;
count_bin[bin_i] += 1;
//resetting the variable that stores the sum for each q-vector
singleChain_localSum = 0;
//loop over chains (cid is chain_id)
for (int cid = myrank * cpp; cid < (1 + myrank) * cpp
&& cid < num_chains; cid++) {
scos_local = 0; //resetting the cos sum for the each chain
ssin_local = 0; //resetting the sin sum for the each chain
//loop over particles
for (int k = cid * chainlength; k < (1 + cid) * chainlength && k < num_part;
k++) {
coordP = config->getCoordinates(k);
scos_local += cos(q * coordP);
ssin_local += sin(q * coordP);
}
//the (summation part of the) single chain structure
// factors are summed up for the averaging at the
// end (over the chains)
singleChain_localSum += scos_local * scos_local
+ ssin_local * ssin_local;
}
if (myrank != 0) {
boost::mpi::reduce(*system.comm, singleChain_localSum, plus<real > (), 0);
}
if (myrank == 0) {
real singleChainSum = 0;
boost::mpi::reduce(*system.comm, singleChain_localSum, singleChainSum, plus<real > (), 0);
sq_bin[bin_i] += singleChainSum;
}
}
}
}
//creates the python list with the results
if (myrank == 0) {
//starting with bin_i = 1 will leave out the value for q=0, otherwise start with bin_i=0
for (int bin_i = 1; bin_i < num_bins; bin_i++) {
real c = (count_bin[bin_i]) ? 1 / (real) count_bin[bin_i] : 0;
sq_bin[bin_i] = n_reci * chainlength_reci * sq_bin[bin_i] * c;
q_bin[bin_i] = q_bin[bin_i] * c;
python::tuple q_Sq_pair;
q_Sq_pair = python::make_tuple(q_bin[bin_i], sq_bin[bin_i]);
pyli.append(q_Sq_pair);
}
}
return pyli;
}
python::list StaticStructF::computeArray(int nqx, int nqy, int nqz,
real bin_factor) const {
time_t start;
time(&start);
cout << "collective calc starts " << ctime(&start) << "\n";
//fist the system coords are saved at each CPU
System& system = getSystemRef();
esutil::Error err(system.comm);
Real3D Li = system.bc->getBoxL(); //Box size (Lx, Ly, Lz)
int nprocs = system.comm->size(); // number of CPUs
int myrank = system.comm->rank(); // current CPU's number
if (myrank == 0) {
cout << "collective calc starts " << ctime(&start) << "\n";
}
int num_part = 0;
ConfigurationPtr config = make_shared<Configuration > ();
// loop over all CPU-numbers - to give all CPUs all particle coords
for (int rank_i = 0; rank_i < nprocs; rank_i++) {
map< size_t, Real3D > conf;
if (rank_i == myrank) {
CellList realCells = system.storage->getRealCells();
for (CellListIterator cit(realCells); !cit.isDone(); ++cit) {
int id = cit->id();
conf[id] = cit->position();
}
}
boost::mpi::broadcast(*system.comm, conf, rank_i);
// for simplicity we will number the particles from 0
for (map<size_t, Real3D>::iterator itr = conf.begin(); itr != conf.end(); ++itr) {
size_t id = itr->first;
Real3D p = itr->second;
config->set(id, p[0], p[1], p[2]);
//config->set(num_part, p[0], p[1], p[2]);
num_part++;
}
}
if (myrank == 0) {
time_t distributed;
time(&distributed);
cout << "particles on all CPUs " << ctime(&distributed) << "\n";
cout << "distribution to CPUs took "
<< difftime(distributed, start) << " seconds \n";
}
// now all CPUs have all particle coords and num_part is the total number
// of particles
// use all CPUs
// TODO it could be a problem if n_nodes > num_part
// here starts calculation of the static structure factor
//step size for qx, qy, qz
real dqs[3];
dqs[0] = 2. * M_PIl / Li[0];
dqs[1] = 2. * M_PIl / Li[1];
dqs[2] = 2. * M_PIl / Li[2];
Real3D q;
//calculations for binning
real bin_size = bin_factor * min(dqs[0], (dqs[1], dqs[2]));
real q_sqr_max = nqx * nqx * dqs[0] * dqs[0]
+ nqy * nqy * dqs[1] * dqs[1]
+ nqz * nqz * dqs[2] * dqs[2];
real q_max = sqrt(q_sqr_max);
int num_bins = (int) ceil(q_max / bin_size);
vector<real> sq_bin;
vector<real> q_bin;
vector<int> count_bin;
sq_bin.resize(num_bins);
q_bin.resize(num_bins);
count_bin.resize(num_bins);
if (myrank == 0) {
cout << nprocs << " CPUs\n\n"
<< "bin size \t" << bin_size << "\n"
<< "q_max \t" << q_max << "\n";
}
real n_reci = 1. / num_part;
real scos_local = 0; //will store cos-sum on each CPU
real ssin_local = 0; //will store sin-sum on each CPU
int ppp = (int) ceil((double) num_part / nprocs); //particles per proc
Real3D coordP;
python::list pyli;
//loop over different q values
//starting from zero because combinations with negative components
//will give the same result in S(q). so S(q) is the same for
//the 8 vectors q=(x,y,z),(-x,y,z), (x,-y,z),(x,y,-z),(-x,-y,z),...
for (int hx = -nqx; hx <= nqx; hx++) {
for (int hy = -nqy; hy <= nqy; hy++) {
for (int hz = 0; hz <= nqz; hz++) {
//values of q-vector
q[0] = hx * dqs[0];
q[1] = hy * dqs[1];
q[2] = hz * dqs[2];
real q_abs = q.abs();
//determining the bin number
int bin_i = (int) floor(q_abs / bin_size);
q_bin[bin_i] += q_abs;
count_bin[bin_i] += 1;
//resetting the variables that store the local sum on each proc
scos_local = 0;
ssin_local = 0;
//loop over particles
for (int k = myrank * ppp; k < (1 + myrank) * ppp && k < num_part;
k++) {
coordP = config->getCoordinates(k);
scos_local += cos(q * coordP);
ssin_local += sin(q * coordP);
}
if (myrank != 0) {
boost::mpi::reduce(*system.comm, scos_local, plus<real > (), 0);
boost::mpi::reduce(*system.comm, ssin_local, plus<real > (), 0);
}
if (myrank == 0) {
real scos = 0;
real ssin = 0;
boost::mpi::reduce(*system.comm, scos_local, scos, plus<real > (), 0);
boost::mpi::reduce(*system.comm, ssin_local, ssin, plus<real > (), 0);
sq_bin[bin_i] += scos * scos + ssin * ssin;
}
}
}
}
//creates the python list with the results
if (myrank == 0) {
//starting with bin_i = 1 will leave out the value for q=0, otherwise start with bin_i=0
for (int bin_i = 1; bin_i < num_bins; bin_i++) {
real c = (count_bin[bin_i]) ? 1 / (real) count_bin[bin_i] : 0;
sq_bin[bin_i] = n_reci * sq_bin[bin_i] * c;
q_bin[bin_i] = q_bin[bin_i] * c;
python::tuple q_Sq_pair;
q_Sq_pair = python::make_tuple(q_bin[bin_i], sq_bin[bin_i]);
pyli.append(q_Sq_pair);
}
}
return pyli;
}
int main(int argc, char *argv[]) {
debugthreads = 1;
Exposure exposure;
unsigned int nImages = 1;
std::string reponame;
std::string filtername;
int c;
int longindex;
double temperature = std::numeric_limits<double>::quiet_NaN();
while (EOF != (c = getopt_long(argc, argv, "b:c:de:f:hn:p:r:t:?",
longopts, &longindex)))
switch (c) {
case 'b':
exposure.mode(Binning(optarg));
break;
case 'c':
Configuration::set_default(optarg);
break;
case 'd':
debuglevel = LOG_DEBUG;
break;
case 'e':
exposure.exposuretime(atof(optarg));
break;
case 'f':
filtername = std::string(optarg);
break;
case 'h':
case '?':
usage(argv[0]);
return EXIT_SUCCESS;
case 'n':
nImages = atoi(optarg);
break;
case 'p':
exposure.purpose(Exposure::string2purpose(optarg));
break;
case 'r':
reponame = std::string(optarg);
break;
case 't':
temperature = atof(optarg);
break;
case 1:
exposure.frame(ImageRectangle(optarg));
break;
default:
throw std::runtime_error("unknown option");
}
// next argument must be instrument name or help
if (optind >= argc) {
std::cerr << "missing instrument name" << std::endl;
return EXIT_FAILURE;
}
std::string instrumentname(argv[optind++]);
// get the configuration
ConfigurationPtr config = Configuration::get();
// backend for instruments
InstrumentBackend instrumentbackend(config->database());
InstrumentPtr instrument = instrumentbackend.get(instrumentname);
// get the image repository
ImageRepoPtr repo(NULL);
if (reponame.size() > 0) {
ImageRepoConfigurationPtr imagerepos
= ImageRepoConfiguration::get(config);
repo = imagerepos->repo(reponame);
}
// prepare a repository from which we can extract the devices
Repository repository;
Devices devices(repository);
// get the devices
CameraPtr camera = devices.getCamera(instrument->getCamera(0).deviceurl());
CcdPtr ccd = devices.getCcd(instrument->getCcd(0).deviceurl());
// If temperature is set, and a cooler is present, initialize the
// cooler and wait until temperature is reached
CoolerPtr cooler(NULL);
if ((temperature == temperature)
&& (instrument->hasCooler())) {
double absolute = 273.15 + temperature;
if (absolute < 0) {
std::string msg
= stringprintf("illegal temperature: %f",
temperature);
debug(LOG_ERR, DEBUG_LOG, 0, "%s", msg.c_str());
throw std::runtime_error(msg);
}
cooler = devices.getCooler(instrument->getCooler(0).deviceurl());
cooler->setTemperature(absolute);
cooler->setOn(true);
double delta;
do {
double actual = cooler->getActualTemperature();
delta = fabs(absolute - actual);
debug(LOG_DEBUG, DEBUG_LOG, 0,
"set: %.1f, actual: %.1f, delta: %.1f",
absolute, actual, delta);
} while (delta > 1);
}
// if the instrument has a filter wheel, we get a pointer to it
// and try
FilterWheelPtr filterwheel(NULL);
if (instrument->hasFilterWheel()) {
filterwheel = devices.getFilterWheel(
instrument->getFilterWheel(0).deviceurl());
filterwheel->wait(20);
if (filtername.size() > 0) {
filterwheel->select(filtername);
filterwheel->wait(20);
}
}
// start the stream
unsigned int imagesRetrieved = 0;
ccd->startStream(exposure);
while (imagesRetrieved < nImages) {
ImagePtr image = ccd->getEntry(true).image;
debug(LOG_DEBUG, DEBUG_LOG, 0, "got image[%u] %s",
++imagesRetrieved,
image->size().toString().c_str());
if (!image->hasMetadata(std::string("INSTRUME"))) {
image->setMetadata(FITSKeywords::meta(
std::string("INSTRUME"), instrument->name()));
}
// do something about the image
if (repo) {
repo->save(image);
}
}
// stop the stream
ccd->stopStream();
// find out how many images were dropped
if (ccd->dropped() > 0) {
std::cerr << "images dropped: " << ccd->dropped() << std::endl;
}
// turn off the cooler
if (cooler) {
cooler->setOn(false);
}
return EXIT_SUCCESS;
}
/**
* \brief Get the device mapper
*/
DeviceMapperPtr DeviceMapperConfigurationBackend::devicemapper() {
return DeviceMapper::get(_config->database());
}