Ejemplo n.º 1
0
void pyne::Material::_load_comp_protocol0(H5::H5File * db, std::string datapath, int row)
{
  H5::Group matgroup = (*db).openGroup(datapath);
  H5::DataSet nucset;

  double nucvalue;
  hsize_t matG = matgroup.getNumObjs();

  // Iterate over datasets in the group.
  for (int matg = 0; matg < matG; matg++)
  {
    std::string nuckey = matgroup.getObjnameByIdx(matg);
    nucset = matgroup.openDataSet(nuckey);
    nucvalue = h5wrap::get_array_index<double>(&nucset, row);

    if (nuckey == "Mass" || nuckey == "MASS" || nuckey == "mass")
      mass = nucvalue;
    else
      comp[pyne::nucname::zzaaam(nuckey)] = nucvalue;

    nucset.close();
  };

  // Set meta data
  name = datapath.substr(datapath.rfind("/")+1, datapath.length());
  atoms_per_mol = -1.0;
};
Ejemplo n.º 2
0
bool loadStackHDF5( const char* fileName, Image4DSimple& img )
{
#ifdef USE_HDF5
    H5::Exception::dontPrint();
    H5::H5File file( fileName, H5F_ACC_RDONLY );

    for ( size_t i = 0; i < file.getObjCount(); i++ )
    {
        H5std_string name = file.getObjnameByIdx( i );
        if ( name == "Channels" )
        {
            H5::Group channels = file.openGroup( name );

            // Grab the attributes
            H5::Attribute attr = channels.openAttribute( "width" );
            H5::DataType type = attr.getDataType();
            long width, height;
            attr.read( type, &width );
            attr.close();

            attr = channels.openAttribute( "height" );
            attr.read( type, &height );
            attr.close();

            int num_channels = 0;
            // Count the number of channels
            for ( size_t obj = 0; obj < channels.getNumObjs(); obj++ )
                if ( channels.getObjTypeByIdx( obj ) == H5G_DATASET )
                    num_channels++;

            int channel_idx = 0;
            for ( size_t obj = 0; obj < channels.getNumObjs(); obj++ )
            {
                if ( channels.getObjTypeByIdx( obj ) == H5G_DATASET )
                {
                    H5std_string ds_name = channels.getObjnameByIdx( obj );
                    H5::DataSet data = channels.openDataSet( ds_name );
                    uint8_t* buffer = new uint8_t[ data.getStorageSize() ];
                    data.read( buffer, data.getDataType() );
                    QByteArray qbarray( ( const char* )buffer, data.getStorageSize() );
                    data.close();

                    if ( !loadIndexedStackFFMpeg( &qbarray, img, channel_idx++, num_channels,
                                                  width, height ) )
                    {
                        v3d_msg( "Error happened in HDF file reading. Stop. \n", false );
                        return false;
                    }

                    delete [] buffer;
                }
            }
        }
    }

#endif

    return true;
}
Ejemplo n.º 3
0
bool Bundle2::checkGeometry_(H5::H5File& file) const {
	bool found = false;

	H5::Group root = file.openGroup("/");

	const hsize_t maxObjs = root.getNumObjs();
	for(hsize_t obj = 0; obj < maxObjs; ++obj) {
		string objName = root.getObjnameByIdx(obj);
		if(objName == string("Geometry")) found = true;
	}

	root.close();
	return found;
}
Ejemplo n.º 4
0
static void attributes_append_group(Attributes &attrs, H5::Group &g, cpath basename, cpath group_path)
{     
  for(uint i=0;i<g.getNumObjs();i++) {
    
    char g_name[1024];
    g.getObjnameByIdx(hsize_t(i), g_name, 1024);
    cpath name = group_path / g_name;
    
    H5G_stat_t stat;
    g.getObjinfo(g_name, false, stat);
    
    if (stat.type == H5G_GROUP) {
      H5::Group sub = g.openGroup(g_name);
      attributes_append_group(attrs, sub, basename, name);
    }
    else if (stat.type == H5G_LINK)
    {
      //FIXME we assume soft link!
      Attribute attr;
      char attr_name[1024];
      char link[1024];
      
      attr.setName(remove_prefix(name, basename));
      
      H5L_info_t info;
      H5Lget_val(g.getId(), g_name, link, 1024, H5P_DEFAULT);
      attr.setLink(remove_prefix(link, basename));
      
      attrs.append(attr);
    }
  }
  
  
  for(int i=0;i<g.getNumAttrs();i++) {
    H5::Attribute h5attr = g.openAttribute(i);
    Attribute attr;
    BaseType type;
    char name[1024];
    
    H5Aget_name(h5attr.getId(), 1024, name);
    read_attr(&attr, g, basename, group_path, name, type);
    
    attrs.append(attr);
  }
}
Ejemplo n.º 5
0
	/**
	 * Returns a pointer to a std::vector<float> containing the values of the selected variable
	 * in the range specified by the startIndex and count (the number of records to read) stored
	 * in the selected file.  This allocates a new std::vector<float> pointer.  Make sure you
	 * delete the contents when you done using it, or you will have a memory leak.
	 * @param variableID
	 * @param startIndex
	 * @param count
	 * @return std::vector<float> containing the values of the selected variable.
	 */
	std::vector<float>* HDF5FileReader::getVariable(long variable, long indexOffset, long count)
	{

		std::vector<float>* variableData = new std::vector<float>();



		//get dim sizes
		H5::Group group = this->current_file->openGroup("Variables");
		//cout << "variable: " << variable << ": " << counts[0] << endl;
		H5::DataSet * dataset = new H5::DataSet(group.openDataSet(group.getObjnameByIdx(variable)));
		H5::DataSpace dataspace = dataset->getSpace();
		int rank = dataspace.getSimpleExtentNdims(); //should be 1
		hsize_t length[1] = {count};
		hsize_t offset[1] = {indexOffset};
		//int ndims = dataspace.getSimpleExtentDims(count, NULL);
		float * buffer = new float[length[0]];



		dataspace.selectHyperslab(H5S_SELECT_SET, length, offset);

		hsize_t dim[] = {length[0]};
		H5::DataSpace memspace( rank, dim);
		memspace.selectHyperslab(H5S_SELECT_SET, dim, offset);

		dataset->read(buffer, H5::PredType::NATIVE_FLOAT, memspace, dataspace);


		//add data to vector type, and delete original array
		variableData->reserve(length[0]);
		for (int i = 0; i < length[0]; i++)
		{
			variableData->push_back(buffer[i]);
		}

		delete[] buffer;
		delete dataset;
		//std::cout << "finished reading " << variable << std::endl;
		//std::cout << "size of variable: " << variableData.size() << std::endl;
		//std::cout << "dimSizes[0]: " << dimSizes[0] << std::endl;
		return variableData;
	}
Ejemplo n.º 6
0
	/**
	 * @param variableNum
	 * @param index
	 * @return
	 */
	float HDF5FileReader::getVariableAtIndex(long variable, long index)
	{

		float value = std::numeric_limits<float>::min();

		//get dim sizes

		H5::Group group = this->current_file->openGroup("Variables");
		//cout << "variable: " << variable << ": " << counts[0] << endl;
		H5::DataSet * dataset = new H5::DataSet(group.openDataSet(group.getObjnameByIdx(variable)));
		H5::DataSpace dataspace = dataset->getSpace();
		int rank = dataspace.getSimpleExtentNdims(); //should be 1
		hsize_t count[1] = {1};
		hsize_t offset[1] = {index};
		//int ndims = dataspace.getSimpleExtentDims(count, NULL);
		float * buffer = new float[count[0]];



		dataspace.selectHyperslab(H5S_SELECT_SET, count, offset);

		hsize_t dim[] = {count[0]};
		H5::DataSpace memspace( rank, dim);
		memspace.selectHyperslab(H5S_SELECT_SET, dim, offset);

		dataset->read(buffer, H5::PredType::NATIVE_FLOAT, memspace, dataspace);


		//add data to vector type, and delete original array
		value = buffer[0];
		delete[] buffer;
		delete dataset;
		return value;
			//std::cout << "finished reading " << variable << std::endl;
			//std::cout << "size of variable: " << variableData.size() << std::endl;
			//std::cout << "dimSizes[0]: " << dimSizes[0] << std::endl;

	}
Ejemplo n.º 7
0
/*********************************************************
FunctionName:RecursiveVisitNode
FunctionDesc:递归创建Group
InputParam:
OutputParam:
Return:
Author:xiaowei.han
*********************************************************/
void RecursiveVisitNode(H5::Group& Node, Hdf5_Wrapper::LP_HDF5_DATA pData)
{
	using namespace H5;
	if (nullptr == pData)
	{
		return;
	}
	//获取节点名称
	pData->strKeyName = Utility::UTF8ToGB2312(Node.getObjName());
	//获取属性个数
	int nAttrNum = static_cast<int>(Node.getNumAttrs());
	for (int i = 0; i < nAttrNum; ++i)
	{
		auto childAttr = Node.openAttribute(i);

		//解析读取属性数据
		//获取数据类型
		auto AttrDataType = childAttr.getDataType();
		//获取数据类型大小
		unsigned int nDataByte = (unsigned int)AttrDataType.getSize();

		boost::scoped_ptr<CAbstractAttrHanlder> pHandler(CreateAttrHandler(childAttr.getTypeClass(), nDataByte));

		if (pHandler)
		{
			pHandler->ReadAttr(childAttr, AttrDataType, pData->AttributeArray);
		}
		childAttr.close();
	}

	//获取节点对象个数
	int nObjNum = static_cast<int>(Node.getNumObjs());

	//遍历子节点信息
	for (int i = 0; i < nObjNum; ++i)
	{
		//NECESSARY_LOG("the node name is [%s],the type is [%d].", Node.getObjnameByIdx(i).c_str(), Node.getObjTypeByIdx(i));
		auto SubNodeType = Node.getObjTypeByIdx(i);
		switch (SubNodeType)
		{
		case H5G_GROUP:
		{
			Hdf5_Wrapper::LP_HDF5_DATA pSubData = new Hdf5_Wrapper::HDF5_DATA;
			if (nullptr != pSubData)
			{
				//添加进去
				pData->SubDataArray.push_back(pSubData);
				auto ChildGroupNode = Node.openGroup(Node.getObjnameByIdx(i));
				RecursiveVisitNode(ChildGroupNode,pSubData);
				ChildGroupNode.close();
			}
		}
		break;
		case H5G_DATASET:
		{
			auto childDataset = Node.openDataSet(Node.getObjnameByIdx(i));

			Hdf5_Wrapper::LP_HDF5_DATA pSubData = new Hdf5_Wrapper::HDF5_DATA;
			if (nullptr != pSubData)
			{
				pSubData->strKeyName = childDataset.getObjName();
				//添加进去
				pData->SubDataArray.push_back(pSubData);
				//获取数据类型
				auto ChildDataSetDataType = childDataset.getDataType();
				//获取类型占用字节数
				unsigned int nDataByte = (unsigned int)ChildDataSetDataType.getSize();
				//判断数据类型
				boost::scoped_ptr<CAbstractDataTypeHandler> pHandlder(CDataTypeHandlerFactory::CreateDataTypeHandler(childDataset.getTypeClass(),nDataByte));
				if (pHandlder)
				{
					pHandlder->ReadDataSet(childDataset, pSubData);
				}
			}
		}
		break;
		default:
			break;
		}	
	}
}
Ejemplo n.º 8
0
//--------------------------------------------------------------------------------------------------
/// 
//--------------------------------------------------------------------------------------------------
TEST(DISABLED_HDFTests, BasicFileRead)
{
    std::string file_path = "D:/ResInsight/SourSim/PKMUNK_NOV_TEST_SS.sourpre.00001";

    try
    {
        H5::Exception::dontPrint();                                // Turn off auto-printing of failures to handle the errors appropriately

        H5::H5File file(file_path.c_str(), H5F_ACC_RDONLY);

        {
            H5::Group        timestep = file.openGroup("Timestep_00001");
            H5::Attribute    attr     = timestep.openAttribute("timestep");

            double timestep_value = 0.0;

            H5::DataType type = attr.getDataType();
            attr.read(type, &timestep_value);

            //std::cout << "Timestep value " << timestep_value << std::endl;
            EXPECT_NEAR(timestep_value, 1.0, 1e-1);
        }


        {
            // Group size is not an attribute!

            H5::Group GridFunctions = file.openGroup("Timestep_00001/GridParts/GridPart_00000/GridFunctions");

            hsize_t   group_size = GridFunctions.getNumObjs();

            //std::cout << "GridFunctions group_size " << group_size << std::endl;
            EXPECT_EQ(size_t(20), group_size);

/*            for (hsize_t i = 0; i < group_size; i++)
            {
                // H5std_string node_name = GridFunctions.getObjnameByIdx(i);     // crashes on VS2017 due to lib/heap/runtime differences to HDF5 VS2015 lib

                std::string node_name;
                node_name.resize(1024);

                ssize_t slen = GridFunctions.getObjnameByIdx(i, &node_name[0], 1023);

                node_name.resize(slen + 1);

                std::cout << "GridFunctions sub-node name " << node_name << std::endl;
            }
*/

            std::string first_subnode(1024, '\0');

            ssize_t slen = GridFunctions.getObjnameByIdx(0, &first_subnode[0], 1023);
            first_subnode.resize(slen + 1);

            EXPECT_TRUE(first_subnode.compare(0, slen, "GridFunction_00002") == 0);
        }


        {
            H5::Group        GridFunction_00002 = file.openGroup("Timestep_00001/GridParts/GridPart_00000/GridFunctions/GridFunction_00002");
            H5::Attribute    attr = GridFunction_00002.openAttribute("limits_max");

            double limits_max = 0.0;
        
            H5::DataType type = attr.getDataType();
            attr.read(type, &limits_max);

//            std::cout << "limits_max " << limits_max << std::endl;
            EXPECT_NEAR(limits_max, 0.3970204292629652, 1e-10);
        }


        {
            H5::Group        GridFunction_00002 = file.openGroup("Timestep_00001/GridParts/GridPart_00000/GridFunctions/GridFunction_00002");
            H5::DataSet        dataset = H5::DataSet(GridFunction_00002.openDataSet("values"));

            hsize_t dims[2];
            H5::DataSpace    dataspace = dataset.getSpace();
            dataspace.getSimpleExtentDims(dims, nullptr);

            std::vector<double> values;
            values.resize(dims[0]);
            dataset.read(values.data(), H5::PredType::NATIVE_DOUBLE);

/*            for (hsize_t i = 0; i < dims[0]; i++)
            {
                std::cout << "value " << i << " " << values[i] << std::endl;

            }
*/
            EXPECT_NEAR(values[0], 0.32356910366452146, 1e-10);
            EXPECT_NEAR(values[dims[0] - 1], 0.12200070891582514, 1e-10);
        }



    }  // end of try block
    
       
    catch (H5::FileIException error)        // catch failure caused by the H5File operations
    {
        std::cout << error.getCDetailMsg();
    }
    
    catch (H5::DataSetIException error)        // catch failure caused by the DataSet operations
    {
        std::cout << error.getCDetailMsg();
    }
    
    catch (H5::DataSpaceIException error)    // catch failure caused by the DataSpace operations
    {
        std::cout << error.getCDetailMsg(); 
    }
    
    catch (H5::DataTypeIException error)        // catch failure caused by the DataSpace operations
    {
        std::cout << error.getCDetailMsg();
    }

}
Ejemplo n.º 9
0
void ossim_hdf5::iterateGroupForDatasetNames(  H5::H5File* file,
                                               const std::string& groupName,
                                               std::vector<std::string>& datasetNames,
                                               ossim_uint32& recursedCount )
{
   if ( file && groupName.size() )
   {
      ++recursedCount;
      
      // std::cout << "iterateGroup: " << groupName << std::endl;
      
      H5::Group* group = new H5::Group( file->openGroup(groupName) );
      
      const hsize_t OBJ_COUNT = group->getNumObjs();
      
      for ( hsize_t i = 0; i < OBJ_COUNT; ++i )
      {
         std::string objName = group->getObjnameByIdx(i);

         if ( objName.size() )
         {
            char separator = '/';
            std::string combinedName;
            combine( groupName, objName, separator, combinedName );
            
            H5G_obj_t objType   = group->getObjTypeByIdx(i);

#if 0
            std::cout << "combinedName: " << combinedName
                      << "\ngetObjnameByIdx[" << i << "]: " << objName
                      << "\ngetObjTypeByIdx[" << i << "]: " << objType
                      << std::endl;
#endif

            if ( objType == H5G_GROUP )
            {
               // Recursive call:
               if ( recursedCount < ossim_hdf5::MAX_RECURSION_LEVEL )
               {
                  ossim_hdf5::iterateGroupForDatasetNames(
                     file, combinedName, datasetNames, recursedCount );
               }
               else
               {
                  ossimNotify(ossimNotifyLevel_WARN)
                     << "ossim_hdf5::iterateGroupForDatasetNames WARNING!"
                     << "\nMax iterations reached!" << std::endl;
               }
            }
            else if ( objType == H5G_DATASET )
            {
               datasetNames.push_back( combinedName );
            }
            else
            {
               ossimNotify(ossimNotifyLevel_WARN)
                     << "ossim_hdf5::iterateGroupForDatasetNames WARNING!"
                     << "\nUnhandled object type: " << objType << std::endl;
            }
         }
      }
      
      group->close();
      delete group;
      group = 0;
      --recursedCount;
      
   } // Matches: if ( file )
   
} // End: void ossim_hdf5::iterateGroupForDatasetNames
Ejemplo n.º 10
0
void ossim_hdf5::printIterative( H5::H5File* file,
                                 const std::string& groupName,
                                 const std::string& prefix,
                                 ossim_uint32& recursedCount,
                                 std::ostream& out )
{
   if ( file && groupName.size() )
   {
      ++recursedCount;
      
      H5::Group* group = new H5::Group( file->openGroup(groupName) );

      // Print attributes:
      const ossim_uint32 ATTRS_COUNT = group->getNumAttrs();
      for ( ossim_uint32 aIdx = 0; aIdx < ATTRS_COUNT; ++aIdx )
      {
         H5::Attribute attr( group->openAttribute( aIdx ) );
         ossim_hdf5::printAttribute( attr, prefix, out );
         attr.close();
      }
      
      const hsize_t OBJ_COUNT = group->getNumObjs();
      for ( hsize_t i = 0; i < OBJ_COUNT; ++i )
      {
         std::string objName = group->getObjnameByIdx(i);

         if ( objName.size() )
         {
            char separator = '/';
            std::string combinedName;
            combine( groupName, objName, separator, combinedName );
            
            separator = '.';
            std::string combinedPrefix;
            combine( prefix, objName, separator, combinedPrefix );
            
            H5G_obj_t objType   = group->getObjTypeByIdx(i);

#if 0
            std::cout << "combinedName: " << combinedName
                      << "\ncombinedPrefix: " << combinedPrefix
                      << "\ngetObjnameByIdx[" << i << "]: " << objName
                      << "\ngetObjTypeByIdx[" << i << "]: " << objType
                      << std::endl;
#endif
            
            if ( objType == H5G_GROUP )
            {
               // Recursive call:
               if ( recursedCount < ossim_hdf5::MAX_RECURSION_LEVEL )
               {
                  ossim_hdf5::printIterative(
                     file, combinedName, combinedPrefix, recursedCount, out );
               }
               else
               {
                  ossimNotify(ossimNotifyLevel_WARN)
                     << "ossim_hdf5::printIterative WARNING!"
                     << "\nMax iterations reached!" << std::endl;
               }
            }
            else if ( objType == H5G_DATASET )
            {
               printObject( file, combinedName, combinedPrefix, out );
            }
            else
            {
               ossimNotify(ossimNotifyLevel_WARN)
                  << "ossim_hdf5::printIterative WARNING!"
                  << "\nUnhandled object type: " << objType << std::endl;
            }
         }
      }
      
      group->close();
      delete group;
      group = 0;
      --recursedCount;
      
   } // Matches: if ( file )
   
} // End: void ossim_hdf5::printIterative method.
Ejemplo n.º 11
0
void Bundle2::loadGeometry_(H5::H5File& file) {
	H5::Group geometryGroup = file.openGroup("/Geometry");

	// Loading poses
	H5::DataSet posesDataSet = geometryGroup.openDataSet("Poses");
	double* posesData = (double*)malloc(frames_.size()*12*sizeof(double));
	posesDataSet.read((void*)posesData, H5::PredType::NATIVE_DOUBLE, H5::DataSpace::ALL, H5::DataSpace::ALL);
	posesDataSet.close();

	size_t i = 0;
	for(deque<Frame*>::iterator it = frames_.begin(); it != frames_.end(); ++it) {
		Pose* pose = new Pose;
		pose->sett(core::RealPoint3D<double>(posesData[i*12], posesData[i*12 + 1], posesData[i*12 + 2]));

		core::Matrix<double> R(3, 3);
		R[0][0] = posesData[i*12 + 3]; R[1][0] = posesData[i*12 + 4]; R[2][0] = posesData[i*12 + 5];
		R[0][1] = posesData[i*12 + 6]; R[1][1] = posesData[i*12 + 7]; R[2][1] = posesData[i*12 + 8];
		R[0][2] = posesData[i*12 + 9]; R[1][2] = posesData[i*12 + 10]; R[2][2] = posesData[i*12 + 11];

		pose->setR(R);
		pose->calcEulerAngles();
		pose->setorientationSynchronWithAngles(true);
		pose->setderivationsSynchronWithAngles(false);

		(*it)->setpose(pose);

		++i;
	}
	free((void*)posesData);

	// Loading points
	H5::DataSet pointsDataSet = geometryGroup.openDataSet("Points");
	double* pointsData = (double*)malloc(tracks_.size()*3*sizeof(double));
	pointsDataSet.read((void*)pointsData, H5::PredType::NATIVE_DOUBLE, H5::DataSpace::ALL, H5::DataSpace::ALL);
	pointsDataSet.close();

	i = 0;
	for(deque<Track*>::iterator it = tracks_.begin(); it != tracks_.end(); it++) {
		Point* point = new Point(core::RealPoint3D<double>(pointsData[i*3], pointsData[i*3 + 1], pointsData[i*3 + 2]));
		(*it)->setpoint(point);

		++i;
	}
	free((void*)pointsData);

	// Loading inlier information
	H5::DataSet inliersDataSet = geometryGroup.openDataSet("Inliers");
	hvl_t* inliersData = (hvl_t*)malloc(frames_.size()*sizeof(hvl_t));
	H5::VarLenType memType(&H5::PredType::NATIVE_UCHAR);
	inliersDataSet.read((void*)inliersData, memType, H5::DataSpace::ALL, H5::DataSpace::ALL);
	memType.close();
	inliersDataSet.close();

	i = 0;
	for(deque<Frame*>::iterator it = frames_.begin(); it != frames_.end(); it++) {
		unsigned char* inl = (unsigned char*)(inliersData[i].p);

        size_t k = 0;
		for(size_t j = 0; j < (*it)->size(); ++j) {
            View& v = (**it)[j];
            for(unsigned int cam = 0; cam < v.numCameras(); ++cam) {
                if(v.inCamera(cam)) {
                    Ray ray;
                    if(inl[k]) ray.setinlier(true);
                    else ray.setinlier(false);

                    v.addRay(cam, ray);
                    ++k;
                }
            }
		}

		++i;
	}

	for(size_t j = 0; j < frames_.size(); ++j) free(inliersData[j].p);
	free((void*)inliersData);

	// Loading curves if they exists
	bool curvesFound = false;
	const hsize_t maxObjs = geometryGroup.getNumObjs();
	for(hsize_t obj = 0; obj < maxObjs; ++obj) {
		string objName = geometryGroup.getObjnameByIdx(obj);
		if(objName == string("Curves")) curvesFound = true;
	}

	if(curvesFound) {
		H5::DataSet curvesDataSet = geometryGroup.openDataSet("Curves");

		hsize_t curvesDim[1];
		H5::DataSpace curvesDS = curvesDataSet.getSpace();
		curvesDS.getSimpleExtentDims(curvesDim);
		curvesDS.close();

		hvl_t* curvesData = (hvl_t*)malloc(curvesDim[0]*sizeof(hvl_t));
		H5::VarLenType memType(&H5::PredType::NATIVE_HSIZE);

		curvesDataSet.read((void*)curvesData, memType, H5::DataSpace::ALL, H5::DataSpace::ALL);

		memType.close();
		curvesDataSet.close();

		for(size_t c = 0; c < curvesDim[0]; ++c) {
			const size_t cur_c = addCurve();

			for(size_t p = 0; p < curvesData[c].len; ++p) {
				curves_[cur_c].addPoint(((size_t*)(curvesData[c].p))[p]);
			}
		}

		for(size_t i = 0; i < curvesDim[0]; ++i) free(curvesData[i].p);
		free((void*)curvesData);
	}

	geometryGroup.close();
}