Detailed Description

Dataset class - cluster data.

These datasets are outputted by a clus block

See also: clus

Definition at line 6 of file irdata_clus.m.

Inheritance diagram for irdata_clus:

Collaboration diagram for irdata_clus:

Public Member Functions
function	irdata_clus (in data)
	Constructor. More...

function get	no (in data)
	no getter More...

function get	nf (in data)
	nf getter More...

function get	nonf (in data)
	nonf getter More...

function get	no_groups (in data)
	no_groups getter More...

function get	nc (in data)
	nc getter More...

function get	width (in data)

function	get_groupidxs_from_groupcodes (in data, in codes)

function	get_obsidxs_from_groupidxs (in data, in groupidxs)

function	get_no_levels (in data)
	Counts to pre-allocate. More...

function	check (in data)
	Checks if internal variables are synchronized with some troubleshooting. More...

function	import_from_struct (in data, in DATA)

function	eliminate_unused_classlabels (in data)

function	mount_from_signal (in signal, in no_inputs, in future)
	Populates from a time series. More...

function	get_props_to_copy (in data)
	This is the maximum number of rows of the dataset before something blows. More...

function	copy_emptyrows (in data)

function	split_map (in data, in map, in feamap, in fext)

function	split_splitidxs (in data)
	prepares a clone, except for the fields in rowfieldnames More...

function	map_rows (in data, in idxnew)

function	select_features (in data, in idxs)

function	transform_linear (in data, in L, in L_fea_prefix)
	irverbose(sprintf('INFO (data_select_features()): # features before: %>d; # features after: %>d. ', nfold, data.nf)); More...

function	get_fea_names (in data, in idxs)
	Returns the names of the features. More...

function	make_groupnumbers (in data)
	fills in the groupnumbers property based on the groupcodes property. More...

function	assert_fix (in data)
	Makes the dataset properties consistent with each other. More...

function	get_weights (in data, in exponent)

function	transpose2 (in data)

function	assert_not_nan (in data)
	Asserts that there is no NaN in data.X. More...

function	get_description (in o, in flag_short)

function	setbatch (in o, in params)
	Sets several properties of an object at once. More...

function	get_methodname (in o, in flag_short)

function	get_report (in o)
	Object reports are plain text. HTML would be cool but c'mon, we don't need that sophistication. More...

function	get_html (in o, in flag_stylesheet)

function	get_params (in o, in data)
	Calls Parameters GUI. More...

function	extract_log (in o)

function	get_ancestry (in o, in flag_title)

Public Attributes
Property	no
	number of "observations" (e.g. spectra) More...

Property	nf
	number of features (i.e., variables) More...

Property	nonf
	a vector [no, nf] More...

Property	no_groups
	number of groups More...

Property	nc
	number of classes More...

Property	X
	[no]x[nf] matrix. Data matrix More...

Property	classes

Property	classlabels
	Cell of strings. Class labels. More...

Property	groupcodes
	(optional) [no]x[1] Cell of strings. Group codes (e.g. patient names) More...

Property	obsnames
	(optional) [no]x[1] Cell of strings. Observation names (e.g. file names of the individual spectra) More...

Property	filename

Property	filetype
	mat or txt More...

Property	fea_x
	feature x-axis More...

Property	fea_names
	(optional) Cell of strings. Name of each feature More...

Property	xname
	x-axis name, defaults to 'Wavenumber (cm^{-1})' More...

Property	xunit
	x-axis unit, defaults to 'cm^{-1}' More...

Property	yname
	y-axis name, defaults to 'Absorbance' More...

Property	yunit
	y-axis unit, defaults to 'a.u.' More...

Property	height
	Height of image. Spectra start counting from the bottom left upwards. More...

Property	width
	Width of image. Width is actually calculated as `no/height` . If result is not integer, an error will occur. More...

Property	direction

Property	Y
	Output (instead of classes). For regression instead of classification. More...

Property	groupnumbers
	For easier access than groupcodes. More...

Property	obsids

Property	splitidxs

Property	title

Property	color

Protected Member Functions
function	do_get_html (in o)
	HTML inner body. More...

function	do_get_report (in o)
	Default report. More...

Protected Attributes
Property	rowfieldnames
	fields to be split or merged when dataset is split or merged More...

Property	flags_cell

Property	classtitle
	Class Title. Should have a descriptive name, as short as possible. More...

Property	short
	Short for the method name. More...

Property	flag_params

Property	flag_ui
	(GUI setting) Whether to "publish" in blockmenu and datatool. Note that a class can be "published" without a GUI (set flag_params=0 in this case, at the class constructor). More...

Property	moreactions
	(GUI setting) String cell containing names of methods that may be called from the GUIs More...

Constructor & Destructor Documentation

function irdata_clus::irdata_clus ( in data )

Constructor.

Member Function Documentation

function irdata::assert_fix ( in data )

inherited

Makes the dataset properties consistent with each other.

This is both an assertion routine and a "fixing" routine. The two parts are implemented sequentially, so it will be easy to split this in the future.

The assertion part will do a number of checks and throw an error if there is no hope of making it a consistent dataset. Fatal problems will be:

not empty row fields (listed in the irdata::rowfieldnames read-only property) of different sizes
irdata::fea_x with number of elements different from irdata::nf

The subsewquent fix part may do a number of works on the dataset:

autofill the "classes" vector if it is empty (and create a default class label)
autogenerate the "fea_x" vector if it is empty
add elements to irdata::classlabels if class numbers surpass the number of labels

function irdata::assert_not_nan ( in data )

inherited

Asserts that there is no NaN in data.X.

function irdata::check ( in data )

inherited

Checks if internal variables are synchronized with some troubleshooting.

function irdata::copy_emptyrows ( in data )

inherited

Makes copy with empty fields whose names are in .rowfieldnames Additionally, resets .height

function irdata::do_get_html ( in o )

protectedinherited

HTML inner body.

function irobj::do_get_report ( in o )

protectedinherited

Default report.

function irdata::eliminate_unused_classlabels ( in data )

inherited

retains only labels corresponding to classes that exist in the dataset, and classes are renumbered accordingly

function irobj::extract_log ( in o )

inherited

Parameters

o

Returns: [o, log]

function irobj::get_ancestry	(	in	o,
		in	flag_title
	)

inherited

Parameters

o
flag_title=1

function irobj::get_description	(	in	o,
		in	flag_short
	)

inherited

Returns description string

Precedence according with flag_short:

0: title > short > classtitle
1: short > title > classtitle

Parameters

flag_short=0 I am sealing this to make sure that no class will try to improvise on this function.

function irdata::get_fea_names	(	in	data,
		in	idxs
	)

inherited

Returns the names of the features.

This function checks the fea_names property and if it is empty, it makes feature names on-the-fly using the fea_x property.

Parameters

idxs	Optional list of indexes to be returned

function irdata::get_groupidxs_from_groupcodes	(	in	data,
		in	codes
	)

inherited

Converts group codes to group indexes Indexes will point to the "unique(data.groupcodes)" vector

function irobj::get_html	(	in	o,
		in	flag_stylesheet
	)

inherited

Parameters

flag_stylesheet=1 Whether to include the stylesheet in the HTML

function irobj::get_methodname	(	in	o,
		in	flag_short
	)

inherited

This is used only to compose sequence string e.g. xxx->yyy->zzz

Parameters

flag_short=0

function irdata::get_no_levels ( in data )

inherited

Counts to pre-allocate.

Loops again to fill Returns the number of levels in classlabels

function irdata::get_obsidxs_from_groupidxs	(	in	data,
		in	groupidxs
	)

inherited

Converts group indexes to observation indexes CAUTION: be sure that idxs_codes contains indexes that point to the "unique(data.groupcodes)" vector

function irobj::get_params	(	in	o,
		in	data
	)

inherited

Calls Parameters GUI.

If flag_params, tries uip_<class>.m. If fails, tries uip_<ancestor>.m and so on

function irdata::get_props_to_copy ( in data )

inherited

This is the maximum number of rows of the dataset before something blows.

Mounts X and Y each data row will stand for [s(n) s(n-1) s(n-2) ...]. This way the dot product between the row and the coefficients of a linear filter is a causal convolution. Gets a list with all properties except the ones that will be split

function irobj::get_report ( in o )

inherited

Object reports are plain text. HTML would be cool but c'mon, we don't need that sophistication.

function irdata::get_weights	(	in	data,
		in	exponent
	)

inherited

Gets weights for each class

Weights are inversely proportional to the number of observations in each class.

Weights are normalized, so that their sum equals one

Parameters

exponent =1. Exponent to power all weights before they are normalized to sum=1

function irdata::import_from_struct	(	in	data,
		in	DATA
	)

inherited

Copies structure fields to object fields Contains a dictionary with many old property names for backward compatibility Also works when the input is an object.

function irdata::make_groupnumbers ( in data )

inherited

fills in the groupnumbers property based on the groupcodes property.

function irdata::map_rows	(	in	data,
		in	idxnew
	)

inherited

Maps rows. Single-output version of split_map()

Returns new object

function irdata::mount_from_signal	(	in	signal,
		in	no_inputs,
		in	future
	)

inherited

Populates from a time series.

This function makes X and Y. X will be a Toeplitz matrix.

Inputs:

Parameters

signal	vector s(n)
no_inputs	dimensionality of the input data space (aka number of features or nf)
future	"prediction task", which will be to predict s(n+future)

function get irdata::nc ( in data )

inherited

nc getter

function get irdata::nf ( in data )

inherited

nf getter

function get irdata::no ( in data )

inherited

no getter

function get irdata::no_groups ( in data )

inherited

no_groups getter

function get irdata::nonf ( in data )

inherited

nonf getter

function irdata::select_features	(	in	data,
		in	idxs
	)

inherited

Manual feature selection.

Inputs: idxs: list of column indexes to select, or cell thereof

function irobj::setbatch	(	in	o,
		in	params
	)

inherited

Sets several properties of an object at once.

Parameters

o
params	Cell followint the pattern {'property1', value1, 'property2', value2, ...}

function irdata::split_map	(	in	data,
		in	map,
		in	feamap,
		in	fext
	)

inherited

Splits dataset into one or more datasets using row maps

Parameters

map	1D or 2D cell array of row indexes
feamap	(optional

Return values

out	Matrix of datasets.

function irdata::split_splitidxs ( in data )

inherited

prepares a clone, except for the fields in rowfieldnames

maps the rowfieldnames fields be used or not as necessary and no error will occur. Splits dataset into one or more datasets using its own splitidxs property

Parameters

map	1D or 2D cell array of row indexes

Return values

out	Matrix of datasets.

function irdata::transform_linear	(	in	data,
		in	L,
		in	L_fea_prefix
	)

inherited

irverbose(sprintf('INFO (data_select_features()): # features before: %>d; # features after: %>d.
', nfold, data.nf));

Transforms dataset using loadings matrix L

data.X = data.X*L; data.xlabel = 'Factor'; data.ylabel = 'Score';

Parameters

L[nf][any]	Loadings matrix
L_fea_prefix=[]	Prefix to make new feature names.

function irdata::transpose2 ( in data )

inherited

Changes direction and swaps width and height

This is called "transpose2" because MATLAB objects have a built-in "transpose" already

function get irdata::width ( in data )

inherited

Member Data Documentation

Property irdata::classes

inherited

[no]x[1] vector. Classes. Zero-based (first class is class zero).

Classes may be negative, with special meanings for negative values (see get_negative_meaning.m)

Definition at line 57 of file irdata.m.

Property irdata::classlabels

inherited

Cell of strings. Class labels.

Definition at line 60 of file irdata.m.

Property irobj::classtitle

protectedinherited

Class Title. Should have a descriptive name, as short as possible.

Definition at line 50 of file irobj.m.

Property irobj::color

inherited

=[0, .8, 0]. multipurpose feature, routines may use it for different things. Major use is to change the background of objtool and blockmenu. See also classes_html.m

Definition at line 42 of file irobj.m.

Property irdata::direction

inherited

='ver'. States how the pixels are organized. 'ver': bottom-up, left-right 'hor': left-right, bottom-up

Definition at line 107 of file irdata.m.

Property irdata::fea_names

inherited

(optional) Cell of strings. Name of each feature

Definition at line 80 of file irdata.m.

Property irdata::fea_x

inherited

feature x-axis

Definition at line 77 of file irdata.m.

Property irdata::filename

inherited

Definition at line 70 of file irdata.m.

Property irdata::filetype

inherited

mat or txt

Definition at line 73 of file irdata.m.

Property irobj::flag_params

protectedinherited

=1. (GUI setting) Whether to call a GUI when the block is selected in blockmenu.m . If true, a routine called "uip_"<class name> will be called.

Definition at line 57 of file irobj.m.

Property irobj::flag_ui

protectedinherited

(GUI setting) Whether to "publish" in blockmenu and datatool. Note that a class can be "published" without a GUI (set flag_params=0 in this case, at the class constructor).

Definition at line 60 of file irobj.m.

Property irdata::flags_cell

protectedinherited

Definition at line 128 of file irdata.m.

Property irdata::groupcodes

inherited

(optional) [no]x[1] Cell of strings. Group codes (e.g. patient names)

Definition at line 64 of file irdata.m.

Property irdata::groupnumbers

inherited

For easier access than groupcodes.

Definition at line 115 of file irdata.m.

Property irdata::height

inherited

Height of image. Spectra start counting from the bottom left upwards.

Definition at line 99 of file irdata.m.

Property irobj::moreactions

protectedinherited

(GUI setting) String cell containing names of methods that may be called from the GUIs

Definition at line 63 of file irobj.m.

Property irdata::nc

inherited

number of classes

Definition at line 48 of file irdata.m.

Property irdata::nf

inherited

number of features (i.e., variables)

Definition at line 39 of file irdata.m.

Property irdata::no

inherited

number of "observations" (e.g. spectra)

Definition at line 36 of file irdata.m.

Property irdata::no_groups

inherited

number of groups

Definition at line 45 of file irdata.m.

Property irdata::nonf

inherited

a vector [no, nf]

Definition at line 42 of file irdata.m.

Property irdata::obsids

inherited

Definition at line 117 of file irdata.m.

Property irdata::obsnames

inherited

(optional) [no]x[1] Cell of strings. Observation names (e.g. file names of the individual spectra)

Definition at line 67 of file irdata.m.

Property irdata::rowfieldnames

protectedinherited

fields to be split or merged when dataset is split or merged

Definition at line 126 of file irdata.m.

Property irobj::short

protectedinherited

Short for the method name.

Definition at line 53 of file irobj.m.

Property irdata::splitidxs

inherited

Definition at line 120 of file irdata.m.

Property irobj::title

inherited

Definition at line 38 of file irobj.m.

Property irdata::width

inherited

Width of image. Width is actually calculated as no/height . If result is not integer, an error will occur.

Definition at line 102 of file irdata.m.

Property irdata::X

inherited

[no]x[nf] matrix. Data matrix

Definition at line 52 of file irdata.m.

Property irdata::xname

inherited

x-axis name, defaults to 'Wavenumber (cm^{-1})'

Definition at line 84 of file irdata.m.

Property irdata::xunit

inherited

x-axis unit, defaults to 'cm^{-1}'

Definition at line 87 of file irdata.m.

Property irdata::Y

inherited

Output (instead of classes). For regression instead of classification.

Definition at line 111 of file irdata.m.

Property irdata::yname

inherited

y-axis name, defaults to 'Absorbance'

Definition at line 90 of file irdata.m.

Property irdata::yunit

inherited

y-axis unit, defaults to 'a.u.'

Definition at line 93 of file irdata.m.

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

irdata_clus.m

Detailed Description

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation