IRootLab
An Open-Source MATLAB toolbox for vibrational biospectroscopy
cascade_decidergrag Class Reference

Detailed Description

Cascade block: decider -> grag_classes_vote.

Definition at line 2 of file cascade_decidergrag.m.

+ Inheritance diagram for cascade_decidergrag:
+ Collaboration diagram for cascade_decidergrag:

Public Member Functions

function cascade_decidergrag ()
 
function get L (in o)
 
function get L_fea_x (in o)
 
function get xname (in o)
 
function get xunit (in o)
 
function get yname (in o)
 
function get yunit (in o)
 
function get classlabels (in o)
 
function get v (in o)
 Retrieves v from last block. More...
 
function get decisionthreshold (in o)
 Retrieves decisionthreshold from the decider that if finds. More...
 
function get no_blocks (in o)
 
function extract_fcon_linear_fixed (in o)
 Extracts fcon_linear_fixed with same Loadings Matrix. More...
 
function get_L_fea_x (in o)
 
function get_xname (in o)
 
function get_xunit (in o)
 Feature names: takes the xname property from the first linear block. More...
 
function get_yname (in o)
 
function get_yunit (in o)
 
function get_methodname (in o, in flag_short)
 Calls get_methodname() for all blocks. More...
 
function get_L_fea_names (in o, in idxs)
 
function get_loadings (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_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 blocks
 Cell of block objects. More...
 
Property flag_crossc
 
Property sgs_crossc
 SGS to do the cross-calculations when necessary. If needed and empty, a default one will be used. More...
 
Property L
 
Property L_fea_names
 Loadings feature names. fcon_linear mimicking. More...
 
Property L_fea_x
 Feature x-axis. fcon_linear mimicking. Retrieves the L_fea_x from the first block. More...
 
Property xname
 x-axis name. fcon_linear mimicking. Retrieves the xname from the first block. More...
 
Property xunit
 
Property yname
 
Property yunit
 
Property classlabels
 Class labels. clssr mimicking. Retrieves the classlabels property from the last block. More...
 
Property v
 Feature indexes. fsel mimicking. Retrieves the v property from the last block. More...
 
Property decisionthreshold
 
Property title
 
Property color
 

Protected Member Functions

function assert_checked (in o)
 BLock needs to keep up-to-date with contents. More...
 
function do_check (in o)
 
function do_boot (in o)
 Boots every encapsulated block. More...
 
function do_train (in o, in data)
 
function do_use (in o, in data)
 
function assert_fcon_linear (in o)
 Makes sure that the block can mimic a linear block. More...
 
function get_linear1 (in o)
 Retrieves the first linear block. More...
 
function do_get_report (in o)
 
function do_get_html (in o)
 Abstract. HTML inner body. More...
 

Protected Attributes

Property no_blocks
 Number of blocks. More...
 
Property flag_fcon_linear
 Whether the block is able to mimic a fcon_linear. This is calculated at boot time. More...
 
Property flag_decider
 Whether the block is able to mimic a decider. This is calculated at boot time. More...
 
Property idx_linear1
 Index of first linear block. This is calculated at boot time. More...
 
Property idx_decider
 Index of decider. This is calculated at boot time. More...
 
Property flag_checked
 
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 cascade_decidergrag::cascade_decidergrag ( )

Member Function Documentation

function block_cascade_base::assert_checked ( in  o)
protectedinherited

BLock needs to keep up-to-date with contents.

function block_cascade_base::assert_fcon_linear ( in  o)
protectedinherited

Makes sure that the block can mimic a linear block.

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 get block_cascade_base::classlabels ( in  o)
inherited

Other getters call yet another function, I don't know exactly why. I won't do this here because this may be called many times.

function get block_cascade_base::decisionthreshold ( in  o)
inherited

Retrieves decisionthreshold from the decider that if finds.

function block_cascade_base::do_boot ( in  o)
protectedinherited

Boots every encapsulated block.

function block_cascade_base::do_check ( in  o)
protectedinherited
function irobj::do_get_html ( in  o)
protectedinherited

Abstract. HTML inner body.

function block_cascade_base::do_get_report ( in  o)
protectedinherited
function block_cascade_base::do_train ( in  o,
in  data 
)
protectedinherited

Trains every encapsulated block

Todo:
think about stacked generalization
function block_cascade_base::do_use ( in  o,
in  data 
)
protectedinherited

output of (k-1)-th block is inputted into k-th block. Final output is the output of the end-th block.

Skips any blmisc_rowsout block (outlier remover)

function block_cascade_base::extract_fcon_linear_fixed ( in  o)
inherited

Extracts fcon_linear_fixed with same Loadings Matrix.

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=0I 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=1Whether to include the stylesheet in the HTML
function block_cascade_base::get_L_fea_names ( in  o,
in  idxs 
)
inherited

Mimicking a fcon_linear::get_L_fea_names()

Calls the get_L_fea_names from the first block that has this method (SEARCHING BACKWARDS)

function block_cascade_base::get_L_fea_x ( in  o)
inherited
function block_cascade_base::get_linear1 ( in  o)
protectedinherited

Retrieves the first linear block.

function block_cascade_base::get_loadings ( in  o)
inherited

Cascades blocks' loadings matrices. Works only if one or all blocks provide one loadings matrix of course, i.e., they all represent linear transforms.

function block_cascade_base::get_methodname ( in  o,
in  flag_short 
)
inherited

Calls get_methodname() for all blocks.

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 block_cascade_base::get_xname ( in  o)
inherited
function block_cascade_base::get_xunit ( in  o)
inherited

Feature names: takes the xname property from the first linear block.

function block_cascade_base::get_yname ( in  o)
inherited

y-name: takes the yname property from the last block that has it

Returns
yname. Defaults to an empty string.
function block_cascade_base::get_yunit ( in  o)
inherited

y-unit: takes the yunit property from the last block that has it

Returns
yunit. Defaults to an empty string.
function get block_cascade_base::L ( in  o)
inherited
function get block_cascade_base::L_fea_x ( in  o)
inherited
function get block_cascade_base::no_blocks ( in  o)
inherited
function irobj::setbatch ( in  o,
in  params 
)
inherited

Sets several properties of an object at once.

Parameters
o
paramsCell 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.

function get block_cascade_base::v ( in  o)
inherited

Retrieves v from last block.

function get block_cascade_base::xname ( in  o)
inherited
function get block_cascade_base::xunit ( in  o)
inherited
function get block_cascade_base::yname ( in  o)
inherited
function get block_cascade_base::yunit ( in  o)
inherited

Member Data Documentation

Property block_cascade_base::blocks
inherited

Cell of block objects.

Definition at line 20 of file block_cascade_base.m.

Property block_cascade_base::classlabels
inherited

Class labels. clssr mimicking. Retrieves the classlabels property from the last block.

Definition at line 57 of file block_cascade_base.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 block_cascade_base::decisionthreshold
inherited

Decision threshold. decider mimicking. Retriever the decisionthreshold property from some decider it finds along the blocks

Definition at line 64 of file block_cascade_base.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_cascade_base::flag_checked
protectedinherited

Definition at line 84 of file block_cascade_base.m.

Property block_cascade_base::flag_crossc
inherited

=1. Whether to cross-calculate outputs when it is the case. The case is: in training; and the component block is level 1 (trainable); and the component block is not the last block. If flag_crossc is false, the same dataset will be used to train and to calculate the block output.

Definition at line 25 of file block_cascade_base.m.

Property block_cascade_base::flag_decider
protectedinherited

Whether the block is able to mimic a decider. This is calculated at boot time.

Definition at line 75 of file block_cascade_base.m.

Property block_cascade_base::flag_fcon_linear
protectedinherited

Whether the block is able to mimic a fcon_linear. This is calculated at boot time.

Definition at line 72 of file block_cascade_base.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_cascade_base::idx_decider
protectedinherited

Index of decider. This is calculated at boot time.

Definition at line 81 of file block_cascade_base.m.

Property block_cascade_base::idx_linear1
protectedinherited

Index of first linear block. This is calculated at boot time.

Definition at line 78 of file block_cascade_base.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 block_cascade_base::L
inherited

Loadings matrix. fcon_linear mimicking. Calculates loadings matrix by multiplying (L = block1.L*block2.L*...).

Definition at line 37 of file block_cascade_base.m.

Property block_cascade_base::L_fea_names
inherited

Loadings feature names. fcon_linear mimicking.

Definition at line 42 of file block_cascade_base.m.

Property block_cascade_base::L_fea_x
inherited

Feature x-axis. fcon_linear mimicking. Retrieves the L_fea_x from the first block.

Definition at line 45 of file block_cascade_base.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 block_cascade_base::no_blocks
protectedinherited

Number of blocks.

Definition at line 69 of file block_cascade_base.m.

Property block_cascade_base::sgs_crossc
inherited

SGS to do the cross-calculations when necessary. If needed and empty, a default one will be used.

Definition at line 28 of file block_cascade_base.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.

Property block_cascade_base::v
inherited

Feature indexes. fsel mimicking. Retrieves the v property from the last block.

Definition at line 60 of file block_cascade_base.m.

Property block_cascade_base::xname
inherited

x-axis name. fcon_linear mimicking. Retrieves the xname from the first block.

Definition at line 48 of file block_cascade_base.m.

Property block_cascade_base::xunit
inherited

Definition at line 50 of file block_cascade_base.m.

Property block_cascade_base::yname
inherited

Definition at line 52 of file block_cascade_base.m.

Property block_cascade_base::yunit
inherited

Definition at line 54 of file block_cascade_base.m.


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