This class retrieves all information from an HDF5 file. More...

#include <HDF5CF.h>

Inheritance diagram for HDF5CF::File:

Collaboration diagram for HDF5CF::File:

Public Member Functions
virtual void	Add_Supplement_Attrs (bool) throw (Exception)
	Add supplemental attributes such as fullpath and original name. More...

virtual void	Adjust_Dim_Name ()=0
	Adjust dimension names based on different products. More...

virtual void	Adjust_Obj_Name ()=0
	Adjust object names based on different products. More...

virtual void	Flatten_Obj_Name (bool) throw (Exception)
	Flatten the object name. More...

const vector< Attribute * > &	getAttributes () const
	Public interface to obtain information of all attributes under the root group. More...

const hid_t	getFileID () const
	Obtain the HDF5 file ID. More...

const vector< Group * > &	getGroups () const
	Public interface to obtain all the group info. More...

const string &	getPath () const
	Obtain the path of the file. More...

const vector< Var * > &	getVars () const
	Public interface to obtain information of all variables. More...

virtual void	Handle_Coor_Attr ()=0
	Handle "coordinates" attributes. More...

virtual void	Handle_CVar ()=0
	Handle coordinate variables. More...

virtual void	Handle_DimNameClashing ()=0
	Handle dimension name clashing. Since COARDS requires the change of cv names, So we need to handle dimension name clashing specially. More...

virtual void	Handle_SpVar ()=0
	Handle special variables. More...

virtual void	Handle_SpVar_Attr ()=0
	Handle special variable attributes. More...

virtual void	Handle_Unsupported_Dspace () throw (Exception)
	Handle unsupported HDF5 dataspaces for datasets. More...

virtual void	Handle_Unsupported_Dtype (bool) throw (Exception)
	Handle unsupported HDF5 datatypes. More...

virtual void	Retrieve_H5_Info (const char *path, hid_t file_id, bool include_attr) throw (Exception)
	Retrieve DDS information from the HDF5 file. The reason to separate reading DDS from DAS is: DAP needs to hold all values of attributes in the memory, building DDS doesn't need the attributes. So to reduce huge memory allocation for some HDF5 files, we separate the access of DAS from DDS although internally they still share common routines. More...

virtual void	Retrieve_H5_Supported_Attr_Values () throw (Exception)
	Retrieve attribute values for the supported HDF5 datatypes. More...

virtual	~File ()

Protected Member Functions
void	Add_One_FakeDim_Name (Dimension *dim) throw (Exception)

void	Add_One_Float_Attr (Attribute *attr, const string &attrname, float float_value) throw (Exception)

void	Add_Str_Attr (Attribute *attr, const string &attrname, const string &strvalue) throw (Exception)

void	Adjust_Duplicate_FakeDim_Name (Dimension *dim) throw (Exception)

void	Change_Attr_One_Str_to_Others (Attribute attr, Var var) throw (Exception)

	File (const char *path, hid_t file_id)

virtual string	get_CF_string (string)

template<typename T >
void	Handle_General_NameClashing (set< string > &objnameset, vector< T * > &objvec) throw (Exception)

void	Handle_GeneralObj_NameClashing (bool, set< string > &objnameset) throw (Exception)

void	Handle_Obj_AttrNameClashing () throw (Exception)

void	Handle_RootGroup_NameClashing (set< string > &objnameset) throw (Exception)

void	Handle_Var_NameClashing (set< string > &objnameset) throw (Exception)

void	Insert_One_NameSizeMap_Element (string name, hsize_t size) throw (Exception)

void	Insert_One_NameSizeMap_Element2 (map< string, hsize_t > &, string name, hsize_t size) throw (Exception)

virtual void	Replace_Var_Attrs (Var src, Var target)

virtual void	Replace_Var_Info (Var src, Var target)

void	Retrieve_H5_Attr_Info (Attribute *, hid_t obj_id, const int j, bool &unsup_attr_dtype) throw (Exception)

void	Retrieve_H5_Attr_Value (Attribute *attr, string) throw (Exception)

void	Retrieve_H5_Obj (hid_t grp_id, const char *gname, bool include_attr) throw (Exception)

void	Retrieve_H5_VarDim (Var *, hid_t dset_id, const string &varname, bool &unsup_var_dspace) throw (Exception)

void	Retrieve_H5_VarType (Var *, hid_t dset_id, const string &varname, bool &unsup_var_dtype) throw (Exception)

Protected Attributes
int	addeddimindex

map< string, hsize_t >	dimname_to_dimsize

set< string >	dimnamelist

map< hsize_t, string >	dimsize_to_fakedimname
	Handle added dimension names. More...

hid_t	fileid

vector< Group * >	groups
	Non-root group vectors. More...

string	path

vector< Attribute * >	root_attrs
	Root attribute vectors. More...

hid_t	rootid

bool	unsupported_attr_dtype

bool	unsupported_var_dspace

bool	unsupported_var_dtype

vector< Var * >	vars
	Var vectors. More...

Detailed Description

This class retrieves all information from an HDF5 file.

Definition at line 506 of file HDF5CF.h.

Constructor & Destructor Documentation

File::~File ( )

virtual

Definition at line 47 of file HDF5CF.cc.

References fileid, groups, root_attrs, rootid, and vars.

HDF5CF::File::File	(	const char *	path,
		hid_t	file_id
	)

inlineprotected

Definition at line 621 of file HDF5CF.h.

Member Function Documentation

void File::Add_One_FakeDim_Name	(	Dimension *	dim	)
throw	(	Exception
	)

protected

Definition at line 1077 of file HDF5CF.cc.

References HDF5CFUtil::gen_unique_name(), throw2, and throw4.

Referenced by HDF5CF::GMFile::Add_Dim_Name_ACOS_L2S(), HDF5CF::GMFile::Add_Dim_Name_GPM(), HDF5CF::GMFile::Add_Dim_Name_Mea_Ozonel3z(), and HDF5CF::GMFile::Add_Dim_Name_SMAP().

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void File::Add_One_Float_Attr	(	Attribute *	attr,
		const string &	attrname,
		float	float_value
	)
throw	(	Exception
	)

protected

Definition at line 1177 of file HDF5CF.cc.

References H5FLOAT32.

Referenced by HDF5CF::GMFile::Add_Aqu_Attrs(), HDF5CF::GMFile::Add_GPM_Attrs(), and HDF5CF::GMFile::Add_SeaWiFS_Attrs().

void File::Add_Str_Attr	(	Attribute *	attr,
		const string &	attrname,
		const string &	strvalue
	)
throw	(	Exception
	)

protected

Definition at line 1163 of file HDF5CF.cc.

References H5FSTRING.

Referenced by HDF5CF::GMFile::Add_Aqu_Attrs(), HDF5CF::GMFile::Add_GPM_Attrs(), HDF5CF::GMFile::Handle_Coor_Attr(), HDF5CF::EOS5File::Handle_Coor_Attr(), HDF5CF::EOS5File::Handle_EOS5CVar_Unit_Attr(), and HDF5CF::GMFile::Handle_GPM_l1_Coor_Attr().

void File::Add_Supplement_Attrs	(	bool	add_path	)
throw	(	Exception
	)

virtual

Add supplemental attributes such as fullpath and original name.

Reimplemented in HDF5CF::EOS5File, and HDF5CF::GMFile.

Definition at line 1322 of file HDF5CF.cc.

Referenced by HDF5CF::GMFile::Add_Supplement_Attrs(), and HDF5CF::EOS5File::Add_Supplement_Attrs().

virtual void HDF5CF::File::Adjust_Dim_Name ( )

pure virtual

Adjust dimension names based on different products.

Implemented in HDF5CF::EOS5File, and HDF5CF::GMFile.

void File::Adjust_Duplicate_FakeDim_Name	(	Dimension *	dim	)
throw	(	Exception
	)

protected

Definition at line 1130 of file HDF5CF.cc.

References HDF5CFUtil::gen_unique_name(), and throw2.

Referenced by HDF5CF::GMFile::Add_Dim_Name_ACOS_L2S(), HDF5CF::GMFile::Add_Dim_Name_Mea_Ozonel3z(), and HDF5CF::GMFile::Add_Dim_Name_SMAP().

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virtual void HDF5CF::File::Adjust_Obj_Name ( )

pure virtual

Adjust object names based on different products.

Implemented in HDF5CF::EOS5File, and HDF5CF::GMFile.

void File::Change_Attr_One_Str_to_Others	(	Attribute *	attr,
		Var *	var
	)
throw	(	Exception
	)

protected

Definition at line 1187 of file HDF5CF.cc.

References H5CHAR, H5FLOAT32, H5FLOAT64, H5FSTRING, H5INT16, H5INT32, H5UCHAR, H5UINT16, H5UINT32, NULL, throw2, throw4, and throw5.

Referenced by HDF5CF::GMFile::Add_GPM_Attrs().

void File::Flatten_Obj_Name	(	bool	include_attr	)
throw	(	Exception
	)

virtual

Flatten the object name.

Reimplemented in HDF5CF::EOS5File, and HDF5CF::GMFile.

Definition at line 866 of file HDF5CF.cc.

Referenced by HDF5CF::GMFile::Flatten_Obj_Name(), and HDF5CF::EOS5File::Flatten_Obj_Name().

string File::get_CF_string ( string s )

protectedvirtual

Reimplemented in HDF5CF::EOS5File, and HDF5CF::GMFile.

Definition at line 1026 of file HDF5CF.cc.

Referenced by HDF5CF::GMFile::get_CF_string(), and HDF5CF::EOS5File::get_CF_string().

const vector< Attribute * >& HDF5CF::File::getAttributes ( ) const

inline

Public interface to obtain information of all attributes under the root group.

Definition at line 578 of file HDF5CF.h.

References root_attrs.

Referenced by gen_eos5_cfdas(), and gen_gmh5_cfdas().

const hid_t HDF5CF::File::getFileID ( ) const

inline

Obtain the HDF5 file ID.

Definition at line 559 of file HDF5CF.h.

References fileid.

Referenced by gen_eos5_cfdds(), and gen_gmh5_cfdds().

const vector< Group * >& HDF5CF::File::getGroups ( ) const

inline

Public interface to obtain all the group info.

Definition at line 584 of file HDF5CF.h.

References groups.

Referenced by gen_eos5_cfdas(), and gen_gmh5_cfdas().

const string& HDF5CF::File::getPath ( ) const

inline

Obtain the path of the file.

Definition at line 566 of file HDF5CF.h.

References path.

Referenced by gen_eos5_cfdds(), and gen_gmh5_cfdds().

const vector< Var * >& HDF5CF::File::getVars ( ) const

inline

Public interface to obtain information of all variables.

Definition at line 572 of file HDF5CF.h.

References vars.

Referenced by gen_eos5_cfdas(), gen_eos5_cfdds(), gen_gmh5_cfdas(), and gen_gmh5_cfdds().

virtual void HDF5CF::File::Handle_Coor_Attr ( )

pure virtual

Handle "coordinates" attributes.

Implemented in HDF5CF::EOS5File, and HDF5CF::GMFile.

virtual void HDF5CF::File::Handle_CVar ( )

pure virtual

Handle coordinate variables.

Implemented in HDF5CF::EOS5File, and HDF5CF::GMFile.

virtual void HDF5CF::File::Handle_DimNameClashing ( )

pure virtual

Handle dimension name clashing. Since COARDS requires the change of cv names, So we need to handle dimension name clashing specially.

Implemented in HDF5CF::EOS5File, and HDF5CF::GMFile.

template<class T >

void File::Handle_General_NameClashing	(	set< string > &	objnameset,
		vector< T * > &	objvec
	)
throw	(	Exception
	)

protected

Definition at line 971 of file HDF5CF.cc.

References HDF5CFUtil::gen_unique_name().

Referenced by HDF5CF::EOS5File::Handle_EOS5CVar_AttrNameClashing(), HDF5CF::GMFile::Handle_GMCVar_AttrNameClashing(), HDF5CF::GMFile::Handle_GMSPVar_AttrNameClashing(), and Handle_Obj_AttrNameClashing().

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void File::Handle_GeneralObj_NameClashing	(	bool	include_attr,
		set< string > &	objnameset
	)
throw	(	Exception
	)

protected

Definition at line 1016 of file HDF5CF.cc.

Referenced by HDF5CF::GMFile::Handle_Obj_NameClashing(), and HDF5CF::EOS5File::Handle_Obj_NameClashing().

void File::Handle_Obj_AttrNameClashing	(		)
throw	(	Exception
	)

protected

Definition at line 939 of file HDF5CF.cc.

References groups, Handle_General_NameClashing(), root_attrs, and vars.

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void File::Handle_RootGroup_NameClashing	(	set< string > &	objnameset	)
throw	(	Exception
	)

protected

Definition at line 911 of file HDF5CF.cc.

References HDF5CFUtil::gen_unique_name().

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virtual void HDF5CF::File::Handle_SpVar ( )

pure virtual

Handle special variables.

Implemented in HDF5CF::EOS5File, and HDF5CF::GMFile.

virtual void HDF5CF::File::Handle_SpVar_Attr ( )

pure virtual

Handle special variable attributes.

Implemented in HDF5CF::EOS5File, and HDF5CF::GMFile.

void File::Handle_Unsupported_Dspace	(		)
throw	(	Exception
	)

virtual

Handle unsupported HDF5 dataspaces for datasets.

Reimplemented in HDF5CF::EOS5File, and HDF5CF::GMFile.

Definition at line 850 of file HDF5CF.cc.

References unsupported_var_dspace, and vars.

Referenced by HDF5CF::GMFile::Handle_Unsupported_Dspace(), and HDF5CF::EOS5File::Handle_Unsupported_Dspace().

void File::Handle_Unsupported_Dtype	(	bool	include_attr	)
throw	(	Exception
	)

virtual

Handle unsupported HDF5 datatypes.

Reimplemented in HDF5CF::EOS5File, and HDF5CF::GMFile.

Definition at line 776 of file HDF5CF.cc.

References HDF5CFUtil::cf_strict_support_type().

Referenced by HDF5CF::GMFile::Handle_Unsupported_Dtype(), and HDF5CF::EOS5File::Handle_Unsupported_Dtype().

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void File::Handle_Var_NameClashing	(	set< string > &	objnameset	)
throw	(	Exception
	)

protected

Definition at line 906 of file HDF5CF.cc.

void File::Insert_One_NameSizeMap_Element	(	string	name,
		hsize_t	size
	)
throw	(	Exception
	)

protected

Definition at line 1044 of file HDF5CF.cc.

References throw4.

Referenced by HDF5CF::GMFile::Add_Dim_Name_Dimscale_General_Product(), HDF5CF::GMFile::Add_Dim_Name_GPM(), HDF5CF::GMFile::Add_Dim_Name_Mea_Ozonel3z(), HDF5CF::GMFile::Add_Dim_Name_Mea_SeaWiFS(), HDF5CF::GMFile::Add_Dim_Name_SMAP(), and HDF5CF::GMFile::Handle_CVar_GPM_L1().

void File::Insert_One_NameSizeMap_Element2	(	map< string, hsize_t > &	name_to_size,
		string	name,
		hsize_t	size
	)
throw	(	Exception
	)

protected

Definition at line 1054 of file HDF5CF.cc.

References throw4.

void File::Replace_Var_Attrs	(	Var *	src,
		Var *	target
	)

protectedvirtual

Definition at line 1424 of file HDF5CF.cc.

References HDF5CF::Var::attrs, HDF5CF::Attribute::count, HDF5CF::Var::dims, HDF5CF::Attribute::dtype, HDF5CF::Attribute::fstrsize, HDF5CF::Attribute::name, HDF5CF::Attribute::newname, HDF5CF::Attribute::strsize, and HDF5CF::Attribute::value.

Referenced by HDF5CF::EOS5File::Replace_Var_Attrs().

void File::Replace_Var_Info	(	Var *	src,
		Var *	target
	)

protectedvirtual

void File::Retrieve_H5_Attr_Info	(	Attribute *	attr,
		hid_t	obj_id,
		const int	j,
		bool &	unsup_attr_dtype
	)
throw	(	Exception
	)

protected

Definition at line 461 of file HDF5CF.cc.

References HDF5CFUtil::cf_strict_support_type(), HDF5CFUtil::H5type_to_H5DAPtype(), NULL, throw1, and throw2.

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void File::Retrieve_H5_Attr_Value	(	Attribute *	attr,
		string	obj_name
	)
throw	(	Exception
	)

protected

Definition at line 614 of file HDF5CF.cc.

References H5FSTRING, HDF5CFUtil::H5type_to_H5DAPtype(), H5VSTRING, NULL, throw2, throw4, and HDF5CFUtil::trim_string().

Referenced by HDF5CF::GMFile::Add_Aqu_Attrs(), HDF5CF::GMFile::Add_Dim_Name_GPM(), HDF5CF::EOS5File::Adjust_Attr_Value(), HDF5CF::EOS5File::Check_Aura_Product_Status(), HDF5CF::GMFile::Check_General_Product_Pattern(), HDF5CF::EOS5File::Handle_EOS5CVar_Special_Attr(), HDF5CF::EOS5File::Handle_EOS5CVar_Unit_Attr(), Retrieve_H5_Supported_Attr_Values(), HDF5CF::GMFile::Retrieve_H5_Supported_Attr_Values(), and HDF5CF::EOS5File::Retrieve_H5_Supported_Attr_Values().

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void File::Retrieve_H5_Info	(	const char *	path,
		hid_t	file_id,
		bool	include_attr
	)
throw	(	Exception
	)

virtual

Retrieve DDS information from the HDF5 file. The reason to separate reading DDS from DAS is: DAP needs to hold all values of attributes in the memory, building DDS doesn't need the attributes. So to reduce huge memory allocation for some HDF5 files, we separate the access of DAS from DDS although internally they still share common routines.

Reimplemented in HDF5CF::EOS5File, and HDF5CF::GMFile.

Definition at line 83 of file HDF5CF.cc.

References throw1.

Referenced by HDF5CF::GMFile::Retrieve_H5_Info(), and HDF5CF::EOS5File::Retrieve_H5_Info().