org.apache.ctakes.ytex.libsvm

Class LibSVMFormatterFactory.LibSVMFormatter

java.lang.Object

org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter

org.apache.ctakes.ytex.libsvm.LibSVMFormatterFactory.LibSVMFormatter

All Implemented Interfaces:

SparseDataFormatter

Direct Known Subclasses:

SparseMatrixFormatterFactory.SparseMatrixDataFormatter, SVMLightFormatterFactory.SVMLightFormatter

Enclosing class:

LibSVMFormatterFactory

public static class LibSVMFormatterFactory.LibSVMFormatter
extends BaseSparseDataFormatter

Field Summary

Fields inherited from class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter

exportProperties, kernelUtil, labelToClassIndexMap, maxAttributeIndex, nominalAttributeMap, numericAttributeMap, outdir

Fields inherited from interface org.apache.ctakes.ytex.kernel.SparseDataFormatter

ATTR_INSTANCE_ID, SCOPE, SCOPE_FOLD, SCOPE_LABEL

Constructor Summary

Constructors

Constructor and Description
LibSVMFormatterFactory.LibSVMFormatter(KernelUtil kernelUtil)

Method Summary

Methods

Modifier and Type	Method and Description
void	clearFold() clean up fold specific state
void	clearLabel()
protected java.util.List<java.lang.Long>	exportDataForInstances(SparseData bagOfWordsData, java.util.SortedMap<java.lang.Long,java.lang.String> instanceClassMap, classToIndexMap, java.io.BufferedWriter wData, java.io.BufferedWriter wId)
protected void	exportDataForLabel(java.lang.String filename, java.lang.String idFilename, SparseData bagOfWordsData, java.util.SortedMap<java.lang.Long,java.lang.String> instanceClassMap, classToIndexMap) Export data file and id file
void	exportFold(SparseData sparseData, java.util.SortedMap<java.lang.Long,java.lang.String> instanceClassMap, boolean train, java.lang.String label, java.lang.Integer run, java.lang.Integer fold) export the given train/test set
void	initializeExport(InstanceData instanceLabel, java.util.Properties properties, SparseData sparseData) get needed properties out of outdir.
void	initializeFold(SparseData sparseData, java.lang.String label, java.lang.Integer run, java.lang.Integer fold, java.util.SortedMap<java.lang.Boolean,java.util.SortedMap<java.lang.Long,java.lang.String>> foldInstanceLabelMap) write a file with the attribute names corresponding to the indices in the libsvm data file
void	initializeLabel(java.lang.String label, java.util.SortedMap<java.lang.Integer,java.util.SortedMap<java.lang.Integer,java.util.SortedMap<java.lang.Boolean,java.util.SortedMap<java.lang.Long,java.lang.String>>>> labelInstances, java.util.Properties properties, SparseData sparseData)
protected void	writeLibsvmLine(java.io.BufferedWriter wData, java.util.SortedMap<java.lang.Integer,java.lang.Double> instanceValues)

Methods inherited from class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter

addNumericAttribute, exportAttributeNames, exportAttributeNames, exportSparseMatrix, exportSparseRow, getSparseLineValues, updateLabelClassMapTransductive

Methods inherited from class java.lang.Object

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

Constructor Detail

LibSVMFormatterFactory.LibSVMFormatter

public LibSVMFormatterFactory.LibSVMFormatter(KernelUtil kernelUtil)

Method Detail

initializeExport

public void initializeExport(InstanceData instanceLabel,
                    java.util.Properties properties,
                    SparseData sparseData)
                      throws java.io.IOException

Description copied from class: BaseSparseDataFormatter

get needed properties out of outdir. convert class names into integers for libsvm. attempt to parse the class name into an integer. if this fails, use an index that we increment. index corresponds to class name's alphabetical order.

Specified by:

initializeExport in interface SparseDataFormatter

Overrides:

initializeExport in class BaseSparseDataFormatter

Throws:

java.io.IOException

initializeLabel

public void initializeLabel(java.lang.String label,
                   java.util.SortedMap<java.lang.Integer,java.util.SortedMap<java.lang.Integer,java.util.SortedMap<java.lang.Boolean,java.util.SortedMap<java.lang.Long,java.lang.String>>>> labelInstances,
                   java.util.Properties properties,
                   SparseData sparseData)
                     throws java.io.IOException

Throws:

java.io.IOException

initializeFold

public void initializeFold(SparseData sparseData,
                  java.lang.String label,
                  java.lang.Integer run,
                  java.lang.Integer fold,
                  java.util.SortedMap<java.lang.Boolean,java.util.SortedMap<java.lang.Long,java.lang.String>> foldInstanceLabelMap)
                    throws java.io.IOException

write a file with the attribute names corresponding to the indices in the libsvm data file

Throws:

java.io.IOException

exportFold

public void exportFold(SparseData sparseData,
              java.util.SortedMap<java.lang.Long,java.lang.String> instanceClassMap,
              boolean train,
              java.lang.String label,
              java.lang.Integer run,
              java.lang.Integer fold)
                throws java.io.IOException

export the given train/test set

Throws:

java.io.IOException

exportDataForLabel

protected void exportDataForLabel(java.lang.String filename,
                      java.lang.String idFilename,
                      SparseData bagOfWordsData,
                      java.util.SortedMap<java.lang.Long,java.lang.String> instanceClassMap,
                       classToIndexMap)
                           throws java.io.IOException

Export data file and id file

Parameters:

filename -

idFilename -

bagOfWordsData -

instanceClassMap -

numericAttributeMap -

nominalAttributeMap -

label -

Throws:

java.io.IOException

exportDataForInstances

protected java.util.List<java.lang.Long> exportDataForInstances(SparseData bagOfWordsData,
                                                    java.util.SortedMap<java.lang.Long,java.lang.String> instanceClassMap,
                                                     classToIndexMap,
                                                    java.io.BufferedWriter wData,
                                                    java.io.BufferedWriter wId)
                                                         throws java.io.IOException

Parameters:

bagOfWordsData - data to be exported

instanceClassMap - instance ids - class name map

classToIndexMap - class name - class id map

wData - file to write data to

wId - file to write ids to

Returns:

list of instance ids corresponding to order with which they were exported

Throws:

java.io.IOException

writeLibsvmLine

protected void writeLibsvmLine(java.io.BufferedWriter wData,
                   java.util.SortedMap<java.lang.Integer,java.lang.Double> instanceValues)
                        throws java.io.IOException

Throws:

java.io.IOException

clearFold

public void clearFold()

clean up fold specific state

clearLabel

public void clearLabel()