Pixel grid metadata and (x, y) -> spectrum_index lookup for MSI data. More...

#include <OpenMS/IMAGING/MSImagingGeometry.h>

Collaboration diagram for MSImagingGeometry:

Classes
struct	Pixel
	A pixel in the imaging grid, linked to one spectrum in the experiment. More...

Public Member Functions
void	setDimensions (UInt width, UInt height)
	Sets the image dimensions.

UInt	getWidth () const
	Image width.

UInt	getHeight () const
	Image height.

void	setPixelSize (double x, double y, const std::string &unit="micrometer")
	Records the physical pixel size and its unit.

double	getPixelSizeX () const
	Physical pixel size along x.

double	getPixelSizeY () const
	Physical pixel size along y.

const std::string &	getPixelSizeUnit () const
	Unit for the pixel size.

void	addPixel (UInt x, UInt y, Size spectrum_index)
	Adds a pixel at (`x`, `y`) bound to `spectrum_index`.

bool	hasPixel (UInt x, UInt y) const
	Tests pixel presence at (`x`, `y`).

Size	getSpectrumIndex (UInt x, UInt y) const
	Looks up the spectrum index at (`x`, `y`).

const std::vector< Pixel > &	getPixels () const
	Pixels in insertion order.

Size	getNumberOfPixels () const
	Total number of pixels with a bound spectrum.

void	clear ()
	Resets all state (dimensions, pixel size, pixels, lookup, regions).

void	addRegion (const MSImagingRegion &region)
	Adds a region to the geometry as a decoupled overlay.

void	removeRegion (Size id)
	Removes the region with the given id.

void	clearRegions ()
	Removes all regions; acquired pixels are left untouched.

const std::vector< MSImagingRegion > &	getRegions () const
	All regions in insertion order.

const MSImagingRegion &	getRegion (Size id) const
	Returns the region with the given id.

Size	getNumberOfRegions () const
	Number of regions in the overlay.

Size	regionOf (UInt x, UInt y) const
	Returns the id of the region owning the acquired pixel at (`x`, `y`).

std::vector< Size >	getRegionPixels (Size id) const
	Acquired pixels belonging to a region, as indices into getPixels().

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

Static Public Attributes
static constexpr Size	NO_REGION = std::numeric_limits<Size>::max()
	Sentinel returned by regionOf() when a coordinate belongs to no region.

Static Private Member Functions
static UInt64	packKey_ (UInt x, UInt y)

Private Attributes
UInt	width_ = 0

UInt	height_ = 0

double	pixel_size_x_ = 1.0

double	pixel_size_y_ = 1.0

std::string	pixel_size_unit_ = "micrometer"

std::vector< Pixel >	pixels_

std::unordered_map< UInt64, Size >	lookup_

std::vector< MSImagingRegion >	regions_

std::unordered_map< Size, Size >	region_id_to_index_

Detailed Description

Pixel grid metadata and (x, y) -> spectrum_index lookup for MSI data.

Coordinates are zero-based. imzML files are one-based; the Phase 2 loader (ImzMLFile) is responsible for normalizing those to zero-based coordinates before populating this geometry.

3D MSI is intentionally not modeled here. Serial-section experiments should be handled as a collection of MSImagingExperiment objects (one per section).

Class Documentation

◆ OpenMS::MSImagingGeometry::Pixel

struct OpenMS::MSImagingGeometry::Pixel

A pixel in the imaging grid, linked to one spectrum in the experiment.

Collaboration diagram for MSImagingGeometry::Pixel:

[legend]

Class Members
Size	spectrum_index = 0	Index into the bound MSExperiment.
UInt	x = 0	Column index (zero-based).
UInt	y = 0	Row index (zero-based).

Member Function Documentation

◆ addPixel()

void addPixel	(	UInt	x,
		UInt	y,
		Size	spectrum_index
	)

Adds a pixel at (x, y) bound to spectrum_index.

Parameters

[in]	x	Column index (zero-based).
[in]	y	Row index (zero-based).
[in]	spectrum_index	Index into the bound MSExperiment.

Exceptions

Exception::InvalidValue on duplicate coordinates, or if dimensions have been set and (x, y) is outside [0, width) x [0, height).

◆ addRegion()

void addRegion ( const MSImagingRegion & region )

Adds a region to the geometry as a decoupled overlay.

Membership of acquired pixels in the region is derived on demand via MSImagingRegion::contains(); no per-pixel region state is stored.

Parameters

[in] region Region footprint to add (copied in).

Exceptions

Exception::InvalidValue if the id equals NO_REGION, the id is already present, or the footprint geometrically overlaps an existing region.

◆ clear()

void clear ( )

Resets all state (dimensions, pixel size, pixels, lookup, regions).

◆ clearRegions()

void clearRegions ( )

Removes all regions; acquired pixels are left untouched.

◆ getHeight()

UInt getHeight ( ) const

Image height.

Returns: Number of rows.

◆ getNumberOfPixels()

Size getNumberOfPixels ( ) const

Total number of pixels with a bound spectrum.

Returns: Size of the pixel list.

◆ getNumberOfRegions()

Size getNumberOfRegions ( ) const

Number of regions in the overlay.

Returns: Size of the region list.

◆ getPixels()

const std::vector< Pixel > & getPixels ( ) const

Pixels in insertion order.

Returns: Reference to the internal pixel list.

◆ getPixelSizeUnit()

const std::string & getPixelSizeUnit ( ) const

Unit for the pixel size.

Returns: Reference to the unit string.

◆ getPixelSizeX()

double getPixelSizeX ( ) const

Physical pixel size along x.

Returns: Stored x pixel size.

◆ getPixelSizeY()

double getPixelSizeY ( ) const

Physical pixel size along y.

Returns: Stored y pixel size.

◆ getRegion()

const MSImagingRegion & getRegion ( Size id ) const

Returns the region with the given id.

Parameters

[in] id Region id to look up.

Returns: Reference to the stored region.

Exceptions

Exception::ElementNotFound if no region with that id exists.

◆ getRegionPixels()

std::vector< Size > getRegionPixels ( Size id ) const

Acquired pixels belonging to a region, as indices into getPixels().

Parameters

[in] id Region id.

Returns: Positions in getPixels() of the member pixels (use to index getPixels()).

Exceptions

Exception::ElementNotFound if no region with that id exists.

◆ getRegions()

const std::vector< MSImagingRegion > & getRegions ( ) const

All regions in insertion order.

Returns: Reference to the internal region list.

◆ getRegionSpectrumIndices()

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

Spectrum indices of the acquired pixels belonging to a region.

Parameters

[in] id Region id.

Returns: The spectrum_index values of the member pixels (use to index the bound MSExperiment).

Exceptions

Exception::ElementNotFound if no region with that id exists.

◆ getSpectrumIndex()

Size getSpectrumIndex	(	UInt	x,
		UInt	y
	)		const

Looks up the spectrum index at (x, y).

Parameters

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

Returns: spectrum_index recorded for that pixel.

Exceptions

Exception::ElementNotFound if no pixel exists at that coordinate.

◆ getWidth()

UInt getWidth ( ) const

Image width.

Returns: Number of columns.

◆ 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 was inserted at that coordinate.

◆ packKey_()

static UInt64 packKey_	(	UInt	x,
		UInt	y
	)

staticprivate

◆ regionOf()

Size regionOf	(	UInt	x,
		UInt	y
	)		const

Returns the id of the region owning the acquired pixel at (x, y).

Parameters

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

Returns: The owning region's id, or NO_REGION if (x, y) is not an acquired pixel or belongs to no region.

◆ removeRegion()

void removeRegion ( Size id )

Removes the region with the given id.

Parameters

[in] id Region id to remove.

Exceptions

Exception::ElementNotFound if no region with that id exists.

◆ setDimensions()

void setDimensions	(	UInt	width,
		UInt	height
	)

Sets the image dimensions.

Parameters

[in]	width	Number of columns.
[in]	height	Number of rows.

◆ setPixelSize()

void setPixelSize	(	double	x,
		double	y,
		const std::string &	unit = `"micrometer"`
	)

Records the physical pixel size and its unit.

Parameters

[in]	x	Pixel size along x.
[in]	y	Pixel size along y.
[in]	unit	Length unit (default "micrometer").

Member Data Documentation

◆ height_

UInt height_ = 0

private

◆ lookup_

std::unordered_map<UInt64, Size> lookup_

private

◆ NO_REGION

constexpr Size NO_REGION = std::numeric_limits<Size>::max()

staticconstexpr

Sentinel returned by regionOf() when a coordinate belongs to no region.

◆ pixel_size_unit_

std::string pixel_size_unit_ = "micrometer"

private

◆ pixel_size_x_

double pixel_size_x_ = 1.0

private

◆ pixel_size_y_

double pixel_size_y_ = 1.0

private

◆ pixels_

std::vector<Pixel> pixels_

private

◆ region_id_to_index_

std::unordered_map<Size, Size> region_id_to_index_

private

◆ regions_

std::vector<MSImagingRegion> regions_

private

◆ width_

UInt width_ = 0

private

Classes

Public Member Functions

Static Public Attributes

Static Private Member Functions

Private Attributes

Detailed Description

Class Documentation

◆ OpenMS::MSImagingGeometry::Pixel

Member Function Documentation

◆ addPixel()

◆ addRegion()

◆ clear()

◆ clearRegions()

◆ getHeight()

◆ getNumberOfPixels()

◆ getNumberOfRegions()

◆ getPixels()

◆ getPixelSizeUnit()

◆ getPixelSizeX()

◆ getPixelSizeY()

◆ getRegion()

◆ getRegionPixels()

◆ getRegions()

◆ getRegionSpectrumIndices()

◆ getSpectrumIndex()

◆ getWidth()

◆ hasPixel()

◆ packKey_()

◆ regionOf()

◆ removeRegion()

◆ setDimensions()

◆ setPixelSize()

Member Data Documentation

◆ height_

◆ lookup_

◆ NO_REGION

◆ pixel_size_unit_

◆ pixel_size_x_

◆ pixel_size_y_

◆ pixels_

◆ region_id_to_index_

◆ regions_

◆ width_