Package weka.filters.unsupervised.attribute

Class OuterProductAnalysis

java.lang.Object

weka.filters.Filter

weka.filters.SimpleFilter

weka.filters.SimpleStreamFilter

weka.filters.unsupervised.attribute.OuterProductAnalysis

All Implemented Interfaces:

Serializable, weka.core.CapabilitiesHandler, weka.core.CapabilitiesIgnorer, weka.core.CommandlineRunnable, weka.core.OptionHandler, weka.core.RevisionHandler, weka.core.TechnicalInformationHandler, weka.filters.StreamableFilter, weka.filters.UnsupervisedFilter

public class OuterProductAnalysis
extends weka.filters.SimpleStreamFilter
implements weka.filters.UnsupervisedFilter, weka.core.TechnicalInformationHandler

Performs Outer Product Analysis (OPA).

For more information, see:
Fabricio S.Terra, Raphael A.Viscarra Rossel, Jose A.M.Dematte (2019). Spectral fusion by Outer Product Analysis (OPA) to improve predictions of soil organic C. Geoderma. 335:35-46. URL https://doi.org/10.1016/j.geoderma.2018.08.005.

Valid options are:

 -first <regexp>
  The first attribute range to use.
  (default: amplitude-.*)

 -second <regexp>
  The second attribute range to use.
  (default: amplitude-.*)

 -prefix <string>
  The prefix to use for the generated attributes.
  (default: opa-)

 -output-debug-info
  If set, filter is run in debug mode and
  may output additional info to the console

 -do-not-check-capabilities
  If set, filter capabilities are not checked before filter is built
  (use with caution).

Author:

fracpete (fracpete at waikato dot ac dot nz)

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static String	DEFAULT_PREFIX
static String	DEFAULT_REGEXP
protected String	m_AttributePrefix	the prefix to use for the generated attributes.
protected int[]	m_First	the positions of the first range.
protected adams.core.base.BaseRegExp	m_FirstRange	the first range of the attributes to use.
protected int[]	m_Positions	the new positions for the attributes.
protected int[]	m_Second	the positions of the second range.
protected adams.core.base.BaseRegExp	m_SecondRange	the second range of the attributes to use.
protected int[]	m_Types	the types of the attributes.

Fields inherited from class weka.filters.Filter

m_Debug, m_DoNotCheckCapabilities, m_FirstBatchDone, m_InputRelAtts, m_InputStringAtts, m_NewBatch, m_OutputRelAtts, m_OutputStringAtts

Constructor Summary

Constructors

Constructor	Description
OuterProductAnalysis()

Method Summary

Modifier and Type	Method	Description
String	attributePrefixTipText()	Returns the tip text for this property.
protected weka.core.Instances	determineOutputFormat(weka.core.Instances inputFormat)	Determines the output format based on the input format and returns this.
String	firstRangeTipText()	Returns the tip text for this property.
String	getAttributePrefix()	Returns the prefix to use for the generated attributes.
weka.core.Capabilities	getCapabilities()	Returns the Capabilities of this filter.
adams.core.base.BaseRegExp	getFirstRange()	Returns the first attribute range to use (regular expression on attribute names).
String[]	getOptions()	Gets the current settings of the Classifier.
String	getRevision()	Returns the revision string.
adams.core.base.BaseRegExp	getSecondRange()	Returns the second attribute range to use (regular expression on attribute names).
weka.core.TechnicalInformation	getTechnicalInformation()	Returns an instance of a TechnicalInformation object, containing detailed information about the technical background of this class, e.g., paper reference or book this class is based on.
String	globalInfo()	Returns a string describing this classifier.
Enumeration<weka.core.Option>	listOptions()	Returns an enumeration describing the available options.
static void	main(String[] args)	Main method for testing this class.
protected weka.core.Instance	process(weka.core.Instance instance)	processes the given instance (may change the provided instance) and returns the modified version.
String	secondRangeTipText()	Returns the tip text for this property.
void	setAttributePrefix(String value)	Sets the second attribute range to use (regular expression on attribute names).
void	setFirstRange(adams.core.base.BaseRegExp value)	Sets the first attribute range to use (regular expression on attribute names).
void	setOptions(String[] options)	Parses a given list of options.
void	setSecondRange(adams.core.base.BaseRegExp value)	Sets the prefix to use for the generated attributes.

Methods inherited from class weka.filters.SimpleStreamFilter

batchFinished, hasImmediateOutputFormat, input, preprocess, process

Methods inherited from class weka.filters.SimpleFilter

reset, setInputFormat

Methods inherited from class weka.filters.Filter

batchFilterFile, bufferInput, copyValues, copyValues, debugTipText, doNotCheckCapabilitiesTipText, filterFile, flushInput, getCapabilities, getDebug, getDoNotCheckCapabilities, getInputFormat, getOutputFormat, initInputLocators, initOutputLocators, inputFormatPeek, isFirstBatchDone, isNewBatch, isOutputFormatDefined, makeCopies, makeCopy, mayRemoveInstanceAfterFirstBatchDone, numPendingOutput, output, outputFormatPeek, outputPeek, postExecution, preExecution, push, push, resetQueue, run, runFilter, setDebug, setDoNotCheckCapabilities, setOutputFormat, testInputFormat, toString, useFilter, wekaStaticWrapper

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

DEFAULT_REGEXP

public static final String DEFAULT_REGEXP

See Also:

Constant Field Values

DEFAULT_PREFIX

public static final String DEFAULT_PREFIX

See Also:

Constant Field Values

m_FirstRange

protected adams.core.base.BaseRegExp m_FirstRange

the first range of the attributes to use.

m_SecondRange

protected adams.core.base.BaseRegExp m_SecondRange

the second range of the attributes to use.

m_AttributePrefix

protected String m_AttributePrefix

the prefix to use for the generated attributes.

m_First

protected int[] m_First

the positions of the first range.

m_Second

protected int[] m_Second

the positions of the second range.

m_Positions

protected int[] m_Positions

the new positions for the attributes.

m_Types

protected int[] m_Types

the types of the attributes.

Constructor Detail

OuterProductAnalysis

public OuterProductAnalysis()

Method Detail

globalInfo

public String globalInfo()

Returns a string describing this classifier.

Specified by:

globalInfo in class weka.filters.SimpleFilter

Returns:

a description of the classifier suitable for displaying in the explorer/experimenter gui

getTechnicalInformation

public weka.core.TechnicalInformation getTechnicalInformation()

Returns an instance of a TechnicalInformation object, containing detailed information about the technical background of this class, e.g., paper reference or book this class is based on.

Specified by:

getTechnicalInformation in interface weka.core.TechnicalInformationHandler

Returns:

the technical information about this class

listOptions

public Enumeration<weka.core.Option> listOptions()

Returns an enumeration describing the available options.

Specified by:

listOptions in interface weka.core.OptionHandler

Overrides:

listOptions in class weka.filters.Filter

Returns:

an enumeration of all the available options.

setOptions

public void setOptions(String[] options)
                throws Exception

Parses a given list of options.

Specified by:

setOptions in interface weka.core.OptionHandler

Overrides:

setOptions in class weka.filters.Filter

Parameters:

options - the list of options as an array of strings

Throws:

Exception - if an option is not supported

getOptions

public String[] getOptions()

Gets the current settings of the Classifier.

Specified by:

getOptions in interface weka.core.OptionHandler

Overrides:

getOptions in class weka.filters.Filter

Returns:

an array of strings suitable for passing to setOptions

setFirstRange

public void setFirstRange(adams.core.base.BaseRegExp value)

Sets the first attribute range to use (regular expression on attribute names).

Parameters:

value - the expression

getFirstRange

public adams.core.base.BaseRegExp getFirstRange()

Returns the first attribute range to use (regular expression on attribute names).

Returns:

the expression

firstRangeTipText

public String firstRangeTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the GUI or for listing the options.

setSecondRange

public void setSecondRange(adams.core.base.BaseRegExp value)

Sets the prefix to use for the generated attributes.

Parameters:

value - the expression

getSecondRange

public adams.core.base.BaseRegExp getSecondRange()

Returns the second attribute range to use (regular expression on attribute names).

Returns:

the expression

secondRangeTipText

public String secondRangeTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the GUI or for listing the options.

setAttributePrefix

public void setAttributePrefix(String value)

Sets the second attribute range to use (regular expression on attribute names).

Parameters:

value - the prefix

getAttributePrefix

public String getAttributePrefix()

Returns the prefix to use for the generated attributes.

Returns:

the prefix

attributePrefixTipText

public String attributePrefixTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the GUI or for listing the options.

getCapabilities

public weka.core.Capabilities getCapabilities()

Returns the Capabilities of this filter. Derived filters have to override this method to enable capabilities.

Specified by:

getCapabilities in interface weka.core.CapabilitiesHandler

Overrides:

getCapabilities in class weka.filters.Filter

Returns:

the capabilities of this object

See Also:

Capabilities

determineOutputFormat

protected weka.core.Instances determineOutputFormat(weka.core.Instances inputFormat)
                                             throws Exception

Determines the output format based on the input format and returns this. In case the output format cannot be returned immediately, i.e., hasImmediateOutputFormat() returns false, then this method will called from batchFinished() after the call of preprocess(Instances), in which, e.g., statistics for the actual processing step can be gathered.

Specified by:

determineOutputFormat in class weka.filters.SimpleStreamFilter

Parameters:

inputFormat - the input format to base the output format on

Returns:

the output format

Throws:

Exception - in case the determination goes wrong

process

protected weka.core.Instance process(weka.core.Instance instance)
                              throws Exception

processes the given instance (may change the provided instance) and returns the modified version.

Specified by:

process in class weka.filters.SimpleStreamFilter

Parameters:

instance - the instance to process

Returns:

the modified data

Throws:

Exception - in case the processing goes wrong

getRevision

public String getRevision()

Returns the revision string.

Specified by:

getRevision in interface weka.core.RevisionHandler

Overrides:

getRevision in class weka.filters.Filter

Returns:

the revision

main

public static void main(String[] args)

Main method for testing this class.

Parameters:

args - should contain arguments to the filter: use -h for help