ImzMLSpectrumRules Class Reference

Per-spectrum rules shared by every imzML access path (in-memory, streaming, metadata-only, index-only and OnDiscImzMLExperiment), so they cannot drift apart. More...

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

Static Public Member Functions
static double	scanStartTime (const MSSpectrum &s)
	Acquisition (scan start) time of an imaging spectrum in seconds.
static bool	isLoadableAuxArray (const std::string &name, uint64_t length, ImzMLSpectrumIndex::DataType type, uint64_t n_peaks, bool warn=false, uint32_t x=0, uint32_t y=0, uint32_t z=0)
	Whether an external auxiliary array is read from the .ibd for a spectrum with n_peaks peaks (it needs an identity, a non-zero length equal to the peak count and a known binary data type). The one rule for every access path.
static void	applyIMPeakType (MSSpectrum &s, bool has_im_array)
	Set the IM peak type after the auxiliary arrays are known: with an ion mobility array, UNKNOWN becomes IM_PROFILE (a type the file declares, e.g. MS:1003441, is kept); without one, the type is UNKNOWN.
static void	attachAuxArray (MSSpectrum &s, const std::string &name, const std::string &unit_accession, const std::vector< float > &values)
	Attach the values of an external auxiliary array read from the .ibd.
static void	pruneEmptyDataArrays (MSSpectrum &s)
	Drop the empty Float/Integer/StringDataArrays left by MzMLHandler for aux arrays that were not filled.

Detailed Description

Per-spectrum rules shared by every imzML access path (in-memory, streaming, metadata-only, index-only and OnDiscImzMLExperiment), so they cannot drift apart.

Member Function Documentation

applyIMPeakType()

static void applyIMPeakType ( MSSpectrum &  s, bool  has_im_array  )

static

Set the IM peak type after the auxiliary arrays are known: with an ion mobility array, UNKNOWN becomes IM_PROFILE (a type the file declares, e.g. MS:1003441, is kept); without one, the type is UNKNOWN.

attachAuxArray()

static void attachAuxArray ( MSSpectrum &  s, const std::string &  name, const std::string &  unit_accession, const std::vector< float > &  values  )

static

Attach the values of an external auxiliary array read from the .ibd.

They go into the first still-empty FloatDataArray named name (MzMLHandler creates one per auxiliary binaryDataArray, with its metadata), so repeated names map 1:1 in order; without one, a new array named name (and unit_accession) is added.

isLoadableAuxArray()

static bool isLoadableAuxArray ( const std::string &  name, uint64_t  length, ImzMLSpectrumIndex::DataType  type, uint64_t  n_peaks, bool  warn = false, uint32_t  x = 0, uint32_t  y = 0, uint32_t  z = 0  )

static

Whether an external auxiliary array is read from the .ibd for a spectrum with n_peaks peaks (it needs an identity, a non-zero length equal to the peak count and a known binary data type). The one rule for every access path.

With warn, a skipped array (other than one of length 0) is logged with the pixel x / y / z.

pruneEmptyDataArrays()

static void pruneEmptyDataArrays ( MSSpectrum &  s )

static

Drop the empty Float/Integer/StringDataArrays left by MzMLHandler for aux arrays that were not filled.

scanStartTime()

static double scanStartTime ( const MSSpectrum &  s )

static

Acquisition (scan start) time of an imaging spectrum in seconds.

Imaging spectra keep RT at -1 and store the time as the MetaValue imzml:scan_start_time. An RT the caller set (>= 0) wins over the MetaValue; a non-numeric, non-finite or negative MetaValue counts as no time (a scan start time is relative to the start of the run, so a negative one is a placeholder).

Returns

The time (>= 0), or the (negative) RT if the spectrum has none.