CDPP / AMDA_Kernel

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src/ParamGetImpl/LocalFileInterface/FileReaderNetCDF.cc 11.7 KB
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/*
 * FileReaderNetCDF.cc
 *
 *  Created on: Feb 08, 2018
 *  Author: AKKA
 */

#include "FileReaderNetCDF.hh"

#include "ParameterManager.hh"
#include "LocalFileInterfaceConfig.hh"
#include "TimeUtil.hh"

#include <boost/shared_ptr.hpp>

namespace AMDA {
namespace LocalFileInterface {

FileReaderNetCDF::FileReaderNetCDF()
{
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	resetFile();
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}

FileReaderNetCDF::~FileReaderNetCDF()
{
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	resetFile();
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}

bool FileReaderNetCDF::open(std::string filePath)
{
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	boost::mutex::scoped_lock scoped_lock(AMDA::Parameters::ParameterManager::mutexNetCDFLib);
	if (isOpened()) {
		return true;
	}

	int status = nc_open(filePath.c_str(), 0, &_file.id);
	if (status != NC_NOERR) {
		LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::open - Cannot open netCDF file : " << getErrorMessage(status))
		resetFile();
		return false;
	}
	return loadNetCDFFileInfo();
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}

bool FileReaderNetCDF::close(void)
{
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	boost::mutex::scoped_lock scoped_lock(AMDA::Parameters::ParameterManager::mutexNetCDFLib);
	if (!isOpened()) {
		return true;
	}
	int status = nc_close(_file.id);
	if (status != NC_NOERR) {
		LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::close - Cannot close netCDF file : " << getErrorMessage(status))
		return false;
	}
	resetFile();
	return true;
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}

bool FileReaderNetCDF::isOpened(void)
{
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	return (_file.id != 0);
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}

std::string FileReaderNetCDF::getTimeParamId(void)
{
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	if (!isOpened()) {
		LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::getTimeParamId - File not opened")
		return "";
	}

	for (std::vector<NetCDFVar>::iterator it =  _file.vars.begin(); it != _file.vars.end(); ++it) {
		std::string name = it->name;
		std::transform(name.begin(), name.end(), name.begin(), ::tolower);
		if ((std::strcmp(name.c_str(),"time") == 0) && (it->type == NC_DOUBLE)) {
			return it->name;
		}
	}

	LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::getTimeParamId - Cannot find the time variable")
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	return "";
}

bool FileReaderNetCDF::getParamInfo(std::string& paramId, LocalParamType& paramType, int& dim1Size, int& dim2Size)
{
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	for (std::vector<NetCDFVar>::iterator it =  _file.vars.begin(); it != _file.vars.end(); ++it) {
		if (std::strcmp(it->name, paramId.c_str()) == 0) {
			if (it->dimids.size() == 1) {
				//scalar
				dim1Size = 1;
				dim2Size = 1;
			}
			else if (it->dimids.size() == 2) {
				//vector
				dim1Size = _file.dims[it->dimids[1]].length;
				dim2Size = 1;
			}
			else if (it->dimids.size() == 3) {
				//Tab2D
				dim1Size = _file.dims[it->dimids[1]].length;
				dim2Size = _file.dims[it->dimids[2]].length;
			}
			else {
				LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::getParamInfo - Variable dimensions not supported")
				return false;
			}
			switch (it->type) {
				case NC_FLOAT :
					paramType = LocalParamType::TYPE_FLOAT;
					break;
				case NC_DOUBLE :
					paramType = LocalParamType::TYPE_DOUBLE;
					break;
				case NC_SHORT :
					paramType = LocalParamType::TYPE_SHORT;
					break;
				case NC_INT :
					paramType = LocalParamType::TYPE_INT;
					break;
				default:
					paramType = LocalParamType::TYPE_UNKNOWN;
					LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::getParamInfo - Unknown variable type")
					return false;
			}
		}
	}
	return true;
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}

int FileReaderNetCDF::getRecordIndex(std::string& timeId, double time)
{
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	boost::mutex::scoped_lock scoped_lock(AMDA::Parameters::ParameterManager::mutexNetCDFLib);
	for (std::vector<NetCDFVar>::iterator it =  _file.vars.begin(); it != _file.vars.end(); ++it) {
		if (std::strcmp(it->name, timeId.c_str()) == 0) {
			if (!loadData(*it)) {
				LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::getRecordIndex - Cannot load time data")
				return -1;
			}
			double* buffer = (double*)it->buffer;
			for (int i = 0; i < getNbVarRecords(*it); ++i) {
				if (time <= buffer[i]) {
					return i;
				}	
			}
		}
	}
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	return -1;
}

FileReaderStatus FileReaderNetCDF::getParamPacketData(std::string& timeId, std::string& paramId,
		int recordIndex, double stopTime, LocalParamDataPacket *packet)
{
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	boost::mutex::scoped_lock scoped_lock(AMDA::Parameters::ParameterManager::mutexNetCDFLib);

	NetCDFVar* timeVar = NULL;
	NetCDFVar* paramVar = NULL;
	for (std::vector<NetCDFVar>::iterator it =  _file.vars.begin(); it != _file.vars.end(); ++it) {
		if (std::strcmp(it->name, timeId.c_str()) == 0) {
			timeVar = &(*it);
		}
		if (std::strcmp(it->name, paramId.c_str()) == 0) {
			paramVar = &(*it);
		}
	}

	if ((timeVar == NULL) || (paramVar == NULL)) {
		LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::getParamPacketData - Cannot retrieve time or param variable")
		return FRS_ERROR;
	}

	if (!loadData(*timeVar) || !loadData(*paramVar)) {
		LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::getParamPacketData - Cannot load time or param data")
		return FRS_ERROR;
	}

	double* time_buffer = (double*)timeVar->buffer;
	bool packetFull = false;
	int nbValues = getNbVarValuesByRecord(*paramVar);
	for (int i = recordIndex; i < getNbVarRecords(*paramVar); ++i) {
		double crtTime = time_buffer[i];
		void* pos = (void*)((char*)paramVar->buffer + paramVar->valuesize * nbValues * i);
		if (crtTime > stopTime) {
			return FRS_FINISH;
		}
		if (!packet->addData(crtTime, pos, packetFull))
		{
			if (packetFull)
				return FRS_MORE;
			LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::getParamPacketData - Error to add data in packet");
			return FRS_ERROR;
                }
	}

	return FRS_EOF;
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}
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bool FileReaderNetCDF::getInfo(const char* pInfoName, std::vector<double>& res)
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{
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	for (std::vector<NetCDFVar>::iterator it =  _file.vars.begin(); it != _file.vars.end(); ++it) {
		if (std::strcmp(it->name, pInfoName) == 0) {
			if (it->dimids.empty()) {
				LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::getInfo - dims error")
				return false;
			}
			int nbValues = 1;
			for (int i = 0; i < (int)it->dimids.size(); ++i) {
				nbValues *= _file.dims[it->dimids[i]].length;
			}
			int valuesize = 0;
			switch (it->type) {
				case NC_FLOAT :
					valuesize = sizeof(float);
					break;
				case NC_DOUBLE :
					valuesize = sizeof(double);
					break;
				case NC_SHORT :
					valuesize = sizeof(short);
					break;
				case NC_INT :
					valuesize = sizeof(int);
					break;
				default:
					LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::getInfo - var type not supported")
					return false;
			}
			int varid;
			int status = nc_inq_varid (_file.id, it->name, &varid);
			if (status != NC_NOERR) {
				LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::getInfo - Cannot load variable data : " << getErrorMessage(status))
				return false;
			}
			void* buffer = std::malloc(nbValues*valuesize);
			status = nc_get_var(_file.id, varid,  buffer);
			if (status != NC_NOERR) {
				LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::getInfo - Cannot load info data : " << getErrorMessage(status))
				std::free(buffer);
				return false;
			}
			for (int i = 0; i < nbValues; ++i) {
				switch (it->type) {
					case NC_FLOAT :
						res.push_back(((float*)buffer)[i]);
						break;
					case NC_DOUBLE :
						res.push_back(((double*)buffer)[i]);
						break;
					case NC_SHORT :
						res.push_back(((short*)buffer)[i]);
						break;
					case NC_INT :
						res.push_back(((int*)buffer)[i]);
						break;
					default:
						return false;
				}
			}
			std::free(buffer);
			return true;
		}
	}

	LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::getInfo - Cannot retrieve data for " << pInfoName)
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	return false;
}
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void FileReaderNetCDF::resetFile() {
	_file.id = 0;
	_file.dims.clear();
	for (std::vector<NetCDFVar>::iterator it = _file.vars.begin(); it != _file.vars.end(); ++it) {
		if (it->buffer != NULL) {
			std::free(it->buffer);
			it->buffer = NULL;
		}
	}
	_file.vars.clear();
	_file.atts.clear();
}

bool FileReaderNetCDF::loadNetCDFFileInfo() {
	if (!isOpened()) {
		LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::loadNetCDFFileInfo - File not opened")
		return false;
	}

	int status, ndims, nvars, ngatts, unlimdimid;
	status = nc_inq(_file.id, &ndims, &nvars, &ngatts, &unlimdimid);

	if (status != NC_NOERR) {
		LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::loadNetCDFFileInfo - Cannot load info in netCDF file : " << getErrorMessage(status))
		return false;
	}

	//Load dims
	for (int i = 0; i < ndims; ++i) {
		NetCDFDim dim;
		status = nc_inq_dim(_file.id, i, dim.name, &dim.length);
		if (status != NC_NOERR) {
			LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::loadNetCDFFileInfo - Cannot load dimension info : " << getErrorMessage(status))
			return false;
		}
		dim.isUnlimited = (i == unlimdimid);
		_file.dims.push_back(dim);
	}

	//Load global attributes
	for (int i = 0; i < ngatts; ++i) {
		NetCDFAtt att;
		status = nc_inq_attname(_file.id, NC_GLOBAL, i, att.name);
		if (status != NC_NOERR) {
			LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::loadNetCDFFileInfo - Cannot load global attribute name : " << getErrorMessage(status))
			return false;
		}
		status = nc_inq_att(_file.id, NC_GLOBAL, att.name, &att.type, &att.length);
		if (status != NC_NOERR) {
			LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::loadNetCDFFileInfo - Cannot load global attribute info : " << getErrorMessage(status))
			return false;
		}
		_file.atts.push_back(att);
	}

	//Load variables
	for (int i = 0; i < nvars; ++i) {
		int natts;
		int ndims;
		int dimids[NC_MAX_VAR_DIMS];
		NetCDFVar var;
		var.buffer = NULL;
		status = nc_inq_var(_file.id, i, var.name, &var.type, &ndims, dimids, &natts);
		if (status != NC_NOERR) {
			LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::loadNetCDFFileInfo - Cannot load variable info : " << getErrorMessage(status))
			return false;
		}
		if (ndims > 3) {
			//Not supported by the kernel
			continue;
		}
		for (int j = 0; j < ndims; ++j) {
			var.dimids.push_back(dimids[j]);
		}
		//Load variable attributes
		for (int j = 0; j < natts; ++j) {
			NetCDFAtt att;
			status = nc_inq_attname(_file.id, i, j, att.name);
			if (status != NC_NOERR) {
				LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::loadNetCDFFileInfo - Cannot load variable attribute : " << getErrorMessage(status))
				return false;
			}
			status = nc_inq_att(_file.id, i, att.name, &att.type, &att.length);
			if (status != NC_NOERR) {
				LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::loadNetCDFFileInfo - Cannot load variable attribute : " << getErrorMessage(status))
				return false;
			}
			var.atts.push_back(att);
		}
		_file.vars.push_back(var);
	}
	return true;
}

int FileReaderNetCDF::getNbVarValuesByRecord(const NetCDFVar& var) {
	if (var.dimids.size() == 1) {
		//scalar
		return 1;
	}
	else if (var.dimids.size() == 2) {
		//vector
		return _file.dims[var.dimids[1]].length;
	}
	else if (var.dimids.size() == 3) {
		//tab2d
		return _file.dims[var.dimids[1]].length * _file.dims[var.dimids[2]].length;
	}
	return 1;
}

int FileReaderNetCDF::getNbVarRecords(const NetCDFVar& var) {
	if (var.dimids.size() < 1)
		return 0;
	return _file.dims[var.dimids[0]].length;
}

bool FileReaderNetCDF::loadData(NetCDFVar& var) {
	if (var.buffer != NULL) {
		return true;
	}
	int nbRecords = getNbVarRecords(var);
	int nbValues = getNbVarValuesByRecord(var);
	int varid;
	int status = nc_inq_varid (_file.id, var.name, &varid);
	if (status != NC_NOERR) {
		LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::loadData - Cannot load variable data : " << getErrorMessage(status))
		return false;
	}
	switch (var.type) {
		case NC_FLOAT :
			var.valuesize = sizeof(float);
			break;
		case NC_DOUBLE :
			var.valuesize = sizeof(double);
			break;
		case NC_SHORT :
			var.valuesize = sizeof(short);
			break;
		case NC_INT :
			var.valuesize = sizeof(int);
			break;
		default:
			return false;
	}
	var.buffer = std::malloc(nbRecords*nbValues*var.valuesize);
	status = nc_get_var(_file.id, varid,  var.buffer);
	if (status != NC_NOERR) {
		LOG4CXX_ERROR(gLogger, "FileReaderNetCDF::loadData - Cannot load variable data : " << getErrorMessage(status))
		std::free(var.buffer);
		var.buffer = NULL;
		return false;
	}
	return true;
}

std::string FileReaderNetCDF::getErrorMessage(int status) {
	if (status == NC_NOERR) {
		return "NO ERROR";
	}
	return nc_strerror(status);
}
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} /* LocalFileInterface */
} /* AMDA */