Data storage and retrieval class for "ranging" a spectra, where overlapping ranges are permitted. More...

#include <multiRange.h>

Public Member Functions
	MultiRange ()

	MultiRange (const AtomProbe::RangeFile &rng, const AtomProbe::AbundanceData &natData)
	Do our best to initialise from a rangefile. More...

bool	operator== (const MultiRange &oth) const
	Check for equality with other multirange. More...

unsigned int	addIon (const std::set< SIMPLE_SPECIES > &molecule, const std::string &name, const RGBf &ionCol)
	Add the ion to the database returns ion ID if successful, -1 otherwise. More...

unsigned int	addIon (const SIMPLE_SPECIES &molecule, const std::string &name, const RGBf &ionCol)
	Add a simple ion to the database - returns ion ID if successful, -1 otherwise. More...

unsigned int	addRange (float start, float end, unsigned int ionID)
	Add a range to the rangefile. Returns ID number of added range if adding successful, (unsigned int)-1 otherwise. More...

unsigned int	addRange (const std::pair< float, float > &rng, unsigned int ionID)
	Convenience wrapper for addRange(float,float, unsigned int) More...

void	setRangeGroups (const std::vector< unsigned int > &groups)
	Set the groupings for the ranges : this is used when splitting overlapping ranges. More...

bool	write (const char *fileName, unsigned int format=MULTIRANGE_FORMAT_XML) const
	Save the structure to a file. format specifies output file format type. More...

bool	open (const char *fileName, unsigned int format=-1)
	read the contents of the file into class More...

unsigned int	getIonID (unsigned int rangeId) const
	Get the ion's ID from a specified mass. More...

void	setIonID (unsigned int range, unsigned int newIonId)
	Set the ion ID for a given range. More...

RGBf	getColour (unsigned int ionID) const
	Obtain the colour for a given ion. More...

void	setColour (unsigned int ionID, const RGBf &r)
	Set the colour using the ion ID. More...

std::string	getErrString () const
	Retrieve the human-readable error associated with the current range file state. More...

std::string	getIonName (unsigned int ionID) const
	Get the name of a specified ionID. More...

unsigned int	getNumRanges () const
	Get the number of unique ranges. More...

unsigned int	getNumRanges (unsigned int ionID) const
	Get the number of ranges for a given ion ID. More...

unsigned int	getNumIons () const
	Get the number of unique ions. More...

std::set< SIMPLE_SPECIES >	getMolecule (unsigned int ionID) const
	Return the molecule that is associated with this ion. More...

std::pair< float, float >	getRange (unsigned int rangeID) const
	Retrieve the start and end of a given range as a pair(start,end) More...

std::vector< unsigned int >	getRanges (float mass) const
	Retrieve all of the ranges that specify the given mass. More...

bool	isRanged (float mass) const
	Returns true if a specified mass is ranged. More...

bool	isRanged (const IonHit &) const
	Returns true if an ion is ranged. More...

void	range (std::vector< IonHit > &ionHits) const
	Clips out ions that are not inside the rangefile's ranges. More...

bool	isSelfConsistent () const
	Check to see if data structure is internally consistent. More...

void	clear ()
	Erase the contents of the rangefile. More...

void	flattenToMassAxis (std::vector< FLATTENED_RANGE > &ionMapping, float tolerance=0) const
	Obtain a projection onto the mass axis of ranges that do not touch one another. More...

void	splitOverlapping (std::vector< MultiRange > &decomposedRanges, float massTolerance=0) const

void	copyDataFromRange (const MultiRange &src, unsigned int srcRngId)
	Copy range from a different multirange into this one, including all dependant data. More...

Detailed Description

Data storage and retrieval class for "ranging" a spectra, where overlapping ranges are permitted.

Definition at line 63 of file multiRange.h.

Constructor & Destructor Documentation

◆ MultiRange() [1/2]

AtomProbe::MultiRange::MultiRange ( )

Definition at line 136 of file multiRange.cpp.

◆ MultiRange() [2/2]

AtomProbe::MultiRange::MultiRange	(	const AtomProbe::RangeFile &	rng,
		const AtomProbe::AbundanceData &	natData
	)

Do our best to initialise from a rangefile.

ions and their child ranges may be dropped if they cannot be identified

Definition at line 141 of file multiRange.cpp.

References ASSERT, AtomProbe::SIMPLE_SPECIES::atomicNumber, AtomProbe::SIMPLE_SPECIES::count, AtomProbe::RangeFile::decomposeIonNames(), AtomProbe::AbundanceData::getAtomicNumber(), AtomProbe::RangeFile::getColour(), AtomProbe::RangeFile::getIonID(), AtomProbe::RangeFile::getName(), AtomProbe::RangeFile::getNumIons(), AtomProbe::RangeFile::getNumRanges(), AtomProbe::RangeFile::getRange(), AtomProbe::AbundanceData::getSymbolIndices(), and isSelfConsistent().

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Member Function Documentation

◆ addIon() [1/2]

unsigned int AtomProbe::MultiRange::addIon	(	const std::set< SIMPLE_SPECIES > &	molecule,
		const std::string &	name,
		const RGBf &	ionCol
	)

Add the ion to the database returns ion ID if successful, -1 otherwise.

Definition at line 271 of file multiRange.cpp.

References ASSERT, and isSelfConsistent().

Referenced by addIon(), AtomProbe::computeRangeAdjacency(), copyDataFromRange(), and AtomProbe::leastSquaresOverlapSolve().

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◆ addIon() [2/2]

unsigned int AtomProbe::MultiRange::addIon	(	const SIMPLE_SPECIES &	molecule,
		const std::string &	name,
		const RGBf &	ionCol
	)

Add a simple ion to the database - returns ion ID if successful, -1 otherwise.

Definition at line 293 of file multiRange.cpp.

References addIon(), ASSERT, and isSelfConsistent().

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◆ addRange() [1/2]

unsigned int AtomProbe::MultiRange::addRange	(	float	start,
		float	end,
		unsigned int	ionID
	)

Add a range to the rangefile. Returns ID number of added range if adding successful, (unsigned int)-1 otherwise.

Note that ranges are, unlike RangeFile, allowed to overlap, and still be self consistent.

Definition at line 303 of file multiRange.cpp.

References ASSERT, and isSelfConsistent().

Referenced by AtomProbe::computeRangeAdjacency(), copyDataFromRange(), and AtomProbe::leastSquaresOverlapSolve().

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◆ addRange() [2/2]

unsigned int AtomProbe::MultiRange::addRange	(	const std::pair< float, float > &	rng,
		unsigned int	ionID
	)

Convenience wrapper for addRange(float,float, unsigned int)

◆ clear()

void AtomProbe::MultiRange::clear ( )

Erase the contents of the rangefile.

Definition at line 831 of file multiRange.cpp.

Referenced by open().

◆ copyDataFromRange()

void AtomProbe::MultiRange::copyDataFromRange	(	const MultiRange &	src,
		unsigned int	srcRngId
	)

Copy range from a different multirange into this one, including all dependant data.

Definition at line 983 of file multiRange.cpp.

References addIon(), addRange(), ASSERT, AtomProbe::SIMPLE_SPECIES::atomicNumber, AtomProbe::ISOTOPE_ENTRY::atomicNumber, AtomProbe::RGBf::blue, AtomProbe::SIMPLE_SPECIES::count, AtomProbe::RGBf::fromHex(), AtomProbe::AbundanceData::generateSingleAtomDist(), getIonName(), getNumIons(), getNumRanges(), AtomProbe::AbundanceData::getSymbolIndices(), AtomProbe::RGBf::green, AtomProbe::AbundanceData::isotope(), isSelfConsistent(), MASS_TOL, open(), AtomProbe::RGBf::red, setRangeGroups(), splitOverlapping(), AtomProbe::AbundanceData::symbolIndex(), TEST, and write().

Referenced by splitOverlapping().

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◆ flattenToMassAxis()

void AtomProbe::MultiRange::flattenToMassAxis	(	std::vector< FLATTENED_RANGE > &	ionMapping,
		float	tolerance = `0`
	)		const

Obtain a projection onto the mass axis of ranges that do not touch one another.

Definition at line 915 of file multiRange.cpp.

References ASSERT, and AtomProbe::FLATTENED_RANGE::startMass.

Referenced by splitOverlapping().

◆ getColour()

RGBf AtomProbe::MultiRange::getColour ( unsigned int ionID ) const

Obtain the colour for a given ion.

Definition at line 785 of file multiRange.cpp.

References ASSERT.

◆ getErrString()

std::string AtomProbe::MultiRange::getErrString ( ) const

Retrieve the human-readable error associated with the current range file state.

Definition at line 693 of file multiRange.cpp.

References ASSERT, and AtomProbe::MULTIRANGE_ERR_ENUM_END.

◆ getIonID()

unsigned int AtomProbe::MultiRange::getIonID ( unsigned int rangeId ) const

Get the ion's ID from a specified mass.

Returns the ions ID if there exists a range that contains this mass. Otherwise (unsigned int)-1 is returned

Definition at line 752 of file multiRange.cpp.

References ASSERT, and range().

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◆ getIonName()

std::string AtomProbe::MultiRange::getIonName ( unsigned int ionID ) const

Get the name of a specified ionID.

Definition at line 733 of file multiRange.cpp.

References ASSERT.

Referenced by copyDataFromRange(), and AtomProbe::leastSquaresOverlapSolve().

◆ getMolecule()

set< SIMPLE_SPECIES > AtomProbe::MultiRange::getMolecule ( unsigned int ionID ) const

Return the molecule that is associated with this ion.

Definition at line 727 of file multiRange.cpp.

References ASSERT.

Referenced by AtomProbe::computeIonDistAdjacency().

◆ getNumIons()

unsigned int AtomProbe::MultiRange::getNumIons ( ) const

Get the number of unique ions.

Definition at line 747 of file multiRange.cpp.

Referenced by AtomProbe::computeIonDistAdjacency(), copyDataFromRange(), and AtomProbe::leastSquaresOverlapSolve().

◆ getNumRanges() [1/2]

unsigned int AtomProbe::MultiRange::getNumRanges ( ) const

Get the number of unique ranges.

Definition at line 720 of file multiRange.cpp.

Referenced by AtomProbe::computeRangeAdjacency(), copyDataFromRange(), and AtomProbe::leastSquaresOverlapSolve().

◆ getNumRanges() [2/2]

unsigned int AtomProbe::MultiRange::getNumRanges ( unsigned int ionID ) const

Get the number of ranges for a given ion ID.

Definition at line 739 of file multiRange.cpp.

References ASSERT.

◆ getRange()

std::pair< float, float > AtomProbe::MultiRange::getRange ( unsigned int rangeID ) const

Retrieve the start and end of a given range as a pair(start,end)

Definition at line 759 of file multiRange.cpp.

References ASSERT.

Referenced by AtomProbe::computeRangeAdjacency().

◆ getRanges()

std::vector< unsigned int > AtomProbe::MultiRange::getRanges ( float mass ) const

Retrieve all of the ranges that specify the given mass.

Definition at line 765 of file multiRange.cpp.

◆ isRanged() [1/2]

bool AtomProbe::MultiRange::isRanged ( float mass ) const

Returns true if a specified mass is ranged.

Definition at line 797 of file multiRange.cpp.

References range().

Referenced by isRanged(), and range().

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◆ isRanged() [2/2]

bool AtomProbe::MultiRange::isRanged ( const IonHit & ion ) const

Returns true if an ion is ranged.

Definition at line 809 of file multiRange.cpp.

References AtomProbe::IonHit::getMassToCharge(), and isRanged().

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◆ isSelfConsistent()

bool AtomProbe::MultiRange::isSelfConsistent ( ) const

Check to see if data structure is internally consistent.

Definition at line 230 of file multiRange.cpp.

Referenced by addIon(), addRange(), copyDataFromRange(), MultiRange(), open(), and write().

◆ open()

bool AtomProbe::MultiRange::open	(	const char *	fileName,
		unsigned int	format = `-1`
	)

read the contents of the file into class

returns true if successful, otherwise false

if not successful then the errState will contain the error information, and the calling object (rangefile) will be in an invalid state

Definition at line 398 of file multiRange.cpp.

Referenced by copyDataFromRange().

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◆ operator==()

bool AtomProbe::MultiRange::operator== ( const MultiRange & oth ) const

Check for equality with other multirange.

Definition at line 208 of file multiRange.cpp.

◆ range()

void AtomProbe::MultiRange::range ( std::vector< IonHit > & ionHits ) const

Clips out ions that are not inside the rangefile's ranges.

Definition at line 814 of file multiRange.cpp.

References isRanged().

Referenced by getIonID(), isRanged(), and setIonID().

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◆ setColour()

void AtomProbe::MultiRange::setColour	(	unsigned int	ionID,
		const RGBf &	r
	)

Set the colour using the ion ID.

Definition at line 791 of file multiRange.cpp.

References ASSERT.

◆ setIonID()

void AtomProbe::MultiRange::setIonID	(	unsigned int	range,
		unsigned int	newIonId
	)

Set the ion ID for a given range.

Definition at line 778 of file multiRange.cpp.

References ASSERT, and range().

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◆ setRangeGroups()

void AtomProbe::MultiRange::setRangeGroups ( const std::vector< unsigned int > & groups )

Set the groupings for the ranges : this is used when splitting overlapping ranges.

When splitting overlapping ranges, "grouped" ranges are considered to be part of the same split grouping. This is typically used for example, to group isotopes that belong to an ion, but of differing charge state. As the intensities for charge state in an experiment are not linked There is no need to link these in the range group. Each range with a shared integer belongs to the same group

the input vector must match range size, or be empty.
range size cannot be changed without changing grouping vector

Definition at line 321 of file multiRange.cpp.

References ASSERT.

Referenced by copyDataFromRange(), and AtomProbe::leastSquaresOverlapSolve().

◆ splitOverlapping()

void AtomProbe::MultiRange::splitOverlapping	(	std::vector< MultiRange > &	decomposedRanges,
		float	massTolerance = `0`
	)		const

Separate out the non-interacting parts of the multi-ranges into their own multiRange entries The vector of maps converts the ionids of the child MultiRange to the parent

Definition at line 844 of file multiRange.cpp.

References ASSERT, copyDataFromRange(), flattenToMassAxis(), AtomProbe::linkIdentifiers(), and AtomProbe::pairOverlaps().

Referenced by copyDataFromRange(), and AtomProbe::leastSquaresOverlapSolve().

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◆ write()

bool AtomProbe::MultiRange::write	(	const char *	fileName,
		unsigned int	format = `MULTIRANGE_FORMAT_XML`
	)		const

Save the structure to a file. format specifies output file format type.

Returns true if successful, otherwise false

Definition at line 327 of file multiRange.cpp.

References ASSERT, AtomProbe::LibVersion::getVersionStr(), isSelfConsistent(), AtomProbe::MULTIRANGE_FORMAT_XML, and AtomProbe::tabs().

Referenced by copyDataFromRange().

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The documentation for this class was generated from the following files:

include/atomprobe/io/multiRange.h
src/io/multiRange.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ MultiRange() [1/2]

◆ MultiRange() [2/2]

Member Function Documentation

◆ addIon() [1/2]

◆ addIon() [2/2]

◆ addRange() [1/2]

◆ addRange() [2/2]

◆ clear()

◆ copyDataFromRange()

◆ flattenToMassAxis()

◆ getColour()

◆ getErrString()

◆ getIonID()

◆ getIonName()

◆ getMolecule()

◆ getNumIons()

◆ getNumRanges() [1/2]

◆ getNumRanges() [2/2]

◆ getRange()

◆ getRanges()

◆ isRanged() [1/2]

◆ isRanged() [2/2]

◆ isSelfConsistent()

◆ open()

◆ operator==()

◆ range()

◆ setColour()

◆ setIonID()

◆ setRangeGroups()

◆ splitOverlapping()

◆ write()