tatami_mtx Namespace Reference

Read tatami matrices from Matrix Market files. More...

Classes
struct	Automatic
	Enable automatic type determination. More...
struct	Options
	Options for load_matrix() and friends. More...

Functions
template<typename Value_ , typename Index_ , typename StoredValue_ = Automatic, typename StoredIndex_ = Automatic>
std::shared_ptr< tatami::Matrix< Value_, Index_ > >	load_matrix (byteme::Reader &reader, const Options &options)
template<typename Value_ , typename Index_ , typename StoredValue_ = Automatic, typename StoredIndex_ = Automatic>
std::shared_ptr< tatami::Matrix< Value_, Index_ > >	load_matrix_from_text_file (const char *filepath, const Options &options)
template<typename Value_ , typename Index_ , typename StoredValue_ = Automatic, typename StoredIndex_ = Automatic>
std::shared_ptr< tatami::Matrix< Value_, Index_ > >	load_matrix_from_gzip_file (const char *filepath, const Options &options)
template<typename Value_ , typename Index_ , typename StoredValue_ = Automatic, typename StoredIndex_ = Automatic>
std::shared_ptr< tatami::Matrix< Value_, Index_ > >	load_matrix_from_some_file (const char *filepath, const Options &options)
template<typename Value_ , typename Index_ , typename StoredValue_ = Automatic, typename StoredIndex_ = Automatic>
std::shared_ptr< tatami::Matrix< Value_, Index_ > >	load_matrix_from_text_buffer (const unsigned char *buffer, size_t n, const Options &options)
template<typename Value_ , typename Index_ , typename StoredValue_ = Automatic, typename StoredIndex_ = Automatic>
std::shared_ptr< tatami::Matrix< Value_, Index_ > >	load_matrix_from_zlib_buffer (const unsigned char *buffer, size_t n, const Options &options)
template<typename Value_ , typename Index_ , typename StoredValue_ = Automatic, typename StoredIndex_ = Automatic>
std::shared_ptr< tatami::Matrix< Value_, Index_ > >	load_matrix_from_some_buffer (const unsigned char *buffer, size_t n, const Options &options)

Detailed Description

Read tatami matrices from Matrix Market files.

Function Documentation

load_matrix()

template<typename Value_ , typename Index_ , typename StoredValue_ = Automatic, typename StoredIndex_ = Automatic>

std::shared_ptr< tatami::Matrix< Value_, Index_ > > tatami_mtx::load_matrix	(	byteme::Reader &	reader,
		const Options &	options
	)

Load a tatami::Matrix from a Matrix Market file. Coordinate formats will yield a sparse matrix, while array formats will yield a dense matrix. The storage types depend on the Matrix Market field type as well as the settings of StoredValue_ and StoredIndex_.

Template Parameters

Value_	Data type for the tatami::Matrix interface.
Index_	Integer index type for the tatami::Matrix interface.
StoredValue_	Matrix data type that is stored in memory. If set to Automatic, it defaults to double for real/double fields and int for integer fields.
StoredIndex_	Index data type that is stored in memory for sparse matrices. If set to Automatic, it defaults to uint8_t if no dimension is greater than 255; uint16_t if no dimension is greater than 65536; and int otherwise.

Parameters

reader	A byteme::Reader instance containing bytes from a Matrix Market file.
options	Options for loading the matrix.

Returns

Pointer to a tatami::Matrix instance containing data from the Matrix Market file.

load_matrix_from_text_file()

template<typename Value_ , typename Index_ , typename StoredValue_ = Automatic, typename StoredIndex_ = Automatic>

std::shared_ptr< tatami::Matrix< Value_, Index_ > > tatami_mtx::load_matrix_from_text_file	(	const char *	filepath,
		const Options &	options
	)

Load a tatami::Matrix from a Matrix Market text file, see load_matrix() for details.

Template Parameters

Value_	Data type for the tatami::Matrix interface.
Index_	Integer index type for the tatami::Matrix interface.
StoredValue_	Matrix data type that is stored in memory, see load_matrix() for details.
StoredIndex_	Index data type that is stored in memory for sparse matrices, see load_matrix() for details.
parallel_	Whether to parallelize the loading and parsing.

Parameters

filepath	Path to a Matrix Market file.
options	Options for loading the matrix.

Returns

Pointer to a tatami::Matrix instance containing data from the Matrix Market file.

load_matrix_from_gzip_file()

template<typename Value_ , typename Index_ , typename StoredValue_ = Automatic, typename StoredIndex_ = Automatic>

std::shared_ptr< tatami::Matrix< Value_, Index_ > > tatami_mtx::load_matrix_from_gzip_file	(	const char *	filepath,
		const Options &	options
	)

Load a tatami::Matrix from a Gzip-compressed Matrix Market file, see load_matrix() for details.

Template Parameters

Value_	Data type for the tatami::Matrix interface.
Index_	Integer index type for the tatami::Matrix interface.
StoredValue_	Matrix data type that is stored in memory, see load_matrix() for details.
StoredIndex_	Index data type that is stored in memory for sparse matrices, see load_matrix() for details.

Parameters

filepath	Path to a Matrix Market file.
options	Options for loading the matrix.

Returns

Pointer to a tatami::Matrix instance containing data from the Matrix Market file.

load_matrix_from_some_file()

template<typename Value_ , typename Index_ , typename StoredValue_ = Automatic, typename StoredIndex_ = Automatic>

std::shared_ptr< tatami::Matrix< Value_, Index_ > > tatami_mtx::load_matrix_from_some_file	(	const char *	filepath,
		const Options &	options
	)

Load a tatami::Matrix from a possibly Gzip-compressed Matrix Market file, see load_matrix() for details.

Template Parameters

Value_	Data type for the tatami::Matrix interface.
Index_	Integer index type for the tatami::Matrix interface.
StoredValue_	Matrix data type that is stored in memory, see load_matrix() for details.
StoredIndex_	Index data type that is stored in memory for sparse matrices, see load_matrix() for details.

Parameters

filepath	Path to a Matrix Market file.
options	Options for loading the matrix.

Returns

Pointer to a tatami::Matrix instance containing data from the Matrix Market file.

load_matrix_from_text_buffer()

template<typename Value_ , typename Index_ , typename StoredValue_ = Automatic, typename StoredIndex_ = Automatic>

std::shared_ptr< tatami::Matrix< Value_, Index_ > > tatami_mtx::load_matrix_from_text_buffer	(	const unsigned char *	buffer,
		size_t	n,
		const Options &	options
	)

Load a tatami::Matrix from a buffer containing a Matrix Market file, see load_matrix() for details.

Template Parameters

Value_	Data type for the tatami::Matrix interface.
Index_	Integer index type for the tatami::Matrix interface.
StoredValue_	Matrix data type that is stored in memory, see load_matrix() for details.
StoredIndex_	Index data type that is stored in memory for sparse matrices, see load_matrix() for details.

Parameters

buffer	Array containing the contents of an uncompressed Matrix Market file.
n	Length of the array.
options	Options for loading the matrix.

Returns

Pointer to a tatami::Matrix instance containing data from the Matrix Market file.

load_matrix_from_zlib_buffer()

template<typename Value_ , typename Index_ , typename StoredValue_ = Automatic, typename StoredIndex_ = Automatic>

std::shared_ptr< tatami::Matrix< Value_, Index_ > > tatami_mtx::load_matrix_from_zlib_buffer	(	const unsigned char *	buffer,
		size_t	n,
		const Options &	options
	)

Load a tatami::Matrix from a buffer containing a Gzip/Zlib-compressed Matrix Market file, see load_matrix() for details.

Template Parameters

Value_	Data type for the tatami::Matrix interface.
Index_	Integer index type for the tatami::Matrix interface.
StoredValue_	Matrix data type that is stored in memory, see load_matrix() for details.
StoredIndex_	Index data type that is stored in memory for sparse matrices, see load_matrix() for details.

Parameters

buffer	Array containing the contents of a Matrix Market file after Gzip/Zlib compression.
n	Length of the array.
options	Options for loading the matrix.

Returns

Pointer to a tatami::Matrix instance containing data from the Matrix Market file.

load_matrix_from_some_buffer()

template<typename Value_ , typename Index_ , typename StoredValue_ = Automatic, typename StoredIndex_ = Automatic>

std::shared_ptr< tatami::Matrix< Value_, Index_ > > tatami_mtx::load_matrix_from_some_buffer	(	const unsigned char *	buffer,
		size_t	n,
		const Options &	options
	)

Load a tatami::Matrix from a buffer containing a possibly Gzip/Zlib-compressed Matrix Market file, see load_matrix() for details.

Template Parameters

Value_	Data type for the tatami::Matrix interface.
Index_	Integer index type for the tatami::Matrix interface.
StoredValue_	Matrix data type that is stored in memory, see load_matrix() for details.
StoredIndex_	Index data type that is stored in memory for sparse matrices, see load_matrix() for details.

Parameters

buffer	Array containing the contents of a Matrix Market file, possibly after Gzip/Zlib compression.
n	Length of the array.
options	Options for loading the matrix.

Returns

Pointer to a tatami::Matrix instance containing data from the Matrix Market file.