io_helpers.cc File Reference

#include <cassert>
#include <cmath>
#include <cstddef>
#include <memory>
#include <array>
#include <string>
#include <vector>
#include "pism/util/ConfigInterface.hh"
#include "pism/util/Context.hh"
#include "pism/util/Grid.hh"
#include "pism/util/Logger.hh"
#include "pism/util/Profiling.hh"
#include "pism/util/Time.hh"
#include "pism/util/VariableMetadata.hh"
#include "pism/util/error_handling.hh"
#include "pism/util/Interpolation1D.hh"
#include "pism/util/io/File.hh"
#include "pism/util/io/IO_Flags.hh"
#include "pism/util/io/LocalInterpCtx.hh"
#include "pism/util/io/io_helpers.hh"
#include "pism/util/pism_utilities.hh"
#include "pism/util/projection.hh"

Go to the source code of this file.

Classes
struct	pism::io::StartCountInfo

Namespaces
namespace	pism
namespace	pism::io
	Input and output code (NetCDF wrappers, etc)

Functions
static void	pism::io::interpolate (const Grid &grid, const LocalInterpCtx &lic, double const *input_array, double *output_array)
	Bi-(or tri-)linear interpolation.
static StartCountInfo	pism::io::compute_start_and_count (std::vector< AxisType > &dim_types, const std::array< int, 4 > &start, const std::array< int, 4 > &count)
void	pism::io::define_dimension (const File &file, unsigned long int length, const VariableMetadata &metadata)
	Define a dimension and the associated coordinate variable. Set attributes.
void	pism::io::define_time (const File &file, const Context &ctx)
	Prepare a file for output.
void	pism::io::define_time (const File &file, const std::string &name, const std::string &calendar, const std::string &units, units::System::Ptr unit_system)
void	pism::io::append_time (const File &file, const Config &config, double time_seconds)
	Prepare a file for output.
void	pism::io::append_time (const File &file, const std::string &name, double value)
	Append to the time dimension.
static void	pism::io::define_dimensions (const SpatialVariableMetadata &var, const Grid &grid, const File &file)
	Define dimensions a variable depends on.
static void	pism::io::write_dimension_data (const File &file, const std::string &name, const std::vector< double > &data)
void	pism::io::write_dimensions (const SpatialVariableMetadata &var, const Grid &grid, const File &file)
static bool	pism::io::transpose (std::vector< AxisType > dimension_types)
static std::vector< AxisType >	pism::io::dimension_types (const File &file, const std::string &var_name, std::shared_ptr< units::System > unit_system)
static void	pism::io::transpose (const double *input, const std::vector< AxisType > &input_axes, const std::array< int, 4 > &count, double *output)
static void	pism::io::check_for_missing_values (const File &file, const std::string &variable_name, double tolerance, const double *buffer, size_t buffer_length)
static void	pism::io::read_distributed_array (const File &file, const std::string &variable_name, std::shared_ptr< units::System > unit_system, const std::array< int, 4 > &start, const std::array< int, 4 > &count, double *output)
	Read an array distributed according to the grid.
void	pism::io::define_spatial_variable (const SpatialVariableMetadata &metadata, const Grid &grid, const File &file, io::Type default_type)
	Define a NetCDF variable corresponding to a VariableMetadata object.
static std::string	pism::io::check_units (const VariableMetadata &variable, const std::string &input_units, const Logger &log)
void	pism::io::read_spatial_variable (const SpatialVariableMetadata &variable, const Grid &grid, const File &file, unsigned int time, double *output)
	Read a variable from a file into an array output.
void	pism::io::write_spatial_variable (const SpatialVariableMetadata &metadata, const Grid &grid, const File &file, const double *input)
	Write a double array to a file.
static void	pism::io::check_grid_overlap (const grid::InputGridInfo &input, const Grid &internal, const std::vector< double > &z_internal)
void	pism::io::check_input_grid (const grid::InputGridInfo &input_grid, const Grid &internal_grid, const std::vector< double > &internal_z_levels)
	Check that x, y, and z coordinates of the input grid are strictly increasing.
void	pism::io::regrid_spatial_variable (const SpatialVariableMetadata &variable, const Grid &target_grid, const LocalInterpCtx &interp_context, const File &file, double *output)
	Regrid from a NetCDF file into a distributed array output.
void	pism::io::define_timeseries (const VariableMetadata &var, const std::string &dimension_name, const File &file, io::Type nctype)
	Define a NetCDF variable corresponding to a time-series.
std::vector< double >	pism::io::read_1d_variable (const File &file, const std::string &variable_name, const std::string &units, std::shared_ptr< units::System > unit_system)
void	pism::io::write_timeseries (const File &file, const VariableMetadata &metadata, size_t t_start, const std::vector< double > &data)
	Write a time-series data to a file.
void	pism::io::define_time_bounds (const VariableMetadata &var, const std::string &dimension_name, const std::string &bounds_name, const File &file, io::Type nctype)
std::vector< double >	pism::io::read_bounds (const File &file, const std::string &bounds_variable_name, const std::string &internal_units, std::shared_ptr< units::System > unit_system)
void	pism::io::write_time_bounds (const File &file, const VariableMetadata &metadata, size_t t_start, const std::vector< double > &data)
void	pism::io::read_time_info (std::shared_ptr< units::System > unit_system, const File &file, const std::string &time_name, const std::string &time_units, std::vector< double > &times, std::vector< double > &bounds)
bool	pism::io::file_exists (MPI_Comm com, const std::string &filename)
VariableMetadata	pism::io::read_attributes (const File &file, const std::string &variable_name, std::shared_ptr< units::System > unit_system)
void	pism::io::write_attributes (const File &file, const VariableMetadata &variable, io::Type nctype)
	Write variable attributes to a NetCDF file.
std::string	pism::io::time_dimension (units::System::Ptr unit_system, const File &file, const std::string &variable_name)
void	pism::io::move_if_exists (MPI_Comm com, const std::string &file_to_move, int rank_to_use)
	Moves the file aside (file.nc -> file.nc~).
void	pism::io::remove_if_exists (MPI_Comm com, const std::string &file_to_remove, int rank_to_use)
	Check if a file is present are remove it.