/******************************************************************************
* Timer callback used during animation playback.
******************************************************************************/
void AnimationSettings::onPlaybackTimer()
{
// Check if the animation playback has been deactivated in the meantime.
if(!_isPlaybackActive)
return;
// Add one frame to current time
int newFrame = timeToFrame(time()) + 1;
TimePoint newTime = frameToTime(newFrame);
// Loop back to first frame if end has been reached.
if(newTime > animationInterval().end())
newTime = animationInterval().start();
// Set new time.
setTime(newTime);
// Wait until the scene is ready. Then jump to the next frame.
dataset()->runWhenSceneIsReady([this]() {
if(_isPlaybackActive) {
_isPlaybackActive = false;
startAnimationPlayback();
}
});
}
TEST(HDF5IO, ReadWrite1D)
{
const unsigned int nelements = 5;
std::vector<float> a(nelements);
for (unsigned int i=0; i < a.size(); i++)
a[i] = 2 * i;
// 1D array
std::vector<unsigned int> rank(1);
rank[0] = a.size();
std::string filename("/tmp/sxmc_test_1d.hdf5");
std::string dataset("/a");
ASSERT_TRUE(write_float_vector_hdf5(filename, dataset, a, rank) >= 0);
///////
std::vector<float> test_a;
std::vector<unsigned int> test_rank;
ASSERT_TRUE(read_float_vector_hdf5(filename, dataset, test_a, test_rank) >= 0);
ASSERT_EQ((unsigned) 1, test_rank.size());
EXPECT_EQ(nelements, test_rank[0]);
ASSERT_EQ(nelements, test_a.size());
for (unsigned int i=0; i < test_a.size(); i++)
EXPECT_EQ(2*i, test_a[i]);
}
double terrama2::core::RiscoDeFogo::XYLinhaCol(double x, double y, const std::string& path, const std::string& filename) const
{
//const auto& prec = *(precipitacao.rbegin()+i);
std::shared_ptr<te::da::DataSource> datasource(te::da::DataSourceFactory::make("GDAL", "file://"+path+filename));
//RAII for open/closing the datasource
terrama2::core::OpenClose<std::shared_ptr<te::da::DataSource> > openClose(datasource);
std::shared_ptr<te::da::DataSourceTransactor> transactor(datasource->getTransactor());
std::shared_ptr<te::da::DataSet> dataset(transactor->getDataSet(filename));
std::shared_ptr<te::rst::Raster> raster(dataset->getRaster(0));
te::rst::Grid* grid = raster->getGrid();
te::rst::Band* band = raster->getBand(0);
double colD, rowD;
grid->geoToGrid(x, y, colD, rowD);
int col = std::round(colD);
int row = std::round(rowD);
double value;
band->getValue(col, row, value);
return value;
}
static unsigned hdf5_read(ndio_t file, nd_t dst)
{ ndio_hdf5_t self=(ndio_hdf5_t)ndioContext(file);
HTRY(H5Dread(dataset(self),dtype(self),H5S_ALL,H5S_ALL,H5P_DEFAULT,nddata(dst)));
return 1;
Error:
return 0;
}
void ANNWrapper::SetPoints(const std::vector <openMVG::Vec3f> &P)
{
dataset = openMVG::Matf(P.size(), dim);
m_nnidx = Eigen::VectorXi(m_k); // allocate near neigh indices
m_dists = new KFLANN::DistanceType[m_k]; // allocate near neighbor m_dists
for (unsigned int i = 0; i < P.size(); i++)
{
dataset(i, 0) = P.at(i).x();
dataset(i, 1) = P.at(i).y();
dataset(i, 2) = P.at(i).z();
}
matcher.Build(dataset.data(), P.size(), dim);
}
/******************************************************************************
* Is called when the user presses the "Open Inspector" button.
******************************************************************************/
void DislocationNetworkEditor::onOpenInspector()
{
DislocationNetwork* dislocationsObj = static_object_cast<DislocationNetwork>(editObject());
if(!dislocationsObj) return;
QMainWindow* inspectorWindow = new QMainWindow(container()->window(), (Qt::WindowFlags)(Qt::Tool | Qt::CustomizeWindowHint | Qt::WindowMaximizeButtonHint | Qt::WindowCloseButtonHint));
inspectorWindow->setWindowTitle(tr("Dislocation Inspector"));
PropertiesPanel* propertiesPanel = new PropertiesPanel(inspectorWindow);
propertiesPanel->hide();
QWidget* mainPanel = new QWidget(inspectorWindow);
QVBoxLayout* mainPanelLayout = new QVBoxLayout(mainPanel);
mainPanelLayout->setStretch(0,1);
mainPanelLayout->setContentsMargins(0,0,0,0);
inspectorWindow->setCentralWidget(mainPanel);
ObjectNode* node = dynamic_object_cast<ObjectNode>(dataset()->selection()->front());
DislocationInspector* inspector = new DislocationInspector(node);
connect(inspector, &QObject::destroyed, inspectorWindow, &QMainWindow::close);
inspector->setParent(propertiesPanel);
inspector->initialize(propertiesPanel, mainWindow(), RolloutInsertionParameters().insertInto(mainPanel));
inspector->setEditObject(dislocationsObj);
inspectorWindow->setAttribute(Qt::WA_DeleteOnClose);
inspectorWindow->resize(1000, 350);
inspectorWindow->show();
}
template<typename Distance, typename IndexType> void
buildIndex_(void*& index, const Mat& data, const IndexParams& params, const Distance& dist = Distance())
{
typedef typename Distance::ElementType ElementType;
if(DataType<ElementType>::type != data.type())
CV_Error_(Error::StsUnsupportedFormat, ("type=%d\n", data.type()));
if(!data.isContinuous())
CV_Error(Error::StsBadArg, "Only continuous arrays are supported");
::cvflann::Matrix<ElementType> dataset((ElementType*)data.data, data.rows, data.cols);
IndexType* _index = new IndexType(dataset, get_params(params), dist);
try
{
_index->buildIndex();
}
catch (...)
{
delete _index;
_index = NULL;
throw;
}
index = _index;
}
/******************************************************************************
* Is called when the user has selected a certain frame in the frame list box.
******************************************************************************/
void FileSourceEditor::onFrameSelected(int index)
{
FileSource* obj = static_object_cast<FileSource>(editObject());
if(!obj) return;
dataset()->animationSettings()->setTime(obj->inputFrameToAnimationTime(index));
}
/**
* @brief TestAlgorithm::run start the search
* @return a list of data packets containing results
*/
QList<DataPacket*> TestAlgorithm::run() {
QList<DataPacket*> list;
SearchResult* result = new SearchResult();
list.append(dynamic_cast<DataPacket*>(result));
for (QString& datasetPath : mQuery->getDatasets()) {
Dataset dataset(datasetPath);
for (Medium* medium : dataset.getMediaList()) {
if (mCancel == true) {
return list;
}
SearchObject* object = new SearchObject();
object->setMedium(medium->getPath());
object->setSourceDataset(dataset.getPath());
//new result element
SearchResultElement* resultElement = new SearchResultElement();
resultElement->setSearchObject(*object);
resultElement->setScore(std::rand() % 20);
//add to result list
result->addResultElement(*resultElement);
}
}
QThread::msleep(1500);
return list;
}
// Calculates log-loss of a dataset using ffm-native-ops C++ library (without GPU).
//
// Arguments:
// --datasetPath <path> (--binModelPath | --textModelPath) <path> [--samplingFactor <float>]
int main(int argc, const char ** argv)
{
Options const & options = parseOptions(argvToArgs(argc, argv));
Dataset dataset(options.datasetPath);
Model model(dataset.numFields);
if (!options.binModelPath.empty()) {
model.binaryDeserialize(options.binModelPath);
} else {
model.importModel(options.textModelPath);
}
LogLossCalculator logLossCalc(options.samplingFactor);
for (int64_t sampleIdx = 0; dataset.hasNext(); ++sampleIdx) {
Dataset::Sample const & sample = dataset.next();
float t = ffmPredict(model.weights.data(), dataset.numFields, sample.data());
int y = sample.back() > 0 ? 1 : -1;
logLossCalc.update(t, y);
std::cout << sampleIdx << " " << y << " " << t << std::endl;
}
std::cout << "Log-loss: " << logLossCalc.get() << std::endl;
return 0;
}
hdf5_iprimitive::read_hdf5_dataset
(
std::wstring* t,
std::size_t data_count,
std::size_t object_number
)
{
BOOST_ASSERT(data_count == 1);
std::string path = create_object_data_path(object_number);
hdf5_dataset dataset(*file_, path);
hdf5_datatype datatype(dataset);
// If you can think of a better way to store wchar_t/wstring objects in HDF5, be my guest...
size_t size = datatype.get_size();
BOOST_ASSERT(size >= sizeof(wchar_t));
std::size_t string_size = size / sizeof(wchar_t) - 1;
t->resize(string_size);
if(string_size) {
std::vector<wchar_t> buffer(string_size + 1);
dataset.read(datatype, &buffer[0]);
t->replace(0, string_size, &buffer[0], string_size);
}
datatype.close();
dataset.close();
}
hdf5_iprimitive::read_hdf5_dataset
(
std::string* t,
std::size_t data_count,
std::size_t object_number
)
{
BOOST_ASSERT(data_count == 1);
std::string path = create_object_data_path(object_number);
hdf5_dataset dataset(*file_, path);
hdf5_datatype datatype(dataset);
if(datatype.is_variable_length_string()) {
char* buffer;
hdf5_dataspace dataspace(dataset);
dataset.read(datatype, &buffer);
*t = buffer;
datatype.reclaim_buffer(dataspace, &buffer);
dataspace.close();
}
else {
size_t size = datatype.get_size();
std::vector<char> buffer(size);
dataset.read(datatype, &buffer[0]);
t->resize(size);
t->replace(0, size, &buffer[0], size);
}
datatype.close();
dataset.close();
}
int main(int argc, char* argv[]) {
if( argc != 4 && argc != 5 ) {
std::cout << "USAGE: ./do2ndLevel_PhotonJet_batch [dataset] [inputFileList] [flags] [useGenJets=false]" << std::endl;
exit(23);
}
std::string dataset(argv[1]);
std::string inputFileList(argv[2]);
std::string flags(argv[3]);
bool useGenJets = false;
if( argc == 5 ) {
std::string useGenJets_str(argv[4]);
if( useGenJets_str=="true" ) useGenJets = true;
}
TRegexp run2010("Run2010");
TRegexp run2011("Run2011");
TRegexp run2012("Run2012");
TString dataset_str(dataset);
if( dataset_str.Contains(run2010) || dataset_str.Contains(run2011) || dataset_str.Contains(run2012) ) { // then it's data
doSingleLoop(inputFileList, dataset, flags, (bool)true, (bool)false);
} else {
doSingleLoop(inputFileList, dataset, flags, (bool)false, useGenJets);
}
}
bool Print::print(const QStringList &commands, State &state)
{
if (commands.isEmpty()) {
std::cout << QObject::tr("print requires a dataset to be named").toStdString() << std::endl;
return true;
}
const QString datasetName = commands.first();
QDir project(state.projectPath());
Dataset dataset(datasetName, state);
if (!dataset.isValid()) {
std::cout << QObject::tr("The dataset %1 could not be loaded; try checking it with the check command").arg(datasetName).toStdString() << std::endl;
return true;
}
QStringList cols;
if (commands.size() > 1) {
cols = commands;
cols.removeFirst();
}
std::cout << dataset.tableHeaders(cols).toStdString() << std::endl;
dataset.eachRow(
[cols](const Dataset::Row &row) {
std::cout << row.toString(cols).toStdString() << std::endl;
});
return true;
}
/******************************************************************************
* Replaces the particle selection.
******************************************************************************/
void ParticleSelectionSet::setParticleSelection(const PipelineFlowState& state, const QBitArray& selection, SelectionMode mode)
{
// Make a backup of the old snapshot so it may be restored.
if(dataset()->undoStack().isRecording())
dataset()->undoStack().push(new ReplaceSelectionOperation(this));
ParticlePropertyObject* identifierProperty = ParticlePropertyObject::findInState(state, ParticleProperty::IdentifierProperty);
if(identifierProperty && useIdentifiers()) {
OVITO_ASSERT(selection.size() == identifierProperty->size());
_selection.clear();
int index = 0;
if(mode == SelectionReplace) {
_selectedIdentifiers.clear();
for(int id : identifierProperty->constIntRange()) {
if(selection.testBit(index++))
_selectedIdentifiers.insert(id);
}
}
else if(mode == SelectionAdd) {
for(int id : identifierProperty->constIntRange()) {
if(selection.testBit(index++))
_selectedIdentifiers.insert(id);
}
}
else if(mode == SelectionSubtract) {
for(int id : identifierProperty->constIntRange()) {
if(selection.testBit(index++))
_selectedIdentifiers.remove(id);
}
}
}
else {
_selectedIdentifiers.clear();
if(mode == SelectionReplace)
_selection = selection;
else if(mode == SelectionAdd) {
_selection.resize(selection.size());
_selection |= selection;
}
else if(mode == SelectionSubtract) {
_selection.resize(selection.size());
_selection &= ~selection;
}
}
notifyDependents(ReferenceEvent::TargetChanged);
}
static void annotate_paint(SkPaint& paint, const char* key, SkData* value) {
SkAutoTUnref<SkDataSet> dataset(SkNEW_ARGS(SkDataSet, (key, value)));
SkAnnotation* ann = SkNEW_ARGS(SkAnnotation, (dataset,
SkAnnotation::kNoDraw_Flag));
paint.setAnnotation(ann)->unref();
SkASSERT(paint.isNoDrawAnnotation());
}
virtual void start_document (
)
{
meta = dataset();
ts.clear();
temp_image = image();
temp_box = box();
}
/*
* Class: org_moa_gpu_bridge_NativeDenseInstanceBatch
* Method: init
* Signature: (Lweka/core/Instances;I)V
*/
JNIEXPORT void JNICALL Java_org_moa_gpu_bridge_NativeDenseInstanceBatch_init (JNIEnv * env, jobject instance_batch, jobject instances, jint num_rows)
{
static jclass _class = env->FindClass(theClazz);
static jfieldID _context_field = env->GetFieldID(_class, "m_native_context", "J");
dataset_interface dataset(env,instances);
dense_instance_batch* batch = new dense_instance_batch(num_rows, dataset.get_num_attributes()-1,get_global_context());
env->SetLongField(instance_batch, _context_field, (jlong)batch);
}
dataobject::dataobject(administrator_basic * adb, administrator_pointer * adp,
const ST::string & n,ofstream * lo,istream * in)
: statobject(adb,n,"dataset",lo,in)
{
adminp_p = adp;
d = dataset(n,adb);
create();
}
TEST(utest_interface_optics, optics_algorithm) {
std::shared_ptr<pyclustering_package> sample = pack(dataset({ { 1.0, 1.0 }, { 1.1, 1.0 }, { 1.2, 1.4 }, { 10.0, 10.3 }, { 10.1, 10.2 }, { 10.2, 10.4 } }));
pyclustering_package * result = optics_algorithm(sample.get(), 4, 2, 2, 0);
ASSERT_EQ((std::size_t) OPTICS_PACKAGE_SIZE, result->size);
delete result;
}
TEST(utest_interface_dbscan, dbscan_algorithm) {
std::shared_ptr<pyclustering_package> sample = pack(dataset({ { 1.0, 1.0 }, { 1.1, 1.0 }, { 1.2, 1.4 }, { 10.0, 10.3 }, { 10.1, 10.2 }, { 10.2, 10.4 } }));
pyclustering_package * result = dbscan_algorithm(sample.get(), 4, 2, 0);
ASSERT_EQ(3U, result->size); /* allocated clustes + noise */
delete result;
}
/******************************************************************************
* Is called when the current animation time has changed.
******************************************************************************/
void AnimationSettings::onTimeChanged(TimePoint newTime)
{
_timeIsChanging++;
dataset()->runWhenSceneIsReady([this] () {
_timeIsChanging--;
Q_EMIT timeChangeComplete();
});
}
af::shared<dataset>
crystal::datasets() const
{
af::shared<dataset> result((af::reserve(n_datasets())));
for(int i_dataset=0; i_dataset<n_datasets(); i_dataset++) {
result.push_back(dataset(*this, i_dataset));
}
return result;
}
///
/// \brief Vespucci::SaveVespucciBinary
/// \param spectra
/// \param x
/// \param y
/// \param abscissa
/// \return
///
bool Vespucci::SaveVespucciBinary(std::string filename, const arma::mat &spectra, const arma::vec &x, const arma::vec &y, const arma::vec &abscissa)
{
bool success;
try{
arma::field<arma::mat> dataset(4);
dataset(0) = spectra;
dataset(1) = abscissa;
dataset(2) = x;
dataset(3) = y;
success = dataset.save(filename, arma::arma_binary);
}
catch(std::exception e){
std::cerr << "See armadillo exception" << std::endl;
std::string str = "Vespucci::SaveVespucciBinary: " + std::string(e.what());
throw std::runtime_error(str);
}
return success;
}
int main( int argc, char* argv[] ) {
if( argc!=3 && argc!=4 && argc!=5 && argc!=6 ) {
std::cout << "USAGE: ./finalize_TTZDilepton [dataset] [selectionType] [bTaggerType=\"SSVHE\"] [PUType=\"HR11_73pb\"] [leptType=\"ALL\"]" <<std::endl;
return 13;
}
std::string dataset(argv[1]);
std::string selectionType(argv[2]);
std::string bTaggerType="SSVHE";
if( argc==4 ) {
std::string bTaggerType_str(argv[3]);
bTaggerType = bTaggerType_str;
}
std::string PUType="HR11_73pb";
if( argc==5 ) {
std::string PUType_str(argv[4]);
PUType = PUType_str;
}
std::string leptType="ALL";
if( argc==6 ) {
std::string leptType_str(argv[5]);
leptType = leptType_str;
}
Ntp1Finalizer_TTZDilepton* nf = new Ntp1Finalizer_TTZDilepton( dataset, selectionType, bTaggerType, PUType, leptType );
nf->set_inputAnalyzerType("TTZ");
if( dataset=="DATA_HR11_v2" ) {
nf->addFile("DoubleMu_Run2011A_FULL"); //first muons! important!
nf->addFile("DoubleMu_Run2011B_v2"); //first muons! important!
nf->addFile("SingleMu_Run2011A_FULL"); //first muons! important!
nf->addFile("SingleMu_Run2011B_v2"); //first muons! important!
nf->addFile("DoubleElectron_Run2011A_FULL");
nf->addFile("DoubleElectron_Run2011B_v2");
} else {
nf->addFile( dataset );
}
nf->finalize();
return 0;
}
/******************************************************************************
* Selects all particles in the given particle data set.
******************************************************************************/
void ParticleSelectionSet::selectAll(const PipelineFlowState& state)
{
// Make a backup of the old selection state so it may be restored.
if(dataset()->undoStack().isRecording())
dataset()->undoStack().push(new ReplaceSelectionOperation(this));
ParticlePropertyObject* identifiers = ParticlePropertyObject::findInState(state, ParticleProperty::IdentifierProperty);
if(useIdentifiers() && identifiers != nullptr) {
_selection.clear();
_selectedIdentifiers.clear();
for(int id : identifiers->constIntRange())
_selectedIdentifiers.insert(id);
}
else {
_selection.fill(true, particleCount(state));
_selectedIdentifiers.clear();
}
notifyDependents(ReferenceEvent::TargetChanged);
}
/******************************************************************************
* Returns the world space point around which the viewport camera orbits.
******************************************************************************/
Point3 ViewportConfiguration::orbitCenter()
{
// Update orbiting center.
if(orbitCenterMode() == ORBIT_SELECTION_CENTER) {
Box3 selectionBoundingBox;
for(SceneNode* node : dataset()->selection()->nodes()) {
selectionBoundingBox.addBox(node->worldBoundingBox(dataset()->animationSettings()->time()));
}
if(!selectionBoundingBox.isEmpty())
return selectionBoundingBox.center();
else {
Box3 sceneBoundingBox = dataset()->sceneRoot()->worldBoundingBox(dataset()->animationSettings()->time());
if(!sceneBoundingBox.isEmpty())
return sceneBoundingBox.center();
}
}
else if(orbitCenterMode() == ORBIT_USER_DEFINED) {
return _userOrbitCenter;
}
return Point3::Origin();
}
inline typename boost::enable_if<is_multi_array<T>, dataset>::type
create_dataset(h5xxObject const& object, std::string const& name, T const& value,
StoragePolicy const& storage_policy = StoragePolicy())
{
typedef typename T::element value_type;
hid_t type_id = ctype<value_type>::hid(); // this ID must not be closed
enum { rank = T::dimensionality };
// --- create a temporary dataspace based on the input array dimensions
boost::array<hsize_t, rank> dims;
std::copy(value.shape(), value.shape() + rank, dims.begin());
return dataset(object, name, type_id, dataspace(dims), storage_policy);
}
/******************************************************************************
* Aligns the current viewing direction to the slicing plane.
******************************************************************************/
void SliceModifierEditor::onAlignViewToPlane()
{
TimeInterval interval;
Viewport* vp = dataset()->viewportConfig()->activeViewport();
if(!vp) return;
// Get the object to world transformation for the currently selected object.
ObjectNode* node = dynamic_object_cast<ObjectNode>(dataset()->selection()->front());
if(!node) return;
const AffineTransformation& nodeTM = node->getWorldTransform(dataset()->animationSettings()->time(), interval);
// Transform the current slicing plane to the world coordinate system.
SliceModifier* mod = static_object_cast<SliceModifier>(editObject());
if(!mod) return;
Plane3 planeLocal = mod->slicingPlane(dataset()->animationSettings()->time(), interval);
Plane3 planeWorld = nodeTM * planeLocal;
// Calculate the intersection point of the current viewing direction with the current slicing plane.
Ray3 viewportRay(vp->cameraPosition(), vp->cameraDirection());
FloatType t = planeWorld.intersectionT(viewportRay);
Point3 intersectionPoint;
if(t != FLOATTYPE_MAX)
intersectionPoint = viewportRay.point(t);
else
intersectionPoint = Point3::Origin() + nodeTM.translation();
if(vp->isPerspectiveProjection()) {
FloatType distance = (vp->cameraPosition() - intersectionPoint).length();
vp->setViewType(Viewport::VIEW_PERSPECTIVE);
vp->setCameraDirection(-planeWorld.normal);
vp->setCameraPosition(intersectionPoint + planeWorld.normal * distance);
}
else {
vp->setViewType(Viewport::VIEW_ORTHO);
vp->setCameraDirection(-planeWorld.normal);
}
vp->zoomToSelectionExtents();
}
/******************************************************************************
* Adopts the selection state from the modifier's input.
******************************************************************************/
void ParticleSelectionSet::resetSelection(const PipelineFlowState& state)
{
// Take a snapshot of the current selection.
ParticlePropertyObject* selProperty = ParticlePropertyObject::findInState(state, ParticleProperty::SelectionProperty);
if(selProperty) {
// Make a backup of the old snapshot so it may be restored.
if(dataset()->undoStack().isRecording())
dataset()->undoStack().push(new ReplaceSelectionOperation(this));
ParticlePropertyObject* identifierProperty = ParticlePropertyObject::findInState(state, ParticleProperty::IdentifierProperty);
if(identifierProperty && useIdentifiers()) {
OVITO_ASSERT(selProperty->size() == identifierProperty->size());
_selectedIdentifiers.clear();
_selection.clear();
const int* s = selProperty->constDataInt();
for(int id : identifierProperty->constIntRange()) {
if(*s++)
_selectedIdentifiers.insert(id);
}
}
else {
// Take a snapshot of the selection state.
_selectedIdentifiers.clear();
_selection.fill(false, selProperty->size());
const int* s = selProperty->constDataInt();
const int* s_end = s + selProperty->size();
for(int index = 0; s != s_end; ++s, index++) {
if(*s) _selection.setBit(index);
}
}
notifyDependents(ReferenceEvent::TargetChanged);
}
else {
// Reset selection snapshot if input doesn't contain a selection state.
clearSelection(state);
}
}