MSImagingRegion Class Reference

A spatial region within an MSI dataset, in global pixel coordinates. More...

#include <OpenMS/IMAGING/MSImagingRegion.h>

Collaboration diagram for MSImagingRegion:

Public Types
enum class	Shape { Rectangle , Mask }
	Discriminates how a region's footprint is represented. More...

Public Member Functions
const std::string &	getName () const
	Region name.
bool	contains (UInt x, UInt y) const
	Tests whether the global coordinate (x, y) is inside the region.
bool	intersects (const MSImagingRegion &other) const
	Tests whether this region's footprint geometrically overlaps other.
Shape	getShape () const
	Region shape (Rectangle or Mask).
Size	getId () const
	Region identifier.
UInt	getMinX () const
	Leftmost column of the global bounding box (inclusive).
UInt	getMinY () const
	Top row of the global bounding box (inclusive).
UInt	getMaxX () const
	Rightmost column of the global bounding box (inclusive).
UInt	getMaxY () const
	Bottom row of the global bounding box (inclusive).
UInt	getBBoxWidth () const
	Bounding box width in pixels (max_x - min_x + 1).
UInt	getBBoxHeight () const
	Bounding box height in pixels (max_y - min_y + 1).
const std::vector< bool > &	getMask () const
	Bbox-local row-major bitmask; empty for a Rectangle.
Size	area () const
	Number of pixels inside the region.

Static Public Member Functions
static MSImagingRegion	rectangle (Size id, const std::string &name, UInt min_x, UInt min_y, UInt max_x, UInt max_y)
	Creates a rectangular region spanning the inclusive bounding box.
static MSImagingRegion	fromMask (Size id, const std::string &name, UInt origin_x, UInt origin_y, UInt width, UInt height, std::vector< bool > mask)
	Creates a masked region from a row-major bitmask over a bounding box.

Private Attributes
Size	id_ {0}
Shape	shape_ = Shape::Rectangle
std::string	name_
std::vector< bool >	mask_
UInt	min_x_ {0}
UInt	min_y_ {0}
UInt	max_x_ {0}
UInt	max_y_ {0}

Detailed Description

A spatial region within an MSI dataset, in global pixel coordinates.

A region is a pure-geometry footprint, either an axis-aligned rectangular bounding box (Shape::Rectangle) or a per-pixel bitmask within a bounding box (Shape::Mask). It knows nothing about acquired pixels or spectra and is reusable as a bare footprint (e.g. a microscopy annotation). Construct via the rectangle() / fromMask() factories. Coordinates are zero-based and bounding boxes are inclusive on both ends.

Member Enumeration Documentation

Shape

enum class Shape

strong

Discriminates how a region's footprint is represented.

Enumerator
Rectangle	grid aligned bounding box (every cell inside the bbox is part of the region)
Mask	per pixel bitmask inside the bounding box

Member Function Documentation

area()

Size area

(

)

const

Number of pixels inside the region.

Returns

Bounding-box area for a Rectangle, set-bit count (popcount) for a Mask.

contains()

bool contains	(	UInt	x,
		UInt	y
	)		const

Tests whether the global coordinate (x, y) is inside the region.

Parameters

[in]	x	Column index (zero-based).
[in]	y	Row index (zero-based).

Returns

true if (x, y) lies within the footprint (bbox for a Rectangle, a set bit for a Mask).

fromMask()

static MSImagingRegion fromMask ( Size  id, const std::string &  name, UInt  origin_x, UInt  origin_y, UInt  width, UInt  height, std::vector< bool >  mask  )

static

Creates a masked region from a row-major bitmask over a bounding box.

The global bounding box is [origin_x, origin_x + width - 1] x [origin_y, origin_y + height - 1]; mask is stored bbox-local.

Parameters

[in]	id	Region identifier.
[in]	name	Human-readable region name.
[in]	origin_x	Leftmost column of the bounding box (zero-based).
[in]	origin_y	Top row of the bounding box (zero-based).
[in]	width	Bounding box width in pixels.
[in]	height	Bounding box height in pixels.
[in]	mask	Row-major bitmask (true = inside), size == width * height.

Returns

A region with Shape::Mask.

Exceptions

Exception::InvalidValue

if width or height is 0, if mask.size() != width * height, or if mask is all-false.

getBBoxHeight()

UInt getBBoxHeight

(

)

const

Bounding box height in pixels (max_y - min_y + 1).

Returns

Bounding box height.

getBBoxWidth()

UInt getBBoxWidth

(

)

const

Bounding box width in pixels (max_x - min_x + 1).

Returns

Bounding box width.

getId()

Size getId

(

)

const

Region identifier.

Returns

The stored id.

getMask()

const std::vector< bool > & getMask

(

)

const

Bbox-local row-major bitmask; empty for a Rectangle.

Returns

Reference to the mask (branch on getShape() before use).

getMaxX()

UInt getMaxX

(

)

const

Rightmost column of the global bounding box (inclusive).

Returns

max x.

getMaxY()

UInt getMaxY

(

)

const

Bottom row of the global bounding box (inclusive).

Returns

max y.

getMinX()

UInt getMinX

(

)

const

Leftmost column of the global bounding box (inclusive).

Returns

min x.

getMinY()

UInt getMinY

(

)

const

Top row of the global bounding box (inclusive).

Returns

min y.

getName()

const std::string & getName

(

)

const

Region name.

Returns

Reference to the stored name.

getShape()

Shape getShape

(

)

const

Region shape (Rectangle or Mask).

Returns

The shape discriminator.

intersects()

bool intersects

(

const MSImagingRegion &

other

)

const

Tests whether this region's footprint geometrically overlaps other.

Symmetric and independent of any acquired pixels: returns true iff some global coordinate lies inside both footprints.

Parameters

[in]

other

The other region.

Returns

true if the footprints share at least one coordinate.

rectangle()

static MSImagingRegion rectangle ( Size  id, const std::string &  name, UInt  min_x, UInt  min_y, UInt  max_x, UInt  max_y  )

static

Creates a rectangular region spanning the inclusive bounding box.

Parameters

[in]	id	Region identifier.
[in]	name	Human-readable region name.
[in]	min_x	Leftmost column (inclusive, zero-based).
[in]	min_y	Top row (inclusive, zero-based).
[in]	max_x	Rightmost column (inclusive, zero-based).
[in]	max_y	Bottom row (inclusive, zero-based).

Returns

A region with Shape::Rectangle.

Exceptions

Exception::InvalidValue

if max_x < min_x or max_y < min_y.

Member Data Documentation

id_

Size id_ {0}

private

mask_

std::vector<bool> mask_

private

max_x_

UInt max_x_ {0}

private

max_y_

UInt max_y_ {0}

private

min_x_

UInt min_x_ {0}

private

min_y_

UInt min_y_ {0}

private

name_

std::string name_

private

shape_

Shape shape_ = Shape::Rectangle

private