Detailed Description

Paul Bassan's Resonant Mie Scattering Correction.

References:

[1] Paul Bassan, Achim Kohler, Harald Martens, Joe Lee, Hugh J. Byrne, Paul Dumas, Ehsan Gazi, Michael Brown, Noel Clarke, Peter Gardner. Resonant Mie Scattering (RMieS) Correction of Infrared Spectra from Highly Scattering Biological Samples (Analyst, DOI:10.1039/B921056C)

[2] Paul Bassan, Hugh J. Byrne, Frank Bonnier, Joe Lee, Paul Dumas, Peter Gardner. Resonant Mie scattering in Infrared spectroscopy of biological materials – understanding the “dispersion artefact” Analyst, 134 (2009), 1586—1593

[3] Kohler, A.; Sule-Suso, J.; Sockalingum, G. D.; Tobin, M.; Bahrami, F.; Yang, Y.; Pijanka, J.; Dumas, P.; Cotte, M.; Martens, H. "Estimating and correcting Mie scattering in synchrotron based microscopic FTIR spectra by extended multiplicative signal correction (EMSC). " Appl Spectrosc 2008, 62, 259-266.

[4] Martens, H.; Stark, E. "Extended Multiplicative Signal Correction and Spectral Interference Subtraction - New Preprocessing Methods for near- Infrared Spectroscopy." Journal of Pharmaceutical and Biomedical Analysis 1991, 9, 625-635.

See also: uip_pre_bc_rmiesc.m

Definition at line 13 of file pre_bc_rmiesc.m.

Inheritance diagram for pre_bc_rmiesc:

Collaboration diagram for pre_bc_rmiesc:

Public Member Functions
function	pre_bc_rmiesc (in o)

function	get_grades (in o, in params)
	Abstract. Method to get the per-feature grades. BMTool stuff. More...

function	get_gradeslegend (in o, in params)
	Abstract. Method to get block title based on passed parameters. BMTool stuff. More...

function	use (in o, in data)
	Applies block to data. More...

function	train (in o, in data, in varargin)
	Trains block. More...

function	boot (in o)
	Configures the structure to deal with new type of data. 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	options

	Property

Property	title

Property	color

Protected Member Functions
function	do_use (in o, in data)

function	do_train (in o, in data)

function	do_boot (in o)
	Boots the block. More...

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

function	do_get_html (in o)
	Abstract. HTML inner body. More...

Protected Attributes
Property	inputclass

Property	flag_bootable
	=0. (High-Level setting and internal function) Whether or not the block is bootable. More...

Property	flag_trainable
	=0. (High-Level + internal function). Whether or not the block can be trained, or completely non-data-based. More...

Property	flag_incrtrain

Property	flag_fixednf
	=1. (internal function) If true, dataset number of features will be checked upon training and using. Ignored if o.flag_trainable is 0. More...

Property	flag_fixedno
	=0. (internal function) If true, dataset number of observations will be checked upon training and using. Ignored if o.flag_trainable is 0. More...

Property	flag_multiin
	=0. (High-Level setting (gencode)) Whether block allows/expects multiple objects as input. More...

Property	flag_out
	=1. (High-Level setting (gencode)) Whether the block generates any output at all (counterexample: vis blocks) More...

Property	flag_train_inliers_only

Property	flag_train_require_inliers

Property	nf
	=-1. Number of features. Cleared at boot(), assigned or reinforced at train(). More...

Property	no
	=-1. Number of observations. More...

Property	flag_trained
	=0. Set to 1 by train() if training is successful; set back to 0 after booting. More...

Property	flag_booted
	=0. Set to 1 by boot() after booting the block More...

Property	time_train
	Trainings time. More...

Property	time_use
	Use time. More...

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 pre_bc_rmiesc::pre_bc_rmiesc ( in o )

Member Function Documentation

function block::boot ( in o )

inherited

Configures the structure to deal with new type of data.

Booting accounts for clearing any recordings; model structure; stored data etc from the object so that it can be re-used anew.

function block::do_boot ( in o )

protectedinherited

Boots the block.

Abstract. Booting accounts for clearing any recordings; model structure; stored data etc from the object so that it can be re-used anew.

function irobj::do_get_html ( in o )

protectedinherited

Abstract. HTML inner body.

function irobj::do_get_report ( in o )

protectedinherited

Default report.

function block::do_train	(	in	o,
		in	data
	)

protectedinherited

function pre_bc_rmiesc::do_use	(	in	o,
		in	data
	)

protected

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 block::get_grades	(	in	o,
		in	params
	)

inherited

Abstract. Method to get the per-feature grades. BMTool stuff.

function block::get_gradeslegend	(	in	o,
		in	params
	)

inherited

Abstract. Method to get block title based on passed parameters. BMTool stuff.

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 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 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 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 block::train	(	in	o,
		in	data,
		in	varargin
	)

inherited

Trains block.

function block::use	(	in	o,
		in	data
	)

inherited

Applies block to data.

Member Data Documentation

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 block::flag_bootable

protectedinherited

=0. (High-Level setting and internal function) Whether or not the block is bootable.

Definition at line 14 of file block.m.

Property block::flag_booted

protectedinherited

=0. Set to 1 by boot() after booting the block

Definition at line 69 of file block.m.

Property block::flag_fixednf

protectedinherited

=1. (internal function) If true, dataset number of features will be checked upon training and using. Ignored if o.flag_trainable is 0.

Definition at line 28 of file block.m.

Property block::flag_fixedno

protectedinherited

=0. (internal function) If true, dataset number of observations will be checked upon training and using. Ignored if o.flag_trainable is 0.

Definition at line 31 of file block.m.

Property block::flag_incrtrain

protectedinherited

=0. (internal function). Whether or not the block accepts incremental training. The meaning is:

If YES, it means that the block can adapt/evolve everytime its train() method is called
If NO, the block can be trained only once, and calling its train() method many times can lead to unpredictable results

Definition at line 23 of file block.m.

Property block::flag_multiin

protectedinherited

=0. (High-Level setting (gencode)) Whether block allows/expects multiple objects as input.

Definition at line 35 of file block.m.

Property block::flag_out

protectedinherited

=1. (High-Level setting (gencode)) Whether the block generates any output at all (counterexample: vis blocks)

Definition at line 38 of file block.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 block::flag_train_inliers_only

protectedinherited

If true, train() will pass on to do_train() a dataset with inliers only. If this flag is true, flag_train_require_inliers will be ignored, because flag_train_inliers_only being true is one way to solve the "inliers requirement".

Definition at line 46 of file block.m.

Property block::flag_train_require_inliers

protectedinherited

=1. If true, train() will give an error if the dataset has outliers. This is true by default, because the developer should be aware of outliers being inputted into a training algorithm.

Definition at line 51 of file block.m.

Property block::flag_trainable

protectedinherited

=0. (High-Level + internal function). Whether or not the block can be trained, or completely non-data-based.

Definition at line 17 of file block.m.

Property block::flag_trained

protectedinherited

=0. Set to 1 by train() if training is successful; set back to 0 after booting.

Definition at line 66 of file block.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 block::inputclass

protectedinherited

='irdata'. (High-Level setting) Class or classes (can be string or cell of strings) that the block can deal with. Allows for objtool and datatool to know (when appropriate) which blocks are applicable to the selected object(s).

Definition at line 11 of file block.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 block::nf

protectedinherited

=-1. Number of features. Cleared at boot(), assigned or reinforced at train().

Definition at line 60 of file block.m.

Property block::no

protectedinherited

=-1. Number of observations.

Definition at line 63 of file block.m.

Property pre_bc_rmiesc::options

Definition at line 18 of file pre_bc_rmiesc.m.

pre_bc_rmiesc::Property

Definition at line 20 of file pre_bc_rmiesc.m.

Property irobj::short

protectedinherited

Short for the method name.

Definition at line 53 of file irobj.m.

Property block::time_train

protectedinherited

Trainings time.

Definition at line 73 of file block.m.

Property block::time_use

protectedinherited

Use time.

Definition at line 76 of file block.m.

Property irobj::title

inherited

Definition at line 38 of file irobj.m.

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

pre_bc_rmiesc.m

Detailed Description

References:

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation