MetaDataset Class Reference

The MetaDataset class A subclass of VespucciDataset for datasets created from multiple other datasets. this stores information about the parents. More...

#include <metadataset.h>

Inheritance diagram for MetaDataset:

Public Member Functions
	MetaDataset (QString name, MainWindow *main_window, QString *directory, QString method_description, MetaMethod::Method method, QList< QSharedPointer< VespucciDataset > > parent_datasets)
	MetaDataset::MetaDataset. More...
vec *	parents ()
Public Member Functions inherited from VespucciDataset
	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

Additional Inherited Members
Public Attributes inherited from VespucciDataset
QTextStream	log_text_stream_
	log_text_stream_ A log of all UI-induced functions called on this dataset More...

Detailed Description

The MetaDataset class A subclass of VespucciDataset for datasets created from multiple other datasets. this stores information about the parents.

Definition at line 30 of file metadataset.h.

Constructor & Destructor Documentation

MetaDataset::MetaDataset	(	QString	name,
		MainWindow *	main_window,
		QString *	directory,
		QString	method_description,
		MetaMethod::Method	method,
		QList< QSharedPointer< VespucciDataset > >	parent_datasets
	)

MetaDataset::MetaDataset.

Parameters

name	Name of this dataset as displayed to user
main_window	Main window of the program
log_file	The log file
directory	The current global working directory
method_description	The description of the method used
endmember_selection	The string used by the user to select endmembers
method	An enum specifying the method
parent_datasets	The datasets from which this dataset is extracted

Definition at line 34 of file metadataset.cpp.

Member Function Documentation

vec * MetaDataset::parents

(

)

Definition at line 152 of file metadataset.cpp.

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

• Projects/VespucciProject/Vespucci/Vespucci/Data/Dataset/metadataset.h
• Projects/VespucciProject/Vespucci/Vespucci/Data/Dataset/metadataset.cpp