void Feature::data(const DataArray &data) {
util::checkEntityInput(data);
if (!data.isValidEntity()) {
throw UninitializedEntity();
}
backend()->data(data.id());
}
typename Wavefunction<Rank>::Ptr Wavefunction<Rank>::CopyDeep() const
{
/* Set up representations and stuff */
Ptr newPsi = Ptr(new Wavefunction());
newPsi->SetRepresentation(this->Repr->Copy());
/* Allocate data */
for (size_t i = 0; i < this->WavefunctionData.size(); i++)
{
//Allocate data buffer in new wavefunction
DataArray oldData ( GetData(i) );
int bufferName = newPsi->AllocateData(oldData.shape());
if (bufferName != (int)i)
{
throw std::runtime_error("What! something is wrong in Wavefunction::CopyDeep()");
}
//Copy data buffer to new wavefunction
DataArray newData ( newPsi->GetData(bufferName) );
newData = oldData;
}
//Set active buffer on the new wavefunction
newPsi->SetActiveBuffer(this->GetActiveBufferName());
return newPsi;
}
void PerconaFTEngine::Stats(Context& ctx, std::string& str)
{
str.append("perconaft_version:").append(stringfromll(DB_VERSION_MAJOR)).append(".").append(stringfromll(DB_VERSION_MINOR)).append(".").append(
stringfromll(DB_VERSION_PATCH)).append("\r\n");
DataArray nss;
ListNameSpaces(ctx, nss);
PerconaFTLocalContext& local_ctx = g_local_ctx.GetValue();
for (size_t i = 0; i < nss.size(); i++)
{
DB* db = GetFTDB(ctx, nss[i], false);
if (NULL == db)
continue;
str.append("\r\nDB[").append(nss[i].AsString()).append("] Stats:\r\n");
DB_BTREE_STAT64 st;
memset(&st, 0, sizeof(st));
db->stat64(db, local_ctx.transc.Peek(), &st);
str.append("bt_nkeys:").append(stringfromll(st.bt_nkeys)).append("\r\n");
str.append("bt_ndata:").append(stringfromll(st.bt_ndata)).append("\r\n");
str.append("bt_fsize:").append(stringfromll(st.bt_fsize)).append("\r\n");
str.append("bt_dsize:").append(stringfromll(st.bt_dsize)).append("\r\n");
str.append("bt_create_time_sec:").append(stringfromll(st.bt_create_time_sec)).append("\r\n");
str.append("bt_modify_time_sec:").append(stringfromll(st.bt_modify_time_sec)).append("\r\n");
str.append("bt_verify_time_sec:").append(stringfromll(st.bt_verify_time_sec)).append("\r\n");
}
}
bool Tag::hasReference(const DataArray &reference) const {
if (!util::checkEntityInput(reference, false)) {
return false;
}
DataArray da = backend()->getReference(reference.name());
return da && da.id() == reference.id();
}
DataView retrieveFeatureData(const Tag &tag, size_t feature_index) {
if (tag.featureCount() == 0) {
throw nix::OutOfBounds("There are no features associated with this tag!", 0);
}
if (feature_index > tag.featureCount()) {
throw nix::OutOfBounds("Feature index out of bounds.", 0);
}
Feature feat = tag.getFeature(feature_index);
DataArray data = feat.data();
if (data == nix::none) {
throw nix::UninitializedEntity();
//return NDArray(nix::DataType::Float,{0});
}
if (feat.linkType() == nix::LinkType::Tagged) {
NDSize offset, count;
getOffsetAndCount(tag, data, offset, count);
if (!positionAndExtentInData(data, offset, count)) {
throw nix::OutOfBounds("Requested data slice out of the extent of the Feature!", 0);
}
DataView io = DataView(data, count, offset);
return io;
}
// for untagged and indexed return the full data
NDSize offset(data.dataExtent().size(), 0);
DataView io = DataView(data, data.dataExtent(), offset);
return io;
}
void findHistogram(IDataArray::Pointer inputData, int32_t* ensembleArray, int32_t* eIds, int NumberOfBins, bool removeBiasedFeatures, bool* biasedFeatures)
{
DataArray<T>* featureArray = DataArray<T>::SafePointerDownCast(inputData.get());
if (NULL == featureArray)
{
return;
}
T* fPtr = featureArray->getPointer(0);
size_t numfeatures = featureArray->getNumberOfTuples();
int32_t bin;
int32_t ensemble;
float min = 1000000.0f;
float max = 0.0f;
float value;
for (size_t i = 1; i < numfeatures; i++)
{
value = fPtr[i];
if(value > max) { max = value; }
if(value < min) { min = value; }
}
float stepsize = (max - min) / NumberOfBins;
for (size_t i = 1; i < numfeatures; i++)
{
if(removeBiasedFeatures == false || biasedFeatures[i] == false)
{
ensemble = eIds[i];
bin = (fPtr[i] - min) / stepsize;
if(bin >= NumberOfBins) { bin = NumberOfBins - 1; }
ensembleArray[(NumberOfBins * ensemble) + bin]++;
}
}
}
Data& getElement(uint32_t idx)
{
if (elements.size() <= idx)
{
elements.resize(idx + 1);
}
return elements[idx];
}
int Engine::FlushAll(Context& ctx)
{
DataArray nss;
ListNameSpaces(ctx, nss);
for (size_t i = 0; i < nss.size(); i++)
{
Flush(ctx, nss[i]);
}
return 0;
}
void SortTimeFunction::f() {
const int n = m_copy.size();
const int elementSize = m_copy.getElementSize();
DataArray data = m_copy;
switch(elementSize) {
case 1 : m_sortMethod->getMethod()(data.getData(), n, elementSize, CountComparator<BYTE>( m_compareCount)); break;
case 2 : m_sortMethod->getMethod()(data.getData(), n, elementSize, CountComparator<unsigned short>(m_compareCount)); break;
default: m_sortMethod->getMethod()(data.getData(), n, elementSize, CountComparator<unsigned int >(m_compareCount)); break;
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void subtractVector3d(DataArray<double>::Pointer data, double* v)
{
size_t count = data->getNumberOfTuples();
for (size_t i = 0; i < count; ++i)
{
double* ptr = data->getPointer(i * 3);
ptr[0] = ptr[0] - v[0];
ptr[1] = ptr[1] - v[1];
ptr[2] = ptr[2] - v[2];
}
}
int Engine::CompactAll(Context& ctx)
{
DataArray nss;
ListNameSpaces(ctx, nss);
for (size_t i = 0; i < nss.size(); i++)
{
KeyObject start, end;
start.SetNameSpace(nss[i]);
Compact(ctx, start, end);
}
return 0;
}
/**
* @brief Static constructor
* @param numTuples The number of tuples in the array.
* @param numComponents The number of Components in each Tuple
* @param name The name of the array
* @return Boost::Shared_Ptr wrapping an instance of DataArrayTemplate<T>
*/
static Pointer CreateArray(size_t numTuples, int numComponents, const std::string &name)
{
DataArray<T>* d = new DataArray<T> (numTuples, numComponents, true);
if (d->Allocate() < 0)
{ // Could not allocate enough memory, reset the pointer to null and return
delete d;
return DataArray<T>::NullPointer();
}
d->SetName(name);
Pointer ptr(d);
return ptr;
}
DataArray createDataArray(const std::string &name,
const std::string &type,
const T &data) {
const Hydra<const T> hydra(data);
DataType dtype = hydra.element_data_type();
const NDSize shape = hydra.shape();
DataArray da = createDataArray(name, type, dtype, shape);
const NDSize offset(shape.size(), 0);
da.setData(data, offset);
return da;
}
/**
* packerに基づきイメージを結合する
*/
static void combineImages(){
// 出力フォーマットの選別
const int ch = getChannels(ofmt_type);
const int type = (ch == 4)? CV_8UC4 : CV_8UC3;
const cv::Scalar scalar = (ch == 4)? cv::Scalar(127, 127, 127, 255) : cv::Scalar(127, 127, 127); // 初期色
cv::Mat dst(cv::Size(packer.getW(), packer.getH()), type, scalar);
int count = 0; // for debug
DataArray::iterator it = inputs.begin();
for(; it != inputs.end(); it++){
if(!it->fit)
continue; // skip
cv::Mat src = cv::imread(it->path, -1);
if(src.channels() != ch){
adjustmentImage(src, ch);
}
cv::Mat roi = dst(cv::Rect(it->fit->rect.getX() + packer.getPadding(), it->fit->rect.getY() + packer.getPadding(), it->w, it->h));
src.copyTo(roi);
// for debug
#if 0
cv::rectangle(dst, cv::Rect(it->fit->rect.getX(), it->fit->rect.getY(), it->fit->rect.getW(), it->fit->rect.getH()), cv::Scalar(255, 255, 255), 1);
std::ostringstream oss;
oss << it->w << "x" << it->h << "(" << count << ")";
count++;
const std::string size = oss.str();
cv::putText(dst, size, cv::Point(it->fit->rect.getX() + 1, it->fit->rect.getY() + 21), cv::FONT_HERSHEY_SIMPLEX, 0.5, cv::Scalar(0, 0, 0), 1);
cv::putText(dst, size, cv::Point(it->fit->rect.getX(), it->fit->rect.getY() + 20), cv::FONT_HERSHEY_SIMPLEX, 0.5, cv::Scalar(255, 255, 255), 1);
#endif
}
// 出力
if((om_type == OutputMode_WriteOnly) || (om_type == OutputMode_Both)){
bool ret = cv::imwrite(output_path, dst, params);
}
if((om_type == OutputMode_DisplayOnly) || (om_type == OutputMode_Both)){
std::ostringstream oss;
oss << "packed image(" << packer.getW() << " x " << packer.getH() << ")";
const std::string name = oss.str();
cv::namedWindow(name, CV_WINDOW_AUTOSIZE | CV_WINDOW_KEEPRATIO);
cv::imshow(name, dst);
if(ch == 4){
std::vector<cv::Mat> mv;
cv::split(dst, mv);
cv::Mat dsta = mv[3].clone();
cv::imshow("packed image(alpha)", dsta);
}
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
std::vector<int32_t> TriangleOps::findAdjacentTriangles(SurfaceMeshDataContainer* sm,
int32_t triangleIndex,
int32_t label)
{
std::vector<int32_t> adjacentTris;
// Get the master list of triangles for the mesh
DREAM3D::SurfaceMesh::FaceList_t::Pointer facesPtr = sm->getFaces();
// DREAM3D::SurfaceMesh::Face_t* faces = facesPtr->GetPointer(0);
IDataArray::Pointer flPtr = sm->getFaceData(DREAM3D::FaceData::SurfaceMeshFaceLabels);
DataArray<int32_t>* faceLabelsPtr = DataArray<int32_t>::SafePointerDownCast(flPtr.get());
int32_t* faceLabels = faceLabelsPtr->GetPointer(0);
// Get the Triangle Neighbor Structure
MeshFaceNeighbors::Pointer triNeighbors = sm->getMeshFaceNeighborLists();
// For the specific triangle that was passed, get its neighbor list
uint16_t count = triNeighbors->getNumberOfFaces(triangleIndex);
int32_t* nList = triNeighbors->getNeighborListPointer(triangleIndex);
if (count < 3)
{
std::cout << "Triangle Neighbor List had only " << count << " neighbors. Must be at least 3." << std::endl;
BOOST_ASSERT(false);
}
else if (count == 3) // This triangle only has 3 neighbors so we are assuming all three have the same label set.
{
for (uint16_t n = 0; n < count; ++n)
{
adjacentTris.push_back(nList[n]);
}
}
else
{
// Iterate over the indices to find triangles that match the label and are NOT the current triangle index
for (uint16_t n = 0; n < count; ++n)
{
int32_t fl_0 = faceLabels[nList[n]*2];
int32_t fl_1 = faceLabels[nList[n]*2 + 1];
if ( (fl_0 == label || fl_1 == label) && (nList[n] != triangleIndex) )
{
// std::cout << " Found Adjacent Triangle: " << t->tIndex << std::endl;
adjacentTris.push_back(nList[n]);
// ++index;
}
}
}
return adjacentTris;
}
int MMKVImpl::SAdd(DBID db, const Data& key, const DataArray& elements)
{
if (m_readonly)
{
return ERR_PERMISSION_DENIED;
}
int err = 0;
RWLockGuard<MemorySegmentManager, WRITE_LOCK> keylock_guard(m_segment);
EnsureWritableValueSpace();
ObjectAllocator allocator = m_segment.MSpaceAllocator<Object>();
StringSet* set = GetObject<StringSet>(db, key, V_TYPE_SET, true, err)(std::less<Object>(), allocator);
if (0 != err)
{
return err;
}
int inserted = 0;
for (size_t i = 0; i < elements.size(); i++)
{
std::pair<StringSet::iterator, bool> ret = set->insert(Object(elements[i], true));
if (ret.second)
{
m_segment.AssignObjectValue(*(ret.first), elements[i], true);
inserted++;
}
}
return inserted;
}
RangeDimension::RangeDimension(const DataArray &array)
: ImplContainer()
{
if (array.dataExtent().size() > 1) {
throw InvalidRank("Error creating RangeDimension with DataArray: array must be 1-D!");
}
}
void Clear()
{
type = 0;
ns.Clear();
key.Clear();
elements.clear();
}
void TestBlock::testMultiTagAccess() {
vector<string> names = { "tag_a", "tag_b", "tag_c", "tag_d", "tag_e" };
// create a valid positions data array below
typedef boost::multi_array<double, 3>::index index;
DataArray positions = block.createDataArray("array_one",
"testdata",
DataType::Double,
nix::NDSize({ 3, 4, 2 }));
boost::multi_array<double, 3> A(boost::extents[3][4][2]);
int values = 0;
for(index i = 0; i != 3; ++i)
for(index j = 0; j != 4; ++j)
for(index k = 0; k != 2; ++k)
A[i][j][k] = values++;
positions.setData(A);
CPPUNIT_ASSERT(block.multiTagCount() == 0);
CPPUNIT_ASSERT(block.multiTags().size() == 0);
CPPUNIT_ASSERT(block.getMultiTag("invalid_id") == false);
vector<string> ids;
for (auto it = names.begin(); it != names.end(); it++) {
MultiTag tag = block.createMultiTag(*it, "segment", positions);
CPPUNIT_ASSERT(tag.name() == *it);
ids.push_back(tag.id());
}
CPPUNIT_ASSERT_THROW(block.createMultiTag(names[0], "segment", positions),
DuplicateName);
CPPUNIT_ASSERT(block.multiTagCount() == names.size());
CPPUNIT_ASSERT(block.multiTags().size() == names.size());
for (auto it = ids.begin(); it != ids.end(); it++) {
MultiTag tag = block.getMultiTag(*it);
CPPUNIT_ASSERT(block.hasMultiTag(*it) == true);
CPPUNIT_ASSERT(tag.id() == *it);
block.deleteMultiTag(*it);
}
CPPUNIT_ASSERT(block.multiTagCount() == 0);
CPPUNIT_ASSERT(block.multiTags().size() == 0);
CPPUNIT_ASSERT(block.getMultiTag("invalid_id") == false);
}
void MultiTag::extents(const DataArray &extents) {
if (extents == none) {
backend()->extents(none);
}
else {
backend()->extents(extents.id());
}
}
static void UpdateInstancingParams (bool allDataDirty,
const DataArray& array,
csRef<iRenderBuffer>& buffer,
csShaderVariable* sv)
{
bool updateData = allDataDirty;
if (!buffer
|| (buffer->GetElementCount() != array.Capacity()))
{
buffer = csRenderBuffer::CreateRenderBuffer (array.Capacity(),
CS_BUF_STREAM, CS_BUFCOMP_FLOAT,
sizeof (typename DataArray::ValueType) / sizeof(float));
sv->SetValue (buffer);
updateData = true;
}
if (updateData) buffer->SetData (array.GetArray());
}
void Feature::data(const DataArray &data) {
if (data == none) {
throw std::runtime_error("Empty data entity (DataArray) given");
}
else {
backend()->data(data.id());
}
}
FeatureHDF5::FeatureHDF5(const shared_ptr<IFile> &file, const shared_ptr<IBlock> &block, const Group &group,
const string &id, DataArray data, LinkType link_type, time_t time)
: EntityHDF5(file, group, id, time), block(block)
{
linkType(link_type);
// TODO: the line below currently throws an exception if the DataArray
// is not in block - to consider if we prefer copying it to the block
this->data(data.id());
}
FeatureFS::FeatureFS(const std::shared_ptr<base::IFile> &file, const std::shared_ptr<base::IBlock> &block, const std::string &loc,
const std::string &id, DataArray data, LinkType link_type, time_t time)
: EntityFS(file, (bfs::path(loc) / bfs::path(id)).string(), id, time), block(block)
{
linkType(link_type);
// TODO: the line below currently throws an exception if the DataArray
// is not in block - to consider if we prefer copying it to the block
this->data(data.id());
}
int MMKVImpl::SDiff(DBID db, const DataArray& keys, const StringArrayResult& diffs)
{
if (keys.size() < 2)
{
return ERR_INVALID_TYPE;
}
RWLockGuard<MemorySegmentManager, READ_LOCK> keylock_guard(m_segment);
return GenericSInterDiffUnion(db, OP_DIFF, keys, NULL, &diffs);
}
/**
* @brief Static constructor
* @param numTuples The number of tuples in the array.
* @param dims The actual dimensions of the attribute on each Tuple
* @param name The name of the array
* @return Boost::Shared_Ptr wrapping an instance of DataArrayTemplate<T>
*/
static Pointer CreateArray(size_t numTuples, QVector<size_t> cDims, const QString& name, bool allocate = true)
{
if (name.isEmpty() == true)
{
return NullPointer();
}
DataArray<T>* d = new DataArray<T>(numTuples, cDims, name, allocate);
if(allocate)
{
if (d->allocate() < 0)
{
// Could not allocate enough memory, reset the pointer to null and return
delete d;
return DataArray<T>::NullPointer();
}
}
Pointer ptr(d);
return ptr;
}
int PerconaFTEngine::ListNameSpaces(Context& ctx, DataArray& nss)
{
RWLockGuard<SpinRWLock> guard(m_lock, true);
FTDBTable::iterator it = m_dbs.begin();
while (it != m_dbs.end())
{
nss.push_back(it->first);
it++;
}
return 0;
}
EllMatrix(index_t rows, index_t cols, index_t nnz_per_row)
: _rows(rows), _cols(cols), nnz_per_row(nnz_per_row) {
static constexpr auto step = align_bytes / sizeof(scalar_t);
auto aligned_rows = rows;
while (aligned_rows % step != 0) {
++aligned_rows;
}
data.resize(aligned_rows, nnz_per_row);
indices.resize(aligned_rows, nnz_per_row);
}
void getOffsetAndCount(const Tag &tag, const DataArray &array, NDSize &offset, NDSize &count) {
vector<double> position = tag.position();
vector<double> extent = tag.extent();
vector<string> units = tag.units();
NDSize temp_offset(position.size());
NDSize temp_count(position.size(), 1);
if (array.dimensionCount() != position.size() || (extent.size() > 0 && extent.size() != array.dimensionCount())) {
throw std::runtime_error("Dimensionality of position or extent vector does not match dimensionality of data!");
}
for (size_t i = 0; i < position.size(); ++i) {
Dimension dim = array.getDimension(i+1);
temp_offset[i] = positionToIndex(position[i], i >= units.size() ? "none" : units[i], dim);
if (i < extent.size()) {
ndsize_t c = positionToIndex(position[i] + extent[i], i >= units.size() ? "none" : units[i], dim) - temp_offset[i];
temp_count[i] = (c > 1) ? c : 1;
}
}
offset = temp_offset;
count = temp_count;
}
bool positionInData(const DataArray &data, const NDSize &position) {
NDSize data_size = data.dataExtent();
bool valid = true;
if (!(data_size.size() == position.size())) {
return false;
}
for (size_t i = 0; i < data_size.size(); i++) {
valid &= position[i] < data_size[i];
}
return valid;
}