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.

IonImage	extractIonImage (double mz, double tolerance_ppm, Size region_id) const
	Extracts an ion image by summing peak intensities inside [mz - dm, mz + dm], with dm = mz * tolerance_ppm * 1e-6. Overloaded with region id to extract a specific region only.

void	validate () const
	Validates that every pixel references an in-range spectrum_index.

std::vector< Size >	getRegionSpectrumIndices (Size region_id) const
	Spectrum indices of the acquired pixels belonging to a region.

Private Member Functions
void	extractIntoImage_ (IonImage &image, double mz_lo, double mz_hi, const std::vector< MSImagingGeometry::Pixel > &pixels, const std::vector< Size > &pixel_indices) const
	extracts the sum of intensities in [mz_lo:mz_hi] into image on a pixel level, indices control which pixels are summed

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

◆ extractIntoImage_()

void extractIntoImage_	(	IonImage &	image,
		double	mz_lo,
		double	mz_hi,
		const std::vector< MSImagingGeometry::Pixel > &	pixels,
		const std::vector< Size > &	pixel_indices
	)		const

private

extracts the sum of intensities in [mz_lo:mz_hi] into image on a pixel level, indices control which pixels are summed

Parameters

image	image values are saved in here
mz_lo	lower m/z bound
mz_hi	upper m/z bound
pixels	Geometry pixels from getPixels()
pixel_indices	indices which pixels are to be summed

◆ extractIonImage() [1/2]

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.

◆ extractIonImage() [2/2]

IonImage extractIonImage	(	double	mz,
		double	tolerance_ppm,
		Size	region_id
	)		const

Extracts an ion image by summing peak intensities inside [mz - dm, mz + dm], with dm = mz * tolerance_ppm * 1e-6. Overloaded with region id to extract a specific region only.

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).
[in]	region_id	region of pixels to be extracted

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.
Exception::ElementNotFound	if an unknown region id is supplied.

◆ 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.

◆ getRegionSpectrumIndices()

std::vector< Size > getRegionSpectrumIndices ( Size region_id ) const

Spectrum indices of the acquired pixels belonging to a region.

Delegates to the geometry; the returned values are spectrum_index values (indices into the bound MSExperiment), not pixel positions.

Parameters

[in] region_id Region id.

Returns: The spectrum_index values of the region's member pixels.

Exceptions

Exception::ElementNotFound if region_id is unknown.

◆ 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

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MSImagingExperiment() [1/2]

◆ MSImagingExperiment() [2/2]

Member Function Documentation

◆ extractIntoImage_()

◆ extractIonImage() [1/2]

◆ extractIonImage() [2/2]

◆ getGeometry() [1/2]

◆ getGeometry() [2/2]

◆ getMSExperiment() [1/2]

◆ getMSExperiment() [2/2]

◆ getNumberOfPixels()

◆ getNumberOfSpectra()

◆ getRegionSpectrumIndices()

◆ getSpectrum() [1/2]

◆ getSpectrum() [2/2]

◆ hasPixel()

◆ operator=()

◆ setGeometry()

◆ setMSExperiment()

◆ validate()

Member Data Documentation

◆ experiment_

◆ geometry_