bool readTBlock(const StormParams::Shape& blockOffset,
const StormParams::Shape& blockShape,
MultiArrayView<STORMPARAMS_N, T> & array, FileType type,
const StormParams::Shape &shape, void *ptr) {
switch(type) {
case TIFF:
{
ImageImportInfo* info = reinterpret_cast<ImageImportInfo*>(ptr);
vigra_precondition(blockOffset[0]==0 && blockOffset[1]==0 &&
blockShape[0]==shape[0] && blockShape[1]==shape[1],
"for Tiff images only complete Frames are currently supported as ROIs");
vigra_precondition(array.size(2)==blockShape[2],"array shape and number of images in ROI for tiff file differ.");
vigra_precondition(blockShape[2] <= info->numImages(), "block shape larger than number of frames in the image");
for(int i = 0; i < blockShape[2]; ++i) {
MultiArrayView <2, T> img = array.bindOuter(i);
BasicImageView <T> v = makeBasicImageView(img);
info->setImageIndex(i+blockOffset[2]);
vigra::importImage(*info, destImage(v));
}
return true;
}
#ifdef HDF5_FOUND
case HDF5:
{
HDF5File* info = reinterpret_cast<HDF5File*>(ptr);
info->readBlock("/data", blockOffset, blockShape, array);
return true;
}
#endif // HDF5_FOUND
default:
return false;
}
}
/*
* HDF5NumAttributeTest.cpp
*
* Created on: 20 oct. 2012
* Author: boubad
*/
#ifndef NO_GTEST
/////////////////////////////
#include <gtest/gtest.h>
/////////////////////////////
#include <hdf5store.h>
/////////////////////////////
template <typename T>
class HDF5NumAttributeTest : public ::testing::Test {
public:
typedef std::vector<T> Vector;
public:
HDF5NumAttributeTest():m_filename("testresults/mytest.h5"),m_grpname("g_initial"){}
virtual ~HDF5NumAttributeTest(){}
protected:
T value_;
std::string m_filename;
std::string m_grpname;
};
typedef ::testing::Types<char, signed char,unsigned char,short,unsigned short,int, unsigned int, long, unsigned long, long long, unsigned long long> MyTypes;
TYPED_TEST_CASE(HDF5NumAttributeTest, MyTypes);
///////////////////////////////////////
using namespace statdata;
using namespace statdata::hdf5;
//////////////////////////////////////
TYPED_TEST(HDF5NumAttributeTest,ScalarAttribute)
{
TypeParam v = (TypeParam)68;
boost::any vv(v);
const std::type_info &tt = vv.type();
HDF5File oFile;
bool bRet = oFile.create(this->m_filename);
ASSERT_TRUE(bRet);
HDF5Group oGroup(&oFile, this->m_grpname, true);
std::string name = std::string("att_") + std::string(tt.name()) + std::string("_scalar");
HDF5Attribute att(&oGroup,name);
bRet = att.write_scalar(v);
ASSERT_TRUE(bRet);
TypeParam actual;
bRet = att.read_scalar(actual);
ASSERT_TRUE(bRet);
ASSERT_EQ(v, actual);
}/* Scalar Attribute */
TYPED_TEST(HDF5NumAttributeTest,VectorAttribute)
{
size_t n = 10;
typename TestFixture::Vector values(n);
for (size_t i = 0; i < n; ++i){
values[i] = (TypeParam)(68 + i);
}// i
TypeParam v = (TypeParam)68;
boost::any vv(v);
const std::type_info &tt = vv.type();
HDF5File oFile;
bool bRet = oFile.create(this->m_filename);
ASSERT_TRUE(bRet);
HDF5Group oGroup(&oFile, this->m_grpname, true);
std::string name = std::string("att_") + std::string(tt.name()) + std::string("_vector");
HDF5Attribute att(&oGroup,name);
bRet = att.write_vector(values);
ASSERT_TRUE(bRet);
typename TestFixture::Vector actual;
bRet = att.read_vector(actual);
ASSERT_TRUE(bRet);
ASSERT_EQ(n, actual.size());
for (size_t i = 0; i < n; ++i){
TypeParam v1 = values[i];
TypeParam v2 = actual[i];
ASSERT_EQ(v1, v2);
}// i
}/* Vector Attribute */
TYPED_TEST(HDF5NumAttributeTest,VectorDataset)
{
size_t n = 10;
typename TestFixture::Vector values(n);
for (size_t i = 0; i < n; ++i){
values[i] = (TypeParam)(68 + i);
}// i
TypeParam v = (TypeParam)68;
boost::any vv(v);
const std::type_info &tt = vv.type();
HDF5File oFile;
bool bRet = oFile.create(this->m_filename);
ASSERT_TRUE(bRet);
HDF5Group oGroup(&oFile, this->m_grpname, true);
std::string name = std::string("dataset_") + std::string(tt.name()) + std::string("_vector");
HDF5Dataset att(&oGroup,name);
bRet = att.write_vector(values);
ASSERT_TRUE(bRet);
typename TestFixture::Vector actual;
bRet = att.read_vector(actual);
ASSERT_TRUE(bRet);
ASSERT_EQ(n, actual.size());
for (size_t i = 0; i < n; ++i){
TypeParam v1 = values[i];
TypeParam v2 = actual[i];
ASSERT_EQ(v1, v2);
}// i
}/* Vector VectorDataset */
// TODO: 0 size plane matrices are not output due to a bug in an older version of HDF5
void RigidBody2DSim::writeBinaryState( HDF5File& output_file ) const
{
// Output the configuration
output_file.write( "q", m_state.q() );
// Output the velocity
output_file.write( "v", m_state.v() );
// Output the mass
{
// Assemble the mass into a single flat vector like q, v, and r
assert( unsigned(m_state.M().nonZeros()) == 3 * m_state.nbodies() );
const VectorXs m{ Eigen::Map<const VectorXs>{ &m_state.M().data().value(0), m_state.q().size() } };
output_file.write( "m", m );
}
{
VectorXu fixed{ numBodies() };
for( int body_index = 0; body_index < fixed.size(); ++body_index )
{
fixed( body_index ) = isKinematicallyScripted( body_index ) ? 1 : 0;
}
output_file.write( "kinematically_scripted", fixed );
}
// Output the simulated geometry
RigidBody2DStateOutput::writeGeometryIndices( m_state.geometry(), m_state.geometryIndices(), "geometry", output_file );
RigidBody2DStateOutput::writeGeometry( m_state.geometry(), "geometry", output_file );
// Output the static geometry
if( !m_state.planes().empty() )
{
RigidBody2DStateOutput::writeStaticPlanes( m_state.planes(), "static_geometry", output_file );
}
if( !m_state.planarPortals().empty() )
{
RigidBody2DStateOutput::writePlanarPortals( m_state.planarPortals(), "static_geometry", output_file );
}
}
bool readTVolume(MultiArrayView<STORMPARAMS_N, T> & array, FileType type, void *ptr) {
switch(type) {
case TIFF:
{
ImageImportInfo* info = reinterpret_cast<ImageImportInfo*>(ptr);
vigra_precondition(array.size(2)==info->numImages(),"array shape and number of images in tiff file differ.");
for(int i = 0; i < info->numImages(); ++i) {
MultiArrayView <2, T> img = array.bindOuter(i);
BasicImageView <T> v = makeBasicImageView(img);
info->setImageIndex(i);
vigra::importImage(*info, destImage(v));
}
return true;
}
#ifdef HDF5_FOUND
case HDF5:
{
HDF5File* info = reinterpret_cast<HDF5File*>(ptr);
info->read("/data", array);
return true;
}
#endif // HDF5_FOUND
default:
return false;
}
}
void CAMCode<B,T,D>::Exec ()
{
_timer.Start ();
MomInit ();
CalcE (_B, _Ua, _dn);
Timer thyb;
do
{
if (_time.Restart ())
{
_time.Print ();
CheckPointLoad ();
_time.SetRestart (false);
}
else
{
_sensmng.SaveAll (_time);
_sensmng.SetNextOutput (_time);
}
CheckPointSave ();
DBG_INFO ("iteration time : "<<thyb);
_timer.Update ();
DBG_INFO ("wallclock time : "<<_timer);
thyb.Reset ();
thyb.Start ();
int nit = _time.HybIters () -_time.Iter ();
Hyb ();
thyb.Stop ();
thyb /= nit;
if (Mpi::Rank () == 0)
{
_itertime.Push (thyb.GetWallclockTime ());
String fname = _sensmng.GetIOManager().GetFileName ("Stat");
HDF5File file (fname, IOFile::suff);
file.Write (_itertime, "Iter");
}
}
while (_time.Iter () < _time.ItersMax ());
_sensmng.SaveAll (_time);
_sensmng.SetNextOutput (_time);
}
/// \brief Open a group if possible, otherwise create a new one
HDF5Group(const HDF5File &file, const std::string &groupname)
: HDF5ID<HDF5Group>(-1)
{
if (!file) {
return;
}
bool print_error = hdf5_error_printing(false);
id_ = ::H5Gopen2(file.id(), groupname.c_str(), H5P_DEFAULT);
hdf5_error_printing(print_error);
if (!good()) {
id_ = ::H5Gcreate2(file.id(), groupname.c_str(), H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);
}
}
template<> Recorder<SAVE>::~Recorder () {
size_t n_samples = _states.size();
if (n_samples == 0)
return;
HDF5File f ("simout.h5", OUT);
NDData<double> times (n_samples);
NDData<double> data (n_samples,3);
for (size_t i = 0; i < n_samples; ++i) {
times [i] = _times[i];
data (i,0) = _states[i][0];
data (i,1) = _states[i][1];
data (i,2) = _states[i][2];
}
f.Write (times, "times");
f.Write (data, "data");
fclose (f);
}
TYPED_TEST(HDF5NumAttributeTest,ScalarAttribute)
{
TypeParam v = (TypeParam)68;
boost::any vv(v);
const std::type_info &tt = vv.type();
HDF5File oFile;
bool bRet = oFile.create(this->m_filename);
ASSERT_TRUE(bRet);
HDF5Group oGroup(&oFile, this->m_grpname, true);
std::string name = std::string("att_") + std::string(tt.name()) + std::string("_scalar");
HDF5Attribute att(&oGroup,name);
bRet = att.write_scalar(v);
ASSERT_TRUE(bRet);
TypeParam actual;
bRet = att.read_scalar(actual);
ASSERT_TRUE(bRet);
ASSERT_EQ(v, actual);
}/* Scalar Attribute */
/*
* HDF5NumAttributeTest.cpp
*
* Created on: 20 oct. 2012
* Author: boubad
*/
#ifndef NO_GTEST
/////////////////////////////
#include <gtest/gtest.h>
/////////////////////////////
#include <hdf5store.h>
/////////////////////////////
template <typename T>
class HDF5NumAttributeTest : public ::testing::Test {
public:
typedef std::vector<T> Vector;
public:
HDF5NumAttributeTest():m_filename("testresults/mytest.h5"),m_grpname("g_initial"){}
virtual ~HDF5NumAttributeTest(){}
protected:
T value_;
std::string m_filename;
std::string m_grpname;
};
typedef ::testing::Types<char, signed char,unsigned char,short,unsigned short,int, unsigned int, long, unsigned long, long long, unsigned long long> MyTypes;
TYPED_TEST_CASE(HDF5NumAttributeTest, MyTypes);
///////////////////////////////////////
using namespace statdata;
using namespace statdata::hdf5;
//////////////////////////////////////
TYPED_TEST(HDF5NumAttributeTest,ScalarAttribute)
{
TypeParam v = (TypeParam)68;
boost::any vv(v);
const std::type_info &tt = vv.type();
HDF5File oFile;
bool bRet = oFile.create(this->m_filename);
ASSERT_TRUE(bRet);
HDF5Group oGroup(&oFile, this->m_grpname, true);
std::string name = std::string("att_") + std::string(tt.name()) + std::string("_scalar");
HDF5Attribute att(&oGroup,name);
bRet = att.write_scalar(v);
ASSERT_TRUE(bRet);
TypeParam actual;
bRet = att.read_scalar(actual);
ASSERT_TRUE(bRet);
ASSERT_EQ(v, actual);
}/* Scalar Attribute */
TYPED_TEST(HDF5NumAttributeTest,VectorAttribute)
{
size_t n = 10;
typename TestFixture::Vector values(n);
for (size_t i = 0; i < n; ++i){
values[i] = (TypeParam)(68 + i);
}// i
TypeParam v = (TypeParam)68;
boost::any vv(v);
const std::type_info &tt = vv.type();
HDF5File oFile;
bool bRet = oFile.create(this->m_filename);
ASSERT_TRUE(bRet);
HDF5Group oGroup(&oFile, this->m_grpname, true);
std::string name = std::string("att_") + std::string(tt.name()) + std::string("_vector");
HDF5Attribute att(&oGroup,name);
bRet = att.write_vector(values);
ASSERT_TRUE(bRet);
typename TestFixture::Vector actual;
bRet = att.read_vector(actual);
ASSERT_TRUE(bRet);
ASSERT_EQ(n, actual.size());
for (size_t i = 0; i < n; ++i){
TypeParam v1 = values[i];
TypeParam v2 = actual[i];
ASSERT_EQ(v1, v2);
}// i
}/* Vector Attribute */
TYPED_TEST(HDF5NumAttributeTest,VectorDataset)
{
size_t n = 10;
typename TestFixture::Vector values(n);
for (size_t i = 0; i < n; ++i){
values[i] = (TypeParam)(68 + i);
}// i
TypeParam v = (TypeParam)68;
boost::any vv(v);
const std::type_info &tt = vv.type();
HDF5File oFile;
bool bRet = oFile.create(this->m_filename);
ASSERT_TRUE(bRet);
HDF5Group oGroup(&oFile, this->m_grpname, true);
std::string name = std::string("dataset_") + std::string(tt.name()) + std::string("_vector");
HDF5Dataset att(&oGroup,name);
bRet = att.write_vector(values);
ASSERT_TRUE(bRet);
typename TestFixture::Vector actual;
bRet = att.read_vector(actual);
ASSERT_TRUE(bRet);
ASSERT_EQ(n, actual.size());
for (size_t i = 0; i < n; ++i){
TypeParam v1 = values[i];
TypeParam v2 = actual[i];
ASSERT_EQ(v1, v2);
}// i
}/* Vector VectorDataset */
TYPED_TEST(HDF5NumAttributeTest,ArrayDataset)
{
size_t nr = 5;
size_t nc = 3;
size_t n = (size_t)(nr * nc);
typename TestFixture::Vector values(n);
for (size_t i = 0; i < nr; ++i){
for (size_t j = 0; j < nc; ++j){
values[i * nc + j] = (TypeParam)(68 + i * nc + j);
}
}// i
TypeParam v = (TypeParam)68;
boost::any vv(v);
const std::type_info &tt = vv.type();
HDF5File oFile;
bool bRet = oFile.create(this->m_filename);
ASSERT_TRUE(bRet);
HDF5Group oGroup(&oFile, this->m_grpname, true);
std::string name = std::string("dataset_") + std::string(tt.name()) + std::string("_array");
HDF5Dataset att(&oGroup,name);
bRet = att.write_array(values,nr,nc);
ASSERT_TRUE(bRet);
typename TestFixture::Vector actual;
size_t nra = 0;
size_t nca = 0;
bRet = att.read_array(actual,nra,nca);
ASSERT_TRUE(bRet);
ASSERT_EQ(nr, nra);
ASSERT_EQ(nc, nca);
ASSERT_EQ(n, actual.size());
for (size_t i = 0; i < nr; ++i){
for (size_t j = 0; j < nc; ++j){
size_t k = i * nc + j;
TypeParam v1 = values[k];
TypeParam v2 = actual[k];
ASSERT_EQ(v1, v2);
}// j
}// i
}/* Vector VectorDataset */
template <class T> inline static bool write (const Matrix<T> A) {
HDF5File nf (fname, WRITE);
nf.Write (A, mname);
return true;
}
void ImpactFrictionMap::exportConstraintForcesToBinaryFile( const VectorXs& q, const std::vector<std::unique_ptr<Constraint>>& constraints, const MatrixXXsc& contact_bases, const VectorXs& alpha, const VectorXs& beta, const scalar& dt, HDF5File& output_file )
{
const unsigned ncons = constraints.size();
assert( ncons == alpha.size() );
assert( std::vector<std::unique_ptr<Constraint>>::size_type( ncons ) == constraints.size() );
assert( alpha.size() == ncons );
const unsigned ambient_space_dims{ static_cast<unsigned>( contact_bases.rows() ) };
assert( ambient_space_dims == 2 || ambient_space_dims == 3 );
assert( beta.size() == ncons * ( ambient_space_dims - 1 ) );
// Write out the number of collisions
output_file.writeScalar( "", "collision_count", ncons );
// NB: Prior to version 1.8.7, HDF5 did not support zero sized dimensions.
// Some versions of Ubuntu still have old versions of HDF5, so workaround.
// TODO: Remove once our servers are updated.
if( ncons == 0 )
{
return;
}
// Write out the indices of all bodies involved
{
// Place all indices into a single matrix for output
Matrix2Xic collision_indices{ 2, ncons };
for( unsigned con = 0; con < ncons; ++con )
{
std::pair<int,int> indices;
assert( constraints[con] != nullptr );
getCollisionIndices( *constraints[con], indices );
collision_indices.col( con ) << indices.first, indices.second;
}
// Output the indices
output_file.writeMatrix( "", "collision_indices", collision_indices );
}
// Write out the world space contact points
{
// Place all contact points into a single matrix for output
MatrixXXsc collision_points{ ambient_space_dims, ncons };
for( unsigned con = 0; con < ncons; ++con )
{
VectorXs contact_point;
assert( constraints[con] != nullptr );
constraints[con]->getWorldSpaceContactPoint( q, contact_point );
assert( contact_point.size() == ambient_space_dims );
collision_points.col( con ) = contact_point;
}
// Output the points
output_file.writeMatrix( "", "collision_points", collision_points );
}
// Write out the world space contact normals
{
// Place all contact normals into a single matrix for output
MatrixXXsc collision_normals{ ambient_space_dims, ncons };
for( unsigned con = 0; con < ncons; ++con )
{
collision_normals.col( con ) = contact_bases.col( ambient_space_dims * con );
}
#ifndef NDEBUG
for( unsigned con = 0; con < ncons; ++con )
{
assert( fabs( collision_normals.col( con ).norm() - 1.0 ) <= 1.0e-6 );
}
#endif
// Output the normals
output_file.writeMatrix( "", "collision_normals", collision_normals );
}
// Write out the collision forces
{
// Place all contact forces into a single matrix for output
MatrixXXsc collision_forces{ ambient_space_dims, ncons };
for( unsigned con = 0; con < ncons; ++con )
{
// Contribution from normal
collision_forces.col( con ) = alpha( con ) * contact_bases.col( ambient_space_dims * con );
// Contribution from friction
for( unsigned friction_sample = 0; friction_sample < ambient_space_dims - 1; ++friction_sample )
{
assert( ( ambient_space_dims - 1 ) * con + friction_sample < beta.size() );
const scalar impulse{ beta( ( ambient_space_dims - 1 ) * con + friction_sample ) };
const unsigned column_number{ ambient_space_dims * con + friction_sample + 1 };
assert( column_number < contact_bases.cols() );
assert( fabs( contact_bases.col( ambient_space_dims * con ).dot( contact_bases.col( column_number ) ) ) <= 1.0e-6 );
collision_forces.col( con ) += impulse * contact_bases.col( column_number );
}
}
// Output the forces
output_file.writeMatrix( "", "collision_forces", collision_forces );
}
}
HDF5DataSet(const HDF5File &file, const std::string &name,
const HDF5DataType &type, const HDF5DataSpace &space)
: HDF5ID<HDF5DataSet>(::H5Dcreate2(file.id(), name.c_str(), type.id(),
space.id(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT))
{
}
HDF5DataSet(const HDF5File &file, const std::string &name)
: HDF5ID<HDF5DataSet>(::H5Dopen2(file.id(), name.c_str(), H5P_DEFAULT))
{
}
HDF5Attribute(const HDF5File &file, const std::string &name)
: HDF5ID<HDF5Attribute>(
::H5Aopen(file.id(), name.c_str(), H5P_DEFAULT))
{
}
bool commit(const HDF5File &file, const std::string &name) const
{
return ::H5Tcommit2(file.id(), name.c_str(), id_, H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);
}