Vespucci  1.0.0
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:
VespucciDataset AbstractDataAnalyzer

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...
 
MapListModelmap_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< AnalysisResultsGetAnalysisResult (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< MapDataGetMapData (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
nameName of this dataset as displayed to user
main_windowMain window of the program
log_fileThe log file
directoryThe current global working directory
method_descriptionThe description of the method used
endmember_selectionThe string used by the user to select endmembers
methodAn enum specifying the method
parent_datasetsThe 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.


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