The VespucciDataset class This is the main class for dealing with hyperspectral data. This handles the import and export of spectra, and the creation of maps. Images are handled by the MapData class. This class is intended to be allocated on the heap inside of a smart pointer, there is no copy constructor. More...

#include <vespuccidataset.h>

Inheritance diagram for VespucciDataset:

Public Member Functions
	VespucciDataset (const QString &h5_filename, MainWindow *main_window, QSharedPointer< VespucciWorkspace > ws)
	VespucciDataset::VespucciDataset. More...

	VespucciDataset (QString text_filename, MainWindow main_window, QString directory, QString name, QString x_axis_description, QString y_axis_description, bool swap_spatial, std::string format)
	VespucciDataset::VespucciDataset. More...

	VespucciDataset (map< pair< int, int >, string > text_filenames, MainWindow main_window, QString directory, QString name, QString x_axis_description, QString y_axis_description, int rows, int cols)

	VespucciDataset (QString name, MainWindow main_window, QString directory, QSharedPointer< VespucciDataset > original, uvec indices)
	VespucciDataset::VespucciDataset. More...

	VespucciDataset (QString name, MainWindow main_window, QString directory)
	VespucciDataset::VespucciDataset. More...

	~VespucciDataset ()
	VespucciDataset::~VespucciDataset. More...

void	Undo ()
	VespucciDataset::Undo Swap spectra_ and spectra_old_ to undo an action. Calling this function again re-does the action that was undid. More...

void	CropSpectra (double x_min, double x_max, double y_min, double y_max, double wl_min, double wl_max)
	VespucciDataset::CropSpectra Crops spectra_ based on. More...

mat	ZScoreNormCopy ()
	VespucciDataset::ZScoreNormCopy For when you want to Z-score normalize without changing spectra_. More...

void	MinMaxNormalize ()
	VespucciDataset::MinMaxNormalize Normalizes each column of spectra_ so that the highest value is 1 and lowest value is 0. More...

void	VectorNormalize (uword norm)
	VespucciDataset::VectorNormalize. More...

void	MeanCenter ()
	VespucciDataset::MeanCenter Subtract the mean of all spectra in the dataset at each wavelength from each wavelength (i.e. in preparation for PCA) More...

void	ZScoreNormalize ()
	VespucciDataset::ZScoreNormalize Normalizes each row using the score of the normal distribution. More...

void	SNVNormalize (double offset, bool center)

void	AbsoluteValue ()

void	PeakIntensityNormalize (double peak_position)

void	PeakIntensityNormalize (double left_bound, double right_bound)
	VespucciDataset::PeakIntensityNormalize. More...

void	Booleanize (double min, double max, bool keep_inside, bool oneify)
	VespucciDataset::Booleanize. More...

void	Clamp (double min, double max)
	VespucciDataset::Clamp. More...

void	ShedZeroSpectra ()

void	ShedZeroWavelengths ()

void	SubtractBackground (const QStringList &data_keys)
	VespucciDataset::SubtractBackground. More...

void	MedianFilter (unsigned int window_size)
	VespucciDataset::MedianFilter performs median filtering on the spectral data. Entries near the boundaries of spectra are not processed. See also VespucciDataset::LinearMovingAverage. More...

void	LinearMovingAverage (unsigned int window_size)
	VespucciDataset::LinearMovingAverage Performs moving average filtering on the spectral data. Entries near the boundaries of spectra are not processed. See also VespucciDataset::MedianFilter. More...

void	SavitzkyGolay (unsigned int derivative_order, unsigned int polynomial_order, unsigned int window_size)
	VespucciDataset::SavitzkyGolay Performs derivatization/Savitzky-Golay smoothing. More...

void	SingularValue (unsigned int singular_values)
	VespucciDataset::SingularValue Denoises the spectra matrix using a truncated singular value decomposition. The first singular_values singular values are used to "reconstruct" the spectra matrix. The function used to find the truncated SVD is Vespucci::Math::DimensionReduction::svds. More...

int	QUIC_SVD (double epsilon)
	VespucciDataset::QUIC_SVD. More...

void	MFBaseline (int window_size, int iterations)
	VespucciDataset::MFBaseline Baseline-adjusts the data. This function uses a median filter with a large window to determine the baseline on the assumption that the median value is more likely to be basline than spectrum. This will complicate things if there are many peaks. Additionally, this significantly narrows the shape of peaks. Other baseline methods may be implemented later. More...

void	RollingBallBaseline (size_t wm, size_t ws)
	VespucciDataset::RollingBallBaseline. More...

void	CWTBaseline (int lambda, int penalty_order, double SNR_threshold, double peak_shape_threshold)

void	IModPolyBaseline (const uword poly_order, const uword max_it, double threshold)

void	RemoveClippedSpectra (double threshold)
	VespucciDataset::RemoveClippedSpectra. More...

void	RemoveFlatSpectra (double threshold)
	VespucciDataset::RemoveFlatSpectra. More...

void	ZeroClippedSpectra (double threshold)
	VespucciDataset::ZeroClippedSpectra. More...

void	ZeroFlatSpectra (double threshold)
	VespucciDataset::ZeroFlatSpectra. More...

void	Scale (double scaling_factor)

void	ShedSpectrum (const uword index)
	VespucciDataset::ShedSpectrum. More...

void	ZeroSpectrum (const uword index)

int	HySime ()
	VespucciDataset::HySime. More...

void	TransformAbscissa (QString input_units, double input_factor, QString output_units, double output_factor, QString description)
	VespucciDataset::TransformAbscissa. More...

void	InterpolateToNewAbscissa (const vec &new_abscissa, unsigned int poly_order, unsigned int window_size)
	VespucciDataset::InterpolateToNewAbscissa. More...

void	InterpolateToNewAbscissa (const vec &new_abscissa)
	VespucciDataset::InterpolateToNewAbscissa. More...

void	FourierTransform (int n)
	VespucciDataset::FourierTransform. More...

void	InverseFourierTransform (int n)

void	ApplyFTWeight (QString type, double param)
	VespucciDataset::ApplyFTWeight. More...

void	ApplyFTWeight (double start_offset, double end_offset, double power)
	VespucciDataset::ApplyFTWeight. More...

vec	PointSpectrum (uword index) const
	VespucciDataset::PointSpectrum. More...

QVector< double >	WavelengthQVector () const

int	FindIndex (int x_value, int y_value) const

uword	FindIndex (double abscissa_value) const

uvec	FindRange (double start, double end) const
	VespucciDataset::FindRange. Finds the index of the wavelength value closest to the specified wavelength range. More...

uword	FindOrigin () const
	VespucciDataset::FindOrigin. More...

int	KeySize () const
	VespucciDataset::KeySize Finds the number of data points in x variable to properly set axes of QCustomPlot objects. More...

int	ValueSize () const
	VespucciDataset::ValueSize Finds number of unique y values for properly setting QCPAxis. More...

QCPRange	KeyRange () const
	VespucciDataset::KeyRange Finds the minima and maxima of x variable to properly set axes of QCustomPlot objects. More...

QCPRange	ValueRange () const
	VespucciDataset::ValueRange Finds the minima and maxima of y variable to properly set axes of QCustomPlot objects. More...

bool	Save (QString filename)

bool	Load (QString filename)

bool	SaveSpectrum (QString filename, uword column, file_type type)

void	Univariate (const QString &name, double &left_bound, double &right_bound, uword bound_window)
	VespucciDataset::Univariate. More...

void	FitPeak (const QString &name, const QString &peak_shape, double &left_bound, double &right_bound)

void	BandRatio (const QString &name, double &first_left_bound, double &first_right_bound, double &second_left_bound, double &second_right_bound, uword bound_window)
	VespucciDataset::BandRatio. More...

void	ClassicalLeastSquares (const QString &name, const QStringList &reference_keys)

void	PartialLeastSquares (const QString &name, uword components)
	VespucciDataset::PartialLeastSquares. More...

void	PLSCalibration (const QString &name, const QStringList &control_keys)

void	TrainPLSDA (const QString &name, const QStringList &label_keys)

void	CorrelationAnalysis (const QString &control_key, QString name)
	VespucciDataset::CorrelationAnalysis. More...

void	VertexComponents (const QString &name, uword endmembers)
	VespucciDataset::VertexComponents. More...

void	KMeans (const QString &name, const QString &metric_text, const QString &partition_policy, bool allow_empty, size_t clusters)
	VespucciDataset::KMeans. More...

void	PrincipalComponents (const QString &name)
	VespucciDataset::PrincipalComponents Perform PCA without creating an image. More...

void	PrincipalComponents (const QString &name, bool scale_data)
	VespucciDataset::PrincipalComponents. More...

void	FindPeaks (const QString &name, double sel, double threshold, uword poly_order, uword window_size)
	VespucciDataset::FindPeaks. More...

void	AgglomerativeClustering (const QString &name, const QString &linkage, const QString &metric)
	VespucciDataset::AgglomerativeClustering. More...

void	CalculateRepresentativeSpectrum (const QString &name, QString statistic, QString metric)
	VespucciDataset::CalculateRepresentativeSpectrum. More...

vec	wavelength () const
	VespucciDataset::wavelength. More...

vec	abscissa () const

vec	x () const
	VespucciDataset::x. More...

vec	y () const
	VespucciDataset::y. More...

vec	x (uvec indices) const
	VespucciDataset::x. More...

vec	y (uvec indices) const
	VespucciDataset::y. More...

double	x (uword index) const

double	y (uword index) const

vec	wavelength (uvec indices) const

mat	spectra (uvec indices) const
	VespucciDataset::spectra. More...

mat	spectra () const
	VespucciDataset::spectra. More...

cx_mat	cx_spectra () const

cx_mat	cx_spectra (uvec indices) const

const QString	name () const
	VespucciDataset::name. More...

vec	indices () const
	VespucciDataset::indices. More...

mat *	indices_ptr ()
	VespucciDataset::indices_ptr. More...

QStringList	operations ()

bool	principal_components_calculated () const

bool	mlpack_pca_calculated () const

bool	vertex_components_calculated () const

bool	partial_least_squares_calculated () const

QList< QSharedPointer< UnivariateData > >	univariate_datas ()

const QString	x_axis_description () const
	VespucciDataset::x_axis_description The x_axis_description is printed on the spectrum viewer. More...

const QString	y_axis_description () const
	VespucciDataset::y_axis_description. More...

void	SetName (QString new_name)
	VespucciDataset::SetName. More...

void	SetData (const mat &spectra, const vec &wavelength, const vec &x, const vec &y)
	VespucciDataset::SetData. More...

void	SetIndices (vec indices)
	VespucciDataset::SetIndices. More...

void	AddMap (QSharedPointer< MapData > map)
	VespucciDataset::AddMap Adds a map to the list of map pointers and adds its name to relevant lists. More...

void	RemoveMap (const QString &name)

int	map_loading_count () const
	VespucciDataset::map_names. More...

void	SetXDescription (QString description)
	VespucciDataset::SetXDescription Sets the value of the spectral abscissa description. More...

void	SetYDescription (QString description)
	VespucciDataset::SetYDescription. More...

QCPRange	WavelengthRange () const
	VespucciDataset::WavelengthRange. More...

QCPRange	PointSpectrumRange (int i) const
	VespucciDataset::PointSpectrumRange. More...

QCPColorGradient	GetGradient (int gradient_number) const
	VespucciDataset::GetGradient Selects the color gradient from list of presets. More...

QCPColorGradient	GetClusterGradient (int clusters) const
	VespucciDataset::GetClusterGradient Cluster gradients are slightly different from the continuous gradients. This selects the right gradient based on the number of clusters. More...

bool	ConstructorCancelled () const
	VespucciDataset::ConstructorCancelled Specifies whether or not the constructor has been canceled. The constructor asks this and cleans everything up in case it is canceled. More...

mat	AverageSpectrum (bool stats) const
	VespucciDataset::AverageSpectrum Finds the average of the spectrum. This can be saved by the user. Probably not all that useful, except for determining a spectrum to use as a background spectrum for other maps. More...

mat *	x_ptr ()
	VespucciDataset::x_ptr. More...

mat *	y_ptr ()
	VespucciDataset::y_ptr. More...

mat *	wavelength_ptr ()

mat *	abscissa_ptr ()
	VespucciDataset::abscissa_ptr. More...

mat *	spectra_ptr ()
	VespucciDataset::spectra_ptr. More...

mat *	spectra_old_ptr (bool *ok)

const mat &	spectra_ref ()
	VespucciDataset::spectra_ref. More...

const vec &	abscissa_ref ()
	VespucciDataset::abscissa_ref. More...

const vec &	x_ref ()
	VespucciDataset::x_ref. More...

const vec &	y_ref ()
	VespucciDataset::y_ref. More...

size_t	columns () const

double	AbscissaMin () const

double	AbscissaMax () const

bool	non_spatial () const
	VespucciDataset::non_spatial. More...

bool	meta () const
	VespucciDataset::meta. More...

void	SetParentDatasetIndices (mat parent_dataset_indices)
	VespucciDataset::SetParentDatasetIndices. More...

mat *	parent_dataset_indices ()

bool	Undoable () const
	VespucciDataset::Undoable. More...

uword	UniqueX () const

uword	UniqueY () const

int	UnivariateCount () const
	VespucciDataset::UnivariateCount. More...

const QString	last_operation () const
	VespucciDataset::last_operation. More...

MapListModel *	map_list_model ()

void	AddAnalysisResult (QSharedPointer< AnalysisResults > analysis_result)

void	AddAnalysisResult (QSharedPointer< AnalysisResults > analysis_result, uword start_row, uword end_row)

QStringList	AnalysisResultsKeys () const
	VespucciDataset::AnalysisResultsKeys. More...

QMap< QString, QStringList >	AnalysisResultsTreeStructure () const
	VespucciDataset::AnalysisResultsTreeStructure. More...

void	ImportAuxiliaryMatrix (const QString &name, const QString &filename)
	VespucciDataset::ImportAuxiliaryMatrix. More...

void	AddAuxiliaryMatrix (const QString &name, mat &matrix)
	VespucciDataset::AddAuxiliaryMatrix. More...

void	AddMatrix (const QString &name, mat &matrix)

QStringList	AuxiliaryMatrixKeys () const
	VespucciDataset::AuxiliaryMatrixKeys. More...

QStringList	CoreMatrixKeys () const
	VespucciDataset::CoreMatrixKeys. More...

const mat &	GetAnalysisResultMatrix (const QString &results_key, const QString &matrix_key) const
	VespucciDataset::GetAnalysisResultMatrix. More...

QSharedPointer< AnalysisResults >	GetAnalysisResult (const QString &key)

const mat &	GetAuxiliaryMatrix (const QString &key) const

const mat &	GetCoreMatrix (const QString &key) const

bool	IsCoreMatrix (const QString &key) const
	VespucciDataset::IsCoreMatrix. More...

QSharedPointer< MapData >	GetMapData (const QString &key)

void	CreateMap (const QString &map_name, const QString &results_key, const QString &matrix_key, uword column, QCPColorGradient gradient)
	VespucciDataset::CreateMap. More...

void	CreateMap (const QString &map_name, const QString &matrix_key, uword column, QCPColorGradient gradient)

bool	ShowMapViewer (const QString &map_key, bool show)

QStringList	MapKeys () const

void	SetOldCopies ()

bool	Contains (const QString &key) const
	VespucciDataset::Contains. More...

bool	IsValid () const

bool	state_changed () const

QString	filename () const

QString	last_save_filename () const

bool	saved () const

Public Member Functions inherited from AbstractDataAnalyzer
virtual	~AbstractDataAnalyzer ()

virtual void	Univariate (const QString &name, double &left_bound, double &right_bound, arma::uword bound_window)=0

virtual void	BandRatio (const QString &name, double &first_left_bound, double &first_right_bound, double &second_left_bound, double &second_right_bound, arma::uword bound_window)=0

virtual void	VertexComponents (const QString &name, arma::uword endmembers)=0

virtual void	PartialLeastSquares (const QString &name, arma::uword components)=0

virtual arma::vec	PointSpectrum (arma::uword index) const =0

Public Attributes
QTextStream	log_text_stream_
	log_text_stream_ A log of all UI-induced functions called on this dataset More...

Detailed Description

The VespucciDataset class This is the main class for dealing with hyperspectral data. This handles the import and export of spectra, and the creation of maps. Images are handled by the MapData class. This class is intended to be allocated on the heap inside of a smart pointer, there is no copy constructor.

Definition at line 75 of file vespuccidataset.h.

Constructor & Destructor Documentation

VespucciDataset::VespucciDataset	(	const QString &	h5_filename,
		MainWindow *	main_window,
		QSharedPointer< VespucciWorkspace >	ws
	)

VespucciDataset::VespucciDataset.

Parameters

name
h5_filename
main_window
directory	Constructor to load dataset from an HDF5 file. Restrictions: Top level DataSets with names "Spectra" and "Spectral Abscissa" are required. Only three levels are recognized, Dataset, AnalysisResult, Matrix All matrices other than "x", "y", "abscissa" or "spectra" will be loaded into the auxiliary_matrices_ object.

All DataSets must have 2 dimensions only (column vectors stored as Nx1 matrices)

Attributes will be used to set metadata

All analysis results groups are added as base AnalysisResults

Definition at line 214 of file vespuccidataset.cpp.

VespucciDataset::VespucciDataset	(	QString	text_filename,
		MainWindow *	main_window,
		QString *	directory,
		QString	name,
		QString	x_axis_description,
		QString	y_axis_description,
		bool	swap_spatial,
		std::string	format
	)

VespucciDataset::VespucciDataset.

Parameters

text_filename	The filename of the text file from which data is imported
main_window	The main window of the program
directory	The current global working directory
name	The name of the dataset displayed to the user
x_axis_description	A description of the spectral abscissa
y_axis_description	A description of the spectral ordinate
swap_spatial	Whether or not y is located in the first column instead of the second (some Horiba spectrometers do this). Main function for processing data from text files to create VespucciDataset objects. Currently written to accept files in "wide" format, will be expanded to deal with different ASCII formats later with conditionals.

Definition at line 360 of file vespuccidataset.cpp.

VespucciDataset::VespucciDataset	(	map< pair< int, int >, string >	text_filenames,
		MainWindow *	main_window,
		QString *	directory,
		QString	name,
		QString	x_axis_description,
		QString	y_axis_description,
		int	rows,
		int	cols
	)

Definition at line 444 of file vespuccidataset.cpp.

VespucciDataset::VespucciDataset	(	QString	name,
		MainWindow *	main_window,
		QString *	directory,
		QSharedPointer< VespucciDataset >	original,
		uvec	indices
	)

VespucciDataset::VespucciDataset.

Parameters

name	The name of the dataset displayed to the user
main_window	The main window of the program
directory	The current global working directory
original	The dataset from which this dataset is "extracted"
indices	The indices of the spectra in the previous dataset that will form this one This is a constructor to create a new dataset by "extracting" spectra from a another dataset based on values on an image.

Definition at line 494 of file vespuccidataset.cpp.

VespucciDataset::VespucciDataset	(	QString	name,
		MainWindow *	main_window,
		QString *	directory
	)

VespucciDataset::VespucciDataset.

Parameters

name	Dataset name
main_window	The
directory	Constructor to create a dataset without spatial and spectral data set (i.e. when using MetaDataset or a factory method). Use SetData() to instantiate dataset members

Definition at line 544 of file vespuccidataset.cpp.

VespucciDataset::~VespucciDataset ( )

VespucciDataset::~VespucciDataset.

Definition at line 35 of file vespuccidataset.cpp.

Member Function Documentation

vec VespucciDataset::abscissa ( ) const

virtual

Implements AbstractDataAnalyzer.

Definition at line 2266 of file vespuccidataset.cpp.

mat * VespucciDataset::abscissa_ptr ( )

VespucciDataset::abscissa_ptr.

Returns

Definition at line 2749 of file vespuccidataset.cpp.

const vec & VespucciDataset::abscissa_ref ( )

VespucciDataset::abscissa_ref.

Returns: abscissa_ as reference

Definition at line 2675 of file vespuccidataset.cpp.

double VespucciDataset::AbscissaMax ( ) const

virtual

Implements AbstractDataAnalyzer.

Definition at line 2708 of file vespuccidataset.cpp.

double VespucciDataset::AbscissaMin ( ) const

virtual

Implements AbstractDataAnalyzer.

Definition at line 2703 of file vespuccidataset.cpp.

void VespucciDataset::AbsoluteValue ( )

Definition at line 919 of file vespuccidataset.cpp.

void VespucciDataset::AddAnalysisResult ( QSharedPointer< AnalysisResults > analysis_result )

Definition at line 2819 of file vespuccidataset.cpp.

void VespucciDataset::AddAnalysisResult	(	QSharedPointer< AnalysisResults >	analysis_result,
		uword	start_row,
		uword	end_row
	)

Definition at line 2833 of file vespuccidataset.cpp.

void VespucciDataset::AddAuxiliaryMatrix	(	const QString &	name,
		mat &	matrix
	)

VespucciDataset::AddAuxiliaryMatrix.

Parameters

name	Display name and internal key of the matrix to add
matrix	Auxiliary matrix to insert into this dataset

Definition at line 2892 of file vespuccidataset.cpp.

void VespucciDataset::AddMap ( QSharedPointer< MapData > map )

VespucciDataset::AddMap Adds a map to the list of map pointers and adds its name to relevant lists.

Parameters

map

Definition at line 2457 of file vespuccidataset.cpp.

void VespucciDataset::AddMatrix	(	const QString &	name,
		mat &	matrix
	)

Definition at line 2904 of file vespuccidataset.cpp.

void VespucciDataset::AgglomerativeClustering	(	const QString &	name,
		const QString &	linkage,
		const QString &	metric
	)

virtual

VespucciDataset::AgglomerativeClustering.

Parameters

name
linkage
metric	linkage and metric must be valid arguments for Vespucci::Math::Clustering::AHCA

Implements AbstractDataAnalyzer.

Definition at line 1842 of file vespuccidataset.cpp.

QStringList VespucciDataset::AnalysisResultsKeys ( ) const

VespucciDataset::AnalysisResultsKeys.

Returns: Get a list of keys for analysis results. Used to update display model.

Definition at line 2852 of file vespuccidataset.cpp.

QMap< QString, QStringList > VespucciDataset::AnalysisResultsTreeStructure ( ) const

VespucciDataset::AnalysisResultsTreeStructure.

Returns: Container parsed by TreeModel

Definition at line 2864 of file vespuccidataset.cpp.

void VespucciDataset::ApplyFTWeight	(	QString	type,
		double	param
	)

VespucciDataset::ApplyFTWeight.

Parameters

type
param

Definition at line 1644 of file vespuccidataset.cpp.

void VespucciDataset::ApplyFTWeight	(	double	start_offset,
		double	end_offset,
		double	power
	)

VespucciDataset::ApplyFTWeight.

Parameters

type
start_offset
end_offset
power

Definition at line 1666 of file vespuccidataset.cpp.

QStringList VespucciDataset::AuxiliaryMatrixKeys ( ) const

VespucciDataset::AuxiliaryMatrixKeys.

Returns: List of names of imported auxiliary matrices Used in updating display model

Definition at line 2924 of file vespuccidataset.cpp.

mat VespucciDataset::AverageSpectrum ( bool stats ) const

VespucciDataset::AverageSpectrum Finds the average of the spectrum. This can be saved by the user. Probably not all that useful, except for determining a spectrum to use as a background spectrum for other maps.

Parameters

stats Whether or not to include standard deviations on the second row.

Returns: The average spectrum

Definition at line 2600 of file vespuccidataset.cpp.

void VespucciDataset::BandRatio	(	const QString &	name,
		double &	first_left_bound,
		double &	first_right_bound,
		double &	second_left_bound,
		double &	second_right_bound,
		uword	bound_window
	)

VespucciDataset::BandRatio.

Parameters

first_left_bound
first_right_bound
second_left_bound
second_right_bound
bound_window

Definition at line 1735 of file vespuccidataset.cpp.

void VespucciDataset::Booleanize	(	double	min,
		double	max,
		bool	keep_inside,
		bool	oneify
	)

VespucciDataset::Booleanize.

Parameters

min
max
keep_inside
oneify

Definition at line 753 of file vespuccidataset.cpp.

void VespucciDataset::CalculateRepresentativeSpectrum	(	const QString &	name,
		QString	statistic,
		QString	metric
	)

VespucciDataset::CalculateRepresentativeSpectrum.

Parameters

name
statistic	Either "centroid" or "medoid"
metric	Valid for DistanceMetricWrapper statist

Definition at line 1872 of file vespuccidataset.cpp.

void VespucciDataset::Clamp	(	double	min,
		double	max
	)

VespucciDataset::Clamp.

Parameters

min
max

Definition at line 787 of file vespuccidataset.cpp.

void VespucciDataset::ClassicalLeastSquares	(	const QString &	name,
		const QStringList &	reference_keys
	)

virtual

Implements AbstractDataAnalyzer.

Definition at line 2066 of file vespuccidataset.cpp.

size_t VespucciDataset::columns ( ) const

virtual

Implements AbstractDataAnalyzer.

Definition at line 2698 of file vespuccidataset.cpp.

bool VespucciDataset::ConstructorCancelled ( ) const

VespucciDataset::ConstructorCancelled Specifies whether or not the constructor has been canceled. The constructor asks this and cleans everything up in case it is canceled.

Returns

Definition at line 2587 of file vespuccidataset.cpp.

bool VespucciDataset::Contains ( const QString & key ) const

VespucciDataset::Contains.

Parameters

key

Returns: Every AnalysisResult and auxiliary matrix must have a unique name. This is called before an object is added to verify that it doesn't already exist The caller will rename the object if it exists by appending a number that is iteratively increased until the name is unique

Definition at line 156 of file vespuccidataset.cpp.

QStringList VespucciDataset::CoreMatrixKeys ( ) const

VespucciDataset::CoreMatrixKeys.

Returns

Definition at line 2933 of file vespuccidataset.cpp.

void VespucciDataset::CorrelationAnalysis	(	const QString &	control_key,
		QString	name
	)

VespucciDataset::CorrelationAnalysis.

Parameters

control_key
name	Object with key control_key must be column vector or else only first column used

Definition at line 2004 of file vespuccidataset.cpp.

void VespucciDataset::CreateMap	(	const QString &	map_name,
		const QString &	results_key,
		const QString &	matrix_key,
		uword	column,
		QCPColorGradient	gradient
	)

VespucciDataset::CreateMap.

Parameters

map_name
results_key
matrix_key
column
gradient
tick_count	Caller should check the number of unique elements in the object before plotting it A cluster color gradient should be used for 8 or less unique elements.

Definition at line 3013 of file vespuccidataset.cpp.

void VespucciDataset::CreateMap	(	const QString &	map_name,
		const QString &	matrix_key,
		uword	column,
		QCPColorGradient	gradient
	)

Definition at line 3035 of file vespuccidataset.cpp.

void VespucciDataset::CropSpectra	(	double	x_min,
		double	x_max,
		double	y_min,
		double	y_max,
		double	wl_min,
		double	wl_max
	)

VespucciDataset::CropSpectra Crops spectra_ based on.

Parameters

x_min	value of x below which spectra are deleted
x_max	value of x above which spectra are deleted
y_min	value of y below which spectra are deleted
y_max	value of y above which spectra are deleted Removes all data points outside of the range. Cannot be undone. It is preferable to create a new dataset rather than crop an old one.

Definition at line 613 of file vespuccidataset.cpp.

void VespucciDataset::CWTBaseline	(	int	lambda,
		int	penalty_order,
		double	SNR_threshold,
		double	peak_shape_threshold
	)

Definition at line 1024 of file vespuccidataset.cpp.

cx_mat VespucciDataset::cx_spectra ( ) const

Definition at line 2373 of file vespuccidataset.cpp.

cx_mat VespucciDataset::cx_spectra ( uvec indices ) const

Definition at line 2381 of file vespuccidataset.cpp.

QString VespucciDataset::filename ( ) const

Definition at line 179 of file vespuccidataset.cpp.

int VespucciDataset::FindIndex	(	int	x_value,
		int	y_value
	)		const

uword VespucciDataset::FindIndex ( double abscissa_value ) const

Definition at line 2145 of file vespuccidataset.cpp.

uword VespucciDataset::FindOrigin ( ) const

VespucciDataset::FindOrigin.

Returns: Find the point closest to (0,0) in the map. If the function fails, find the index in the middle of the spatial data.

Definition at line 2113 of file vespuccidataset.cpp.

void VespucciDataset::FindPeaks	(	const QString &	name,
		double	sel,
		double	threshold,
		uword	poly_order,
		uword	window_size
	)

VespucciDataset::FindPeaks.

Parameters

sel	The amount above the surrounding data for a peak to be identified
threshold	A value which peaks must be larger than to be maxima
poly_order	Polynomial order for Savitzky-Golay derivatization
window_size	Window size for Savitzky-Golay derivatization

Definition at line 1812 of file vespuccidataset.cpp.

uvec VespucciDataset::FindRange	(	double	start,
		double	end
	)		const

VespucciDataset::FindRange. Finds the index of the wavelength value closest to the specified wavelength range.

Parameters

start	the first wavelength in the spectral region of interest
end	the second wavelength in the spectral region of interest

Returns

Definition at line 2100 of file vespuccidataset.cpp.

void VespucciDataset::FitPeak	(	const QString &	name,
		const QString &	peak_shape,
		double &	left_bound,
		double &	right_bound
	)

virtual

Implements AbstractDataAnalyzer.

Definition at line 1714 of file vespuccidataset.cpp.

void VespucciDataset::FourierTransform ( int n )

VespucciDataset::FourierTransform.

Parameters

n

Definition at line 1597 of file vespuccidataset.cpp.

QSharedPointer< AnalysisResults > VespucciDataset::GetAnalysisResult ( const QString & key )

Definition at line 2956 of file vespuccidataset.cpp.

const mat & VespucciDataset::GetAnalysisResultMatrix	(	const QString &	results_key,
		const QString &	matrix_key
	)		const

VespucciDataset::GetAnalysisResultMatrix.

Parameters

results_key
matrix_key

Returns: Currently iterates over all results (O(n)) could change structure to use binary tree (O(log n)) but I don't think it should ever be necessary.

Definition at line 2945 of file vespuccidataset.cpp.

const mat & VespucciDataset::GetAuxiliaryMatrix ( const QString & key ) const

Definition at line 2968 of file vespuccidataset.cpp.

QCPColorGradient VespucciDataset::GetClusterGradient ( int clusters ) const

VespucciDataset::GetClusterGradient Cluster gradients are slightly different from the continuous gradients. This selects the right gradient based on the number of clusters.

Parameters

clusters Number of clusters

Returns: Proper color gradient for number of clusters

Definition at line 2565 of file vespuccidataset.cpp.

const mat & VespucciDataset::GetCoreMatrix ( const QString & key ) const

Definition at line 2975 of file vespuccidataset.cpp.

QCPColorGradient VespucciDataset::GetGradient ( int gradient_number ) const

VespucciDataset::GetGradient Selects the color gradient from list of presets.

Parameters

gradient_number

Returns

Definition at line 2511 of file vespuccidataset.cpp.

QSharedPointer< MapData > VespucciDataset::GetMapData ( const QString & key )

Definition at line 2995 of file vespuccidataset.cpp.

int VespucciDataset::HySime ( )

VespucciDataset::HySime.

Returns: Dimensionality predicted by HySime algorithm

Definition at line 1407 of file vespuccidataset.cpp.

void VespucciDataset::IModPolyBaseline	(	const uword	poly_order,
		const uword	max_it,
		double	threshold
	)

Definition at line 1029 of file vespuccidataset.cpp.

void VespucciDataset::ImportAuxiliaryMatrix	(	const QString &	name,
		const QString &	filename
	)

VespucciDataset::ImportAuxiliaryMatrix.

Parameters

name
filename	Load a file into the auxiliary matrix map

Definition at line 2877 of file vespuccidataset.cpp.

vec VespucciDataset::indices ( ) const

VespucciDataset::indices.

Returns: The indices_ vector

Definition at line 2289 of file vespuccidataset.cpp.

mat * VespucciDataset::indices_ptr ( )

VespucciDataset::indices_ptr.

Returns: A pointer to the indices_ vector

Definition at line 2298 of file vespuccidataset.cpp.

void VespucciDataset::InterpolateToNewAbscissa	(	const vec &	new_abscissa,
		unsigned int	poly_order,
		unsigned int	window_size
	)

VespucciDataset::InterpolateToNewAbscissa.

Parameters

new_abscissa
polynomial_order
window_size	Spline interpolation to new abscissa

Definition at line 1555 of file vespuccidataset.cpp.

void VespucciDataset::InterpolateToNewAbscissa ( const vec & new_abscissa )

VespucciDataset::InterpolateToNewAbscissa.

Parameters

new_abscissa Linear interpolation to new abscissa

Definition at line 1576 of file vespuccidataset.cpp.

void VespucciDataset::InverseFourierTransform ( int n )

Definition at line 1617 of file vespuccidataset.cpp.

bool VespucciDataset::IsCoreMatrix ( const QString & key ) const

VespucciDataset::IsCoreMatrix.

Parameters

key

Returns: Check whether the DatasetTreeItem child is core matrix or not DataViewer needs to know whether to use GetCoreMatrix or GetAuxiliaryMatrix after action is performed on a MatrixTreeItem that is child of DatasetTreeItem

Definition at line 2990 of file vespuccidataset.cpp.

bool VespucciDataset::IsValid ( ) const

Definition at line 162 of file vespuccidataset.cpp.

QCPRange VespucciDataset::KeyRange ( ) const

VespucciDataset::KeyRange Finds the minima and maxima of x variable to properly set axes of QCustomPlot objects.

Returns

Definition at line 2171 of file vespuccidataset.cpp.

int VespucciDataset::KeySize ( ) const

VespucciDataset::KeySize Finds the number of data points in x variable to properly set axes of QCustomPlot objects.

Returns: number of unique x values

Definition at line 2185 of file vespuccidataset.cpp.

void VespucciDataset::KMeans	(	const QString &	name,
		const QString &	metric_text,
		const QString &	partition_policy,
		bool	allow_empty,
		size_t	clusters
	)

virtual

VespucciDataset::KMeans.

Implements K-means clustering using MLPACK

Parameters

clusters	Number of clusters to find
metric	Distance metric
name	Name of map in workspace.

Implements AbstractDataAnalyzer.

Definition at line 2041 of file vespuccidataset.cpp.

const QString VespucciDataset::last_operation ( ) const

VespucciDataset::last_operation.

Returns: Description of last pre-processing operation performed

Definition at line 2813 of file vespuccidataset.cpp.

QString VespucciDataset::last_save_filename ( ) const

Definition at line 184 of file vespuccidataset.cpp.

void VespucciDataset::LinearMovingAverage ( unsigned int window_size )

VespucciDataset::LinearMovingAverage Performs moving average filtering on the spectral data. Entries near the boundaries of spectra are not processed. See also VespucciDataset::MedianFilter.

Parameters

window_size - an odd number representing the width of the window.

Definition at line 1225 of file vespuccidataset.cpp.

bool VespucciDataset::Load ( QString filename )

MapListModel* VespucciDataset::map_list_model ( )

int VespucciDataset::map_loading_count ( ) const

VespucciDataset::map_names.

Returns: list of names of the maps created from this dataset VespucciDataset::map_loading_count; number of maps created for this dataset

Definition at line 2446 of file vespuccidataset.cpp.

QStringList VespucciDataset::MapKeys ( ) const

Definition at line 3067 of file vespuccidataset.cpp.

void VespucciDataset::MeanCenter ( )

VespucciDataset::MeanCenter Subtract the mean of all spectra in the dataset at each wavelength from each wavelength (i.e. in preparation for PCA)

Definition at line 712 of file vespuccidataset.cpp.

void VespucciDataset::MedianFilter ( unsigned int window_size )

VespucciDataset::MedianFilter performs median filtering on the spectral data. Entries near the boundaries of spectra are not processed. See also VespucciDataset::LinearMovingAverage.

Parameters

window_size - an odd number representing the width of the window.

Definition at line 1201 of file vespuccidataset.cpp.

bool VespucciDataset::meta ( ) const

VespucciDataset::meta.

Returns: Whether or not this is an instance of MetaDataset

Definition at line 2790 of file vespuccidataset.cpp.

void VespucciDataset::MFBaseline	(	int	window_size,
		int	iterations
	)

VespucciDataset::MFBaseline Baseline-adjusts the data. This function uses a median filter with a large window to determine the baseline on the assumption that the median value is more likely to be basline than spectrum. This will complicate things if there are many peaks. Additionally, this significantly narrows the shape of peaks. Other baseline methods may be implemented later.

Parameters

method
window_size

Definition at line 977 of file vespuccidataset.cpp.

void VespucciDataset::MinMaxNormalize ( )

VespucciDataset::MinMaxNormalize Normalizes each column of spectra_ so that the highest value is 1 and lowest value is 0.

Definition at line 663 of file vespuccidataset.cpp.

bool VespucciDataset::mlpack_pca_calculated ( ) const

const QString VespucciDataset::name ( ) const

VespucciDataset::name.

Returns: member name_, the name of the dataset as seen by the user

Definition at line 2403 of file vespuccidataset.cpp.

bool VespucciDataset::non_spatial ( ) const

VespucciDataset::non_spatial.

Returns: True if map has empty x_ and y_

Definition at line 2781 of file vespuccidataset.cpp.

QStringList VespucciDataset::operations ( )

Definition at line 2303 of file vespuccidataset.cpp.

mat * VespucciDataset::parent_dataset_indices ( )

Definition at line 2804 of file vespuccidataset.cpp.

bool VespucciDataset::partial_least_squares_calculated ( ) const

void VespucciDataset::PartialLeastSquares	(	const QString &	name,
		uword	components
	)

VespucciDataset::PartialLeastSquares.

Parameters

components Perform partial least squares without creating an image

Definition at line 1940 of file vespuccidataset.cpp.

void VespucciDataset::PeakIntensityNormalize ( double peak_position )

void VespucciDataset::PeakIntensityNormalize	(	double	left_bound,
		double	right_bound
	)

VespucciDataset::PeakIntensityNormalize.

Parameters

left_bound
right_bound

Definition at line 732 of file vespuccidataset.cpp.

void VespucciDataset::PLSCalibration	(	const QString &	name,
		const QStringList &	control_keys
	)

virtual

Implements AbstractDataAnalyzer.

Definition at line 1965 of file vespuccidataset.cpp.

vec VespucciDataset::PointSpectrum ( uword index ) const

VespucciDataset::PointSpectrum.

Parameters

index

Returns

Definition at line 2129 of file vespuccidataset.cpp.

QCPRange VespucciDataset::PointSpectrumRange ( int i ) const

VespucciDataset::PointSpectrumRange.

Parameters

i	col of spectra_ containing desired spectrum

Returns: the range of y values for the point spectra at i

Definition at line 2495 of file vespuccidataset.cpp.

bool VespucciDataset::principal_components_calculated ( ) const

void VespucciDataset::PrincipalComponents ( const QString & name )

virtual

VespucciDataset::PrincipalComponents Perform PCA without creating an image.

Implements AbstractDataAnalyzer.

Definition at line 1787 of file vespuccidataset.cpp.

void VespucciDataset::PrincipalComponents	(	const QString &	name,
		bool	scale_data
	)

virtual

VespucciDataset::PrincipalComponents.

Parameters

scaleData
recalculate	Perform PCA using MLPACK's implementation. This is designed for dimensionality reduction, not classification, so there is no corresponding imaging function

Implements AbstractDataAnalyzer.

Definition at line 1768 of file vespuccidataset.cpp.

int VespucciDataset::QUIC_SVD ( double epsilon )

VespucciDataset::QUIC_SVD.

Parameters

epsilon Error tolerance fraction for calculated subspace Use the QUIC-SVD algorithm to denoise the spectra by finding a lower-rank approximation of the matrix.

Definition at line 1285 of file vespuccidataset.cpp.

void VespucciDataset::RemoveClippedSpectra ( double threshold )

VespucciDataset::RemoveClippedSpectra.

Parameters

threshold Removes spectra with a maximum value at or above the threshold

Definition at line 1078 of file vespuccidataset.cpp.

void VespucciDataset::RemoveFlatSpectra ( double threshold )

VespucciDataset::RemoveFlatSpectra.

Parameters

threshold Removes "flat" spectra whose maximum is less than the threshold

Definition at line 1109 of file vespuccidataset.cpp.

void VespucciDataset::RemoveMap ( const QString & name )

Definition at line 2467 of file vespuccidataset.cpp.

void VespucciDataset::RollingBallBaseline	(	size_t	wm,
		size_t	ws
	)

VespucciDataset::RollingBallBaseline.

Parameters

wm
ws

Definition at line 1004 of file vespuccidataset.cpp.

bool VespucciDataset::Save ( QString filename )

Definition at line 42 of file vespuccidataset.cpp.

bool VespucciDataset::saved ( ) const

Definition at line 189 of file vespuccidataset.cpp.

bool VespucciDataset::SaveSpectrum	(	QString	filename,
		uword	column,
		file_type	type
	)

Definition at line 123 of file vespuccidataset.cpp.

void VespucciDataset::SavitzkyGolay	(	unsigned int	derivative_order,
		unsigned int	polynomial_order,
		unsigned int	window_size
	)

VespucciDataset::SavitzkyGolay Performs derivatization/Savitzky-Golay smoothing.

Parameters

derivative_order	The order of the derivative.
polynomial_order	The order of the polynomial
window_size	The size of the filter window.

Definition at line 1320 of file vespuccidataset.cpp.

void VespucciDataset::Scale ( double scaling_factor )

Definition at line 1346 of file vespuccidataset.cpp.

void VespucciDataset::SetData	(	const mat &	spectra,
		const vec &	wavelength,
		const vec &	x,
		const vec &	y
	)

VespucciDataset::SetData.

Parameters

spectra	Spectra
wavelength	Spectral abscissa
x	vec of horizontal axis spatial data
y	vec of vertical axis spatial data Set the data of the dataset. Used by the MetaDataset constructor

Definition at line 2424 of file vespuccidataset.cpp.

void VespucciDataset::SetIndices ( vec indices )

VespucciDataset::SetIndices.

Parameters

indices A new indices_ vector

Definition at line 2312 of file vespuccidataset.cpp.

void VespucciDataset::SetName ( QString new_name )

VespucciDataset::SetName.

Parameters

new_name new name of dataset

Definition at line 2412 of file vespuccidataset.cpp.

void VespucciDataset::SetOldCopies ( )

Definition at line 140 of file vespuccidataset.cpp.

void VespucciDataset::SetParentDatasetIndices ( mat parent_dataset_indices )

VespucciDataset::SetParentDatasetIndices.

Parameters

parent_dataset_indices Set the parent_dataset_indices_ variable. Used by the MetaDataset constructor.

Definition at line 2799 of file vespuccidataset.cpp.

void VespucciDataset::SetXDescription ( QString description )

VespucciDataset::SetXDescription Sets the value of the spectral abscissa description.

Parameters

description

Definition at line 2629 of file vespuccidataset.cpp.

void VespucciDataset::SetYDescription ( QString description )

VespucciDataset::SetYDescription.

Parameters

description Sets the value of the spectral ordinate axis description

Definition at line 2638 of file vespuccidataset.cpp.

void VespucciDataset::ShedSpectrum ( const uword index )

VespucciDataset::ShedSpectrum.

Parameters

index Index of spectrum to shed. Removes a spectrum from the dataset

Definition at line 1366 of file vespuccidataset.cpp.

void VespucciDataset::ShedZeroSpectra ( )

Definition at line 807 of file vespuccidataset.cpp.

void VespucciDataset::ShedZeroWavelengths ( )

Definition at line 832 of file vespuccidataset.cpp.

bool VespucciDataset::ShowMapViewer	(	const QString &	map_key,
		bool	show
	)

Definition at line 3053 of file vespuccidataset.cpp.

void VespucciDataset::SingularValue ( unsigned int singular_values )

VespucciDataset::SingularValue Denoises the spectra matrix using a truncated singular value decomposition. The first singular_values singular values are used to "reconstruct" the spectra matrix. The function used to find the truncated SVD is Vespucci::Math::DimensionReduction::svds.

Parameters

singular_values Number of singular values to use.

Definition at line 1252 of file vespuccidataset.cpp.

void VespucciDataset::SNVNormalize	(	double	offset,
		bool	center
	)

Definition at line 902 of file vespuccidataset.cpp.

mat VespucciDataset::spectra ( uvec indices ) const

VespucciDataset::spectra.

Parameters

indices Vector of indices

Returns: Submat of spectra at indices

Definition at line 2394 of file vespuccidataset.cpp.

mat VespucciDataset::spectra ( ) const

VespucciDataset::spectra.

Returns: member spectra_

Definition at line 2368 of file vespuccidataset.cpp.

mat* VespucciDataset::spectra_old_ptr ( bool * ok )

mat * VespucciDataset::spectra_ptr ( )

VespucciDataset::spectra_ptr.

Returns

Definition at line 2657 of file vespuccidataset.cpp.

const mat & VespucciDataset::spectra_ref ( )

VespucciDataset::spectra_ref.

Returns: spectra_ as reference

Definition at line 2666 of file vespuccidataset.cpp.

bool VespucciDataset::state_changed ( ) const

Definition at line 174 of file vespuccidataset.cpp.

void VespucciDataset::SubtractBackground ( const QStringList & data_keys )

VespucciDataset::SubtractBackground.

Parameters

data_keys location of matrix in workspace

Definition at line 942 of file vespuccidataset.cpp.

void VespucciDataset::TrainPLSDA	(	const QString &	name,
		const QStringList &	label_keys
	)

virtual

Implements AbstractDataAnalyzer.

Definition at line 1982 of file vespuccidataset.cpp.

void VespucciDataset::TransformAbscissa	(	QString	input_units,
		double	input_factor,
		QString	output_units,
		double	output_factor,
		QString	description
	)

VespucciDataset::TransformAbscissa.

Parameters

input_units
input_factor
output_units
output_factor

Definition at line 1435 of file vespuccidataset.cpp.

void VespucciDataset::Undo ( )

VespucciDataset::Undo Swap spectra_ and spectra_old_ to undo an action. Calling this function again re-does the action that was undid.

Definition at line 568 of file vespuccidataset.cpp.

bool VespucciDataset::Undoable ( ) const

VespucciDataset::Undoable.

Returns: Whether or not the last operation can be undone

Definition at line 2718 of file vespuccidataset.cpp.

uword VespucciDataset::UniqueX ( ) const

Definition at line 2723 of file vespuccidataset.cpp.

uword VespucciDataset::UniqueY ( ) const

Definition at line 2729 of file vespuccidataset.cpp.

void VespucciDataset::Univariate	(	const QString &	name,
		double &	left_bound,
		double &	right_bound,
		uword	bound_window
	)

VespucciDataset::Univariate.

Parameters

left_bound
right_bound
bound_window

Definition at line 1691 of file vespuccidataset.cpp.

QList<QSharedPointer<UnivariateData> > VespucciDataset::univariate_datas ( )

int VespucciDataset::UnivariateCount ( ) const

VespucciDataset::UnivariateCount.

Returns: Number of univariate/band ratio data objects have been created

Definition at line 2740 of file vespuccidataset.cpp.

QCPRange VespucciDataset::ValueRange ( ) const

VespucciDataset::ValueRange Finds the minima and maxima of y variable to properly set axes of QCustomPlot objects.

Returns

Definition at line 2158 of file vespuccidataset.cpp.

int VespucciDataset::ValueSize ( ) const

VespucciDataset::ValueSize Finds number of unique y values for properly setting QCPAxis.

Returns: number of unique y values

Definition at line 2220 of file vespuccidataset.cpp.

void VespucciDataset::VectorNormalize ( uword norm )

VespucciDataset::VectorNormalize.

Parameters

norm	If 1, unit area, if 2 unit length

Definition at line 691 of file vespuccidataset.cpp.

bool VespucciDataset::vertex_components_calculated ( ) const

void VespucciDataset::VertexComponents	(	const QString &	name,
		uword	endmembers
	)

VespucciDataset::VertexComponents.

Parameters

endmembers Perform VCA without creating an image

Definition at line 1895 of file vespuccidataset.cpp.

vec VespucciDataset::wavelength ( ) const

VespucciDataset::wavelength.

Returns: member abscissa_ (spectrum key values)

Definition at line 2261 of file vespuccidataset.cpp.

vec VespucciDataset::wavelength ( uvec indices ) const

Definition at line 2271 of file vespuccidataset.cpp.

mat * VespucciDataset::wavelength_ptr ( )

Definition at line 2754 of file vespuccidataset.cpp.

QVector< double > VespucciDataset::WavelengthQVector ( ) const

Definition at line 2134 of file vespuccidataset.cpp.

QCPRange VespucciDataset::WavelengthRange ( ) const

VespucciDataset::WavelengthRange.

Returns: the range of the wavlength vector (for plotting point spectra)

Definition at line 2482 of file vespuccidataset.cpp.

vec VespucciDataset::x ( ) const

VespucciDataset::x.

Returns: member x_

Definition at line 2280 of file vespuccidataset.cpp.

vec VespucciDataset::x ( uvec indices ) const

VespucciDataset::x.

Parameters

indices Vector of indices

Returns: Subvec of x corresponding to valeus in indices

Definition at line 2322 of file vespuccidataset.cpp.

double VespucciDataset::x ( uword index ) const

Definition at line 2327 of file vespuccidataset.cpp.

const QString VespucciDataset::x_axis_description ( ) const

VespucciDataset::x_axis_description The x_axis_description is printed on the spectrum viewer.

Returns: Spectral abscissa description.

Definition at line 2619 of file vespuccidataset.cpp.

mat * VespucciDataset::x_ptr ( )

VespucciDataset::x_ptr.

Returns

Definition at line 2763 of file vespuccidataset.cpp.

const vec & VespucciDataset::x_ref ( )

VespucciDataset::x_ref.

Returns: x_ as reference

Definition at line 2684 of file vespuccidataset.cpp.

vec VespucciDataset::y ( ) const

VespucciDataset::y.

Returns: member y_

Definition at line 2341 of file vespuccidataset.cpp.

vec VespucciDataset::y ( uvec indices ) const

VespucciDataset::y.

Parameters

indices Vector of indices

Returns: Subvec of y at indices

Definition at line 2351 of file vespuccidataset.cpp.

double VespucciDataset::y ( uword index ) const

Definition at line 2356 of file vespuccidataset.cpp.

const QString VespucciDataset::y_axis_description ( ) const

VespucciDataset::y_axis_description.

Returns: The spectral ordinate axis description.

Definition at line 2647 of file vespuccidataset.cpp.

mat * VespucciDataset::y_ptr ( )

VespucciDataset::y_ptr.

Returns

Definition at line 2772 of file vespuccidataset.cpp.

const vec & VespucciDataset::y_ref ( )

VespucciDataset::y_ref.

Returns: y_ as reference

Definition at line 2693 of file vespuccidataset.cpp.

void VespucciDataset::ZeroClippedSpectra ( double threshold )

VespucciDataset::ZeroClippedSpectra.

Parameters

threshold

Definition at line 1140 of file vespuccidataset.cpp.

void VespucciDataset::ZeroFlatSpectra ( double threshold )

VespucciDataset::ZeroFlatSpectra.

Parameters

threshold

Definition at line 1169 of file vespuccidataset.cpp.

void VespucciDataset::ZeroSpectrum ( const uword index )

Definition at line 1387 of file vespuccidataset.cpp.

void VespucciDataset::ZScoreNormalize ( )

VespucciDataset::ZScoreNormalize Normalizes each row using the score of the normal distribution.

Definition at line 881 of file vespuccidataset.cpp.

mat VespucciDataset::ZScoreNormCopy ( )

VespucciDataset::ZScoreNormCopy For when you want to Z-score normalize without changing spectra_.

Returns: A normalized copy of the matrix.

Definition at line 861 of file vespuccidataset.cpp.

Member Data Documentation

QTextStream VespucciDataset::log_text_stream_

log_text_stream_ A log of all UI-induced functions called on this dataset

Definition at line 301 of file vespuccidataset.h.

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

Projects/VespucciProject/Vespucci/Vespucci/Data/Dataset/vespuccidataset.h
Projects/VespucciProject/Vespucci/Vespucci/Data/Dataset/vespuccidataset.cpp

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation