MSImagingExperiment Class Reference

In-memory model for a 2D imaging mass spectrometry dataset. More...

#include <OpenMS/IMAGING/MSImagingExperiment.h>

Collaboration diagram for MSImagingExperiment:

Public Member Functions
	MSImagingExperiment ()=default
	MSImagingExperiment (MSExperiment exp)
	Constructs an MSImagingExperiment wrapping exp with an empty geometry.
MSImagingExperiment &	operator= (MSExperiment exp)
	Replaces the owned MSExperiment and resets the geometry.
MSExperiment &	getMSExperiment ()
	Mutable access to the owned MSExperiment.
const MSExperiment &	getMSExperiment () const
	Read access to the owned MSExperiment.
void	setMSExperiment (MSExperiment exp)
	Replaces the owned MSExperiment.
MSImagingGeometry &	getGeometry ()
	Mutable access to the owned geometry.
const MSImagingGeometry &	getGeometry () const
	Read access to the owned geometry.
void	setGeometry (MSImagingGeometry geom)
	Replaces the owned geometry.
Size	getNumberOfPixels () const
	Number of pixels in the geometry.
Size	getNumberOfSpectra () const
	Number of spectra in the underlying experiment.
bool	hasPixel (UInt x, UInt y) const
	Tests pixel presence at (x, y).
MSSpectrum &	getSpectrum (UInt x, UInt y)
	Mutable access to the spectrum bound to the pixel at (x, y).
const MSSpectrum &	getSpectrum (UInt x, UInt y) const
	Read access to the spectrum bound to the pixel at (x, y).
IonImage	extractIonImage (double mz, double tolerance_ppm) const
	Extracts an ion image by summing peak intensities inside [mz - dm, mz + dm], with dm = mz * tolerance_ppm * 1e-6.
void	validate () const
	Validates that every pixel references an in-range spectrum_index.

Private Attributes
MSExperiment	experiment_
MSImagingGeometry	geometry_

Detailed Description

In-memory model for a 2D imaging mass spectrometry dataset.

Owns an MSExperiment (spectra) and an MSImagingGeometry (pixel grid + pixel -> spectrum index mapping). Provides pixel-based spectrum access and a simple sum-based ion image extraction.

A 3D / serial-section experiment is modeled as a collection of MSImagingExperiment objects, one per section.

Constructor & Destructor Documentation

MSImagingExperiment() [1/2]

MSImagingExperiment ( )

default

MSImagingExperiment() [2/2]

MSImagingExperiment ( MSExperiment  exp )

explicit

Constructs an MSImagingExperiment wrapping exp with an empty geometry.

Parameters

[in]

exp

MSExperiment to take ownership of (moved in).

Member Function Documentation

extractIonImage()

IonImage extractIonImage	(	double	mz,
		double	tolerance_ppm
	)		const

Extracts an ion image by summing peak intensities inside [mz - dm, mz + dm], with dm = mz * tolerance_ppm * 1e-6.

Preconditions: each referenced spectrum must be sorted by m/z. Phase 2's ImzMLFile loader will guarantee this; Phase 1 callers must ensure it manually.

Pixels not present in the geometry remain invalid in the returned image. Pixels with a spectrum but no peaks in the window are marked valid with intensity 0. The returned image's m/z range is set to [mz - dm, mz + dm].

Parameters

[in]	mz	m/z center of the extraction window (>= 0).
[in]	tolerance_ppm	Half-window width in ppm (>= 0).

Returns

Image of the same dimensions as the geometry.

Exceptions

Exception::InvalidValue	if mz or tolerance_ppm is negative or non-finite, or if any pixel references a missing spectrum_index.
Exception::IndexOverflow	if a pixel coordinate falls outside the geometry's declared dimensions.

getGeometry() [1/2]

MSImagingGeometry & getGeometry

(

)

Mutable access to the owned geometry.

Returns

Reference to the owned geometry.

getGeometry() [2/2]

const MSImagingGeometry & getGeometry

(

)

const

Read access to the owned geometry.

Returns

Const reference to the owned geometry.

getMSExperiment() [1/2]

MSExperiment & getMSExperiment

(

)

Mutable access to the owned MSExperiment.

Returns

Reference to the owned experiment.

getMSExperiment() [2/2]

const MSExperiment & getMSExperiment

(

)

const

Read access to the owned MSExperiment.

Returns

Const reference to the owned experiment.

getNumberOfPixels()

Size getNumberOfPixels

(

)

const

Number of pixels in the geometry.

Returns

Geometry pixel count.

getNumberOfSpectra()

Size getNumberOfSpectra

(

)

const

Number of spectra in the underlying experiment.

Returns

Spectrum count.

getSpectrum() [1/2]

MSSpectrum & getSpectrum	(	UInt	x,
		UInt	y
	)

Mutable access to the spectrum bound to the pixel at (x, y).

Parameters

[in]	x	Column index.
[in]	y	Row index.

Returns

Reference to the bound spectrum.

Exceptions

Exception::ElementNotFound	if no pixel exists at that coordinate.
Exception::InvalidValue	if the pixel references a spectrum_index outside the underlying experiment.

getSpectrum() [2/2]

const MSSpectrum & getSpectrum	(	UInt	x,
		UInt	y
	)		const

Read access to the spectrum bound to the pixel at (x, y).

Parameters

[in]	x	Column index.
[in]	y	Row index.

Returns

Const reference to the bound spectrum.

Exceptions

Exception::ElementNotFound	if no pixel exists at that coordinate.
Exception::InvalidValue	if the pixel references a spectrum_index outside the underlying experiment.

hasPixel()

bool hasPixel	(	UInt	x,
		UInt	y
	)		const

Tests pixel presence at (x, y).

Parameters

[in]	x	Column index.
[in]	y	Row index.

Returns

true if a pixel exists at that coordinate.

operator=()

MSImagingExperiment & operator=

(

MSExperiment

exp

)

Replaces the owned MSExperiment and resets the geometry.

The previous geometry's spectrum indices are tied to the previous experiment's spectrum order and become meaningless after assignment, so the geometry is cleared. Use setMSExperiment() if you want to keep the existing geometry.

Parameters

[in]

exp

MSExperiment to take ownership of (moved in).

Returns

Reference to *this.

setGeometry()

void setGeometry

(

MSImagingGeometry

geom

)

Replaces the owned geometry.

Parameters

[in]

geom

New geometry (moved in).

setMSExperiment()

void setMSExperiment

(

MSExperiment

exp

)

Replaces the owned MSExperiment.

Parameters

[in]

exp

New experiment (moved in).

validate()

void validate

(

)

const

Validates that every pixel references an in-range spectrum_index.

Exceptions

Exception::InvalidValue

on the first dangling reference.

Member Data Documentation

experiment_

MSExperiment experiment_

private

geometry_

MSImagingGeometry geometry_

private