Spectral Library is a class that loads and saves SLZ files and holds information from them for use with the Pipeline Object (or independently) More...

#include <spectral_library.h>

Public Member Functions
	spectral_library ()

	spectral_library (std::string filename)

	spectral_library (arma::fvec wavelengths, std::vector< std::string > labels, arma::fmat endmembers)

virtual	~spectral_library ()

void	load (std::string filename)
	load() initialises the spectral library object that it is called on with the data in the specified file. More...

void	save (std::string filename)
	save() saves the contents of the spectral_library to the specified SLZ file More...

void	set_wavelengths (const arma::fvec &in)

arma::fvec	wavelengths () const

void	set_metadata (const std::string &in)

std::string	metadata () const

std::vector< std::string >	labels (std::string filename="") const

std::vector< std::string >	loaded_files () const

std::vector< std::string >	loaded_file_list () const

void	set_endmembers (const arma::fmat &in_endmembers, const std::vector< std::string > &in_labels)

arma::fmat	endmembers (std::string label="", std::string filename="") const

arma::fmat	endmembers_mean () const

std::vector< std::string >	labels_mean () const

void	add_endmembers (const arma::fmat &in_endmembers, const std::vector< std::string > &in_labels, std::string filename="")
	Append endmembers onto the list currently held by the object. More...

void	delete_endmembers (std::string label="", std::string filename="")
	Delete endmembers from the list currently held by the object by label name and or filename. More...

void	add_library (std::string filename, bool re_evaluate=false)
	Append the contents of a SLZ file to the current contents of the object. More...

void	add_library (scyl::spectral_library &in, std::string name="nofile", bool re_evaluate=false)
	Append the contents of a spectral_library object to the current contents of the object. More...

unsigned int	bands ()

unsigned int	num_endmembers ()

void	print ()

Private Attributes
arma::fvec	m_wavelengths

std::vector< std::tuple < std::string, std::string, arma::fvec > >	m_endmember_list

scyl::iotools::slz	m_slz

unsigned int	m_bands

std::string	m_metadata

Detailed Description

Spectral Library is a class that loads and saves SLZ files and holds information from them for use with the Pipeline Object (or independently)

At the most basic level, the spectral_library can be used as follows:

scyl::spectral_library speclib = scyl::spectral_library("/path/to/file.slz");

To add a spectral_library to the Pipeline:

std::shared_ptr<scyl::spectral_library>  spec_lib  = std::make_shared<scyl::spectral_library>("/path/to/file.slz");
scyl::pipeline pipeline = scyl::pipeline();
pipeline.set_spectral_library(speclib);

Constructor & Destructor Documentation

scyl::spectral_library::spectral_library ( )

Spectral_Library Constructor Creates an empty spectral library object.

scyl::spectral_library::spectral_library ( std::string filename )

Spectral Library Constructor Creates a spectral library object based on the contents of a loaded file.

Parameters

filename The path to the SLZ file to be loaded into this object.

scyl::spectral_library::spectral_library	(	arma::fvec	wavelengths,
		std::vector< std::string >	labels,
		arma::fmat	endmembers
	)

Spectral Library Constructor Creates a spectral library object with contents as given in the constructor arguments.

Parameters

wavelengths	- Vector of wavelength values for the given endmembers (bands)
labels	- String label descriptions of the endmembers (num_endmembers)
endmembers	- Matrix of endmembers, each row is one endmember. (m_bands x num_endmembers)

scyl::spectral_library::~spectral_library ( )

virtual

Spectral Library Destructor

Member Function Documentation

void scyl::spectral_library::add_endmembers	(	const arma::fmat &	in_endmembers,
		const std::vector< std::string > &	in_labels,
		std::string	filename = `""`
	)

Append endmembers onto the list currently held by the object.

To add data that has a different number of bands, use add_library() with re_evaluate set to true, or use scyl::spectral_library::resample_endmembers on the data first to make it the correct size.

Parameters

in_endmembers	- endmembers to add
in_labels	- corresponding labels
filename	- source tag (eg, the file the data came from or some other identifying category)

void scyl::spectral_library::add_library	(	std::string	filename,
		bool	re_evaluate = `false`
	)

Append the contents of a SLZ file to the current contents of the object.

This function can concatenate end members that have a different number of bands onto the object using NURBS interpolation to adjust the number of bands in the input data.

Parameters

filename
re_evaluate	set to true to use NURBS to interpolate data of incompatible size.

void scyl::spectral_library::add_library	(	scyl::spectral_library &	in,
		std::string	name = `"nofile"`,
		bool	re_evaluate = `false`
	)

Append the contents of a spectral_library object to the current contents of the object.

This function can concatenate end members that have a different number of bands onto the object using NURBS interpolation to adjust the number of bands in the input data.

Parameters

in	The object to be added
name	The name of the library (for the purpose of recalling where each group of spectra is from)
re_evaluate	set to true to use NURBS to interpolate data of incompatible size.

unsigned int scyl::spectral_library::bands ( )

Get bands

Returns: bands

void scyl::spectral_library::delete_endmembers	(	std::string	label = `""`,
		std::string	filename = `""`
	)

Delete endmembers from the list currently held by the object by label name and or filename.

This function takes a list of labels, and looks them up in the endmember list to find their indexes before calling the uvec version of this function. If a label appears multiple times, all instance will be removed.

Example:

std::vector<std::string> removes;
removes.pushback("label1");
spectral_library.delete_endmembers(removes);

Parameters

label	- the label to delete
filename	- The filename to delete

arma::fmat scyl::spectral_library::endmembers	(	std::string	label = `""`,
		std::string	filename = `""`
	)		const

Gets endmembers (Get the corresponding labels using labels() with identical arguments)

Optional filters are available to narrow the returned results if desired. The label filter will filter endmembers matching that label (exactly), the filename filter will filter labels loaded from that file (you can use loaded_files() to get the list of filenames) Leaving both as "" will return all endmembers. Leaving label as "" and setting filename will return all endmembers for a specific file. Leaving filename as "" and setting label will return only endmembers that match that label.

Parameters

label	- String filter for desired label
filename	- String filter for desired filename

Returns: List of matching endmembers (each row is one endmember)

arma::fmat scyl::spectral_library::endmembers_mean ( ) const

Gets mean endmembers (use label_mean() to get corresponding labels)

If there are multiple identical labels in the library, this function will reduce then to a set of unique label endmembers (if multiple identical labels are found their endmembers are averaged)

Returns: List of unique averaged endmembers (each row is one endmember)

std::vector< std::string > scyl::spectral_library::labels ( std::string filename = "" ) const

Gets labels

if the filename argument is set to "" (default) then all labels are returned, otherwise only labels that are associated (were loaded from) the given filename are returned. You can get the list of loaded files using loaded_files().

Parameters

filename An optional filter of the filename the labels were loaded from

Returns: A vector of the string names for each endmember.

std::vector< std::string > scyl::spectral_library::labels_mean ( ) const

Gets mean endmember labels (use endmember_mean() to get corresponding endmembers)

If there are multiple identical labels in the library, this function will reduce then to a set of unique labels.

Returns: List of unique labels

void scyl::spectral_library::load ( std::string filename )

load() initialises the spectral library object that it is called on with the data in the specified file.

load() will overwrite the entire contents of the spectral_library object it is called upon. It populates the following member variables:

- wavelengths
- bands
- labels
- endmembers

Parameters

filename The path to the SLZ file to be loaded into this object.

std::vector< std::string > scyl::spectral_library::loaded_file_list ( ) const

Gets the list of files corresponding to each endmember.

Returns: A vector of the string representations of filename for each endmember.

std::vector< std::string > scyl::spectral_library::loaded_files ( ) const

Gets the list of files that have been loaded into the spectral_library.

Returns: A vector of the string representations of each file that has been loaded.

std::string scyl::spectral_library::metadata ( ) const

Gets metadata

Returns: metadata

unsigned int scyl::spectral_library::num_endmembers ( )

Get num_endmembers

Returns: num_endmembers

void scyl::spectral_library::print ( )

void scyl::spectral_library::save ( std::string filename )

save() saves the contents of the spectral_library to the specified SLZ file

Parameters

filename The path to the SLZ file to be saved.

void scyl::spectral_library::set_endmembers	(	const arma::fmat &	in_endmembers,
		const std::vector< std::string > &	in_labels
	)

Sets endmembers (pair of label vector and endmember matrix)

Parameters

in_endmembers	endmembers
in_labels	vector of corresponding labels

void scyl::spectral_library::set_metadata ( const std::string & in )

Sets metadata

Parameters

in	string of metadata

void scyl::spectral_library::set_wavelengths ( const arma::fvec & in )

Sets wavelengths

If the wavelength vector's length doesn't match the number of bands of the currently held elements, the class is flushed before setting the new wavelengths.

Parameters

in	Vector of wavelengths

arma::fvec scyl::spectral_library::wavelengths ( ) const

Gets wavelengths

Returns: wavelengths

Member Data Documentation

unsigned int scyl::spectral_library::m_bands

private

std::vector<std::tuple<std::string, std::string, arma::fvec> > scyl::spectral_library::m_endmember_list

private

std::string scyl::spectral_library::m_metadata

private

scyl::iotools::slz scyl::spectral_library::m_slz

private

arma::fvec scyl::spectral_library::m_wavelengths

private

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

src/pipeline/spectral_library.h
src/pipeline/spectral_library.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation