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Minor HDF adjustments (#7577)

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* #7575 Summary HDF : Do not import summary if no UNSRMY file is found
* #7575 Summary HDF : Add optional check on time stamp of h5 file
* Use std::filesystem to check file access
* Do not keep h5 file open
This commit is contained in:
Magne Sjaastad
2021-04-16 10:52:30 +02:00
committed by GitHub
parent a44378e2f5
commit 52799e8b4c
15 changed files with 353 additions and 361 deletions
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243
ApplicationLibCode/FileInterface/RifHdf5SummaryReader.cpp
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@@ -18,7 +18,6 @@
#include "RifHdf5SummaryReader.h"
#include "RiaLogging.h"
#include "RiaQDateTimeTools.h"
#include "RiaTimeTTools.h"
#include "RifHdf5Reader.h"
@@ -33,17 +32,7 @@
//--------------------------------------------------------------------------------------------------
RifHdf5SummaryReader::RifHdf5SummaryReader( const QString& fileName )
{
try
{
m_hdfFile = new H5::H5File( fileName.toStdString().c_str(), H5F_ACC_RDONLY );
}
catch ( ... )
{
RiaLogging::error( "Failed to open HDF file " + fileName );
delete m_hdfFile;
m_hdfFile = nullptr;
}
m_fileName = fileName.toStdString();
}
//--------------------------------------------------------------------------------------------------
@@ -51,21 +40,6 @@ RifHdf5SummaryReader::RifHdf5SummaryReader( const QString& fileName )
//--------------------------------------------------------------------------------------------------
RifHdf5SummaryReader::~RifHdf5SummaryReader()
{
if ( m_hdfFile )
{
m_hdfFile->close();
delete m_hdfFile;
m_hdfFile = nullptr;
}
}
//--------------------------------------------------------------------------------------------------
///
//--------------------------------------------------------------------------------------------------
bool RifHdf5SummaryReader::isValid() const
{
return ( m_hdfFile != nullptr );
}
//--------------------------------------------------------------------------------------------------
@@ -73,11 +47,13 @@ bool RifHdf5SummaryReader::isValid() const
//--------------------------------------------------------------------------------------------------
std::vector<std::string> RifHdf5SummaryReader::vectorNames()
{
if ( m_hdfFile )
try
{
auto h5File = H5::H5File( m_fileName.c_str(), H5F_ACC_RDONLY );
std::vector<std::string> names;
auto groupNames = RifHdf5ReaderTools::getSubGroupNames( m_hdfFile, "summary_vectors" );
auto groupNames = RifHdf5ReaderTools::getSubGroupNames( &h5File, "summary_vectors" );
names.reserve( groupNames.size() );
for ( const auto& name : groupNames )
{
@@ -86,6 +62,9 @@ std::vector<std::string> RifHdf5SummaryReader::vectorNames()
return names;
}
catch ( ... )
{
}
return {};
}
@@ -95,36 +74,47 @@ std::vector<std::string> RifHdf5SummaryReader::vectorNames()
//--------------------------------------------------------------------------------------------------
std::vector<time_t> RifHdf5SummaryReader::timeSteps() const
{
std::vector<time_t> times;
// TODO: This function uses code taken from ESmry::dates(). There is conversion from time_t to
// chrono::system_clock::time_points, and then back to time_t again. Consider using one representation
double time_unit = 24 * 3600;
using namespace std::chrono;
using TP = time_point<system_clock>;
using DoubSec = duration<double, seconds::period>;
auto timeDeltasInDays = values( "TIME" );
std::vector<std::chrono::system_clock::time_point> timePoints;
TP startDat = std::chrono::system_clock::from_time_t( startDate() );
timePoints.reserve( timeDeltasInDays.size() );
for ( const auto& t : timeDeltasInDays )
try
{
timePoints.push_back( startDat + duration_cast<TP::duration>( DoubSec( t * time_unit ) ) );
auto h5File = H5::H5File( m_fileName.c_str(), H5F_ACC_RDONLY );
std::vector<time_t> times;
// TODO: This function uses code taken from ESmry::dates(). There is conversion from time_t to
// chrono::system_clock::time_points, and then back to time_t again. Consider using one representation
double time_unit = 24 * 3600;
using namespace std::chrono;
using TP = time_point<system_clock>;
using DoubSec = duration<double, seconds::period>;
auto timeDeltasInDays = values( "TIME" );
std::vector<std::chrono::system_clock::time_point> timePoints;
TP startDat = std::chrono::system_clock::from_time_t( startDate() );
timePoints.reserve( timeDeltasInDays.size() );
for ( const auto& t : timeDeltasInDays )
{
timePoints.push_back( startDat + duration_cast<TP::duration>( DoubSec( t * time_unit ) ) );
}
for ( const auto& d : timePoints )
{
auto timeAsTimeT = std::chrono::system_clock::to_time_t( d );
times.push_back( timeAsTimeT );
}
return times;
}
for ( const auto& d : timePoints )
catch ( ... )
{
auto timeAsTimeT = std::chrono::system_clock::to_time_t( d );
times.push_back( timeAsTimeT );
}
return times;
return {};
}
//--------------------------------------------------------------------------------------------------
@@ -132,35 +122,33 @@ std::vector<time_t> RifHdf5SummaryReader::timeSteps() const
//--------------------------------------------------------------------------------------------------
std::vector<double> RifHdf5SummaryReader::values( const std::string& vectorName, int smspecKeywordIndex ) const
{
if ( m_hdfFile )
try
{
try
auto h5File = H5::H5File( m_fileName.c_str(), H5F_ACC_RDONLY );
H5::Exception::dontPrint(); // Turn off auto-printing of failures to handle the errors appropriately
std::string idText = std::to_string( smspecKeywordIndex );
std::string groupPath = "summary_vectors/" + vectorName + "/" + idText;
{
H5::Exception::dontPrint(); // Turn off auto-printing of failures to handle the errors appropriately
H5::Group generalGroup = h5File.openGroup( groupPath.c_str() );
H5::DataSet dataset = H5::DataSet( generalGroup.openDataSet( "values" ) );
std::string idText = std::to_string( smspecKeywordIndex );
hsize_t dims[2];
H5::DataSpace dataspace = dataset.getSpace();
dataspace.getSimpleExtentDims( dims, nullptr );
std::string groupPath = "summary_vectors/" + vectorName + "/" + idText;
std::vector<double> values;
values.resize( dims[0] );
dataset.read( values.data(), H5::PredType::NATIVE_DOUBLE );
{
H5::Group generalGroup = m_hdfFile->openGroup( groupPath.c_str() );
H5::DataSet dataset = H5::DataSet( generalGroup.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 );
return values;
}
}
catch ( ... )
{
return values;
}
}
catch ( ... )
{
}
return {};
}
@@ -170,37 +158,36 @@ std::vector<double> RifHdf5SummaryReader::values( const std::string& vectorName,
//--------------------------------------------------------------------------------------------------
std::vector<double> RifHdf5SummaryReader::values( const std::string& vectorName ) const
{
if ( m_hdfFile )
try
{
try
auto h5File = H5::H5File( m_fileName.c_str(), H5F_ACC_RDONLY );
H5::Exception::dontPrint(); // Turn off auto-printing of failures to handle the errors appropriately
std::string groupPath = "summary_vectors/" + vectorName;
auto groupNames = RifHdf5ReaderTools::getSubGroupNames( &h5File, groupPath );
if ( !groupNames.empty() )
{
H5::Exception::dontPrint(); // Turn off auto-printing of failures to handle the errors appropriately
groupPath = groupPath + "/" + groupNames[0];
std::string groupPath = "summary_vectors/" + vectorName;
H5::Group generalGroup = h5File.openGroup( groupPath.c_str() );
H5::DataSet dataset = H5::DataSet( generalGroup.openDataSet( "values" ) );
auto groupNames = RifHdf5ReaderTools::getSubGroupNames( m_hdfFile, groupPath );
if ( !groupNames.empty() )
{
groupPath = groupPath + "/" + groupNames[0];
hsize_t dims[2];
H5::DataSpace dataspace = dataset.getSpace();
dataspace.getSimpleExtentDims( dims, nullptr );
H5::Group generalGroup = m_hdfFile->openGroup( groupPath.c_str() );
H5::DataSet dataset = H5::DataSet( generalGroup.openDataSet( "values" ) );
std::vector<double> values;
values.resize( dims[0] );
dataset.read( values.data(), H5::PredType::NATIVE_DOUBLE );
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 );
return values;
}
}
catch ( ... )
{
return values;
}
}
catch ( ... )
{
}
return {};
}
@@ -210,48 +197,44 @@ std::vector<double> RifHdf5SummaryReader::values( const std::string& vectorName
//--------------------------------------------------------------------------------------------------
time_t RifHdf5SummaryReader::startDate() const
{
if ( m_hdfFile )
try
{
try
{
H5::Exception::dontPrint(); // Turn off auto-printing of failures to handle the errors appropriately
auto h5File = H5::H5File( m_fileName.c_str(), H5F_ACC_RDONLY );
QString groupPath = QString( "general" );
H5::Exception::dontPrint(); // Turn off auto-printing of failures to handle the errors appropriately
H5::Group GridFunction_00002 = m_hdfFile->openGroup( groupPath.toStdString().c_str() );
H5::DataSet dataset = H5::DataSet( GridFunction_00002.openDataSet( "start_date" ) );
QString groupPath = QString( "general" );
hsize_t dims[2];
H5::DataSpace dataspace = dataset.getSpace();
dataspace.getSimpleExtentDims( dims, nullptr );
H5::Group GridFunction_00002 = h5File.openGroup( groupPath.toStdString().c_str() );
H5::DataSet dataset = H5::DataSet( GridFunction_00002.openDataSet( "start_date" ) );
std::vector<int> values;
values.resize( dims[0] );
dataset.read( values.data(), H5::PredType::NATIVE_INT );
hsize_t dims[2];
H5::DataSpace dataspace = dataset.getSpace();
dataspace.getSimpleExtentDims( dims, nullptr );
int day = values[0];
int month = values[1];
int year = values[2];
int hour = values[3];
int minute = values[4];
int second = values[5];
std::vector<int> values;
values.resize( dims[0] );
dataset.read( values.data(), H5::PredType::NATIVE_INT );
QDate date( year, month, day );
QTime time( hour, minute, second );
int day = values[0];
int month = values[1];
int year = values[2];
int hour = values[3];
int minute = values[4];
int second = values[5];
QDateTime dt( date, time );
QDate date( year, month, day );
QTime time( hour, minute, second );
QDateTime reportDateTime = RiaQDateTimeTools::createUtcDateTime( dt );
QDateTime dt( date, time );
time_t myTime = RiaTimeTTools::fromQDateTime( reportDateTime );
return myTime;
}
catch ( ... )
{
}
QDateTime reportDateTime = RiaQDateTimeTools::createUtcDateTime( dt );
time_t myTime = RiaTimeTTools::fromQDateTime( reportDateTime );
return myTime;
}
catch ( ... )
{
}
RiaLogging::error( "Not able to read start_date from HDF5 " );
return {};
}