MSImagingGeometry Class Reference

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).

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_

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).

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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:

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).

clear()

void clear

(

)

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

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.

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.

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

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

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

width_

UInt width_ = 0

private