ImzMLBinaryIO Class Reference

Shared .ibd binary array decode utilities for imzML handlers. More...

#include <OpenMS/FORMAT/HANDLERS/ImzMLHandlerHelper.h>

Static Public Member Functions
static void	readMzArray (FILE *ibd, uint64_t offset, uint64_t count, ImzMLSpectrumIndex::DataType dt, std::vector< double > &out, const std::string &ibd_path)
	Read an m/z array from the companion .ibd file.
static void	readIntArray (FILE *ibd, uint64_t offset, uint64_t count, ImzMLSpectrumIndex::DataType dt, std::vector< float > &out, const std::string &ibd_path)
	Read an intensity array from the companion .ibd file.
static void	readAuxArray (FILE *ibd, uint64_t offset, uint64_t count, ImzMLSpectrumIndex::DataType dt, std::vector< float > &out, const std::string &ibd_path, const std::string &array_name)
	Read an auxiliary (non-m/z, non-intensity) array from the .ibd file.
static void	writeFloat32Array (FILE *ibd, const float *data, uint64_t count, const std::string &ibd_path)
	Write a float32 array to the companion .ibd file (little-endian).
static void	writeMzAsFloat32 (FILE *ibd, const std::vector< double > &mz, const std::string &ibd_path)
	Write m/z values as float32 to the companion .ibd file.
static void	writeFloat64Array (FILE *ibd, const double *data, uint64_t count, const std::string &ibd_path)
	Write a float64 array to the companion .ibd file (little-endian).
static void	writeMzAsFloat64 (FILE *ibd, const std::vector< double > &mz, const std::string &ibd_path)
	Write m/z values as float64 to the companion .ibd file.

Detailed Description

Shared .ibd binary array decode utilities for imzML handlers.

Member Function Documentation

readAuxArray()

static void readAuxArray ( FILE *  ibd, uint64_t  offset, uint64_t  count, ImzMLSpectrumIndex::DataType  dt, std::vector< float > &  out, const std::string &  ibd_path, const std::string &  array_name  )

static

Read an auxiliary (non-m/z, non-intensity) array from the .ibd file.

imzML permits additional binaryDataArray entries per spectrum beyond the mandatory m/z and intensity pair — most notably ion mobility arrays such as MS:1003006 "mean inverse reduced ion mobility array". Values are returned as float because OpenMS stores auxiliary spectrum data in MSSpectrum::FloatDataArray.

Parameters

[in]	ibd	Open binary file handle.
[in]	offset	Byte offset (IMS:1000102).
[in]	count	Element count (IMS:1000103).
[in]	dt	Scalar type of stored values.
[out]	out	Decoded values as float (FloatDataArray storage).
[in]	ibd_path	Path used in error messages.
[in]	array_name	Array name used in error messages (e.g. the CV term name).

Note

Compressed external arrays (any child of MS:1000572 other than uncompressed MS:1000576) are not decoded; callers must reject them before invoking this method. IMS:1000104 is then required to know how many compressed bytes to read.

Exceptions

Exception::ParseError

if seek or read fails.

readIntArray()

static void readIntArray ( FILE *  ibd, uint64_t  offset, uint64_t  count, ImzMLSpectrumIndex::DataType  dt, std::vector< float > &  out, const std::string &  ibd_path  )

static

Read an intensity array from the companion .ibd file.

Exceptions

Exception::ParseError

if seek or read fails.

readMzArray()

static void readMzArray ( FILE *  ibd, uint64_t  offset, uint64_t  count, ImzMLSpectrumIndex::DataType  dt, std::vector< double > &  out, const std::string &  ibd_path  )

static

Read an m/z array from the companion .ibd file.

Parameters

[in]	ibd	Open binary file handle.
[in]	offset	Byte offset (IMS:1000102).
[in]	count	Element count (IMS:1000103).
[in]	dt	Scalar type of stored values.
[out]	out	Decoded m/z values.
[in]	ibd_path	Path used in error messages.

Exceptions

Exception::ParseError

if seek or read fails.

writeFloat32Array()

static void writeFloat32Array ( FILE *  ibd, const float *  data, uint64_t  count, const std::string &  ibd_path  )

static

Write a float32 array to the companion .ibd file (little-endian).

Exceptions

Exception::ParseError

if write fails.

writeFloat64Array()

static void writeFloat64Array ( FILE *  ibd, const double *  data, uint64_t  count, const std::string &  ibd_path  )

static

Write a float64 array to the companion .ibd file (little-endian).

Exceptions

Exception::ParseError

if write fails.

writeMzAsFloat32()

static void writeMzAsFloat32 ( FILE *  ibd, const std::vector< double > &  mz, const std::string &  ibd_path  )

static

Write m/z values as float32 to the companion .ibd file.

Exceptions

Exception::ParseError

if write fails.

writeMzAsFloat64()

static void writeMzAsFloat64 ( FILE *  ibd, const std::vector< double > &  mz, const std::string &  ibd_path  )

static

Write m/z values as float64 to the companion .ibd file.

Exceptions

Exception::ParseError

if write fails.