AtomProbe Namespace Reference

Classes
class	AbundanceData
	Class to load abundance information for natural isotopes. More...
struct	ATO_ENTRY
class	AxisCompare
	Functor allowing for sorting of points in 3D. More...
struct	BACKGROUND_PARAMS
class	BodyCentredCubicGen
class	BoundCube
	Helper class to define a bounding cube. More...
class	ComparePairFirst
class	ComparePairFirstReverse
class	ComparePairSecond
class	CrystalGen
struct	DATA_FIT
class	EPOS_ENTRY
class	FaceCentredCubicGen
struct	FLATTENED_RANGE
	Structure that allows for the multirange data to be mapped into. More...
class	GnomonicProjection
class	IonHit
	This is a data holding class for POS file ions, from. More...
struct	IONHIT
	Record as stored in a .POS file. More...
struct	ISOTOPE_ENTRY
class	K3DNodeApprox
	Node Class for storing point. More...
class	K3DNodeExact
	Node Class for storing point. More...
class	K3DTreeApprox
	3D specific KD tree More...
class	K3DTreeExact
	3D specific KD tree More...
class	LibVersion
	Class to hold the library version data. More...
class	LINE
class	LinearFeedbackShiftReg
	This class implements a Linear Feedback Shift Register (in software) More...
class	MassTool
	Class that brute-force solves the knapsack problem. More...
class	Mesh
	Simple mesh class for storing and manipulating meshes consisting of 2 and 3D simplexes (triangles or tetrahedra) More...
class	MILLER_TRIPLET
class	ModifiedFocusSphericProjection
class	MultiRange
	Data storage and retrieval class for "ranging" a spectra, where overlapping ranges are permitted. More...
struct	OVERLAP_PROBLEM_SETTINGS
class	Point3D
	A 3D point data class storage. More...
struct	Point3f
	Data storage structure for points. More...
class	ProgressBar
struct	Quaternion
	Data storage structure for quaternions. More...
class	RandNumGen
struct	RANGE_MOLECULE
class	RangeFile
	Data storage and retrieval class for various range files. More...
class	ReconstructionSphereOnCone
class	RGBf
	Data holder for colour as float. More...
struct	SIMPLE_SPECIES
class	SimpleCubicGen
struct	SINGLE_HIT
	Single 3DAP hit event. More...
class	SphericPlaneProjection
struct	SphericProjectionParams
class	StereographicProjection
class	TETRAHEDRON
struct	THREEDAP_DATA
	experimental setup data More...
struct	THREEDAP_EXPERIMENT
	Data structure that contains the experiment information present in a 3Dap file. More...
class	TRIANGLE
struct	TriangleWithIndexedVertices
class	TriangleWithVertexNorm
struct	VOLTAGE_DATA
	Voltage data structure – these updates occur periodically during the experiment. More...
class	Voxels
	Template class that stores 3D voxel data. More...
class	Weight
	Placeholder class for containing input weights for MassTool. More...
struct	ZECH_ROOT

Typedefs
typedef struct AtomProbe::ATO_ENTRY	ATO_ENTRY
typedef struct AtomProbe::IONHIT	IONHIT
	Record as stored in a .POS file. More...

Enumerations
enum	{ HULL_SURFREDUCE_NEGATIVE_SCALE_FACT =1, HULL_ERR_USER_ABORT, HULL_ERR_NO_MEM }
enum	PointDir { POINTDIR_TOGETHER =0, POINTDIR_IN_COMMON, POINTDIR_APART }
enum	{   BOUND_CLIP =1, BOUND_HOLD, BOUND_DERIV_HOLD, BOUND_MIRROR,   BOUND_ZERO, BOUND_ENUM_END }
	Boundary clipping mode. More...
enum	{ VOX_INTERP_NONE, VOX_INTERP_LINEAR, VOX_INTERP_ENUM_END }
enum	{ ADJ_ALL, ADJ_PLUS }
enum	{ VOXELS_BAD_FILE_READ =1, VOXELS_BAD_FILE_OPEN, VOXELS_BAD_FILE_SIZE, VOXELS_OUT_OF_MEMORY }
enum	{ CLIP_NONE =0, CLIP_LOWER_SOUTH_WEST, CLIP_UPPER_NORTH_EAST }
	Clipping direction constants. More...
enum	{ VOXEL_ABORT_ERR, VOXEL_MEMORY_ERR, VOXEL_BOUNDS_INVALID_ERR }
enum	{ PROP_PARSE_ERR = 1, PROP_BAD_ATT }
enum	{   RECORDREAD_ERR_GET_FILESIZE =1, RECORDREAD_ERR_FILESIZE_MODULO, RECORDREAD_ERR_FILE_OPEN, RECORDREAD_ERR_NOMEM,   RECORDREAD_BAD_FILEREAD, RECORDREAD_ERR_CHUNKOFFSET, RECORDREAD_BAD_RECORD }
enum	{   ATO_OPEN_FAIL =1, ATO_EMPTY_FAIL, ATO_SIZE_ERR, ATO_VERSIONCHECK_ERR,   ATO_MEM_ERR, ATO_BAD_ENDIAN_DETECT, ATO_ENUM_END }
enum	{ TEXT_ERR_FILE_OPEN =1, TEXT_ERR_FILE_NUM_FIELDS, TEXT_ERR_FILE_FORMAT }
enum	{   OPSREADER_FORMAT_CLINE_ERR =1, OPSREADER_FORMAT_DETECTORLINE_ERR, OPSREADER_FORMAT_LINE_DASH_ERR, OPSREADER_FORMAT_LINE_VOLTAGE_ERR,   OPSREADER_FORMAT_LINE_VOLTAGE_NOBETA, OPSREADER_FORMAT_LINE_VOLTAGE_DATA_ERR, OPSREADER_FORMAT_LINE_VOLTAGE_DATACOUNT_ERR, OPSREADER_FORMAT_LINETYPE_ERR,   OPSREADER_FORMAT_CHANNELS_ERR, OPSREADER_CHANNELS_DATA_ERR, OPSREADER_FORMAT_SLINE_EVENTCOUNT_ERR, OPSREADER_FORMAT_SLINE_EVENTDATA_ERR,   OPSREADER_FORMAT_SLINE_FORMAT_ERR, OPSREADER_FORMAT_SLINE_PREFIX_ERR, OPSREADER_FORMAT_DUPLICATE_SYSDATA, OPSREADER_FORMAT_DUPLICATE_DETECTORSIZE,   OPSREADER_FORMAT_TRAILING_DASH_ERR, OPSREADER_FORMAT_DOUBLEDASH, OPSREADER_OPEN_ERR, OPSREADER_READ_ERR,   OPSREADER_ABORT_ERR, OPSREADER_ENUM_END }
	Error codes for OPS file loading. More...
enum	{ MULTIRANGE_FORMAT_XML }
enum	{   RANGE_FORMAT_ORNL, RANGE_FORMAT_DBL_ORNL, RANGE_FORMAT_ENV, RANGE_FORMAT_RRNG,   RANGE_FORMAT_END_OF_ENUM }
enum	{   RANGE_ERR_FORMAT =1, RANGE_ERR_FORMAT_HEADER, RANGE_ERR_EMPTY, RANGE_ERR_FORMAT_LONGNAME,   RANGE_ERR_FORMAT_SHORTNAME, RANGE_ERR_FORMAT_COLOUR, RANGE_ERR_FORMAT_TABLESEPARATOR, RANGE_ERR_FORMAT_RANGE_DUMMYCHARS,   RANGE_ERR_FORMAT_MASS_PAIR, RANGE_ERR_FORMAT_TABLE_ENTRY, PARSE_RANGE_FORMAT_GENERIC_FAIL, RANGE_ERR_DATA_TOO_MANY_USELESS_RANGES,   RANGE_ERR_DATA_FLIPPED, RANGE_ERR_DATA_INCONSISTENT, RANGE_ERR_DATA_NOMAPPED_IONNAME, RANGE_ERR_OPEN,   RANGE_ERR_FORMAT_RANGETABLE, RANGE_ERR_FORMAT_TABLEHEADER_NUMIONS, RANGE_ERR_NONUNIQUE_POLYATOMIC, RANGE_ERR_TOO_LARGE,   RANGE_ERR_DASHHEADER, RANGE_ERR_IONBLOCK_CONTENT, RANGE_ERR_NUMIONS, RANGE_ERR_NUMIONS_DUPLICATED,   RANGE_ERR_TOO_MANYIONS, RANGE_ERR_ION_BLOCK_NOT_PRESENT, RANGE_ERR_DUPLICATE_NUMRANGES, RANGE_ERR_NUMRANGE_PARSE,   RANGE_ERR_RRNG_IONS_TOOSHORT, RANGE_ERR_RRNG_COLON_SEPARATOR, RANGE_ERR_BADCOLOUR, RANGE_ERR_ION_NOT_MAPPED,   RANGE_ERR_BADSTART, RANGE_ERR_BADEND, RANGE_ERR_NAME_EMPTY, RANGE_ERR_BAD_LINE_RANGEBLOCK,   RANGE_ERR_MISSING_IONBLOCK, RANGE_ERR_NO_RANGES, RANGE_ERR_NO_BASIC_IONS, RANGE_ERR_MISMATCHED_NUMRANGES,   RANGE_ERR_RANGEBLOCK_FORMAT, RANGE_ERR_BAD_MULTIPLICITY, RANGE_ERR_VOLUME_PARSE, RANGE_ERR_FORMAT_EMPTY_RANGEROW,   RANGE_ERR_FILESIZE, RANGE_ERR_ENUM_END }
enum	{   COMPPARSE_BAD_INPUT_FORMAT =1, COMPPARSE_BAD_COMP_VALUE, COMPPARSE_BAD_BAL_USAGE, COMPPARSE_BAD_SYMBOL,   COMPPARSE_DUPLICATE_SYMBOL, COMPPARSE_BAD_TOTAL_COMP }
	composition parsing error messages More...
enum	{ CRYSTAL_BAD_UNIT_CELL, CRYSTAL_ENUM_END }
enum	{ LATTICE_FCC, LATTICE_BCC, LATTICE_HCP, LATTICE_END_OF_ENUM }
enum	{ ELEMENT_TRIANGLE =1, ELEMENT_TETRAHEDRON =2, ELEMENT_LINE =4 }
enum	{ EVOLUTION_MODE_SHANKANGLE }
enum	{ BACK_FIT_MODE_CONST_TOF, BACK_FIT_MODE_ENUM_END }
	Background fitting modes. More...
enum	{   POS_ALLOC_FAIL =1, POS_OPEN_FAIL, POS_SIZE_MODULUS_ERR, POS_SIZE_EMPTY_ERR,   POS_READ_FAIL, POS_NAN_LOAD_ERROR, POS_FILE_ENUM_END }
enum	{ TAPSIM_FILE_FORMAT_FAIL =1, TAPSIM_OPEN_FAIL }
enum	{   MULTIRANGE_ERR_NO_PARSER =1, MULTIRANGE_ERR_NO_XML_DOC, MULTIRANGE_ERR_NO_XML_CONTEXT, MULTIRANGE_ERR_NO_NODEPTR,   MULTIRANGE_NOT_VALID_ROOTNODE, MULTIRANGE_ERR_NO_CONTENT, MULTIRANGE_ERR_NO_TIMESTAMP, MULTIRANGE_ERR_NO_MOLECULES,   MULTIRANGE_ERR_NO_MOLECULE_ENTRIES, MULTIRANGE_ERR_MOL_MISSING_ENTRY, MULTIRANGE_ERR_MOL_MISSING_NAME, MULTIRANGE_ERR_MOL_MISSING_COMPONENTS,   MULTIRANGE_ERR_BAD_RANGE, MULTIRANGE_ERR_BAD_RANGES, MULTIRANGE_ERR_MOL_MISSING_COLOUR, MULTIRANGE_ERR_MOL_BAD_COLOUR,   MULTIRANGE_ERR_NO_RANGES, MULTIRANGE_ERR_BAD_GROUP, MULTIRANGE_ERR_SELF_INCONSISTENT, MULTIRANGE_ERR_RANGE_NOPARENT,   MULTIRANGE_ERR_ENUM_END }
enum	{   MESH_LOAD_UNSPECIFIED_ERROR =1, MESH_LOAD_BAD_NODECOUNT, MESH_LOAD_BAD_ELEMENTCOUNT, MESH_LOAD_IS_INSANE,   MESH_LOAD_ENUM_END }

Functions
unsigned int	generate1DAxialDistHist (const std::vector< Point3D > &pointList, K3DTreeExact &tree, const Point3D &axisDir, float distMax, std::vector< unsigned int > &histogram)
	Generate a 1D axial distribution function,. More...
unsigned int	generate1DAxialDistHistSweep (const std::vector< Point3D > &pointList, K3DTreeExact &tree, float distMax, float dTheta, float dPhi, AtomProbe::ProgressBar &prog, std::vector< std::vector< std::vector< unsigned int > > > &histogram)
	Generate a series of 1D distribution functions, one per pixel in a 2D grid of spherical coordinate directions. More...
void	computeIonDistAdjacency (const MultiRange &mrf, const AbundanceData &abundance, const OVERLAP_PROBLEM_SETTINGS &settings, gsl_matrix *&m, gsl_vector *&vOwnership, gsl_vector *&vMass)
	Calculate the adjacency matrix for the ions in a multirange. More...
unsigned int	GetReducedHullPts (const std::vector< IonHit > &points, float reductionDim, unsigned int *progress, bool(*callback)(bool), std::vector< IonHit > &pointResult)
	Obtain a set of points that are a subset of points the convex hull that are at least "reductionDim" away from the hull itself. More...
unsigned int	computeConvexHull (const std::vector< IonHit > &data, unsigned int *progress, bool(*callback)(bool), std::vector< Point3D > &curHull, bool freeHull)
	Obtain the convex hull of a set of ions. More...
void	filterPeakNeedBiggerObs (const AtomProbe::AbundanceData &massTable, const std::vector< float > &peakData, float tolerance, size_t solutionCharge, std::vector< std::vector< AtomProbe::ISOTOPE_ENTRY > > &solutions)
void	filterBySolutionPPM (const AtomProbe::AbundanceData &massTable, float minPpm, std::vector< std::vector< AtomProbe::ISOTOPE_ENTRY > > &solutions)
	Use the maximum possible PPM for each isotopic combination to filter possible solutions. More...
std::vector< float >	maxExplainedFraction (const std::vector< std::pair< float, float > > &massData, float peakMass, float massWidth, const std::vector< std::vector< AtomProbe::ISOTOPE_ENTRY > > &solutions, const AtomProbe::AbundanceData &massTable, float massDistTol, unsigned int solutionCharge)
	Compute the fraction of the data that has been explained, using the natural abundance information, and intensity data. More...
bool	correlationHistogram (const std::vector< EPOS_ENTRY > &eposIons, std::vector< std::vector< unsigned int > > &histogram, float stepMass, float endMass, bool lowerTriangular=false)
	Generates an ion "correlation histogram" from a vector of EPOS ions. The input vector MUST More...
bool	accumulateCorrelationHistogram (const std::vector< EPOS_ENTRY > &eposIons, std::vector< std::vector< unsigned int > > &histogram, float stepMass, float endMass, bool lowerTriangular=true)
	Increments a correlation histogram, as per correlationHistogram,. More...
template<class T >
void	linearHistogram (const std::vector< T > &data, T start, T end, T step, std::vector< T > &histVals)
void	marchingCubes (const Voxels< float > &v, float isoValue, std::vector< TriangleWithVertexNorm > &tVec)
void	checkMassRangingCorrectness (const AtomProbe::RangeFile &rng, AtomProbe::AbundanceData &massTable, float massTolerance, unsigned int maxChargeState, unsigned int maxComponents, std::vector< bool > &badRanges)
	Ensure that each mass given spans a peak that should exist. More...
void	computeRotationMatrix (const Point3D &ur1, const Point3D &ur2, const Point3D &r1, const Point3D &r2, gsl_matrix *m)
void	computeRotationMatrix (const Point3D &ur1, const Point3D &ur2, const Point3D &r1, const Point3D &r2, std::vector< std::vector< float > > &m)
	Convenience wrapper for conputeRotationMatrix, which uses vector containers. More...
unsigned int	computeRotationMatrixWahba (const std::vector< Point3D > &unrotated, const std::vector< Point3D > &rotated, const std::vector< float > &weights, gsl_matrix *&R)
	Given a series of paired observations of directions, compute the least squares rotation matrix between them. More...
bool	leastSquaresOverlapSolve (const AtomProbe::MultiRange &rangeData, const AtomProbe::AbundanceData &abundance, const std::vector< IonHit > &hits, float(*backgroundEstimator)(float, float), std::vector< std::pair< unsigned int, float > > &decomposedHits, float rangeTolerance=0)
	Solve overlaps using least squares for given multi-range. More...
void	setHardAssert (bool enabled)
	Do assertions cause a straight up crash (enabled), or write a mesage to stderr (disabled)? By default, hard crash. More...
void	askAssert (const char *, unsigned int)
	Either abort program, or ask the user what to do for an assertion. depending on hardAssert setting. More...
void	computeComposition (const std::vector< unsigned int > &countData, std::vector< float > &compositionData)
void	convertEPOStoPos (const std::vector< EPOS_ENTRY > &eposEntry, std::vector< IonHit > &posFile)
	Convert an incoming entry of EPOS files to pos, and the append this to the pos vector given. More...
void	gsl_matrix_mult (const gsl_matrix *A, const gsl_matrix *B, gsl_matrix *&res, bool alloc=false)
unsigned int	estimateRank (const gsl_matrix *m, float tolerance=sqrt(std::numeric_limits< float >::epsilon()))
	Estimate the rank of the given matrix. More...
bool	solveLeastSquares (gsl_matrix *m, gsl_vector *b, gsl_vector *&x)
	Use an SVD based least-squares solver to solve Mx=b (for x). More...
template<class T >
T	weightedMean (const std::vector< T > &values, const std::vector< T > &weight)
template<typename T >
void	meanAndStdev (const std::vector< T > &f, float &meanVal, float &stdevVal, bool normalCorrection=true)
unsigned int	vectorPointDir (const Point3D &pA, const Point3D &pB, const Point3D &vC, const Point3D &vD)
	Check which way vectors attached to two 3D points "point",. More...
float	distanceToSegment (const Point3D &fA, const Point3D &fB, const Point3D &p)
float	signedDistanceToFacet (const Point3D &fA, const Point3D &fB, const Point3D &fC, const Point3D &normal, const Point3D &p)
	Find the distance between a point, and a triangular facet – may be positive or negative. More...
float	distanceToFacet (const Point3D &fA, const Point3D &fB, const Point3D &fC, const Point3D &normal, const Point3D &p)
float	dotProduct (float a1, float a2, float a3, float b1, float b2, float b3)
	Inline func for calculating a(dot)b. More...
double	det3by3 (const double *ptArray)
double	pyramidVol (const Point3D *planarPts, const Point3D &apex)
bool	triIsDegenerate (const Point3D &fA, const Point3D &fB, const Point3D &fC)
void	quat_rot (Point3D &p, const Point3D &r, float angle)
	Rotate a point around a given rotation axis by a specified angle. More...
void	quat_rot (Point3f *point, const Point3f *rotVec, float angle)
	Rotate a point around a given vector, with specified angle. More...
void	quat_rot_array (Point3f *point, unsigned int n, const Point3f *rotVec, float angle)
	Rotate each point in array of size n around a given vector, with specified angle. More...
void	quat_rot_array (Point3D *point, unsigned int n, const Point3f *rotVec, float angle)
	Rotate each point in array of size n around a given vector, with specified angle. More...
void	quat_get_rot_quat (const Point3f *rotVec, float angle, Quaternion *rotQuat)
	Compute the quaternion for specified rotation. More...
void	quat_rot_apply_quat (Point3f *point, const Quaternion *rotQuat)
	Use previously generated quats from quat_get_rot_quats to rotate a point. More...
template<class T >
bool	tolEqual (const T &a, const T &b, const T &f)
	Test for equality within tolerance f (||a-b|| < f) More...
template<class T >
void	selectElements (const std::vector< T > &in, const std::vector< unsigned int > &indices, std::vector< T > &out)
	Obtain the elements at positions indicies in the input vector, copy to output. More...
template<class T >
void	transposeVector (std::vector< std::vector< T > > &v)
	Perform an out-of-place tranposition of a given vector. More...
template<class T >
void	vectorMultiErase (std::vector< T > &vec, const std::vector< bool > &wantKill)
	Remove elements from the vector, without preserving order. More...
void	sampleIons (const std::vector< IonHit > &ions, float sampleFactor, std::vector< IonHit > &sampled, bool strongRandom=true)
template<class T >
size_t	randomSelect (std::vector< T > &result, const std::vector< T > &source, size_t num, gsl_rng *rng)
template<class T >
void	randomIndices (std::vector< T > &res, size_t num, size_t nMax, gsl_rng *rng)
template<class T1 , class T2 >
bool	stream_cast (T1 &result, const T2 &obj)
	Template function to cast and object to another by the stringstream. More...
template<class T >
void	strAppend (std::string s, const T &a)
void	genColString (unsigned char r, unsigned char g, unsigned char b, unsigned char a, std::string &s)
void	genColString (unsigned char r, unsigned char g, unsigned char b, std::string &s)
bool	parseColString (const std::string &str, unsigned char &r, unsigned char &g, unsigned char &b, unsigned char &a)
	Parse a colour string containing rgb[a]; hex for with leading #. More...
std::string	digitString (unsigned int thisDigit, unsigned int maxDigit)
	Generate a string with leading digits up to maxDigit (eg, if maxDigit is 424, and thisDigit is 1. More...
std::string	stripWhite (const std::string &str)
	Strip whitespace, (eg tab,space) from either side of a string. More...
std::string	stripChars (const std::string &Str, const char *chars)
std::string	lowercase (std::string s)
	Return a lowercase version for a given string. More...
std::string	uppercase (std::string s)
	Return a uppercase version for a given string. More...
void	stripZeroEntries (std::vector< std::string > &s)
void	splitStrsRef (const char *cpStr, const char delim, std::vector< std::string > &v)
	Split string references using a single delimiter. More...
void	splitStrsRef (const char *cpStr, const char *delim, std::vector< std::string > &v)
	Split string references using any of a given string of delimiters. More...
std::string	onlyFilename (const std::string &path)
	Return only the filename component. More...
std::string	onlyDir (const std::string &path)
	Return only the directory name component of the full path. More...
std::string	convertFileStringToNative (const std::string &s)
	Convert a path format into a native path from unix format. More...
std::string	convertFileStringToCanonical (const std::string &s)
	Convert a path format into a unix path from native format. More...
std::string	tabs (unsigned int nTabs)
std::string	stlWStrToStlStr (const std::wstring &s)
std::wstring	stlStrToStlWStr (const std::string &s)
void	nullifyMarker (char *buffer, char marker)
template<class T , class U >
void	castVoxels (const Voxels< T > &src, Voxels< U > &dest)
	Convert one type of voxel into another by assignment operator. More...
template<class T , class U >
void	sumVoxels (const Voxels< T > &src, U &counter)
	Use one counting type to sum counts in a voxel of given type. More...
unsigned int	XMLHelpNextType (xmlNodePtr &node, int)
unsigned int	XMLHelpFwdToElem (xmlNodePtr &node, const char *nodeName)
unsigned int	XMLHelpFwdNotElem (xmlNodePtr &node, const char *nodeName)
unsigned int	XMLHelpFwdToList (xmlNodePtr &node, const std::vector< std::string > &nodeList)
std::string	XMLHelpGetText (xmlNodePtr &node)
void	XMLFreeDoc (void *data)
	Free a xmlDoc pointer. For use in conjunction with std::unique_ptr for auto-deallocation. More...
template<class T >
unsigned int	XMLHelpGetProp (T &prop, xmlNodePtr node, std::string propName)
template<class T >
bool	XMLGetNextElemAttrib (xmlNodePtr &nodePtr, T &v, const char *nodeName, const char *attrib)
	Grab the specified attribute from the next element, then stream_cast() it into the passed-in object. Returns true on success, false on error. More...
const char *	getRecordReadErrString (unsigned int errCode)
const char *	getAtoErrString (unsigned int errCode)
unsigned int	loadPosFile (std::vector< IonHit > &posIons, const char *posFile)
	Load a pos file directly into a single ion list. More...
unsigned int	loadPosFile (std::vector< IonHit > &posIons, const char *posFile, unsigned int nSamplesMax)
	As per loadPosFile, but with an additional setting for the maximum number of ions to load. More...
const char *	getPosFileErrString (unsigned int errMesg)
unsigned int	savePosFile (const std::vector< Point3D > &points, float mass, const char *name, bool append=false)
	Save a vector of Point3Ds into a pos file, using a fixed mass, return nonzero on error. More...
unsigned int	savePosFile (const std::vector< IonHit > &data, const char *name, bool append=false)
	Save a vector of IonHits into a "pos" file, return nonzero on error. More...
unsigned int	saveTapsimBin (const std::vector< IonHit > &posIons, std::ostream &f)
	Write a tapsim file from a vector of IonHits. More...
unsigned int	saveTapsimBin (const std::vector< IonHit > &posIons, const char *filename)
	Write a tapsim file from a vector of ionHits. More...
size_t	loadEposFile (std::vector< EPOS_ENTRY > &outData, const char *filename)
	Load an entire "EPOS" File. More...
size_t	chunkLoadEposFile (std::vector< EPOS_ENTRY > &outData, const char *filename, unsigned int chunkSize, unsigned int chunkOffset, unsigned int &nEntriesLeft)
	Load an "EPOS" file, with a maximum chunk size. More...
unsigned int	loadTextData (const char *cpFilename, std::vector< std::vector< float > > &dataVec, std::vector< std::string > &headerVec, const char *delim="\", bool allowNan=true, bool allowConvFails=false, unsigned int headerCount=-1)
	Load a CSV, TSV or similar text file. Assumes "C" Locale for input (ie "." as decimal separator). More...
unsigned int	readPosapOps (const char *file, THREEDAP_EXPERIMENT &data, unsigned int &badLine, unsigned int &progress, std::atomic< bool > &wantAbort, unsigned int nDelayLines=2, bool strictMode=false)
	Function to read POSAP "OPS" files. More...
unsigned int	loadATOFile (const char *fileName, std::vector< ATO_ENTRY > &ions, unsigned int forceEndian=0)
	Load a LAWATAP "ATO" file. More...
bool	operator< (const SIMPLE_SPECIES &a, const SIMPLE_SPECIES &b)
unsigned int	parseCompositionData (const std::vector< std::string > &s, const AbundanceData &atomTable, std::map< unsigned int, double > &atomData)
	Convert atomic string label data, in the form "Fe 0.81" to fraction map. More...
void	convertMolToMass (const AbundanceData &atomTable, const std::map< unsigned int, double > &compositionMols, std::map< unsigned int, double > &compositionMass)
	Convert the given composition from molar fraction data to mass fraction. More...
void	convertMassToMol (const AbundanceData &atomTable, const std::map< unsigned int, double > &compositionMass, std::map< unsigned int, double > &compositionMols)
	Convert the given composition from mass fraction data to molar fraction. More...
void	findOverlaps (const AbundanceData &natData, const RangeFile &rng, float massDelta, unsigned int maxCharge, std::vector< std::pair< size_t, size_t > > &overlapIdx, std::vector< std::pair< float, float > > &overlapMasses)
	Find the overlaps stemming from a given rangefile. More...
void	findOverlaps (const AbundanceData &natData, const std::vector< std::string > &ions, float massDelta, unsigned int maxCharge, std::vector< std::pair< size_t, size_t > > &overlapIdx, std::vector< std::pair< float, float > > &overlapMasses)
	As per findOverlaps(...Rangefile ...) , but uses a vector of ions instead. More...
void	findOverlapsFromSpectra (const std::vector< std::vector< std::pair< float, float > > > &massDistributions, float massDelta, const std::set< unsigned int > &skipIDs, std::vector< std::pair< size_t, size_t > > &overlapIdx, std::vector< std::pair< float, float > > &overlapMasses)
	Find overlaps in the given mass distributions, as per findOverlaps(...Rangefile...) More...
bool	reconstructTest ()
bool	fitVoigt (const std::vector< double > &x, const std::vector< double > &y, double &sigma, double &gamma, double &mu, double &amp, bool autoInit=true)
	Fit a Voigt function to the given X/Y values. Internally, a function minimiser is used. More...
void	voigtProfile (const std::vector< double > &x, double sigma, double gamma, double mu, double amp, std::vector< double > &y)
	Generate a shifted voigt profile. More...
bool	fitDoniachSunjic (const std::vector< double > &x, const std::vector< double > &y, double &a, double &f, double &mu, double &amp, bool autoInit=true)
	Fit a Doniach-Sunjic curve. More...
void	doniachSunjic (const std::vector< double > &x, double &a, double &F, double &mu, double &amp, std::vector< double > &y)
	generate a Doniach-Sunjic profile More...
bool	fitLikeLogGaussian (const std::vector< double > &x, const std::vector< double > &y, double &lambda, double &sigma, double &xp, double &amp, double &h, bool autoInit=true)
	Fit a smoothed log-gaussian curve (arxiv:0711.4449) More...
void	likeLogGaussian (const std::vector< double > &x, double &xp, double &sigma, double &lambda, double &amp, double &h, std::vector< double > &y)
	Generate a smoothed log-gaussian curve. More...
bool	fitExpNorm (const std::vector< double > &x, const std::vector< double > &y, double &K, double &mu, double &sigma, double &amp, bool autoInit=true)
	Fit a smoothed log-gaussian curve (arxiv:0711.4449) More...
void	expNorm (const std::vector< double > &x, double &K, double &mu, double &sigma, double &amp, std::vector< double > &y)
	Exponentially decaying normal distribution. More...
double	lsq (const std::vector< double > &y, const std::vector< double > &yFit)
unsigned int	doFitBackground (const std::vector< float > &massData, BACKGROUND_PARAMS &params)
	Perform a background fit, assuming constant TOF noise, from 0->inf time. More...
std::string	getFitErrorMsg (unsigned int errCode)
void	createMassBackground (float massStart, float massEnd, unsigned int nBinsMass, float tofBackIntensity, std::vector< float > &histogram)
	Build a histogram of the background counts. More...
void	findPeaks (const std::vector< float > &x0, std::vector< unsigned int > &peakInds, float sel, bool autoSel=true, bool includeEndpoints=true)
	Simple peak-finding algorithm. More...
void	poissonConfidenceObservation (float counts, float alpha, float &lBound, float &uBound)
	Obtain poisson confidence limits for the mean of a poisson distribution. More...
bool	numericalEstimatePoissRatioConf (float lambda1, float lambda2, float alpha, unsigned int nTrials, gsl_rng *r, float &lBound, float &uBound)
	Brute-force poisson ratio confidence estimator. Returns the confidence interval in the estimate of the mean, at the given rates. More...
bool	numericalEstimateGaussRatioConf (float mu1, float mu2, float var1, float var2, float alpha, unsigned int nTrials, gsl_rng *r, float &lBound, float &uBound)
	Brute-force guassian ratio confidence estimator. More...
bool	numericalEstimateSkellamConf (float lambda1, float lambda2, float alpha, unsigned int nTrials, gsl_rng *r, float &lBound, float &uBound)
	Brute-force the confidence bounds of a skellam distribution. More...
bool	zechConfidenceLimits (float lambdaBack, unsigned int observation, float alpha, float &estimate)
	Provides a best estimate for true signal when true signal, background. More...
bool	rangeOverlaps (const pair< float, float > &r1, const pair< float, float > &r2)
void	computeRangeAdjacency (const MultiRange &mrf, const OVERLAP_PROBLEM_SETTINGS &settings, gsl_matrix *&m)
void	freeConvexHull ()
unsigned int	doHull (unsigned int bufferSize, double *buffer, vector< Point3D > &resHull, Point3D &midPoint, bool freeHullOnExit)
unsigned int	countIntensityEvents (const vector< pair< float, float > > &data, float minV, float maxV)
void	buildFrequencyTable (const vector< ISOTOPE_ENTRY > &solutionVec, vector< size_t > &solutionElements, vector< size_t > &solutionFrequency)
vector< float >	maxExplainedFraction (const vector< pair< float, float > > &intensityData, float peakMass, float massWidth, const vector< vector< ISOTOPE_ENTRY > > &solutions, const AbundanceData &massTable, float massDistTol, unsigned int solutionCharge)
bool	incrementCorrelationHist (const std::vector< EPOS_ENTRY > &eposIons, std::vector< std::vector< unsigned int > > &histogram, float stepMass, float endMass)
template<class T >
void	removeElements (const std::vector< size_t > &elems, std::vector< T > &vec)
bool	pairContains (const pair< float, float > &p, float m)
RANGE_MOLECULE	getRangeMolecule (const AbundanceData &massTable, const RangeFile &rng, unsigned int rangeId)
double	gsl_matrix_det (gsl_matrix *A, bool inPlace=false)
gsl_matrix *	getRotationMatrix (const Point3D &pt, float theta)
float	nullBackground (float rangeStart, float rangeEnd)
bool	getHardAssert ()
char *	myStrDup (const char *s)
void	pushLocale (const char *newLocale, int type)
void	popLocale ()
bool	getFilesize (const char *fname, size_t &size)
void	gsl_print_matrix (const gsl_matrix *m)
void	gsl_print_vector (const gsl_vector *v)
float	gsl_determinant (const gsl_matrix *m)
bool	isNotDirectory (const char *filename)
int	fpeek (FILE *stream)
void	quat_mult_no_second_a (Quaternion *result, const Quaternion *q1, const Quaternion *q2)
void	quat_pointmult (Point3f *result, const Quaternion *q1, const Quaternion *q2)
void	quat_invert (Quaternion *quat)
void	ucharToHexStr (unsigned char c, std::string &s)
void	hexStrToUChar (const std::string &s, unsigned char &c)
string	XMLHelpGetText (xmlNodePtr node)
template<class T >
unsigned int	fixedRecordReader (const char *filename, bool(*recordReader)(const char *bufRead, const char *destBuf), size_t recordSize, std::vector< T > &outputData)
template<class T >
unsigned int	fixedRecordChunkReader (const char *filename, bool(*recordReader)(const char *bufRead, const char *destBuf), size_t recordSize, std::vector< T > &outputData, unsigned int chunkSize, unsigned int chunkOffset, unsigned int &nEntriesLeft)
unsigned int	loadTapsimBinFile (vector< IonHit > &posIons, const char *posfile)
bool	readEposRecord (const char *src, const char *dest)
bool	strhas (const char *cpTest, const char *cpPossible)
template<class T >
void	linkIdentifiers (vector< T > &link)
bool	pairOverlaps (float aStart, float aEnd, float bStart, float bEnd)
bool	isValidElementSymbol (std::string &symbol)
string	rangeToStr (const pair< float, float > &rng)
bool	matchComposedName (const std::map< string, size_t > &composedNames, const vector< pair< string, size_t > > &namesToFind, size_t &matchOffset)
void	findOverlapsFromSpectra (const vector< vector< pair< float, float > > > &massDistributions, float massDelta, const set< unsigned int > &skipIDs, vector< pair< size_t, size_t > > &overlapIdx, vector< pair< float, float > > &overlapMasses)
void	findOverlaps (const AbundanceData &natData, const RangeFile &rng, float massDelta, unsigned int maxCharge, vector< pair< size_t, size_t > > &overlapIdx, vector< pair< float, float > > &overlapMasses)
void	findOverlaps (const AbundanceData &natData, const vector< string > &ionNames, float massDelta, unsigned int maxCharge, vector< pair< size_t, size_t > > &overlapIdx, vector< pair< float, float > > &overlapMasses)
int	gcd (int a, int b)
std::ostream &	operator<< (std::ostream &stream, const BoundCube &b)
std::ostream &	operator<< (std::ostream &stream, const IonHit &ion)
bool	antiRotateMatch (const unsigned int *a, const unsigned int *b, size_t n)
bool	rotateMatch (const unsigned int *a, const unsigned int *b, size_t n, bool directionForwards=true)
float	signVal (unsigned int val)
size_t	findMaxLessThanOrEq (const vector< std::pair< size_t, size_t > > &v, size_t value)
float	Determinant (float **a, int n)
float	fourDeterminant (const Point3D &a, const Point3D &b, const Point3D &c, const Point3D &d)
unsigned int	edgeIdx (unsigned int i, unsigned int j)
int	intersect_RayTriangle (const Point3D &rayStart, const Point3D &rayEnd, Point3D *tri, Point3D &I)
void	findNearVerticies (float tolerance, const vector< Point3D > &ptVec, vector< std::pair< size_t, vector< size_t > > > &clusterList)
void	findNearVerticies (float tolerance, const vector< Point3D > &ptVec, std::list< std::pair< size_t, vector< size_t > > > &clusterList)
std::ostream &	operator<< (std::ostream &stream, const Point3D &pt)
double	SphericProjectionEqn (double eta, void *p)
void	voigtProfile (const vector< double > &x, double sigma, double gamma, vector< double > &y)
double	fitVoigtFunc (const gsl_vector *v, void *params)
double	fitDoniachSunjic (const gsl_vector *v, void *params)
double	fitLikeLogGaussian (const gsl_vector *v, void *params)
double	fitExpNorm (const gsl_vector *v, void *params)
void	expNormLSQDerivs (const gsl_vector *v, void *params, gsl_vector *df)
template<class T >
bool	andersonDarlingStatistic (std::vector< T > vals, float &meanV, float &stdevVal, float &statistic, size_t &undefCount, bool computeMeanAndStdev=true)
void	makeHistogram (const vector< float > &data, float start, float end, float step, vector< float > &histVals)
void	diff (const vector< float > &in, vector< float > &out)
template<class T , class T2 >
std::iterator_traits< T >::value_type	kahansum (T begin, T end, T2 other)
double	zechRoot (double sigGuess, void *params)
template<class T >
void	cumTrapezoid (const vector< T > &x, const vector< T > &vals, vector< T > &res)
double	gauss_ratio_pdf (double x, double muX, double muY, double varX, double varY)

Variables
LibVersion	libVersion
RandNumGen	randGen
const char *	RECORDREAD_ERR_STRINGS []
const char *	ATO_ERR_STRINGS []
	Human readable error messages for use with ATO reader return values. More...
const char *	OPS_ENUM_ERRSTRINGS []
const unsigned int	NUM_ELEMENTS =119
const size_t	EPOS_RECORD_SIZE = 11*4
const unsigned int	ELEM_SINGLE_NODE_POINT =15
const unsigned int	ELEM_TWO_NODE_LINE =1
const unsigned int	ELEM_THREE_NODE_TRIANGLE =2
const unsigned int	ELEM_FOUR_NODE_TETRAHEDRON =4
const char *	MESH_LOAD_ERRS []
bool	qhullInited =false
const unsigned int	HULL_GRAB_SIZE =4096
int	aiCubeEdgeFlags [256]
int	a2iTriangleConnectionTable [256][16]
const unsigned int	VERTEX_OFFSET [8][3]
int	edgeRemap [12]
bool	hardAssert =true
const size_t	maximumLinearTable []
const char	MULTIRANGE_FORMAT_VERSION [] = "0.0.1"
const size_t	MAX_LINE_SIZE = 16536
const size_t	MAX_RANGEFILE_SIZE = 50*1024*1024
const char *	RANGE_EXTS []
const char *	elementList []
const char *	ABUNDANCE_ERROR []
const size_t	PROGRESS_REDUCE =500

Typedef Documentation

ATO_ENTRY

typedef struct AtomProbe::ATO_ENTRY AtomProbe::ATO_ENTRY

IONHIT

typedef struct AtomProbe::IONHIT AtomProbe::IONHIT

Record as stored in a .POS file.

Enumeration Type Documentation

anonymous enum

anonymous enum

Enumerator
HULL_SURFREDUCE_NEGATIVE_SCALE_FACT
HULL_ERR_USER_ABORT
HULL_ERR_NO_MEM

Definition at line 26 of file convexHull.h.

anonymous enum

anonymous enum

Enumerator
ATO_OPEN_FAIL
ATO_EMPTY_FAIL
ATO_SIZE_ERR
ATO_VERSIONCHECK_ERR
ATO_MEM_ERR
ATO_BAD_ENDIAN_DETECT
ATO_ENUM_END

Definition at line 49 of file dataFiles.h.

anonymous enum

anonymous enum

Enumerator
TEXT_ERR_FILE_OPEN
TEXT_ERR_FILE_NUM_FIELDS
TEXT_ERR_FILE_FORMAT

Definition at line 60 of file dataFiles.h.

anonymous enum

anonymous enum

Error codes for OPS file loading.

Enumerator
OPSREADER_FORMAT_CLINE_ERR
OPSREADER_FORMAT_DETECTORLINE_ERR
OPSREADER_FORMAT_LINE_DASH_ERR
OPSREADER_FORMAT_LINE_VOLTAGE_ERR
OPSREADER_FORMAT_LINE_VOLTAGE_NOBETA
OPSREADER_FORMAT_LINE_VOLTAGE_DATA_ERR
OPSREADER_FORMAT_LINE_VOLTAGE_DATACOUNT_ERR
OPSREADER_FORMAT_LINETYPE_ERR
OPSREADER_FORMAT_CHANNELS_ERR
OPSREADER_CHANNELS_DATA_ERR
OPSREADER_FORMAT_SLINE_EVENTCOUNT_ERR
OPSREADER_FORMAT_SLINE_EVENTDATA_ERR
OPSREADER_FORMAT_SLINE_FORMAT_ERR
OPSREADER_FORMAT_SLINE_PREFIX_ERR
OPSREADER_FORMAT_DUPLICATE_SYSDATA
OPSREADER_FORMAT_DUPLICATE_DETECTORSIZE
OPSREADER_FORMAT_TRAILING_DASH_ERR
OPSREADER_FORMAT_DOUBLEDASH
OPSREADER_OPEN_ERR
OPSREADER_READ_ERR
OPSREADER_ABORT_ERR
OPSREADER_ENUM_END

Definition at line 183 of file dataFiles.h.

anonymous enum

anonymous enum

Enumerator
MULTIRANGE_FORMAT_XML

Definition at line 57 of file multiRange.h.

anonymous enum

anonymous enum

Enumerator
RANGE_FORMAT_ORNL
RANGE_FORMAT_DBL_ORNL
RANGE_FORMAT_ENV
RANGE_FORMAT_RRNG
RANGE_FORMAT_END_OF_ENUM

Definition at line 37 of file ranges.h.

anonymous enum

anonymous enum

Enumerator
RANGE_ERR_FORMAT
RANGE_ERR_FORMAT_HEADER
RANGE_ERR_EMPTY
RANGE_ERR_FORMAT_LONGNAME
RANGE_ERR_FORMAT_SHORTNAME
RANGE_ERR_FORMAT_COLOUR
RANGE_ERR_FORMAT_TABLESEPARATOR
RANGE_ERR_FORMAT_RANGE_DUMMYCHARS
RANGE_ERR_FORMAT_MASS_PAIR
RANGE_ERR_FORMAT_TABLE_ENTRY
PARSE_RANGE_FORMAT_GENERIC_FAIL
RANGE_ERR_DATA_TOO_MANY_USELESS_RANGES
RANGE_ERR_DATA_FLIPPED
RANGE_ERR_DATA_INCONSISTENT
RANGE_ERR_DATA_NOMAPPED_IONNAME
RANGE_ERR_OPEN
RANGE_ERR_FORMAT_RANGETABLE
RANGE_ERR_FORMAT_TABLEHEADER_NUMIONS
RANGE_ERR_NONUNIQUE_POLYATOMIC
RANGE_ERR_TOO_LARGE
RANGE_ERR_DASHHEADER
RANGE_ERR_IONBLOCK_CONTENT
RANGE_ERR_NUMIONS
RANGE_ERR_NUMIONS_DUPLICATED
RANGE_ERR_TOO_MANYIONS
RANGE_ERR_ION_BLOCK_NOT_PRESENT
RANGE_ERR_DUPLICATE_NUMRANGES
RANGE_ERR_NUMRANGE_PARSE
RANGE_ERR_RRNG_IONS_TOOSHORT
RANGE_ERR_RRNG_COLON_SEPARATOR
RANGE_ERR_BADCOLOUR
RANGE_ERR_ION_NOT_MAPPED
RANGE_ERR_BADSTART
RANGE_ERR_BADEND
RANGE_ERR_NAME_EMPTY
RANGE_ERR_BAD_LINE_RANGEBLOCK
RANGE_ERR_MISSING_IONBLOCK
RANGE_ERR_NO_RANGES
RANGE_ERR_NO_BASIC_IONS
RANGE_ERR_MISMATCHED_NUMRANGES
RANGE_ERR_RANGEBLOCK_FORMAT
RANGE_ERR_BAD_MULTIPLICITY
RANGE_ERR_VOLUME_PARSE
RANGE_ERR_FORMAT_EMPTY_RANGEROW
RANGE_ERR_FILESIZE
RANGE_ERR_ENUM_END

Definition at line 44 of file ranges.h.

anonymous enum

anonymous enum

composition parsing error messages

Enumerator
COMPPARSE_BAD_INPUT_FORMAT
COMPPARSE_BAD_COMP_VALUE
COMPPARSE_BAD_BAL_USAGE
COMPPARSE_BAD_SYMBOL
COMPPARSE_DUPLICATE_SYMBOL
COMPPARSE_BAD_TOTAL_COMP

Definition at line 26 of file massconvert.h.

anonymous enum

anonymous enum

Enumerator
CRYSTAL_BAD_UNIT_CELL
CRYSTAL_ENUM_END

Definition at line 96 of file generate.h.

anonymous enum

anonymous enum

Enumerator
LATTICE_FCC
LATTICE_BCC
LATTICE_HCP
LATTICE_END_OF_ENUM

Definition at line 28 of file millerIndex.h.

anonymous enum

anonymous enum

Boundary clipping mode.

These constants defines the behaviour of the routines when presented with a boundary value problem, such as in convolution.

Enumerator
BOUND_CLIP
BOUND_HOLD
BOUND_DERIV_HOLD
BOUND_MIRROR
BOUND_ZERO
BOUND_ENUM_END

Definition at line 47 of file voxels.h.

anonymous enum

anonymous enum

Enumerator
ELEMENT_TRIANGLE
ELEMENT_TETRAHEDRON
ELEMENT_LINE

Definition at line 44 of file mesh.h.

anonymous enum

anonymous enum

Enumerator
EVOLUTION_MODE_SHANKANGLE

Definition at line 29 of file reconstruction-simple.h.

anonymous enum

anonymous enum

Background fitting modes.

Enumerator
BACK_FIT_MODE_CONST_TOF
BACK_FIT_MODE_ENUM_END

Definition at line 22 of file processing.h.

anonymous enum

anonymous enum

Enumerator
POS_ALLOC_FAIL
POS_OPEN_FAIL
POS_SIZE_MODULUS_ERR
POS_SIZE_EMPTY_ERR
POS_READ_FAIL
POS_NAN_LOAD_ERROR
POS_FILE_ENUM_END

Definition at line 53 of file dataFiles.cpp.

anonymous enum

anonymous enum

Enumerator
TAPSIM_FILE_FORMAT_FAIL
TAPSIM_OPEN_FAIL

Definition at line 65 of file dataFiles.cpp.

anonymous enum

anonymous enum

Enumerator
MULTIRANGE_ERR_NO_PARSER
MULTIRANGE_ERR_NO_XML_DOC
MULTIRANGE_ERR_NO_XML_CONTEXT
MULTIRANGE_ERR_NO_NODEPTR
MULTIRANGE_NOT_VALID_ROOTNODE
MULTIRANGE_ERR_NO_CONTENT
MULTIRANGE_ERR_NO_TIMESTAMP
MULTIRANGE_ERR_NO_MOLECULES
MULTIRANGE_ERR_NO_MOLECULE_ENTRIES
MULTIRANGE_ERR_MOL_MISSING_ENTRY
MULTIRANGE_ERR_MOL_MISSING_NAME
MULTIRANGE_ERR_MOL_MISSING_COMPONENTS
MULTIRANGE_ERR_BAD_RANGE
MULTIRANGE_ERR_BAD_RANGES
MULTIRANGE_ERR_MOL_MISSING_COLOUR
MULTIRANGE_ERR_MOL_BAD_COLOUR
MULTIRANGE_ERR_NO_RANGES
MULTIRANGE_ERR_BAD_GROUP
MULTIRANGE_ERR_SELF_INCONSISTENT
MULTIRANGE_ERR_RANGE_NOPARENT
MULTIRANGE_ERR_ENUM_END

Definition at line 48 of file multiRange.cpp.

anonymous enum

anonymous enum

Enumerator
MESH_LOAD_UNSPECIFIED_ERROR
MESH_LOAD_BAD_NODECOUNT
MESH_LOAD_BAD_ELEMENTCOUNT
MESH_LOAD_IS_INSANE
MESH_LOAD_ENUM_END

Definition at line 44 of file mesh.cpp.

anonymous enum

anonymous enum

Enumerator
VOX_INTERP_NONE
VOX_INTERP_LINEAR
VOX_INTERP_ENUM_END

Definition at line 57 of file voxels.h.

anonymous enum

anonymous enum

Enumerator
ADJ_ALL
ADJ_PLUS

Definition at line 64 of file voxels.h.

anonymous enum

anonymous enum

Enumerator
VOXELS_BAD_FILE_READ
VOXELS_BAD_FILE_OPEN
VOXELS_BAD_FILE_SIZE
VOXELS_OUT_OF_MEMORY

Definition at line 70 of file voxels.h.

anonymous enum

anonymous enum

Clipping direction constants.

Controls the clipping direction when performing clipping operations

Enumerator
CLIP_NONE
CLIP_LOWER_SOUTH_WEST
CLIP_UPPER_NORTH_EAST

Definition at line 81 of file voxels.h.

anonymous enum

anonymous enum

Enumerator
VOXEL_ABORT_ERR
VOXEL_MEMORY_ERR
VOXEL_BOUNDS_INVALID_ERR

Definition at line 88 of file voxels.h.

anonymous enum

anonymous enum

Enumerator
PROP_PARSE_ERR
PROP_BAD_ATT

Definition at line 36 of file XMLHelper.h.

anonymous enum

anonymous enum

Enumerator
RECORDREAD_ERR_GET_FILESIZE
RECORDREAD_ERR_FILESIZE_MODULO
RECORDREAD_ERR_FILE_OPEN
RECORDREAD_ERR_NOMEM
RECORDREAD_BAD_FILEREAD
RECORDREAD_ERR_CHUNKOFFSET
RECORDREAD_BAD_RECORD

Definition at line 34 of file dataFiles.h.

PointDir

enum AtomProbe::PointDir

Enumerator
POINTDIR_TOGETHER
POINTDIR_IN_COMMON
POINTDIR_APART

Definition at line 33 of file misc.h.

Function Documentation

accumulateCorrelationHistogram()

bool AtomProbe::accumulateCorrelationHistogram	(	const std::vector< EPOS_ENTRY > &	eposIons,
		std::vector< std::vector< unsigned int > > &	histogram,
		float	stepMass,
		float	endMass,
		bool	lowerTriangular = true
	)

Increments a correlation histogram, as per correlationHistogram,.

For input parameters, see correlationHistogram(...). This version will have lower peak memory input, as eposIons can be chunked.

• The input histogram must be zero sized, or have the correct size when used. If zero sized, it will be resized and zeroed appropriately to contents
• The default here is that the lower triangular is true, unlike in correlationHistogram(...) so when performing the final accumulation, you may wish to set this to false, to ensure that histogram_ij = histogram_ji.
• Do not change endMass or stepMass between calls on the same histogram

Definition at line 119 of file histogram.cpp.

References incrementCorrelationHist().

Referenced by main().

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andersonDarlingStatistic()

template<class T >

bool AtomProbe::andersonDarlingStatistic	(	std::vector< T >	vals,
		float &	meanV,
		float &	stdevVal,
		float &	statistic,
		size_t &	undefCount,
		bool	computeMeanAndStdev = true
	)

Definition at line 51 of file processing.cpp.

References meanAndStdev().

Referenced by doFitBackground().

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antiRotateMatch()

bool AtomProbe::antiRotateMatch	(	const unsigned int *	a,
		const unsigned int *	b,
		size_t	n
	)

Definition at line 63 of file mesh.cpp.

Referenced by AtomProbe::TRIANGLE::edgesMismatch().

askAssert()

void AtomProbe::askAssert	(	const char *	filename,
		unsigned int	lineNumber
	)

Either abort program, or ask the user what to do for an assertion. depending on hardAssert setting.

Definition at line 35 of file aptAssert.cpp.

buildFrequencyTable()

void AtomProbe::buildFrequencyTable	(	const vector< ISOTOPE_ENTRY > &	solutionVec,
		vector< size_t > &	solutionElements,
		vector< size_t > &	solutionFrequency
	)

Definition at line 50 of file filter.cpp.

References ASSERT.

Referenced by filterPeakNeedBiggerObs(), and maxExplainedFraction().

castVoxels()

template<class T , class U >

void AtomProbe::castVoxels	(	const Voxels< T > &	src,
		Voxels< U > &	dest
	)

Convert one type of voxel into another by assignment operator.

Definition at line 368 of file voxels.h.

checkMassRangingCorrectness()

void AtomProbe::checkMassRangingCorrectness	(	const AtomProbe::RangeFile &	rng,
		AtomProbe::AbundanceData &	massTable,
		float	massTolerance,
		unsigned int	maxChargeState,
		unsigned int	maxComponents,
		std::vector< bool > &	badRanges
	)

Ensure that each mass given spans a peak that should exist.

Each entry in badRanges is true if an inconsistent range is detected. There will be one entry per range in the parent rangefile Some ranges may be skipped if they cannot be understood maxComponents will skip checks for ions with more than this many atoms in the ionic molecule. Eg H2 would not be checked if maxComponents=1

Definition at line 101 of file rangeCheck.cpp.

References AtomProbe::RangeFile::addIon(), AtomProbe::RangeFile::addRange(), AtomProbe::RGBf::blue, AtomProbe::RANGE_MOLECULE::components, AtomProbe::AbundanceData::generateIsotopeDist(), AtomProbe::RangeFile::getNumRanges(), AtomProbe::RangeFile::getRange(), getRangeMolecule(), AtomProbe::RGBf::green, AtomProbe::RANGE_MOLECULE::isOK, AtomProbe::RangeFile::moveBothRanges(), AtomProbe::AbundanceData::open(), pairContains(), AtomProbe::RGBf::red, and TEST.

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chunkLoadEposFile()

size_t AtomProbe::chunkLoadEposFile	(	std::vector< EPOS_ENTRY > &	outData,
		const char *	filename,
		unsigned int	chunkSize,
		unsigned int	chunkOffset,
		unsigned int &	nEntriesLeft
	)

Load an "EPOS" file, with a maximum chunk size.

This is useful to avoid out-of-memory situations when working with large datasets If the file has fewer EPOS entries left than the chunk size, only the remaining entries will be read. Increment chunkOffset to seek to the next part of the file The file will be re-opened each time, so larger chunk sizes will increase speed at the cost of memory.

outData : the output to write the epos data to filename : the name of the EPOS formatted file to open chunkSize : the maximum number of entries to read in one go chunkOffset : the position (in chunks) of the file to start reading from, the caller must increment this to prevent the same section being re-read nEntriesLeft : returns the number of entries left in the file, The return value is nonzero on error, and is part of the RECORDREAD_ERR enum

Definition at line 765 of file dataFiles.cpp.

References EPOS_RECORD_SIZE, fixedRecordChunkReader(), and readEposRecord().

Referenced by getAtoErrString(), and main().

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computeComposition()

void AtomProbe::computeComposition	(	const std::vector< unsigned int > &	countData,
		std::vector< float > &	compositionData
	)

Definition at line 29 of file composition.cpp.

Referenced by main().

computeConvexHull()

unsigned int AtomProbe::computeConvexHull	(	const std::vector< IonHit > &	data,
		unsigned int *	progress,
		bool(*)(bool)	callback,
		std::vector< Point3D > &	curHull,
		bool	freeHull
	)

Obtain the convex hull of a set of ions.

An existing set of points on the convex hull, "curHull", can be given as a starting set, optionally. For the last call to this routine , set "freeHull" to true. Returns 0 on success, nonzero on error, with error codes in above enum

Definition at line 149 of file convexHull.cpp.

References callback(), doHull(), HULL_ERR_NO_MEM, HULL_ERR_USER_ABORT, PROGRESS_REDUCE, and AtomProbe::Point3D::sqrDist().

Referenced by GetReducedHullPts().

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computeIonDistAdjacency()

void AtomProbe::computeIonDistAdjacency	(	const MultiRange &	mrf,
		const AbundanceData &	abundance,
		const OVERLAP_PROBLEM_SETTINGS &	settings,
		gsl_matrix *&	m,
		gsl_vector *&	vOwnership,
		gsl_vector *&	vMass
	)

Calculate the adjacency matrix for the ions in a multirange.

Uses tolerance and other data in settings. Range data is NOT used. Vectors and matrices should not be allocated, but must be freed using gsl_matrix_free and gsl_vector_free after use. Return values are a 0/1 adjacency matrix, and two vectors, one describing the owner index of each ion and the other the mass. return matrix will be square, and vectors will have same size as matrix

Definition at line 40 of file componentAnalysis.cpp.

References ASSERT, AtomProbe::AbundanceData::generateIsotopeDist(), AtomProbe::MultiRange::getMolecule(), AtomProbe::MultiRange::getNumIons(), AtomProbe::OVERLAP_PROBLEM_SETTINGS::intensityTolerance, AtomProbe::OVERLAP_PROBLEM_SETTINGS::massTolerance, AtomProbe::OVERLAP_PROBLEM_SETTINGS::maxDefaultCharge, AtomProbe::AbundanceData::symbolIdxFromAtomicNumber(), and vectorMultiErase().

Referenced by computeRangeAdjacency().

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computeRangeAdjacency()

void AtomProbe::computeRangeAdjacency	(	const MultiRange &	mrf,
		const OVERLAP_PROBLEM_SETTINGS &	settings,
		gsl_matrix *&	m
	)

Definition at line 172 of file componentAnalysis.cpp.

References AtomProbe::MultiRange::addIon(), AtomProbe::MultiRange::addRange(), ASSERT, AtomProbe::SIMPLE_SPECIES::atomicNumber, AtomProbe::RGBf::blue, computeIonDistAdjacency(), AtomProbe::SIMPLE_SPECIES::count, AtomProbe::AbundanceData::getAtomicNumber(), AtomProbe::MultiRange::getNumRanges(), AtomProbe::MultiRange::getRange(), AtomProbe::RGBf::green, gsl_print_matrix(), AtomProbe::OVERLAP_PROBLEM_SETTINGS::intensityTolerance, AtomProbe::OVERLAP_PROBLEM_SETTINGS::massTolerance, AtomProbe::OVERLAP_PROBLEM_SETTINGS::maxDefaultCharge, AtomProbe::AbundanceData::open(), rangeOverlaps(), AtomProbe::RGBf::red, AtomProbe::AbundanceData::symbolIndex(), TEST, and WARN.

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computeRotationMatrix() [1/2]

void AtomProbe::computeRotationMatrix	(	const Point3D &	ur1,
		const Point3D &	ur2,
		const Point3D &	r1,
		const Point3D &	r2,
		gsl_matrix *	m
	)

Given two orthogonal and normal basis vectors, r1 and r2, and two matching rotated vectors ur1 and ur2, compute the rotation matrix that will transform between them.

i.e. r = M*ur, vector pairs (ur1,ur2) and (r1,r2) should be orthogonal and normalised matrix m must be pre-allocated as a 3x3 matrix, using e.g gsl_matrix_alloc(3,3)

Definition at line 83 of file rotations.cpp.

References ASSERT, AtomProbe::Point3D::crossProd(), gsl_determinant(), and AtomProbe::Point3D::sqrMag().

Referenced by computeRotationMatrix(), getRotationMatrix(), and main().

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computeRotationMatrix() [2/2]

void AtomProbe::computeRotationMatrix	(	const Point3D &	ur1,
		const Point3D &	ur2,
		const Point3D &	r1,
		const Point3D &	r2,
		std::vector< std::vector< float > > &	m
	)

Convenience wrapper for conputeRotationMatrix, which uses vector containers.

output vectors will be 3x3, indexed vector[row][column]. Presizing is not required

Definition at line 67 of file rotations.cpp.

References computeRotationMatrix().

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computeRotationMatrixWahba()

unsigned int AtomProbe::computeRotationMatrixWahba	(	const std::vector< Point3D > &	unrotated,
		const std::vector< Point3D > &	rotated,
		const std::vector< float > &	weights,
		gsl_matrix *&	R
	)

Given a series of paired observations of directions, compute the least squares rotation matrix between them.

This computes the least-squares rotation matrix that transforms the unrotated points to the rotated ones. rotated points and unrotated points must be the same size, must have >=2 entries, and must not be degenerate. Each point must be normalised. Weights is a series of weighting factor (e.g. inverse error) for each point. If R is nullptr on input, then it will be replaced with a matrix allocated by gsl_matrix_alloc(). The caller should deallocate this with gsl_matrix_free() after use.

Definition at line 147 of file rotations.cpp.

References ASSERT, gsl_determinant(), and gsl_matrix_mult().

Referenced by getRotationMatrix().

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convertEPOStoPos()

void AtomProbe::convertEPOStoPos	(	const std::vector< EPOS_ENTRY > &	eposEntry,
		std::vector< IonHit > &	posFile
	)

Convert an incoming entry of EPOS files to pos, and the append this to the pos vector given.

Definition at line 29 of file convert.cpp.

convertFileStringToCanonical()

std::string AtomProbe::convertFileStringToCanonical

(

const std::string &

s

)

Convert a path format into a unix path from native format.

Referenced by strAppend().

convertFileStringToNative()

std::string AtomProbe::convertFileStringToNative

(

const std::string &

s

)

Convert a path format into a native path from unix format.

Referenced by strAppend().

convertMassToMol()

void AtomProbe::convertMassToMol	(	const AbundanceData &	atomTable,
		const std::map< unsigned int, double > &	compositionMass,
		std::map< unsigned int, double > &	compositionMols
	)

Convert the given composition from mass fraction data to molar fraction.

inputs are: compositionMass - relative mass fractions (this will be normalised automatically) massValues - weights of the masses input compositionMols - output results

Definition at line 74 of file massconvert.cpp.

References AtomProbe::AbundanceData::getNominalMass().

Referenced by parseCompositionData().

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convertMolToMass()

void AtomProbe::convertMolToMass	(	const AbundanceData &	atomTable,
		const std::map< unsigned int, double > &	compositionMols,
		std::map< unsigned int, double > &	compositionMass
	)

Convert the given composition from molar fraction data to mass fraction.

Inputs are:

• atomTable - the natural abundance table, to provide weights
• compositionMols : relative molar fractions (this will be normalised automatically). First entry in map is ion index in abundance table. Second is relative fraction.

Outputs are:

• compositionMass : output results, as mass fractions First entry is the position in the abundance table, second is relative fraction

Definition at line 41 of file massconvert.cpp.

References ASSERT, and AtomProbe::AbundanceData::getNominalMass().

Referenced by parseCompositionData().

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correlationHistogram()

bool AtomProbe::correlationHistogram	(	const std::vector< EPOS_ENTRY > &	eposIons,
		std::vector< std::vector< unsigned int > > &	histogram,
		float	stepMass,
		float	endMass,
		bool	lowerTriangular = false
	)

Generates an ion "correlation histogram" from a vector of EPOS ions. The input vector MUST

The nature of the plot is described in the following paper (Saxey et al, 2011): DOI : 10.1016/j.ultramic.2010.11.021, see e.g, Figure 3a.

The histogram will be allocated for you - do not pre-allocate

As the plot is symmetric around the m1=m2 line, the lowerTriangular setting controls if mirroring of the calculation is done. Setting this to true will ensure that only the lower half of the data field is calculated (faster).

StepMass > 0 EndMass > 0

in both cases, the histogram will use the full rectangular memory space (arrays will not be ragged)

Definition at line 85 of file histogram.cpp.

References incrementCorrelationHist().

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countIntensityEvents()

unsigned int AtomProbe::countIntensityEvents	(	const vector< pair< float, float > > &	data,
		float	minV,
		float	maxV
	)

Definition at line 36 of file filter.cpp.

Referenced by maxExplainedFraction().

createMassBackground()

void AtomProbe::createMassBackground	(	float	massStart,
		float	massEnd,
		unsigned int	nBinsMass,
		float	tofBackIntensity,
		std::vector< float > &	histogram
	)

Build a histogram of the background counts.

• Inputs : Start and end mass for background window, and bin count
• tofBackIntensity is the intensity level per unit time (proportional to sqrt mass) in the background, as obtained by doFitBackground.

Note : You may need to divide by bin width, depending on your application

Definition at line 224 of file processing.cpp.

Referenced by findPeaks().

cumTrapezoid()

template<class T >

void AtomProbe::cumTrapezoid	(	const vector< T > &	x,
		const vector< T > &	vals,
		vector< T > &	res
	)

Definition at line 461 of file confidence.cpp.

References ASSERT, and kahansum().

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det3by3()

double AtomProbe::det3by3

(

const double *

ptArray

)

Definition at line 256 of file misc.cpp.

Referenced by dotProduct(), and pyramidVol().

Determinant()

float AtomProbe::Determinant	(	float **	a,
		int	n
	)

Definition at line 172 of file mesh.cpp.

References ASSERT, and signVal().

Referenced by fourDeterminant().

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diff()

void AtomProbe::diff	(	const vector< float > &	in,
		vector< float > &	out
	)

Definition at line 249 of file processing.cpp.

Referenced by findPeaks().

digitString()

std::string AtomProbe::digitString	(	unsigned int	thisDigit,
		unsigned int	maxDigit
	)

Generate a string with leading digits up to maxDigit (eg, if maxDigit is 424, and thisDigit is 1.

Definition at line 115 of file stringFuncs.cpp.

References stream_cast().

Referenced by strAppend().

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distanceToFacet()

float AtomProbe::distanceToFacet	(	const Point3D &	fA,
		const Point3D &	fB,
		const Point3D &	fC,
		const Point3D &	normal,
		const Point3D &	p
	)

Definition at line 250 of file misc.cpp.

References signedDistanceToFacet().

Referenced by GetReducedHullPts(), and meanAndStdev().

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distanceToSegment()

float AtomProbe::distanceToSegment	(	const Point3D &	fA,
		const Point3D &	fB,
		const Point3D &	p
	)

Definition at line 156 of file misc.cpp.

References AtomProbe::Point3D::crossProd(), POINTDIR_TOGETHER, AtomProbe::Point3D::sqrDist(), AtomProbe::Point3D::sqrMag(), and vectorPointDir().

Referenced by meanAndStdev(), and signedDistanceToFacet().

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doFitBackground()

unsigned int AtomProbe::doFitBackground	(	const std::vector< float > &	massData,
		BACKGROUND_PARAMS &	params
	)

Perform a background fit, assuming constant TOF noise, from 0->inf time.

• Background params has the input and output data for the fit.

dataIn requires raw mass data, not histogram counts.

• returns zero on success, nonzero on error Return value is stored in params.intensity, as counts/bin. Use createMassBackground to re-generate the histogram

Definition at line 160 of file processing.cpp.

References andersonDarlingStatistic(), ASSERT, AtomProbe::BACKGROUND_PARAMS::binWidth, AtomProbe::BACKGROUND_PARAMS::FIT_FAIL_AVG_COUNTS, AtomProbe::BACKGROUND_PARAMS::FIT_FAIL_DATA_NON_GAUSSIAN, AtomProbe::BACKGROUND_PARAMS::FIT_FAIL_INSUFF_DATA, AtomProbe::BACKGROUND_PARAMS::FIT_FAIL_MIN_REQ_BINS, AtomProbe::BACKGROUND_PARAMS::intensity, makeHistogram(), AtomProbe::BACKGROUND_PARAMS::massEnd, AtomProbe::BACKGROUND_PARAMS::massStart, and AtomProbe::BACKGROUND_PARAMS::stdev.

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doHull()

unsigned int AtomProbe::doHull	(	unsigned int	bufferSize,
		double *	buffer,
		vector< Point3D > &	resHull,
		Point3D &	midPoint,
		bool	freeHullOnExit
	)

Definition at line 53 of file convexHull.cpp.

References HULL_ERR_NO_MEM.

Referenced by computeConvexHull().

doniachSunjic()

void AtomProbe::doniachSunjic	(	const std::vector< double > &	x,
		double &	a,
		double &	F,
		double &	mu,
		double &	amp,
		std::vector< double > &	y
	)

generate a Doniach-Sunjic profile

Definition at line 502 of file fitting.cpp.

References M_PI.

Referenced by fitDoniachSunjic().

dotProduct()

float AtomProbe::dotProduct ( float  a1, float  a2, float  a3, float  b1, float  b2, float  b3  )

inline

Inline func for calculating a(dot)b.

Definition at line 128 of file misc.h.

References det3by3(), pyramidVol(), and triIsDegenerate().

Referenced by GetReducedHullPts().

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edgeIdx()

unsigned int AtomProbe::edgeIdx	(	unsigned int	i,
		unsigned int	j
	)

Definition at line 249 of file mesh.cpp.

References ASSERT.

estimateRank()

unsigned int AtomProbe::estimateRank	(	const gsl_matrix *	m,
		float	tolerance = sqrt(std::numeric_limits<float>::epsilon())
	)

Estimate the rank of the given matrix.

Definition at line 58 of file misc.cpp.

Referenced by leastSquaresOverlapSolve(), and pyramidVol().

expNorm()

void AtomProbe::expNorm	(	const std::vector< double > &	x,
		double &	K,
		double &	mu,
		double &	sigma,
		double &	amp,
		std::vector< double > &	y
	)

Exponentially decaying normal distribution.

Definition at line 532 of file fitting.cpp.

Referenced by fitExpNorm(), and main().

expNormLSQDerivs()

void AtomProbe::expNormLSQDerivs	(	const gsl_vector *	v,
		void *	params,
		gsl_vector *	df
	)

Definition at line 551 of file fitting.cpp.

References M_PI, AtomProbe::DATA_FIT::x, and AtomProbe::DATA_FIT::y.

filterBySolutionPPM()

void AtomProbe::filterBySolutionPPM	(	const AtomProbe::AbundanceData &	massTable,
		float	minPpm,
		std::vector< std::vector< AtomProbe::ISOTOPE_ENTRY > > &	solutions
	)

Use the maximum possible PPM for each isotopic combination to filter possible solutions.

For example, 17^O:17^O:17^O in a naturally abundant mix has a maximum possible concentration of 5e-11 at. fraction. Isotope group tolerance is used to group the abundance distribution of nearby isotopes

massTable - a table of natural abundances minPpm - Minimum PPM below which to discard solutions solutions - list of solutions, which will be culled.

Definition at line 83 of file filter.cpp.

References AtomProbe::ISOTOPE_ENTRY::abundance, AtomProbe::AbundanceData::isotope(), and vectorMultiErase().

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filterPeakNeedBiggerObs()

void AtomProbe::filterPeakNeedBiggerObs	(	const AtomProbe::AbundanceData &	massTable,
		const std::vector< float > &	peakData,
		float	tolerance,
		size_t	solutionCharge,
		std::vector< std::vector< AtomProbe::ISOTOPE_ENTRY > > &	solutions
	)

Remove peaks for which an experimental set of observed peaks do not show a peak at a position which is expected from the peak distribution for this element. Only works with single-atom peaks

• Solutions are the input solutions,
• peakData is a list of peak mass positions
• tolerance is the error allowed to fit a peak (+/-)
• solutionCharge - charge state for the input isotope entries

Definition at line 119 of file filter.cpp.

References ASSERT, buildFrequencyTable(), AtomProbe::AbundanceData::generateIsotopeDist(), and vectorMultiErase().

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findMaxLessThanOrEq()

size_t AtomProbe::findMaxLessThanOrEq	(	const vector< std::pair< size_t, size_t > > &	v,
		size_t	value
	)

Definition at line 155 of file mesh.cpp.

References ASSERT.

findNearVerticies() [1/2]

void AtomProbe::findNearVerticies	(	float	tolerance,
		const vector< Point3D > &	ptVec,
		vector< std::pair< size_t, vector< size_t > > > &	clusterList
	)

Definition at line 365 of file mesh.cpp.

References ASSERT.

Referenced by AtomProbe::Mesh::mergeDuplicateVertices(), and AtomProbe::Mesh::setTriangleMesh().

findNearVerticies() [2/2]

void AtomProbe::findNearVerticies	(	float	tolerance,
		const vector< Point3D > &	ptVec,
		std::list< std::pair< size_t, vector< size_t > > > &	clusterList
	)

Definition at line 404 of file mesh.cpp.

References ASSERT.

findOverlaps() [1/4]

void AtomProbe::findOverlaps	(	const AbundanceData &	natData,
		const RangeFile &	rng,
		float	massDelta,
		unsigned int	maxCharge,
		std::vector< std::pair< size_t, size_t > > &	overlapIdx,
		std::vector< std::pair< float, float > > &	overlapMasses
	)

Find the overlaps stemming from a given rangefile.

An overlap is defined as "natural abundances within +-massDelta at same mass to charge"

• Species not in the rangefile will not be marked as overlapping
• FIXME: The output index is abused at this time, the range's index is actually given by dividing the output by the mass to charge. The charge state is given by modulo (massToCharge) +1
• The range mass information in the rangefile is not used - it is abused as an ion list

Inputs are:

• rng: The rangefile to use. The species in the rangefile are used to compute the overlaps
• massDelta: tolerance in amu,
• maxCharge: the maximum charge that species can be estimated to have

Outputs are:

• overlapIdx: the range indices of the overlapping species (ion index in rangefile)
• overlapMasses: the masses of the overlapping species, which should be within +-massDelta of one another

Note that ion's names will be decomposed, so Fe2H will be considered an Fe-Fe-H molecule

Referenced by findOverlaps(), and main().

findOverlaps() [2/4]

void AtomProbe::findOverlaps	(	const AbundanceData &	natData,
		const std::vector< std::string > &	ions,
		float	massDelta,
		unsigned int	maxCharge,
		std::vector< std::pair< size_t, size_t > > &	overlapIdx,
		std::vector< std::pair< float, float > > &	overlapMasses
	)

As per findOverlaps(...Rangefile ...) , but uses a vector of ions instead.

findOverlaps() [3/4]

void AtomProbe::findOverlaps	(	const AbundanceData &	natData,
		const RangeFile &	rng,
		float	massDelta,
		unsigned int	maxCharge,
		vector< pair< size_t, size_t > > &	overlapIdx,
		vector< pair< float, float > > &	overlapMasses
	)

Definition at line 94 of file overlaps.cpp.

References ASSERT, AtomProbe::RangeFile::decomposeIonById(), findOverlapsFromSpectra(), AtomProbe::AbundanceData::generateGroupedIsotopeDist(), AtomProbe::AbundanceData::getAtomicNumber(), AtomProbe::RangeFile::getNumIons(), AtomProbe::AbundanceData::getSymbolIndices(), and vectorMultiErase().

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findOverlaps() [4/4]

void AtomProbe::findOverlaps	(	const AbundanceData &	natData,
		const vector< string > &	ionNames,
		float	massDelta,
		unsigned int	maxCharge,
		vector< pair< size_t, size_t > > &	overlapIdx,
		vector< pair< float, float > > &	overlapMasses
	)

Definition at line 218 of file overlaps.cpp.

References AtomProbe::RangeFile::addIon(), AtomProbe::RangeFile::addRange(), AtomProbe::RGBf::blue, findOverlaps(), AtomProbe::RGBf::green, AtomProbe::AbundanceData::open(), AtomProbe::RGBf::red, and TEST.

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findOverlapsFromSpectra() [1/2]

void AtomProbe::findOverlapsFromSpectra	(	const vector< vector< pair< float, float > > > &	massDistributions,
		float	massDelta,
		const set< unsigned int > &	skipIDs,
		vector< pair< size_t, size_t > > &	overlapIdx,
		vector< pair< float, float > > &	overlapMasses
	)

Definition at line 46 of file overlaps.cpp.

References EQ_TOLV.

findOverlapsFromSpectra() [2/2]

void AtomProbe::findOverlapsFromSpectra	(	const std::vector< std::vector< std::pair< float, float > > > &	massDistributions,
		float	massDelta,
		const std::set< unsigned int > &	skipIDs,
		std::vector< std::pair< size_t, size_t > > &	overlapIdx,
		std::vector< std::pair< float, float > > &	overlapMasses
	)

Find overlaps in the given mass distributions, as per findOverlaps(...Rangefile...)

Referenced by findOverlaps().

findPeaks()

void AtomProbe::findPeaks	(	const std::vector< float > &	x0,
		std::vector< unsigned int > &	peakInds,
		float	sel,
		bool	autoSel = true,
		bool	includeEndpoints = true
	)

Simple peak-finding algorithm.

Adapted from Nathaniel Yoder's: https://uk.mathworks.com/matlabcentral/fileexchange/25500-peakfinder-x0-sel-thresh-extrema-includeendpoints-interpolate which is BSD licenced.

The performance of this function may or may not be suitable for your application, and your histogram may require pre-processing to optimise false postive/false-negative performance

• x0 : input mass histogram, must be > 2 elements
• sel : Selectivity for peaks - larger is more selective
• autosel : whether to determine sel automatically, or not
• includeEndpoints : allow edge values to be peaks

Definition at line 268 of file processing.cpp.

References ASSERT, createMassBackground(), diff(), makeHistogram(), NUM_IONS, and selectElements().

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fitDoniachSunjic() [1/2]

bool AtomProbe::fitDoniachSunjic	(	const std::vector< double > &	x,
		const std::vector< double > &	y,
		double &	a,
		double &	f,
		double &	mu,
		double &	amp,
		bool	autoInit = true
	)

Fit a Doniach-Sunjic curve.

Definition at line 204 of file fitting.cpp.

References weightedMean(), AtomProbe::DATA_FIT::x, and AtomProbe::DATA_FIT::y.

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fitDoniachSunjic() [2/2]

double AtomProbe::fitDoniachSunjic	(	const gsl_vector *	v,
		void *	params
	)

Definition at line 60 of file fitting.cpp.

References doniachSunjic(), lsq(), AtomProbe::DATA_FIT::x, and AtomProbe::DATA_FIT::y.

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fitExpNorm() [1/2]

bool AtomProbe::fitExpNorm	(	const std::vector< double > &	x,
		const std::vector< double > &	y,
		double &	K,
		double &	mu,
		double &	sigma,
		double &	amp,
		bool	autoInit = true
	)

Fit a smoothed log-gaussian curve (arxiv:0711.4449)

Definition at line 280 of file fitting.cpp.

References weightedMean(), AtomProbe::DATA_FIT::x, and AtomProbe::DATA_FIT::y.

Referenced by main().

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fitExpNorm() [2/2]

double AtomProbe::fitExpNorm	(	const gsl_vector *	v,
		void *	params
	)

Definition at line 103 of file fitting.cpp.

References expNorm(), lsq(), AtomProbe::DATA_FIT::x, and AtomProbe::DATA_FIT::y.

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fitLikeLogGaussian() [1/2]

bool AtomProbe::fitLikeLogGaussian	(	const std::vector< double > &	x,
		const std::vector< double > &	y,
		double &	lambda,
		double &	sigma,
		double &	xp,
		double &	amp,
		double &	h,
		bool	autoInit = true
	)

Fit a smoothed log-gaussian curve (arxiv:0711.4449)

Definition at line 360 of file fitting.cpp.

References weightedMean(), AtomProbe::DATA_FIT::x, and AtomProbe::DATA_FIT::y.

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fitLikeLogGaussian() [2/2]

double AtomProbe::fitLikeLogGaussian	(	const gsl_vector *	v,
		void *	params
	)

Definition at line 80 of file fitting.cpp.

References likeLogGaussian(), lsq(), AtomProbe::DATA_FIT::x, and AtomProbe::DATA_FIT::y.

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fitVoigt()

bool AtomProbe::fitVoigt	(	const std::vector< double > &	x,
		const std::vector< double > &	y,
		double &	sigma,
		double &	gamma,
		double &	mu,
		double &	amp,
		bool	autoInit = true
	)

Fit a Voigt function to the given X/Y values. Internally, a function minimiser is used.

Voigt functions are used in spectroscopy as a general curve for fitting spectra. they are symmetric, and won't fit "tailed" curves well

autoinit : If true, then initial values are chosen automatically and heuristically, if false, input parameters must be given, and are used to seed the minimiser outputs are sigma/gamma (voigt parameters), mu (x shift) and amp (y-scale)

Definition at line 123 of file fitting.cpp.

References fitVoigtFunc(), weightedMean(), AtomProbe::DATA_FIT::x, and AtomProbe::DATA_FIT::y.

Referenced by main().

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fitVoigtFunc()

double AtomProbe::fitVoigtFunc	(	const gsl_vector *	v,
		void *	params
	)

Definition at line 44 of file fitting.cpp.

References lsq(), voigtProfile(), AtomProbe::DATA_FIT::x, and AtomProbe::DATA_FIT::y.

Referenced by fitVoigt().

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fixedRecordChunkReader()

template<class T >

unsigned int AtomProbe::fixedRecordChunkReader	(	const char *	filename,
		bool(*)(const char *bufRead, const char *destBuf)	recordReader,
		size_t	recordSize,
		std::vector< T > &	outputData,
		unsigned int	chunkSize,
		unsigned int	chunkOffset,
		unsigned int &	nEntriesLeft
	)

Definition at line 144 of file dataFiles.cpp.

References getFilesize(), RECORDREAD_BAD_FILEREAD, RECORDREAD_BAD_RECORD, RECORDREAD_ERR_CHUNKOFFSET, RECORDREAD_ERR_FILE_OPEN, RECORDREAD_ERR_FILESIZE_MODULO, RECORDREAD_ERR_GET_FILESIZE, and RECORDREAD_ERR_NOMEM.

Referenced by chunkLoadEposFile().

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fixedRecordReader()

template<class T >

unsigned int AtomProbe::fixedRecordReader	(	const char *	filename,
		bool(*)(const char *bufRead, const char *destBuf)	recordReader,
		size_t	recordSize,
		std::vector< T > &	outputData
	)

Definition at line 93 of file dataFiles.cpp.

References getFilesize(), RECORDREAD_BAD_FILEREAD, RECORDREAD_BAD_RECORD, RECORDREAD_ERR_FILE_OPEN, RECORDREAD_ERR_FILESIZE_MODULO, RECORDREAD_ERR_GET_FILESIZE, and RECORDREAD_ERR_NOMEM.

Referenced by loadEposFile().

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fourDeterminant()

float AtomProbe::fourDeterminant	(	const Point3D &	a,
		const Point3D &	b,
		const Point3D &	c,
		const Point3D &	d
	)

Definition at line 212 of file mesh.cpp.

References Determinant().

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fpeek()

int AtomProbe::fpeek ( FILE *  stream )

inline

Definition at line 69 of file helpFuncs.h.

Referenced by AtomProbe::RangeFile::rangeTypeString().

freeConvexHull()

void AtomProbe::freeConvexHull

(

)

Definition at line 47 of file convexHull.cpp.

Referenced by GetReducedHullPts().

gauss_ratio_pdf()

double AtomProbe::gauss_ratio_pdf	(	double	x,
		double	muX,
		double	muY,
		double	varX,
		double	varY
	)

Definition at line 483 of file confidence.cpp.

References M_PI.

gcd()

int AtomProbe::gcd	(	int	a,
		int	b
	)

Definition at line 28 of file millerIndex.cpp.

Referenced by AtomProbe::MILLER_TRIPLET::simplify().

genColString() [1/2]

void AtomProbe::genColString	(	unsigned char	r,
		unsigned char	g,
		unsigned char	b,
		unsigned char	a,
		std::string &	s
	)

Referenced by strAppend(), and AtomProbe::RGBf::toHex().

genColString() [2/2]

void AtomProbe::genColString	(	unsigned char	r,
		unsigned char	g,
		unsigned char	b,
		std::string &	s
	)

Definition at line 308 of file stringFuncs.cpp.

References ucharToHexStr().

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generate1DAxialDistHist()

unsigned int AtomProbe::generate1DAxialDistHist	(	const std::vector< Point3D > &	pointList,
		K3DTreeExact &	tree,
		const Point3D &	axisDir,
		float	distMax,
		std::vector< unsigned int > &	histogram
	)

Generate a 1D axial distribution function,.

This generates a histogram of point-point distances, from the points in the point list to the points in the tree, within a specified radius of the source point.

This is variously called a 1D "Spatial Distribution Map (SDM)" "Atom Vicinity" or similar

• pointList : the source points for the distribution function
• tree : a pre-generated KD tree with the target points
• distMax : radius of the points around which to search
• histogram : a vector with the number of bins that are required for output. Does not need to be zero filled

Definition at line 37 of file axialdf.cpp.

References ASSERT, AtomProbe::K3DTreeExact::getPtRef(), AtomProbe::K3DTreeExact::ptsInSphere(), AtomProbe::BoundCube::setBounds(), AtomProbe::Point3D::sqrDist(), and AtomProbe::Point3D::sqrMag().

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generate1DAxialDistHistSweep()

unsigned int AtomProbe::generate1DAxialDistHistSweep	(	const std::vector< Point3D > &	pointList,
		K3DTreeExact &	tree,
		float	distMax,
		float	dTheta,
		float	dPhi,
		AtomProbe::ProgressBar &	prog,
		std::vector< std::vector< std::vector< unsigned int > > > &	histogram
	)

Generate a series of 1D distribution functions, one per pixel in a 2D grid of spherical coordinate directions.

Using a stepped spherical coordinates in equal delta-Theta, delta-Phi increments pointList : the source points from which to search tree : K3D Tree of target points distMax : maximum distance around which to search dTheta : step size in theta (radiians). dPhi : step size in phi (radiians) prog : Progress bar histogram : resultant data as a 2D vector, one bin per angular entry. Each vector will have the same size. The inner most vector contains the analysis data, over +-distMax

Definition at line 131 of file axialdf.cpp.

References ASSERT, AtomProbe::Point3D::dotProd(), AtomProbe::K3DTreeExact::getPtRef(), M_PI, AtomProbe::K3DTreeExact::ptsInSphere(), AtomProbe::BoundCube::setBounds(), AtomProbe::Point3D::setISOSpherical(), AtomProbe::K3DTreeExact::size(), AtomProbe::Point3D::sqrDist(), and AtomProbe::ProgressBar::update().

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getAtoErrString()

const char* AtomProbe::getAtoErrString ( unsigned int  errCode )

inline

Definition at line 82 of file dataFiles.h.

References chunkLoadEposFile(), getPosFileErrString(), loadEposFile(), loadPosFile(), loadTextData(), AtomProbe::ATO_ENTRY::mass, savePosFile(), and saveTapsimBin().

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getFilesize()

bool AtomProbe::getFilesize	(	const char *	fname,
		size_t &	size
	)

Definition at line 107 of file helpFuncs.cpp.

Referenced by fixedRecordChunkReader(), fixedRecordReader(), AtomProbe::RangeFile::openFormat(), AtomProbe::ComparePairFirstReverse::operator()(), and readPosapOps().

getFitErrorMsg()

string AtomProbe::getFitErrorMsg

(

unsigned int

errCode

)

Obtain a human readable error, which has arison when using doFitBackground Input is the error code from doFitBackground

Definition at line 146 of file processing.cpp.

References ASSERT, and AtomProbe::BACKGROUND_PARAMS::FIT_FAIL_END.

getHardAssert()

bool AtomProbe::getHardAssert

(

)

Definition at line 25 of file aptAssert.cpp.

References hardAssert.

getPosFileErrString()

const char * AtomProbe::getPosFileErrString

(

unsigned int

errMesg

)

Definition at line 238 of file dataFiles.cpp.

References ARRAYSIZE, and POS_FILE_ENUM_END.

Referenced by getAtoErrString(), and main().

getRangeMolecule()

RANGE_MOLECULE AtomProbe::getRangeMolecule	(	const AbundanceData &	massTable,
		const RangeFile &	rng,
		unsigned int	rangeId
	)

Definition at line 55 of file rangeCheck.cpp.

References AtomProbe::RANGE_MOLECULE::components, AtomProbe::RangeFile::decomposeIonNames(), AtomProbe::RangeFile::getIonID(), AtomProbe::RangeFile::getName(), AtomProbe::RANGE_MOLECULE::isOK, AtomProbe::RANGE_MOLECULE::name, and AtomProbe::AbundanceData::symbolIndex().

Referenced by checkMassRangingCorrectness().

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getRecordReadErrString()

const char* AtomProbe::getRecordReadErrString ( unsigned int  errCode )

inline

Definition at line 46 of file dataFiles.h.

GetReducedHullPts()

unsigned int AtomProbe::GetReducedHullPts	(	const std::vector< IonHit > &	points,
		float	reductionDim,
		unsigned int *	progress,
		bool(*)(bool)	callback,
		std::vector< IonHit > &	pointResult
	)

Obtain a set of points that are a subset of points the convex hull that are at least "reductionDim" away from the hull itself.

Definition at line 289 of file convexHull.cpp.

References ASSERT, callback(), computeConvexHull(), distanceToFacet(), dotProduct(), freeConvexHull(), HULL_SURFREDUCE_NEGATIVE_SCALE_FACT, NUM_IONS, pyramidVol(), SCALE, and triIsDegenerate().

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getRotationMatrix()

gsl_matrix* AtomProbe::getRotationMatrix	(	const Point3D &	pt,
		float	theta
	)

Definition at line 246 of file rotations.cpp.

References ASSERT, computeRotationMatrix(), computeRotationMatrixWahba(), gsl_determinant(), AtomProbe::Point3D::normalise(), quat_rot(), AtomProbe::Point3D::sqrDist(), TEST, and AtomProbe::Point3D::transform3x3().

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gsl_determinant()

float AtomProbe::gsl_determinant

(

const gsl_matrix *

m

)

Definition at line 143 of file helpFuncs.cpp.

References ASSERT.

Referenced by computeRotationMatrix(), computeRotationMatrixWahba(), getRotationMatrix(), and AtomProbe::ComparePairFirstReverse::operator()().

gsl_matrix_det()

double AtomProbe::gsl_matrix_det	(	gsl_matrix *	A,
		bool	inPlace = false
	)

Definition at line 37 of file rotations.cpp.

gsl_matrix_mult()

void AtomProbe::gsl_matrix_mult	(	const gsl_matrix *	A,
		const gsl_matrix *	B,
		gsl_matrix *&	res,
		bool	alloc = false
	)

Definition at line 24 of file misc.cpp.

References ASSERT.

Referenced by computeRotationMatrixWahba(), and main().

gsl_print_matrix()

void AtomProbe::gsl_print_matrix

(

const gsl_matrix *

m

)

Definition at line 122 of file helpFuncs.cpp.

Referenced by computeRangeAdjacency(), and AtomProbe::ComparePairFirstReverse::operator()().

gsl_print_vector()

void AtomProbe::gsl_print_vector

(

const gsl_vector *

v

)

Definition at line 134 of file helpFuncs.cpp.

Referenced by AtomProbe::ComparePairFirstReverse::operator()().

hexStrToUChar()

void AtomProbe::hexStrToUChar	(	const std::string &	s,
		unsigned char &	c
	)

Definition at line 92 of file stringFuncs.cpp.

References ASSERT.

Referenced by parseColString().

incrementCorrelationHist()

bool AtomProbe::incrementCorrelationHist	(	const std::vector< EPOS_ENTRY > &	eposIons,
		std::vector< std::vector< unsigned int > > &	histogram,
		float	stepMass,
		float	endMass
	)

Definition at line 29 of file histogram.cpp.

Referenced by accumulateCorrelationHistogram(), and correlationHistogram().

intersect_RayTriangle()

int AtomProbe::intersect_RayTriangle	(	const Point3D &	rayStart,
		const Point3D &	rayEnd,
		Point3D *	tri,
		Point3D &	I
	)

Definition at line 280 of file mesh.cpp.

References AtomProbe::Point3D::crossProd(), AtomProbe::Point3D::dotProd(), AtomProbe::Point3D::normalise(), and AtomProbe::Point3D::sqrMag().

Referenced by AtomProbe::Mesh::pointsInside().

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isNotDirectory()

bool AtomProbe::isNotDirectory

(

const char *

filename

)

Definition at line 170 of file helpFuncs.cpp.

Referenced by AtomProbe::RangeFile::detectFileType(), loadTextData(), and AtomProbe::ComparePairFirstReverse::operator()().

isValidElementSymbol()

bool AtomProbe::isValidElementSymbol

(

std::string &

symbol

)

Definition at line 86 of file ranges.cpp.

kahansum()

template<class T , class T2 >

std::iterator_traits<T>::value_type AtomProbe::kahansum	(	T	begin,
		T	end,
		T2	other
	)

Definition at line 49 of file confidence.cpp.

Referenced by cumTrapezoid().

leastSquaresOverlapSolve()

bool AtomProbe::leastSquaresOverlapSolve	(	const AtomProbe::MultiRange &	rangeData,
		const AtomProbe::AbundanceData &	abundance,
		const std::vector< IonHit > &	hits,
		float(*)(float, float)	backgroundEstimator,
		std::vector< std::pair< unsigned int, float > > &	decomposedHits,
		float	rangeTolerance = 0
	)

Solve overlaps using least squares for given multi-range.

Definition at line 47 of file deconvolution.cpp.

References AtomProbe::AbundanceData::abundanceBetweenLimits(), AtomProbe::MultiRange::addIon(), AtomProbe::MultiRange::addRange(), ASSERT, AtomProbe::SIMPLE_SPECIES::atomicNumber, AtomProbe::RGBf::blue, AtomProbe::SIMPLE_SPECIES::count, estimateRank(), AtomProbe::MultiRange::getIonName(), AtomProbe::MultiRange::getNumIons(), AtomProbe::MultiRange::getNumRanges(), AtomProbe::RandNumGen::getRng(), AtomProbe::RGBf::green, AtomProbe::AbundanceData::isotopes(), meanAndStdev(), AtomProbe::AbundanceData::open(), randGen, AtomProbe::RGBf::red, AtomProbe::MultiRange::setRangeGroups(), solveLeastSquares(), AtomProbe::MultiRange::splitOverlapping(), AtomProbe::AbundanceData::symbolIdxFromAtomicNumber(), AtomProbe::AbundanceData::symbolIndex(), and WARN.

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likeLogGaussian()

void AtomProbe::likeLogGaussian	(	const std::vector< double > &	x,
		double &	xp,
		double &	sigma,
		double &	lambda,
		double &	amp,
		double &	h,
		std::vector< double > &	y
	)

Generate a smoothed log-gaussian curve.

xp : positioning lambda :asymmetry h : FWHM (>0) amp : vertical rescale sigma : width

Definition at line 510 of file fitting.cpp.

References M_PI.

Referenced by fitLikeLogGaussian().

linearHistogram()

template<class T >

void AtomProbe::linearHistogram	(	const std::vector< T > &	data,
		T	start,
		T	end,
		T	step,
		std::vector< T > &	histVals
	)

Make a linearly spaced histogram with the given spacings Takes a vector of floats as input,

Parameters

data

Definition at line 75 of file histogram.h.

References ASSERT.

Referenced by main().

linkIdentifiers()

template<class T >

void AtomProbe::linkIdentifiers

(

vector< T > &

link

)

Definition at line 88 of file multiRange.cpp.

Referenced by AtomProbe::MultiRange::splitOverlapping().

loadATOFile()

unsigned int AtomProbe::loadATOFile	(	const char *	fileName,
		std::vector< ATO_ENTRY > &	ions,
		unsigned int	forceEndian = 0
	)

Load a LAWATAP "ATO" file.

ATO files contain a mix of experiment and analysis data, including voltage, positioning and reconstructed data. There are specific algorithm generated data (eg clustering) which are not loaded in structures in this library to reduce memory consumption. Returns 0 on success, nonzero on error

• Filename : the name of the data file to read
• ions : the returned entries from the file
• forceEndian : if nonzero, this wil force the use of either little-endian reading (1), or big-endian(2). If zero, the routine will try to automatically determine endianness from the file contents.

Returned code if nonzero can be converted to human readable form using ATO_ERR_STRINGS. Note if calling from outside C++, use getAtoErrString(...) to return the error string

Definition at line 1212 of file dataFiles.cpp.

References ASSERT, ATO_EMPTY_FAIL, ATO_MEM_ERR, ATO_OPEN_FAIL, ATO_SIZE_ERR, ATO_VERSIONCHECK_ERR, floatSwapBytes(), AtomProbe::RandNumGen::getRng(), randGen, and randomIndices().

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loadEposFile()

size_t AtomProbe::loadEposFile	(	std::vector< EPOS_ENTRY > &	outData,
		const char *	filename
	)

Load an entire "EPOS" File.

Epos files are very large and unwieldy. Ensure that you really want to do this, as it is possible you will run out of memory. Consider using the "chunkLoadEposFile" to process your data if possible. The file contains x,y,z,m-to-c,tof(uncorrected?). The return value is nonzero on error, and is part of the RECORDREAD_ERR enum

Definition at line 756 of file dataFiles.cpp.

References EPOS_RECORD_SIZE, fixedRecordReader(), and readEposRecord().

Referenced by getAtoErrString(), and main().

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loadPosFile() [1/2]

unsigned int AtomProbe::loadPosFile	(	std::vector< IonHit > &	posIons,
		const char *	posFile
	)

Load a pos file directly into a single ion list.

Load a pos file from a file. Returns nonzero on exit.

Pos files are fixed record size files, with data stored as 4byte big endian floating point. (IEEE 754?). Data is stored as x,y,z,mass/charge.

Currently loads entire file in one gulp. This is bad from the point of view of gigabyte size pos files generated by laser atom probes.. Returns 0 on ok, nonzero on success.

arguments : posfile | path to pos-formatted file posIons | will return any ions that are loaded from the dataset. Behaviour for loading into * a non-empty vector is undefined Return code can be decoded with getPosFileErrString

Definition at line 256 of file dataFiles.cpp.

References ASSERT, AtomProbe::IonHit::hasNaN(), AtomProbe::IONHIT::massToCharge, AtomProbe::IONHIT::pos, POS_ALLOC_FAIL, POS_NAN_LOAD_ERROR, POS_OPEN_FAIL, POS_READ_FAIL, POS_SIZE_EMPTY_ERR, POS_SIZE_MODULUS_ERR, AtomProbe::IonHit::setMassToCharge(), and AtomProbe::IonHit::setPos().

Referenced by getAtoErrString(), loadPosFile(), and main().

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loadPosFile() [2/2]

unsigned int AtomProbe::loadPosFile	(	std::vector< IonHit > &	posIons,
		const char *	posFile,
		unsigned int	nSamplesMax
	)

As per loadPosFile, but with an additional setting for the maximum number of ions to load.

Ions will be randomly sampled to form nSamples. This will be likely much slower than loading a full file, depending on the size of nSamples. The samples are not guaranteed to be the same for each load. Speed will be nlogn in nSamplesMax, o(1) in posIons.

Definition at line 364 of file dataFiles.cpp.

References AtomProbe::RandNumGen::getRng(), loadPosFile(), AtomProbe::IONHIT::massToCharge, AtomProbe::IONHIT::pos, POS_ALLOC_FAIL, POS_NAN_LOAD_ERROR, POS_OPEN_FAIL, POS_READ_FAIL, POS_SIZE_EMPTY_ERR, POS_SIZE_MODULUS_ERR, randGen, and randomIndices().

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loadTapsimBinFile()

unsigned int AtomProbe::loadTapsimBinFile	(	vector< IonHit > &	posIons,
		const char *	posfile
	)

Definition at line 538 of file dataFiles.cpp.

References AtomProbe::IonHit::setMassToCharge(), AtomProbe::IonHit::setPos(), splitStrsRef(), stream_cast(), TAPSIM_FILE_FORMAT_FAIL, and TAPSIM_OPEN_FAIL.

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loadTextData()

unsigned int AtomProbe::loadTextData	(	const char *	cpFilename,
		std::vector< std::vector< float > > &	dataVec,
		std::vector< std::string > &	headerVec,
		const char *	delim = "\t,",
		bool	allowNan = true,
		bool	allowConvFails = false,
		unsigned int	headerCount = -1
	)

Load a CSV, TSV or similar text file. Assumes "C" Locale for input (ie "." as decimal separator).

Maximum line length is 4K. Data will be given out as a vector v[Column][line] in the input text file. this allows for ready column extraction.

headerVec - strings used to represent columns allowConvFails - replace strings that cannot be converted to float with NaN allowNan - return error if the input file contains nan headerCount - the maximum number of lines to consider before declaring that line as the header. if -1, this parameter has no effect

Note the function transposeVector may be of interest

Definition at line 1504 of file dataFiles.cpp.

References isNotDirectory(), splitStrsRef(), stream_cast(), strhas(), stripZeroEntries(), TEXT_ERR_FILE_FORMAT, TEXT_ERR_FILE_NUM_FIELDS, and TEXT_ERR_FILE_OPEN.

Referenced by getAtoErrString(), and main().

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lowercase()

std::string AtomProbe::lowercase

(

std::string

s

)

Return a lowercase version for a given string.

Definition at line 176 of file stringFuncs.cpp.

Referenced by AtomProbe::RangeFile::detectFileType(), main(), parseCompositionData(), AtomProbe::RangeFile::rangeTypeString(), strAppend(), and AtomProbe::AbundanceData::symbolIndex().

lsq()

double AtomProbe::lsq	(	const std::vector< double > &	y,
		const std::vector< double > &	yFit
	)

Definition at line 27 of file fitting.cpp.

References voigtProfile(), AtomProbe::DATA_FIT::x, and AtomProbe::DATA_FIT::y.

Referenced by fitDoniachSunjic(), fitExpNorm(), fitLikeLogGaussian(), fitVoigtFunc(), and main().

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makeHistogram()

void AtomProbe::makeHistogram	(	const vector< float > &	data,
		float	start,
		float	end,
		float	step,
		vector< float > &	histVals
	)

Definition at line 126 of file processing.cpp.

References ASSERT.

Referenced by doFitBackground(), and findPeaks().

marchingCubes()

void AtomProbe::marchingCubes	(	const Voxels< float > &	v,
		float	isoValue,
		std::vector< TriangleWithVertexNorm > &	tVec
	)

Definition at line 494 of file isoSurface.cpp.

References ASSERT, AtomProbe::BoundCube::containsPt(), AtomProbe::Voxels< T >::deprecatedGetEdgeUniqueIndex(), AtomProbe::Voxels< T >::fill(), AtomProbe::Voxels< T >::getBounds(), AtomProbe::Voxels< T >::getData(), AtomProbe::Voxels< T >::getEdgeEndApproxVals(), AtomProbe::Voxels< T >::getEdgeEnds(), AtomProbe::Voxels< T >::getMaxBounds(), AtomProbe::Voxels< T >::getMinBounds(), AtomProbe::Voxels< T >::getPitch(), AtomProbe::Voxels< T >::getSize(), AtomProbe::TriangleWithVertexNorm::isDegenerate(), AtomProbe::TriangleWithVertexNorm::normal, AtomProbe::TriangleWithVertexNorm::p, AtomProbe::TriangleWithIndexedVertices::p, AtomProbe::TRIANGLE::p, AtomProbe::TRIANGLE::physGroup, removeElements(), AtomProbe::Voxels< T >::resize(), AtomProbe::TriangleWithVertexNorm::safeComputeACWNormal(), AtomProbe::BoundCube::setBounds(), AtomProbe::Voxels< T >::setData(), and TEST.

Referenced by main().

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matchComposedName()

bool AtomProbe::matchComposedName	(	const std::map< string, size_t > &	composedNames,
		const vector< pair< string, size_t > > &	namesToFind,
		size_t &	matchOffset
	)

Definition at line 297 of file ranges.cpp.

References AtomProbe::RangeFile::decomposeIonNames().

Referenced by AtomProbe::RangeFile::open().

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maxExplainedFraction() [1/2]

std::vector<float> AtomProbe::maxExplainedFraction	(	const std::vector< std::pair< float, float > > &	massData,
		float	peakMass,
		float	massWidth,
		const std::vector< std::vector< AtomProbe::ISOTOPE_ENTRY > > &	solutions,
		const AtomProbe::AbundanceData &	massTable,
		float	massDistTol,
		unsigned int	solutionCharge
	)

Compute the fraction of the data that has been explained, using the natural abundance information, and intensity data.

Specifically, this returns the maximum possible fraction of this peak that is explained by the isotopic fingerprint for a given solution set, and the count data given. This is returned as a vector with a value for each proposed solution Note the solutions do not need to sum to 1

massData - list of location and intensities for peaks in dataset peakMass - peak we wish to query. Must be present (within tolerance) in peak list (massData) massWidth - tolerance width (+-) when locating peaks solutions - list of candidate solutions we want to find the explained fraction for massDistTol - tolerance to use when checking for peaks in mass distribution solutionCharge - charge state to apply to isotope distribuion

Referenced by maxExplainedFraction().

maxExplainedFraction() [2/2]

vector<float> AtomProbe::maxExplainedFraction	(	const vector< pair< float, float > > &	intensityData,
		float	peakMass,
		float	massWidth,
		const vector< vector< ISOTOPE_ENTRY > > &	solutions,
		const AbundanceData &	massTable,
		float	massDistTol,
		unsigned int	solutionCharge
	)

Definition at line 221 of file filter.cpp.

References ASSERT, buildFrequencyTable(), countIntensityEvents(), AtomProbe::AbundanceData::generateGroupedIsotopeDist(), AtomProbe::AbundanceData::getMajorIsotopeFromElemIdx(), AtomProbe::AbundanceData::isotope(), AtomProbe::ISOTOPE_ENTRY::mass, maxExplainedFraction(), AtomProbe::AbundanceData::open(), AtomProbe::AbundanceData::symbolIndex(), and TEST.

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meanAndStdev()

template<typename T >

void AtomProbe::meanAndStdev	(	const std::vector< T > &	f,
		float &	meanVal,
		float &	stdevVal,
		bool	normalCorrection = true
	)

Definition at line 76 of file misc.h.

References distanceToFacet(), distanceToSegment(), signedDistanceToFacet(), and vectorPointDir().

Referenced by andersonDarlingStatistic(), and leastSquaresOverlapSolve().

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myStrDup()

char* AtomProbe::myStrDup

(

const char *

s

)

Definition at line 39 of file helpFuncs.cpp.

Referenced by pushLocale().

nullBackground()

float AtomProbe::nullBackground	(	float	rangeStart,
		float	rangeEnd
	)

Definition at line 41 of file deconvolution.cpp.

nullifyMarker()

void AtomProbe::nullifyMarker	(	char *	buffer,
		char	marker
	)

Definition at line 55 of file stringFuncs.cpp.

Referenced by AtomProbe::RangeFile::rangeTypeString(), and stlStrToStlWStr().

numericalEstimateGaussRatioConf()

bool AtomProbe::numericalEstimateGaussRatioConf	(	float	mu1,
		float	mu2,
		float	var1,
		float	var2,
		float	alpha,
		unsigned int	nTrials,
		gsl_rng *	r,
		float &	lBound,
		float &	uBound
	)

Brute-force guassian ratio confidence estimator.

Performs monte-carlo trials to determine the distribution of Z=X/Y. where X~Gaussian(L1), Y~max(Gaussian(L2),1)

Biased, as it enforces 1, in the denominator of L1/L2 (ie L2=0 has p=0) returns false if either bound could not be computed

• mu1 : Mean 1 (must be +ve)
• mu2 : Mean 2 (must be +ve)
• var1 : Variance 1 (must be +ve)
• var2 : Variance 2 (must be +ve)
• alpha : confidence interval in distribution
• nTrials : number of computations of Z.
• lBound : returned lower bound at confidence alpha
• uBound : returned upper bound at confidence alpha

Note that the estimator seems to biased to the number of trials, and needs to be improved.

Definition at line 275 of file confidence.cpp.

References ASSERT.

Referenced by poissonConfidenceObservation().

numericalEstimatePoissRatioConf()

bool AtomProbe::numericalEstimatePoissRatioConf	(	float	lambda1,
		float	lambda2,
		float	alpha,
		unsigned int	nTrials,
		gsl_rng *	r,
		float &	lBound,
		float &	uBound
	)

Brute-force poisson ratio confidence estimator. Returns the confidence interval in the estimate of the mean, at the given rates.

Performs monte-carlo trials to determine the distribution of Z=X/Y. where X~Poisson(L1), Y~Poisson(L2) Biased, as it enforces 1, in the denominator of L1/L2 (ie L2=0 has p=0) returns false if either bound could not be computed

• lambda1 : Poisson rate 1 (must be +ve)
• lambda2 : Poisson rate 2 (must be +ve)
• alpha : confidence interval in distribution
• nTrials : number of computations of Z.
• lBound : returned lower bound at confidence alpha. This is interpolated, so is a real number
• uBound : returned upper bound at confidence alpha. This is interpolated, so is a real number.

Note that the estimator seems to slightly biased to the number of trials, and needs to be improved.

Definition at line 68 of file confidence.cpp.

References ASSERT.

Referenced by main(), and poissonConfidenceObservation().

numericalEstimateSkellamConf()

bool AtomProbe::numericalEstimateSkellamConf	(	float	lambda1,
		float	lambda2,
		float	alpha,
		unsigned int	nTrials,
		gsl_rng *	r,
		float &	lBound,
		float &	uBound
	)

Brute-force the confidence bounds of a skellam distribution.

Performs monte-carlo trials to determine Z = X - Y, where X, Y are poisson (Lambda1, Lambda2).

• Lambda1 : poisson rate for X
• Lambda2: poisson rate for Y
• alpha : confidence bound
• nTrials : number of computations of Z.
• lBound : returned lower bound at confidence alpha. This is interpolated, so is a real number
• uBound : returned upper bound at confidence alpha. This is interpolated, so is a real number

Definition at line 173 of file confidence.cpp.

References ASSERT.

Referenced by poissonConfidenceObservation().

onlyDir()

std::string AtomProbe::onlyDir

(

const std::string &

path

)

Return only the directory name component of the full path.

Definition at line 44 of file stringFuncs.cpp.

Referenced by strAppend().

onlyFilename()

std::string AtomProbe::onlyFilename

(

const std::string &

path

)

Return only the filename component.

Definition at line 33 of file stringFuncs.cpp.

Referenced by strAppend().

operator<()

bool AtomProbe::operator<	(	const SIMPLE_SPECIES &	a,
		const SIMPLE_SPECIES &	b
	)

Definition at line 117 of file multiRange.cpp.

References AtomProbe::SIMPLE_SPECIES::atomicNumber, and AtomProbe::SIMPLE_SPECIES::count.

operator<<() [1/3]

std::ostream& AtomProbe::operator<<	(	std::ostream &	stream,
		const IonHit &	ion
	)

Definition at line 181 of file ionhit.cpp.

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

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operator<<() [2/3]

std::ostream& AtomProbe::operator<<	(	std::ostream &	stream,
		const Point3D &	pt
	)

Definition at line 417 of file point3D.cpp.

operator<<() [3/3]

std::ostream& AtomProbe::operator<<	(	std::ostream &	stream,
		const BoundCube &	b
	)

Definition at line 563 of file boundcube.cpp.

pairContains()

bool AtomProbe::pairContains	(	const pair< float, float > &	p,
		float	m
	)

Definition at line 46 of file rangeCheck.cpp.

References ASSERT.

Referenced by checkMassRangingCorrectness().

pairOverlaps()

bool AtomProbe::pairOverlaps	(	float	aStart,
		float	aEnd,
		float	bStart,
		float	bEnd
	)

Definition at line 122 of file multiRange.cpp.

References ASSERT.

Referenced by AtomProbe::MultiRange::splitOverlapping().

parseColString()

bool AtomProbe::parseColString	(	const std::string &	str,
		unsigned char &	r,
		unsigned char &	g,
		unsigned char &	b,
		unsigned char &	a
	)

Parse a colour string containing rgb[a]; hex for with leading #.

Definition at line 269 of file stringFuncs.cpp.

References hexStrToUChar().

Referenced by AtomProbe::RGBf::fromHex(), AtomProbe::MultiRange::open(), AtomProbe::RangeFile::rangeTypeString(), and strAppend().

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parseCompositionData()

unsigned int AtomProbe::parseCompositionData	(	const std::vector< std::string > &	s,
		const AbundanceData &	atomTable,
		std::map< unsigned int, double > &	atomData
	)

Convert atomic string label data, in the form "Fe 0.81" to fraction map.

The input type (mol/mass) is not relevant for this function, but should be in fraction the label "bal" can be used in place of a composition value exactly once to provide "balance" mass to sum to 1 returns 0 on success, nonzero on error (see COMPPARSE enum)

Definition at line 100 of file massconvert.cpp.

References COMPPARSE_BAD_BAL_USAGE, COMPPARSE_BAD_COMP_VALUE, COMPPARSE_BAD_INPUT_FORMAT, COMPPARSE_BAD_SYMBOL, COMPPARSE_BAD_TOTAL_COMP, COMPPARSE_DUPLICATE_SYMBOL, convertMassToMol(), convertMolToMass(), lowercase(), AtomProbe::AbundanceData::open(), splitStrsRef(), stream_cast(), stripWhite(), stripZeroEntries(), AtomProbe::AbundanceData::symbolIndex(), and TEST.

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poissonConfidenceObservation()

void AtomProbe::poissonConfidenceObservation	(	float	counts,
		float	alpha,
		float &	lBound,
		float &	uBound
	)

Obtain poisson confidence limits for the mean of a poisson distribution.

Definition at line 508 of file confidence.cpp.

References ASSERT, AtomProbe::RandNumGen::getRng(), numericalEstimateGaussRatioConf(), numericalEstimatePoissRatioConf(), numericalEstimateSkellamConf(), randGen, TEST, and zechConfidenceLimits().

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popLocale()

void AtomProbe::popLocale

(

)

Definition at line 96 of file helpFuncs.cpp.

Referenced by AtomProbe::RangeFile::openFormat().

pushLocale()

void AtomProbe::pushLocale	(	const char *	newLocale,
		int	type
	)

Definition at line 62 of file helpFuncs.cpp.

References ASSERT, and myStrDup().

Referenced by AtomProbe::RangeFile::openFormat().

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pyramidVol()

double AtomProbe::pyramidVol	(	const Point3D *	planarPts,
		const Point3D &	apex
	)

Definition at line 290 of file misc.cpp.

References ASSERT, det3by3(), and estimateRank().

Referenced by dotProduct(), and GetReducedHullPts().

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quat_get_rot_quat()

void AtomProbe::quat_get_rot_quat	(	const Point3f *	rotVec,
		float	angle,
		Quaternion *	rotQuat
	)

Compute the quaternion for specified rotation.

angle is in radians. pass to quat_rot_apply_quat to compute rotation

Definition at line 184 of file quat.cpp.

References AtomProbe::Quaternion::a, ASSERT, AtomProbe::Quaternion::b, AtomProbe::Quaternion::c, AtomProbe::Quaternion::d, AtomProbe::Point3f::fx, AtomProbe::Point3f::fy, and AtomProbe::Point3f::fz.

Referenced by AtomProbe::Mesh::rotate().

quat_invert()

void AtomProbe::quat_invert

(

Quaternion *

quat

)

Definition at line 219 of file quat.cpp.

References AtomProbe::Quaternion::b, AtomProbe::Quaternion::c, and AtomProbe::Quaternion::d.

quat_mult_no_second_a()

void AtomProbe::quat_mult_no_second_a	(	Quaternion *	result,
		const Quaternion *	q1,
		const Quaternion *	q2
	)

Definition at line 39 of file quat.cpp.

References AtomProbe::Quaternion::a, AtomProbe::Quaternion::b, AtomProbe::Quaternion::c, and AtomProbe::Quaternion::d.

Referenced by quat_rot(), quat_rot_apply_quat(), and quat_rot_array().

quat_pointmult()

void AtomProbe::quat_pointmult	(	Point3f *	result,
		const Quaternion *	q1,
		const Quaternion *	q2
	)

Definition at line 50 of file quat.cpp.

References AtomProbe::Quaternion::a, AtomProbe::Quaternion::b, AtomProbe::Quaternion::c, AtomProbe::Quaternion::d, AtomProbe::Point3f::fx, AtomProbe::Point3f::fy, and AtomProbe::Point3f::fz.

Referenced by quat_rot(), quat_rot_apply_quat(), and quat_rot_array().

quat_rot() [1/2]

void AtomProbe::quat_rot	(	Point3D &	p,
		const Point3D &	r,
		float	angle
	)

Rotate a point around a given rotation axis by a specified angle.

This is not efficient for large numbers of points, as this will recompute the quaternion each time

Definition at line 59 of file quat.cpp.

References AtomProbe::Point3f::fx, AtomProbe::Point3f::fy, and AtomProbe::Point3f::fz.

Referenced by getRotationMatrix().

quat_rot() [2/2]

void AtomProbe::quat_rot	(	Point3f *	point,
		const Point3f *	rotVec,
		float	angle
	)

Rotate a point around a given vector, with specified angle.

This is not efficient for large numbers of points, as this will recompute the quaternion each time. angle (radians) is anti-clockwise as viewed from positive side of vector (right-handed)

Definition at line 77 of file quat.cpp.

References AtomProbe::Quaternion::a, ASSERT, AtomProbe::Quaternion::b, AtomProbe::Quaternion::c, AtomProbe::Quaternion::d, AtomProbe::Point3f::fx, AtomProbe::Point3f::fy, AtomProbe::Point3f::fz, quat_mult_no_second_a(), and quat_pointmult().

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quat_rot_apply_quat()

void AtomProbe::quat_rot_apply_quat	(	Point3f *	point,
		const Quaternion *	rotQuat
	)

Use previously generated quats from quat_get_rot_quats to rotate a point.

Rotation is in-place, on single point

Definition at line 206 of file quat.cpp.

References AtomProbe::Quaternion::b, AtomProbe::Quaternion::c, AtomProbe::Quaternion::d, AtomProbe::Point3f::fx, AtomProbe::Point3f::fy, AtomProbe::Point3f::fz, quat_mult_no_second_a(), and quat_pointmult().

Referenced by AtomProbe::Mesh::rotate().

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quat_rot_array() [1/2]

void AtomProbe::quat_rot_array	(	Point3f *	point,
		unsigned int	n,
		const Point3f *	rotVec,
		float	angle
	)

Rotate each point in array of size n around a given vector, with specified angle.

rotVec is the rotation, angle is the anti-clockwise angle as viewed from positive side of vector ( right-handed) rotation of points is in-place

Definition at line 139 of file quat.cpp.

References AtomProbe::Quaternion::a, ASSERT, AtomProbe::Quaternion::b, AtomProbe::Quaternion::c, AtomProbe::Quaternion::d, AtomProbe::Point3f::fx, AtomProbe::Point3f::fy, AtomProbe::Point3f::fz, quat_mult_no_second_a(), and quat_pointmult().

Referenced by quat_rot_array().

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quat_rot_array() [2/2]

void AtomProbe::quat_rot_array	(	Point3D *	point,
		unsigned int	n,
		const Point3f *	rotVec,
		float	angle
	)

Rotate each point in array of size n around a given vector, with specified angle.

rotVec is the rotation, angle is the anti-clockwise angle as viewed from positive side of vector ( right-handed). rotation of points is in-place

Definition at line 115 of file quat.cpp.

References AtomProbe::Point3f::fx, AtomProbe::Point3f::fy, AtomProbe::Point3f::fz, and quat_rot_array().

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randomIndices()

template<class T >

void AtomProbe::randomIndices	(	std::vector< T > &	res,
		size_t	num,
		size_t	nMax,
		gsl_rng *	rng
	)

Definition at line 113 of file sampling.h.

Referenced by loadATOFile(), and loadPosFile().

randomSelect()

template<class T >

size_t AtomProbe::randomSelect	(	std::vector< T > &	result,
		const std::vector< T > &	source,
		size_t	num,
		gsl_rng *	rng
	)

Definition at line 40 of file sampling.h.

References AtomProbe::LinearFeedbackShiftReg::clock(), AtomProbe::LinearFeedbackShiftReg::setMaskPeriod(), and AtomProbe::LinearFeedbackShiftReg::setState().

Referenced by sampleIons().

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rangeOverlaps()

bool AtomProbe::rangeOverlaps	(	const pair< float, float > &	r1,
		const pair< float, float > &	r2
	)

Definition at line 150 of file componentAnalysis.cpp.

Referenced by computeRangeAdjacency().

rangeToStr()

string AtomProbe::rangeToStr

(

const pair< float, float > &

rng

)

Definition at line 111 of file ranges.cpp.

References stream_cast().

Referenced by AtomProbe::RangeFile::isSelfConsistent().

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readEposRecord()

bool AtomProbe::readEposRecord	(	const char *	src,
		const char *	dest
	)

Definition at line 711 of file dataFiles.cpp.

References AtomProbe::EPOS_ENTRY::deltaPulse, floatSwapBytes(), AtomProbe::EPOS_ENTRY::hitMultiplicity, int4SwapBytes(), AtomProbe::EPOS_ENTRY::massToCharge, AtomProbe::EPOS_ENTRY::timeOfFlight, AtomProbe::EPOS_ENTRY::voltDC, AtomProbe::EPOS_ENTRY::voltPulse, AtomProbe::EPOS_ENTRY::x, AtomProbe::EPOS_ENTRY::xDetector, AtomProbe::EPOS_ENTRY::y, AtomProbe::EPOS_ENTRY::yDetector, and AtomProbe::EPOS_ENTRY::z.

Referenced by chunkLoadEposFile(), and loadEposFile().

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readPosapOps()

unsigned int AtomProbe::readPosapOps	(	const char *	file,
		THREEDAP_EXPERIMENT &	data,
		unsigned int &	badLine,
		unsigned int &	progress,
		std::atomic< bool > &	wantAbort,
		unsigned int	nDelayLines = 2,
		bool	strictMode = false
	)

Function to read POSAP "OPS" files.

OPS files contain data on voltage, positioned hits and time of flights as well as some instrument parameters. This format is not standardised, so variants may exist

• badLine returns the line on which an error was encountered.
• progress gives a 0-100% progress value (counted in file size). Can be used to multithread monitor progress
• nDelayLines - The number of delay lines in the system. Usually 2, possibly 3.
• strictMode - enable to throw errors in cases where files appear to be badly formatted TODO: Can we work out how to obtain nDelayLines from parsing the file?

Definition at line 805 of file dataFiles.cpp.

References AtomProbe::THREEDAP_DATA::alpha, ARRAYSIZE, ASSERT, AtomProbe::VOLTAGE_DATA::beta, AtomProbe::THREEDAP_DATA::beta, AtomProbe::THREEDAP_DATA::detectorChannels, AtomProbe::THREEDAP_DATA::detectorRadius, AtomProbe::THREEDAP_EXPERIMENT::eventData, AtomProbe::THREEDAP_EXPERIMENT::eventPulseNumber, AtomProbe::THREEDAP_DATA::flightPath, getFilesize(), AtomProbe::VOLTAGE_DATA::nextHitGroupOffset, OPSREADER_ABORT_ERR, OPSREADER_CHANNELS_DATA_ERR, OPSREADER_ENUM_END, OPSREADER_FORMAT_CHANNELS_ERR, OPSREADER_FORMAT_CLINE_ERR, OPSREADER_FORMAT_DETECTORLINE_ERR, OPSREADER_FORMAT_DOUBLEDASH, OPSREADER_FORMAT_DUPLICATE_DETECTORSIZE, OPSREADER_FORMAT_DUPLICATE_SYSDATA, OPSREADER_FORMAT_LINE_DASH_ERR, OPSREADER_FORMAT_LINE_VOLTAGE_DATA_ERR, OPSREADER_FORMAT_LINE_VOLTAGE_DATACOUNT_ERR, OPSREADER_FORMAT_LINE_VOLTAGE_NOBETA, OPSREADER_FORMAT_LINETYPE_ERR, OPSREADER_FORMAT_SLINE_EVENTCOUNT_ERR, OPSREADER_FORMAT_SLINE_EVENTDATA_ERR, OPSREADER_FORMAT_SLINE_FORMAT_ERR, OPSREADER_FORMAT_SLINE_PREFIX_ERR, OPSREADER_FORMAT_TRAILING_DASH_ERR, OPSREADER_OPEN_ERR, OPSREADER_READ_ERR, AtomProbe::THREEDAP_EXPERIMENT::params, AtomProbe::VOLTAGE_DATA::pulseVolt, splitStrsRef(), stream_cast(), stripWhite(), stripZeroEntries(), AtomProbe::SINGLE_HIT::tof, AtomProbe::THREEDAP_DATA::tZero, AtomProbe::VOLTAGE_DATA::voltage, and AtomProbe::THREEDAP_EXPERIMENT::voltageData.

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reconstructTest()

bool AtomProbe::reconstructTest

(

)

Referenced by AtomProbe::ReconstructionSphereOnCone::reconstruct(), and runTests().

removeElements()

template<class T >

void AtomProbe::removeElements	(	const std::vector< size_t > &	elems,
		std::vector< T > &	vec
	)

Definition at line 64 of file isoSurface.cpp.

References ASSERT.

Referenced by marchingCubes().

rotateMatch()

bool AtomProbe::rotateMatch	(	const unsigned int *	a,
		const unsigned int *	b,
		size_t	n,
		bool	directionForwards = true
	)

Definition at line 100 of file mesh.cpp.

Referenced by AtomProbe::TRIANGLE::edgesMismatch().

sampleIons()

void AtomProbe::sampleIons	(	const std::vector< IonHit > &	ions,
		float	sampleFactor,
		std::vector< IonHit > &	sampled,
		bool	strongRandom = true
	)

Definition at line 30 of file sampling.cpp.

References AtomProbe::RandNumGen::getRng(), randGen, randomSelect(), and TEST.

Referenced by main().

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savePosFile() [1/2]

unsigned int AtomProbe::savePosFile	(	const std::vector< Point3D > &	points,
		float	mass,
		const char *	name,
		bool	append = false
	)

Save a vector of Point3Ds into a pos file, using a fixed mass, return nonzero on error.

Create an pos file from a vector of points, and a given mass.

A nonzero return code can be decoded with getPosFileErrString, which will provide a human readable error message

• if append is true, the the file will be appended to.

Definition at line 499 of file dataFiles.cpp.

References floatSwapBytes().

Referenced by getAtoErrString(), main(), and AtomProbe::ReconstructionSphereOnCone::reconstruct().

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savePosFile() [2/2]

unsigned int AtomProbe::savePosFile	(	const std::vector< IonHit > &	data,
		const char *	name,
		bool	append = false
	)

Save a vector of IonHits into a "pos" file, return nonzero on error.

Create an pos file from a vector of IonHits.

Definition at line 463 of file dataFiles.cpp.

References floatSwapBytes().

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saveTapsimBin() [1/2]

unsigned int AtomProbe::saveTapsimBin	(	const std::vector< IonHit > &	posIons,
		std::ostream &	f
	)

Write a tapsim file from a vector of IonHits.

Note: there is some data loss here. Tapsim data basically writes a short header and then the ion data is little endian stored, not big-endian. Finally, m/c data is written as short, hence data loss

Definition at line 667 of file dataFiles.cpp.

References ASSERT, floatSwapBytes(), and stream_cast().

Referenced by getAtoErrString(), and saveTapsimBin().

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saveTapsimBin() [2/2]

unsigned int AtomProbe::saveTapsimBin	(	const std::vector< IonHit > &	posIons,
		const char *	filename
	)

Write a tapsim file from a vector of ionHits.

Convenience Wrapper for other saveTapsimBin(...) function

Definition at line 703 of file dataFiles.cpp.

References saveTapsimBin().

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selectElements()

template<class T >

void AtomProbe::selectElements	(	const std::vector< T > &	in,
		const std::vector< unsigned int > &	indices,
		std::vector< T > &	out
	)

Obtain the elements at positions indicies in the input vector, copy to output.

Definition at line 67 of file misc.h.

Referenced by findPeaks().

setHardAssert()

void AtomProbe::setHardAssert

(

bool

enabled

)

Do assertions cause a straight up crash (enabled), or write a mesage to stderr (disabled)? By default, hard crash.

Definition at line 30 of file aptAssert.cpp.

signedDistanceToFacet()

float AtomProbe::signedDistanceToFacet	(	const Point3D &	fA,
		const Point3D &	fB,
		const Point3D &	fC,
		const Point3D &	normal,
		const Point3D &	p
	)

Find the distance between a point, and a triangular facet – may be positive or negative.

Definition at line 172 of file misc.cpp.

References ASSERT, distanceToSegment(), AtomProbe::Point3D::dotProd(), AtomProbe::Point3D::mag(), and AtomProbe::Point3D::sqrDist().

Referenced by distanceToFacet(), AtomProbe::Mesh::getNearestTri(), and meanAndStdev().

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signVal()

float AtomProbe::signVal

(

unsigned int

val

)

Definition at line 147 of file mesh.cpp.

Referenced by Determinant().

solveLeastSquares()

bool AtomProbe::solveLeastSquares	(	gsl_matrix *	m,
		gsl_vector *	b,
		gsl_vector *&	x
	)

Use an SVD based least-squares solver to solve Mx=b (for x).

Definition at line 94 of file misc.cpp.

Referenced by leastSquaresOverlapSolve().

SphericProjectionEqn()

double AtomProbe::SphericProjectionEqn	(	double	eta,
		void *	p
	)

Definition at line 42 of file projection.cpp.

References AtomProbe::SphericProjectionParams::focusDist, and AtomProbe::SphericProjectionParams::theta.

Referenced by AtomProbe::StereographicProjection::thetaToEta(), and AtomProbe::ModifiedFocusSphericProjection::thetaToEta().

splitStrsRef() [1/2]

void AtomProbe::splitStrsRef	(	const char *	cpStr,
		const char	delim,
		std::vector< std::string > &	v
	)

Split string references using a single delimiter.

Definition at line 187 of file stringFuncs.cpp.

Referenced by AtomProbe::RangeFile::detectFileType(), AtomProbe::Mesh::loadGmshMesh(), loadTapsimBinFile(), loadTextData(), main(), AtomProbe::Point3D::parse(), parseCompositionData(), AtomProbe::RangeFile::rangeTypeString(), readPosapOps(), and strAppend().

splitStrsRef() [2/2]

void AtomProbe::splitStrsRef	(	const char *	cpStr,
		const char *	delim,
		std::vector< std::string > &	v
	)

Split string references using any of a given string of delimiters.

Definition at line 221 of file stringFuncs.cpp.

stlStrToStlWStr()

std::wstring AtomProbe::stlStrToStlWStr ( const std::string &  s )

inline

Definition at line 115 of file stringFuncs.h.

References nullifyMarker().

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stlWStrToStlStr()

std::string AtomProbe::stlWStrToStlStr ( const std::wstring &  s )

inline

Definition at line 108 of file stringFuncs.h.

strAppend()

template<class T >

void AtomProbe::strAppend	(	std::string	s,
		const T &	a
	)

Definition at line 41 of file stringFuncs.h.

References convertFileStringToCanonical(), convertFileStringToNative(), digitString(), genColString(), lowercase(), onlyDir(), onlyFilename(), parseColString(), splitStrsRef(), stream_cast(), stripChars(), stripWhite(), stripZeroEntries(), and uppercase().

Referenced by AtomProbe::RangeFile::isSelfConsistent().

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stream_cast()

template<class T1 , class T2 >

bool AtomProbe::stream_cast	(	T1 &	result,
		const T2 &	obj
	)

Template function to cast and object to another by the stringstream.

Definition at line 32 of file stringFuncs.h.

Referenced by AtomProbe::RangeFile::decomposeIonNames(), AtomProbe::RangeFile::detectFileType(), digitString(), AtomProbe::LibVersion::getVersionStr(), AtomProbe::Mesh::loadGmshMesh(), loadTapsimBinFile(), loadTextData(), main(), AtomProbe::MultiRange::open(), AtomProbe::RangeFile::open(), AtomProbe::Point3D::parse(), parseCompositionData(), rangeToStr(), AtomProbe::RangeFile::rangeTypeString(), readPosapOps(), saveTapsimBin(), strAppend(), XMLGetNextElemAttrib(), and XMLHelpGetProp().

strhas()

bool AtomProbe::strhas	(	const char *	cpTest,
		const char *	cpPossible
	)

Definition at line 1485 of file dataFiles.cpp.

Referenced by loadTextData().

stripChars()

std::string AtomProbe::stripChars	(	const std::string &	Str,
		const char *	chars
	)

Definition at line 137 of file stringFuncs.cpp.

Referenced by AtomProbe::RangeFile::rangeTypeString(), strAppend(), and stripWhite().

stripWhite()

std::string AtomProbe::stripWhite

(

const std::string &

str

)

Strip whitespace, (eg tab,space) from either side of a string.

Definition at line 132 of file stringFuncs.cpp.

References stripChars().

Referenced by AtomProbe::RangeFile::detectFileType(), main(), AtomProbe::Point3D::parse(), parseCompositionData(), AtomProbe::RangeFile::rangeTypeString(), readPosapOps(), and strAppend().

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stripZeroEntries()

void AtomProbe::stripZeroEntries

(

std::vector< std::string > &

s

)

Definition at line 155 of file stringFuncs.cpp.

Referenced by AtomProbe::RangeFile::detectFileType(), loadTextData(), main(), parseCompositionData(), AtomProbe::RangeFile::rangeTypeString(), readPosapOps(), and strAppend().

sumVoxels()

template<class T , class U >

void AtomProbe::sumVoxels	(	const Voxels< T > &	src,
		U &	counter
	)

Use one counting type to sum counts in a voxel of given type.

Definition at line 376 of file voxels.h.

References AtomProbe::Voxels< T >::getData(), AtomProbe::Voxels< T >::getSize(), and AtomProbe::Voxels< T >::size().

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tabs()

std::string AtomProbe::tabs ( unsigned int  nTabs )

inline

Definition at line 99 of file stringFuncs.h.

Referenced by AtomProbe::MultiRange::write().

tolEqual()

template<class T >

bool AtomProbe::tolEqual	(	const T &	a,
		const T &	b,
		const T &	f
	)

Test for equality within tolerance f (||a-b|| < f)

Definition at line 59 of file misc.h.

Referenced by AtomProbe::ModifiedFocusSphericProjection::scaleUp().

transposeVector()

template<class T >

void AtomProbe::transposeVector

(

std::vector< std::vector< T > > &

v

)

Perform an out-of-place tranposition of a given vector.

The nested vector may be ragged (ie not a rectangular array) This will temporarily double memory use due to copy

Definition at line 81 of file misc.h.

Referenced by main().

triIsDegenerate()

bool AtomProbe::triIsDegenerate	(	const Point3D &	fA,
		const Point3D &	fB,
		const Point3D &	fC
	)

Definition at line 266 of file misc.cpp.

References AtomProbe::Point3D::mag().

Referenced by dotProduct(), and GetReducedHullPts().

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ucharToHexStr()

void AtomProbe::ucharToHexStr	(	unsigned char	c,
		std::string &	s
	)

Definition at line 68 of file stringFuncs.cpp.

Referenced by genColString().

uppercase()

std::string AtomProbe::uppercase

(

std::string

s

)

Return a uppercase version for a given string.

Referenced by strAppend().

vectorMultiErase()

template<class T >

void AtomProbe::vectorMultiErase	(	std::vector< T > &	vec,
		const std::vector< bool > &	wantKill
	)

Remove elements from the vector, without preserving order.

Definition at line 112 of file misc.h.

Referenced by computeIonDistAdjacency(), AtomProbe::RangeFile::decomposeIonNames(), AtomProbe::RangeFile::eraseIon(), filterBySolutionPPM(), filterPeakNeedBiggerObs(), findOverlaps(), AtomProbe::AbundanceData::generateIsotopeDist(), AtomProbe::RangeFile::makeSelfConsistent(), and FixedStack< T >::~FixedStack().

vectorPointDir()

unsigned int AtomProbe::vectorPointDir	(	const Point3D &	pA,
		const Point3D &	pB,
		const Point3D &	vC,
		const Point3D &	vD
	)

Check which way vectors attached to two 3D points "point",.

Two vectors may point "together", /__\ "apart" __/ or "In common" /__/ or __\

Definition at line 127 of file misc.cpp.

References ASSERT, POINTDIR_APART, POINTDIR_IN_COMMON, and POINTDIR_TOGETHER.

Referenced by distanceToSegment(), and meanAndStdev().

voigtProfile() [1/2]

void AtomProbe::voigtProfile	(	const std::vector< double > &	x,
		double	sigma,
		double	gamma,
		double	mu,
		double	amp,
		std::vector< double > &	y
	)

Generate a shifted voigt profile.

Definition at line 486 of file fitting.cpp.

References AtomProbe::DATA_FIT::x.

Referenced by fitVoigtFunc(), lsq(), and main().

voigtProfile() [2/2]

void AtomProbe::voigtProfile	(	const vector< double > &	x,
		double	sigma,
		double	gamma,
		vector< double > &	y
	)

Definition at line 449 of file fitting.cpp.

References M_PI.

weightedMean()

template<class T >

T AtomProbe::weightedMean	(	const std::vector< T > &	values,
		const std::vector< T > &	weight
	)

Definition at line 52 of file misc.h.

Referenced by fitDoniachSunjic(), fitExpNorm(), fitLikeLogGaussian(), fitVoigt(), and AtomProbe::AbundanceData::generateGroupedIsotopeDist().

XMLFreeDoc()

void AtomProbe::XMLFreeDoc

(

void *

data

)

Free a xmlDoc pointer. For use in conjunction with std::unique_ptr for auto-deallocation.

Definition at line 23 of file XMLHelper.cpp.

Referenced by AtomProbe::MultiRange::open().

XMLGetNextElemAttrib()

template<class T >

bool AtomProbe::XMLGetNextElemAttrib	(	xmlNodePtr &	nodePtr,
		T &	v,
		const char *	nodeName,
		const char *	attrib
	)

Grab the specified attribute from the next element, then stream_cast() it into the passed-in object. Returns true on success, false on error.

Definition at line 112 of file XMLHelper.h.

References stream_cast(), and XMLHelpFwdToElem().

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XMLHelpFwdNotElem()

unsigned int AtomProbe::XMLHelpFwdNotElem	(	xmlNodePtr &	node,
		const char *	nodeName
	)

Definition at line 53 of file XMLHelper.cpp.

XMLHelpFwdToElem()

unsigned int AtomProbe::XMLHelpFwdToElem	(	xmlNodePtr &	node,
		const char *	nodeName
	)

Definition at line 41 of file XMLHelper.cpp.

Referenced by AtomProbe::AbundanceData::open(), AtomProbe::MultiRange::open(), and XMLGetNextElemAttrib().

XMLHelpFwdToList()

unsigned int AtomProbe::XMLHelpFwdToList	(	xmlNodePtr &	node,
		const std::vector< std::string > &	nodeList
	)

XMLHelpGetProp()

template<class T >

unsigned int AtomProbe::XMLHelpGetProp	(	T &	prop,
		xmlNodePtr	node,
		std::string	propName
	)

Definition at line 87 of file XMLHelper.h.

References PROP_BAD_ATT, PROP_PARSE_ERR, and stream_cast().

Referenced by AtomProbe::AbundanceData::open(), and AtomProbe::MultiRange::open().

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XMLHelpGetText() [1/2]

string AtomProbe::XMLHelpGetText

(

xmlNodePtr

node

)

Definition at line 64 of file XMLHelper.cpp.

References XMLHelpNextType().

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XMLHelpGetText() [2/2]

std::string AtomProbe::XMLHelpGetText

(

xmlNodePtr &

node

)

XMLHelpNextType()

unsigned int AtomProbe::XMLHelpNextType	(	xmlNodePtr &	node,
		int	nodeType
	)

Definition at line 28 of file XMLHelper.cpp.

Referenced by XMLHelpGetText().

zechConfidenceLimits()

bool AtomProbe::zechConfidenceLimits	(	float	lambdaBack,
		unsigned int	observation,
		float	alpha,
		float &	estimate
	)

Provides a best estimate for true signal when true signal, background.

Nuclear Instruments and Methods in Physics Research A, 1989 608-610 "Upper limits in Experiments with Background or Measurement Errors" This is numerically unstable for large counts A similar problem is tackled by Bityukov, arxiv:hep-ex/0108020v1 Equation 3.5, but is less numerically stable

lambdaBack : background rate observation : Observed signal+background alpha : confidence parameter, (0,1) estimate : estimate for signal at confidence bound, specified by alpha Returns true if calculation succeeds, false otherwise. Note :this involves a root-finding approach, so may be slow

NOTE: may not be numerically stable for high lambdaback/observation, or lambdaback>>observation. This may cause GSL to error out.

Definition at line 406 of file confidence.cpp.

References AtomProbe::ZECH_ROOT::alpha, ASSERT, AtomProbe::ZECH_ROOT::lambdaBack, AtomProbe::ZECH_ROOT::observation, and zechRoot().

Referenced by poissonConfidenceObservation(), and zechCorrect().

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zechRoot()

double AtomProbe::zechRoot	(	double	sigGuess,
		void *	params
	)

Definition at line 386 of file confidence.cpp.

References AtomProbe::ZECH_ROOT::alpha, AtomProbe::ZECH_ROOT::lambdaBack, and AtomProbe::ZECH_ROOT::observation.

Referenced by zechConfidenceLimits().

Variable Documentation

a2iTriangleConnectionTable

int AtomProbe::a2iTriangleConnectionTable[256][16]

Definition at line 194 of file isoSurface.cpp.

ABUNDANCE_ERROR

const char* AtomProbe::ABUNDANCE_ERROR[]

Initial value:

= { "Unable to read abundance data (opening file)",
                 "Unable to create XML reader.",
                 "Bad property found in XML file",
                 "XML document did not match expected layout (DTD validation)",
                 "Unable to find required node during parse",
                 "Root node missing, expect <atomic-mass-table>!",
                 "Found incorrect root node. Expected <atomic-mass-table>"
}

Definition at line 49 of file abundance.cpp.

aiCubeEdgeFlags

int AtomProbe::aiCubeEdgeFlags[256]

Initial value:

=
{
        0x000, 0x109, 0x203, 0x30a, 0x406, 0x50f, 0x605, 0x70c, 0x80c, 0x905, 0xa0f, 0xb06, 0xc0a, 0xd03, 0xe09, 0xf00, 
        0x190, 0x099, 0x393, 0x29a, 0x596, 0x49f, 0x795, 0x69c, 0x99c, 0x895, 0xb9f, 0xa96, 0xd9a, 0xc93, 0xf99, 0xe90, 
        0x230, 0x339, 0x033, 0x13a, 0x636, 0x73f, 0x435, 0x53c, 0xa3c, 0xb35, 0x83f, 0x936, 0xe3a, 0xf33, 0xc39, 0xd30, 
        0x3a0, 0x2a9, 0x1a3, 0x0aa, 0x7a6, 0x6af, 0x5a5, 0x4ac, 0xbac, 0xaa5, 0x9af, 0x8a6, 0xfaa, 0xea3, 0xda9, 0xca0, 
        0x460, 0x569, 0x663, 0x76a, 0x066, 0x16f, 0x265, 0x36c, 0xc6c, 0xd65, 0xe6f, 0xf66, 0x86a, 0x963, 0xa69, 0xb60, 
        0x5f0, 0x4f9, 0x7f3, 0x6fa, 0x1f6, 0x0ff, 0x3f5, 0x2fc, 0xdfc, 0xcf5, 0xfff, 0xef6, 0x9fa, 0x8f3, 0xbf9, 0xaf0, 
        0x650, 0x759, 0x453, 0x55a, 0x256, 0x35f, 0x055, 0x15c, 0xe5c, 0xf55, 0xc5f, 0xd56, 0xa5a, 0xb53, 0x859, 0x950, 
        0x7c0, 0x6c9, 0x5c3, 0x4ca, 0x3c6, 0x2cf, 0x1c5, 0x0cc, 0xfcc, 0xec5, 0xdcf, 0xcc6, 0xbca, 0xac3, 0x9c9, 0x8c0, 
        0x8c0, 0x9c9, 0xac3, 0xbca, 0xcc6, 0xdcf, 0xec5, 0xfcc, 0x0cc, 0x1c5, 0x2cf, 0x3c6, 0x4ca, 0x5c3, 0x6c9, 0x7c0, 
        0x950, 0x859, 0xb53, 0xa5a, 0xd56, 0xc5f, 0xf55, 0xe5c, 0x15c, 0x055, 0x35f, 0x256, 0x55a, 0x453, 0x759, 0x650, 
        0xaf0, 0xbf9, 0x8f3, 0x9fa, 0xef6, 0xfff, 0xcf5, 0xdfc, 0x2fc, 0x3f5, 0x0ff, 0x1f6, 0x6fa, 0x7f3, 0x4f9, 0x5f0, 
        0xb60, 0xa69, 0x963, 0x86a, 0xf66, 0xe6f, 0xd65, 0xc6c, 0x36c, 0x265, 0x16f, 0x066, 0x76a, 0x663, 0x569, 0x460, 
        0xca0, 0xda9, 0xea3, 0xfaa, 0x8a6, 0x9af, 0xaa5, 0xbac, 0x4ac, 0x5a5, 0x6af, 0x7a6, 0x0aa, 0x1a3, 0x2a9, 0x3a0, 
        0xd30, 0xc39, 0xf33, 0xe3a, 0x936, 0x83f, 0xb35, 0xa3c, 0x53c, 0x435, 0x73f, 0x636, 0x13a, 0x033, 0x339, 0x230, 
        0xe90, 0xf99, 0xc93, 0xd9a, 0xa96, 0xb9f, 0x895, 0x99c, 0x69c, 0x795, 0x49f, 0x596, 0x29a, 0x393, 0x099, 0x190, 
        0xf00, 0xe09, 0xd03, 0xc0a, 0xb06, 0xa0f, 0x905, 0x80c, 0x70c, 0x605, 0x50f, 0x406, 0x30a, 0x203, 0x109, 0x000
}

Definition at line 166 of file isoSurface.cpp.

ATO_ERR_STRINGS

const char * AtomProbe::ATO_ERR_STRINGS

Initial value:

= { "",
                "Error opening file",
                "File is empty",
                "Filesize does not match expected format",
                "File version number not <4, as expected",
                "Unable to allocate memory to store data",
                "Unable to detect endian-ness in file"
                }

Human readable error messages for use with ATO reader return values.

Definition at line 73 of file dataFiles.cpp.

edgeRemap

int AtomProbe::edgeRemap[12]

Initial value:

={ 0,6,1,4,
              2,7,3,5,
              8,10,11,9}

Definition at line 488 of file isoSurface.cpp.

ELEM_FOUR_NODE_TETRAHEDRON

const unsigned int AtomProbe::ELEM_FOUR_NODE_TETRAHEDRON =4

Definition at line 38 of file mesh.h.

Referenced by AtomProbe::Mesh::loadGmshMesh(), and AtomProbe::Mesh::saveGmshMesh().

ELEM_SINGLE_NODE_POINT

const unsigned int AtomProbe::ELEM_SINGLE_NODE_POINT =15

Definition at line 35 of file mesh.h.

Referenced by AtomProbe::Mesh::loadGmshMesh(), and AtomProbe::Mesh::saveGmshMesh().

ELEM_THREE_NODE_TRIANGLE

const unsigned int AtomProbe::ELEM_THREE_NODE_TRIANGLE =2

Definition at line 37 of file mesh.h.

Referenced by AtomProbe::Mesh::loadGmshMesh(), and AtomProbe::Mesh::saveGmshMesh().

ELEM_TWO_NODE_LINE

const unsigned int AtomProbe::ELEM_TWO_NODE_LINE =1

Definition at line 36 of file mesh.h.

Referenced by AtomProbe::Mesh::loadGmshMesh(), and AtomProbe::Mesh::saveGmshMesh().

elementList

const char* AtomProbe::elementList[]

Initial value:

= { 
"H", "He", "Li", "Be",  "B", "C", "N",  "O",  "F", "Ne",

"Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", 

"K", "Ca", "Sc","Ti",  "V", "Cr",  "Mn", "Fe",  "Co", "Ni",  
   "Cu",  "Zn", "Ga", "Ge", "As", "Se",  "Br", "Kr",

"Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd",
   "Ag",  "Cd", "In", "Sn", "Sb", "Te",  "I", "Xe",

"Cs",  "Ba", "La",  "Ce", "Pr",  "Nd", "Pm", "Sm",  "Eu", "Gd",
    "Tb",  "Dy",  "Ho", "Er",  "Tm", "Yb", "Lu",  "Hf", "Ta",
    "W",  "Re", "Os",  "Ir", "Pt", "Au", "Hg",  "Tl", "Pb",
     "Bi",  "Po", "At", "Rn",

"Fr", "Ra",  "Ac", "Th",  "Pa", "U",  "Np", "Pu",  "Am", "Cm",
    "Bk", "Cf",  "Es", "Fm",  "Md",  "No",  "Lr",  "Rf",  "Db",
    "Sg",  "Bh",  "Hs",  "Mt",  "Ds",  "Rg",  "Cn",  "Uut",  "Fl",
     "Uup",  "Lv",  "Uus", "Uuo", ""
}

Definition at line 63 of file ranges.cpp.

EPOS_RECORD_SIZE

const size_t AtomProbe::EPOS_RECORD_SIZE = 11*4

Definition at line 144 of file ionHit.h.

Referenced by chunkLoadEposFile(), and loadEposFile().

hardAssert

bool AtomProbe::hardAssert =true

Definition at line 23 of file aptAssert.cpp.

Referenced by getHardAssert().

HULL_GRAB_SIZE

const unsigned int AtomProbe::HULL_GRAB_SIZE =4096

Definition at line 42 of file convexHull.cpp.

libVersion

LibVersion AtomProbe::libVersion

Definition at line 28 of file atomprobe.cpp.

Referenced by AtomProbe::RandNumGen::getRng().

MAX_LINE_SIZE

const size_t AtomProbe::MAX_LINE_SIZE = 16536

Definition at line 51 of file ranges.cpp.

Referenced by AtomProbe::RangeFile::open(), and AtomProbe::RangeFile::rangeTypeString().

MAX_RANGEFILE_SIZE

const size_t AtomProbe::MAX_RANGEFILE_SIZE = 50*1024*1024

Definition at line 53 of file ranges.cpp.

maximumLinearTable

const size_t AtomProbe::maximumLinearTable[]

Definition at line 39 of file lfsr.cpp.

Referenced by AtomProbe::LinearFeedbackShiftReg::verifyTable().

MESH_LOAD_ERRS

const char * AtomProbe::MESH_LOAD_ERRS

Initial value:

= {  "",
    "Missing error message. This is a bug, please report it",
    "Node count was different to number of present nodes",
    "Element count was less than number of present elements",
    "Mesh loaded, but failed to pass sanity checks"
}

Definition at line 53 of file mesh.cpp.

MULTIRANGE_FORMAT_VERSION

const char AtomProbe::MULTIRANGE_FORMAT_VERSION[] = "0.0.1"

Definition at line 46 of file multiRange.cpp.

NUM_ELEMENTS

const unsigned int AtomProbe::NUM_ELEMENTS =119

Definition at line 35 of file ranges.h.

OPS_ENUM_ERRSTRINGS

const char * AtomProbe::OPS_ENUM_ERRSTRINGS

Initial value:

=
{
    "",
        "\"C\" line (exp. parameters) not in expected format",
    "\"I\"  line (Detector parameters) not in expected format",
    "\"-\" line (Time-of-flights) not in expected format",
    "\"V\" line (voltage data) not in expected format",
    "Error interpreting \"V\" line (voltage data) data",
    "Missing beta value from \"V\" line - needs to be in voltage, or in system header (\"C\" line",
    "Incorrect number of \"V\" line (voltage data) data entries",
    "Unknown linetype in data file",
    "\"P\" line (detector channels) not in expected format",
    "Unable to interpret channels line",
    "Incorrect number of events in \"S\" (hit position) line",
    "Unable to interpret event data on \"S\" (hit position) line",
    "Unable to parse \"S\" (hit position) line event count (eg 8 in S8 ...)",
    "\"S\" (hit position) line data not preceded by TOF data, as it should have been",
    "Duplicate system data/experiment setup (\"C\") entry found -- there can only be one",
    "Duplicate detector (\"I\") data entry found -- there can only be one",
    "Trailing \"-\" line found -- should have be followed by a \"S\" line, but wasn't.",
    "Duplicate\"-\" line found -- should have be followed by a \"S\" line, but wasn't.",
    "Unable to open file",
    "unable to read file, after opening",
    "Abort requested"
}

Definition at line 776 of file dataFiles.cpp.

PROGRESS_REDUCE

const size_t AtomProbe::PROGRESS_REDUCE =500

Definition at line 61 of file mesh.cpp.

Referenced by AtomProbe::K3DTreeExact::build(), computeConvexHull(), and AtomProbe::Mesh::pointsInside().

qhullInited

bool AtomProbe::qhullInited =false

Definition at line 39 of file convexHull.cpp.

randGen

RandNumGen AtomProbe::randGen

Definition at line 29 of file atomprobe.cpp.

Referenced by AtomProbe::RandNumGen::getRng(), leastSquaresOverlapSolve(), loadATOFile(), loadPosFile(), main(), poissonConfidenceObservation(), and sampleIons().

RANGE_EXTS

const char* AtomProbe::RANGE_EXTS[]

Initial value:

= { "rng",
              "env",
              "rng",
              "rrng",
                ""}

Definition at line 55 of file ranges.cpp.

RECORDREAD_ERR_STRINGS

const char * AtomProbe::RECORDREAD_ERR_STRINGS

Initial value:

= { "",
                    "Unable to determine filesize",
                    "Filesize indicates that file contains a non-integer number of entries",
                    "Unable to open file",
                    "Unable to allocate memory for reading file contents",
                    "Unable to perform read  operation on file",
                    "Read past end of file requested",
                    "Entry in file appears to be invalid",
    }

Definition at line 82 of file dataFiles.cpp.

Referenced by main().

VERTEX_OFFSET

const unsigned int AtomProbe::VERTEX_OFFSET[8][3]

Initial value:

= 
{
        {0, 0, 0},{1, 0, 0},{1, 1, 0},{0, 1, 0},
        {0, 0, 1},{1, 0, 1},{1, 1, 1},{0, 1, 1}
}

Definition at line 462 of file isoSurface.cpp.