Per-spectrum binary index entry for an imzML dataset. More...

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

Classes
struct	AuxArray
	Index entry for one auxiliary (non-m/z, non-intensity) external array. More...

Public Types
enum class	DataType : uint8_t { FLOAT32 , FLOAT64 , INT32 , INT64 , UNKNOWN }
	Scalar type identifier for binary array elements. More...

Public Attributes
int32_t	index {0}
	0-based document order

uint32_t	x {0}
	Pixel column (1-based, IMS:1000050)

uint32_t	y {0}
	Pixel row (1-based, IMS:1000051)

uint32_t	z {1}
	Depth slice (1-based, IMS:1000052)

uint64_t	mz_offset {0}
	Byte offset of m/z array (IMS:1000102)

uint64_t	mz_length {0}
	Element count (IMS:1000103)

DataType	mz_type {DataType::UNKNOWN}

bool	mz_compressed {false}
	Compressed (not MS:1000576) on m/z array.

uint64_t	int_offset {0}
	Byte offset of intensity array.

uint64_t	int_length {0}
	Element count.

DataType	int_type {DataType::UNKNOWN}

bool	int_compressed {false}
	Compressed (not MS:1000576) on intensity array.

std::vector< AuxArray >	aux
	Extra external arrays (IM, …) in document order.

Detailed Description

Per-spectrum binary index entry for an imzML dataset.

Records the byte offset and element count for the m/z and intensity arrays in the companion .ibd file, together with the pixel (x,y,z) coordinates and zlib-compression flags (MS:1000574). Built during ImzMLHandler parsing and stored inside OnDiscImzMLExperiment so that random-access spectrum decoding requires only a single fseek + fread per call. Compressed m/z, intensity, and auxiliary arrays (any child of MS:1000572 other than uncompressed MS:1000576) are rejected at decode time (inflate / numpress of external arrays is not supported).

Optional aux entries describe additional external arrays (ion mobility and other FloatDataArray values). Both in-memory ImzMLFile::load and OnDiscImzMLExperiment::getSpectrum() attach those as FloatDataArray on the returned spectrum when present.

Class Documentation

◆ OpenMS::ImzMLSpectrumIndex::AuxArray

struct OpenMS::ImzMLSpectrumIndex::AuxArray

Index entry for one auxiliary (non-m/z, non-intensity) external array.

Used for ion mobility and other per-peak FloatDataArrays so on-disc and in-memory loaders expose the same viewer contract (containsIMData(), equal length to peaks).

Class Members
string	accession	MS accession (e.g. MS:1003006), may be empty.
bool	compressed {false}	Child of MS:1000572 other than MS:1000576 (unsupported)
uint64_t	encoded_bytes {0}	IMS:1000104 byte length on disk.
uint64_t	length {0}	IMS:1000103 element count.
string	name	Ontology / free-text array name (FloatDataArray::getName)
uint64_t	offset {0}	IMS:1000102.
DataType	type {DataType::UNKNOWN}
string	unit_accession	unitAccession on the array-identity cvParam (may be empty)

Member Enumeration Documentation

◆ DataType

enum class DataType : uint8_t

strong

Scalar type identifier for binary array elements.

Enumerator
FLOAT32
FLOAT64
INT32
INT64
UNKNOWN

Member Data Documentation

◆ aux

std::vector<AuxArray> aux

Extra external arrays (IM, …) in document order.

◆ index

int32_t index {0}

0-based document order

◆ int_compressed

bool int_compressed {false}

Compressed (not MS:1000576) on intensity array.

◆ int_length

uint64_t int_length {0}

Element count.

◆ int_offset

uint64_t int_offset {0}

Byte offset of intensity array.

◆ int_type

DataType int_type {DataType::UNKNOWN}

◆ mz_compressed

bool mz_compressed {false}

Compressed (not MS:1000576) on m/z array.

◆ mz_length

uint64_t mz_length {0}

Element count (IMS:1000103)

◆ mz_offset

uint64_t mz_offset {0}

Byte offset of m/z array (IMS:1000102)

◆ mz_type

DataType mz_type {DataType::UNKNOWN}

◆ x

uint32_t x {0}

Pixel column (1-based, IMS:1000050)

◆ y

uint32_t y {0}

Pixel row (1-based, IMS:1000051)

◆ z

uint32_t z {1}

Depth slice (1-based, IMS:1000052)

Classes

Public Types

Public Attributes