/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -folds <folds>
* The number of folds for splitting the training set into
* train and test set. The first fold is always the training
* set. With '-V' you can invert this, i.e., instead of 20/80
* for 5 folds you'll get 80/20.
* (default 5)</pre>
*
* <pre> -V
* Inverts the fold selection, i.e., instead of using the first
* fold for the training set it is used for test set and the
* remaining folds for training.</pre>
*
* <pre> -verbose
* Whether to print some more information during building the
* classifier.
* (default is off)</pre>
*
* <pre> -insight
* Whether to use the labels of the original test set for more
* statistics (not used for learning!).
* (default is off)</pre>
*
* <pre> -S <num>
* Random number seed.
* (default 1)</pre>
*
* <pre> -D
* If set, classifier is run in debug mode and
* may output additional info to the console</pre>
*
* <pre> -naive
* Uses a sorted list (ordered according to distance) instead of the
* KDTree for finding the neighbors.
* (default is KDTree)</pre>
*
* <pre> -I
* Weight neighbours by the inverse of their distance
* (use when k > 1)</pre>
*
* <pre> -F
* Weight neighbours by 1 - their distance
* (use when k > 1)</pre>
*
* <pre> -K <number of neighbors>
* Number of nearest neighbours (k) used in classification.
* (Default = 1)</pre>
*
* <pre> -A
* The nearest neighbour search algorithm to use (default: LinearNN).
* </pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
super.setOptions(options);
setUseNaiveSearch(Utils.getFlag("naive", options));
m_Classifier.setOptions(options);
m_KNN = m_Classifier.getKNN(); // backup KNN
m_Classifier.setCrossValidate(true); // always on!
m_Classifier.setWindowSize(0); // always off!
m_Classifier.setMeanSquared(false); // always off!
}
/**
* Parses a given list of options. Valid options are:
*
* <p>-D <br>
* If set, clusterer is run in debug mode and may output additional info to the console.
*
* <p>-do-not-check-capabilities <br>
* If set, clusterer capabilities are not checked before clusterer is built (use with caution).
*
* <p>
*
* @param options the list of options as an array of strings
* @exception Exception if an option is not supported
*/
@Override
public void setOptions(String[] options) throws Exception {
Option.setOptionsForHierarchy(options, this, AbstractClusterer.class);
setDebug(Utils.getFlag("output-debug-info", options));
setDoNotCheckCapabilities(Utils.getFlag("do-not-check-capabilities", options));
}
/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -find <regexp>
* The regular expression that the attribute names must match.
* (default: ([\s\S]+))</pre>
*
* <pre> -replace <string>
* The string to replace the regular expression of matching attributes with.
* Cannot be used in conjunction with '-remove'.
* (default: $0)</pre>
*
* <pre> -remove
* In case the matching string needs to be removed instead of replaced.
* Cannot be used in conjunction with '-replace <string>'.
* (default: off)</pre>
*
* <pre> -all
* Replaces all occurrences instead of just the first.
* (default: only first occurrence)</pre>
*
* <pre> -R <range>
* The attribute range to work on.
* This is a comma separated list of attribute indices, with "first" and "last" valid values.
* Specify an inclusive range with "-".
* E.g: "first-3,5,6-10,last".
* (default: first-last)</pre>
*
* <pre> -V
* Inverts the attribute selection range.
* (default: off)</pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
String tmpStr;
tmpStr = Utils.getOption("find", options);
if (tmpStr.length() != 0) setFind(tmpStr);
else setFind("([\\s\\S]+)");
if (Utils.getFlag("remove", options)) {
setReplace("");
} else {
tmpStr = Utils.getOption("replace", options);
if (tmpStr.length() > 0) setReplace(tmpStr);
else setReplace("$0");
}
setReplaceAll(Utils.getFlag("all", options));
tmpStr = Utils.getOption("R", options);
if (tmpStr.length() != 0) setAttributeIndices(tmpStr);
else setAttributeIndices("first-last");
setInvertSelection(Utils.getFlag("V", options));
if (getInputFormat() != null) setInputFormat(getInputFormat());
}
/**
* Parses a given list of options controlling the behaviour of this object. Valid options are:
*
* <p>-l "directory name"<br>
* Specifies name of directory.
*
* <p>-m "model name"<br>
* Specifies name of model.
*
* <p>-e "encoding"<br>
* Specifies encoding.
*
* <p>-n<br>
* Specifies number of phrases to be output (default: 5).
*
* <p>-d<br>
* Turns debugging mode on.
*
* <p>-a<br>
* Also write stemmed phrase and score into ".key" file.
*
* <p>
*
* @param options the list of options as an array of strings
* @exception Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
String dirName = Utils.getOption('l', options);
if (dirName.length() > 0) {
setDirName(dirName);
} else {
setDirName(null);
throw new Exception("Name of directory required argument.");
}
String modelName = Utils.getOption('m', options);
if (modelName.length() > 0) {
setModelName(modelName);
} else {
setModelName(null);
throw new Exception("Name of model required argument.");
}
String encoding = Utils.getOption('e', options);
if (encoding.length() > 0) {
setEncoding(encoding);
} else {
setEncoding("default");
}
String numPhrases = Utils.getOption('n', options);
if (numPhrases.length() > 0) {
setNumPhrases(Integer.parseInt(numPhrases));
} else {
setNumPhrases(5);
}
setDebug(Utils.getFlag('d', options));
setAdditionalInfo(Utils.getFlag('a', options));
Utils.checkForRemainingOptions(options);
}
/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -R <col1,col2-col4,...>
* Specifies list of columns to Discretize. First and last are valid indexes.
* (default none)</pre>
*
* <pre> -V
* Invert matching sense of column indexes.</pre>
*
* <pre> -D
* Output binary attributes for discretized attributes.</pre>
*
* <pre> -Y
* Use bin numbers rather than ranges for discretized attributes.</pre>
*
* <pre> -E
* Use better encoding of split point for MDL.</pre>
*
* <pre> -K
* Use Kononenko's MDL criterion.</pre>
*
* <pre> -precision <integer>
* Precision for bin boundary labels.
* (default = 6 decimal places).</pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
@Override
public void setOptions(String[] options) throws Exception {
setMakeBinary(Utils.getFlag('D', options));
setUseBinNumbers(Utils.getFlag('Y', options));
setUseBetterEncoding(Utils.getFlag('E', options));
setUseKononenko(Utils.getFlag('K', options));
setInvertSelection(Utils.getFlag('V', options));
String convertList = Utils.getOption('R', options);
if (convertList.length() != 0) {
setAttributeIndices(convertList);
} else {
setAttributeIndices("first-last");
}
String precisionS = Utils.getOption("precision", options);
if (precisionS.length() > 0) {
setBinRangePrecision(Integer.parseInt(precisionS));
}
if (getInputFormat() != null) {
setInputFormat(getInputFormat());
}
Utils.checkForRemainingOptions(options);
}
/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -B
* Binary splits (convert nominal attributes to binary ones) </pre>
*
* <pre> -P
* Use error on probabilities instead of misclassification error for stopping criterion of LogitBoost.
* </pre>
*
* <pre> -I <numIterations>
* Set fixed number of iterations for LogitBoost (instead of using cross-validation)</pre>
*
* <pre> -F <modelType>
* Set Funtional Tree type to be generate: 0 for FT, 1 for FTLeaves and 2 for FTInner</pre>
*
* <pre> -M <numInstances>
* Set minimum number of instances at which a node can be split (default 15)</pre>
*
* <pre> -W <beta>
* Set beta for weight trimming for LogitBoost. Set to 0 (default) for no weight trimming.</pre>
*
* <pre> -A
* The AIC is used to choose the best iteration.</pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
setBinSplit(Utils.getFlag('B', options));
setErrorOnProbabilities(Utils.getFlag('P', options));
String optionString = Utils.getOption('I', options);
if (optionString.length() != 0) {
setNumBoostingIterations((new Integer(optionString)).intValue());
}
optionString = Utils.getOption('F', options);
if (optionString.length() != 0) {
setModelType(new SelectedTag(Integer.parseInt(optionString), TAGS_MODEL));
// setModelType((new Integer(optionString)).intValue());
}
optionString = Utils.getOption('M', options);
if (optionString.length() != 0) {
setMinNumInstances((new Integer(optionString)).intValue());
}
optionString = Utils.getOption('W', options);
if (optionString.length() != 0) {
setWeightTrimBeta((new Double(optionString)).doubleValue());
}
setUseAIC(Utils.getFlag('A', options));
Utils.checkForRemainingOptions(options);
}
/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -C
* Set whether or not use empirical
* log-odds cut-off instead of 0</pre>
*
* <pre> -R <numOfRuns>
* Set the number of multiple runs
* needed for searching the MLE.</pre>
*
* <pre> -S <num>
* Random number seed.
* (default 1)</pre>
*
* <pre> -D
* If set, classifier is run in debug mode and
* may output additional info to the console</pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
setDebug(Utils.getFlag('D', options));
setUsingCutOff(Utils.getFlag('C', options));
String runString = Utils.getOption('R', options);
if (runString.length() != 0) setNumRuns(Integer.parseInt(runString));
else setNumRuns(1);
super.setOptions(options);
}
/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre>
* -C <pruning confidence>
* Set confidence threshold for pruning.
* (default 0.25)
* </pre>
*
* <pre>
* -M <minimum number of objects>
* Set minimum number of objects per leaf.
* (default 2)
* </pre>
*
* <pre>
* -R
* Use reduced error pruning.
* </pre>
*
* <pre>
* -N <number of folds>
* Set number of folds for reduced error
* pruning. One fold is used as pruning set.
* (default 3)
* </pre>
*
* <pre>
* -B
* Use binary splits only.
* </pre>
*
* <pre>
* -U
* Generate unpruned decision list.
* </pre>
*
* <pre>
* -J
* Do not use MDL correction for info gain on numeric attributes.
* </pre>
*
* <pre>
* -Q <seed>
* Seed for random data shuffling (default 1).
* </pre>
*
* <pre>
* -doNotMakeSplitPointActualValue
* Do not make split point actual value.
* </pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
@Override
public void setOptions(String[] options) throws Exception {
// Pruning options
m_unpruned = Utils.getFlag('U', options);
m_reducedErrorPruning = Utils.getFlag('R', options);
m_binarySplits = Utils.getFlag('B', options);
m_useMDLcorrection = !Utils.getFlag('J', options);
m_doNotMakeSplitPointActualValue = Utils.getFlag("doNotMakeSplitPointActualValue", options);
String confidenceString = Utils.getOption('C', options);
if (confidenceString.length() != 0) {
if (m_reducedErrorPruning) {
throw new Exception("Setting CF doesn't make sense " + "for reduced error pruning.");
} else {
m_CF = (new Float(confidenceString)).floatValue();
if ((m_CF <= 0) || (m_CF >= 1)) {
throw new Exception("CF has to be greater than zero and smaller than one!");
}
}
} else {
m_CF = 0.25f;
}
String numFoldsString = Utils.getOption('N', options);
if (numFoldsString.length() != 0) {
if (!m_reducedErrorPruning) {
throw new Exception(
"Setting the number of folds"
+ " does only make sense for"
+ " reduced error pruning.");
} else {
m_numFolds = Integer.parseInt(numFoldsString);
}
} else {
m_numFolds = 3;
}
// Other options
String minNumString = Utils.getOption('M', options);
if (minNumString.length() != 0) {
m_minNumObj = Integer.parseInt(minNumString);
} else {
m_minNumObj = 2;
}
String seedString = Utils.getOption('Q', options);
if (seedString.length() != 0) {
m_Seed = Integer.parseInt(seedString);
} else {
m_Seed = 1;
}
super.setOptions(options);
}
/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre>
* -N
* Sets if binary attributes are to be coded as nominal ones.
* </pre>
*
* <pre>
* -A
* For each nominal value a new attribute is created,
* not only if there are more than 2 values.
* </pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
@Override
public void setOptions(String[] options) throws Exception {
setBinaryAttributesNominal(Utils.getFlag('N', options));
setTransformAllValues(Utils.getFlag('A', options));
if (getInputFormat() != null) {
setInputFormat(getInputFormat());
}
Utils.checkForRemainingOptions(options);
}
/**
* Parses a given list of options.
*
* <p>Valid options are:
*
* <p>-P <start set> <br>
* Specify a starting set of attributes. Eg 1,4,7-9.
*
* <p>-D <0 = forward selection | 1 = floating forward selection> <br>
* Forward selection method of the search. (default = 0).
*
* <p>-N <num> <br>
* Number of non improving nodes to consider before terminating search. (default = 5).
*
* <p>-I <br>
* Perform initial ranking to select top-ranked attributes.
*
* <p>-K <num> <br>
* Number of top-ranked attributes that are taken into account.
*
* <p>-T <0 = fixed-set | 1 = fixed-width> <br>
* Typ of Linear Forward Selection (default = 0).
*
* <p>-S <num> <br>
* Size of lookup cache for evaluated subsets. Expressed as a multiple of the number of attributes
* in the data set. (default = 1).
*
* <p>-Z <br>
* verbose on/off.
*
* <p>
*
* @param options the list of options as an array of strings
* @exception Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
String optionString;
resetOptions();
optionString = Utils.getOption('P', options);
if (optionString.length() != 0) {
setStartSet(optionString);
}
optionString = Utils.getOption('D', options);
if (optionString.length() != 0) {
setForwardSelectionMethod(
new SelectedTag(Integer.parseInt(optionString), TAGS_SEARCH_METHOD));
} else {
setForwardSelectionMethod(new SelectedTag(SEARCH_METHOD_FORWARD, TAGS_SEARCH_METHOD));
}
optionString = Utils.getOption('N', options);
if (optionString.length() != 0) {
setSearchTermination(Integer.parseInt(optionString));
}
setPerformRanking(Utils.getFlag('I', options));
optionString = Utils.getOption('K', options);
if (optionString.length() != 0) {
setNumUsedAttributes(Integer.parseInt(optionString));
}
optionString = Utils.getOption('T', options);
if (optionString.length() != 0) {
setType(new SelectedTag(Integer.parseInt(optionString), TAGS_TYPE));
} else {
setType(new SelectedTag(TYPE_FIXED_SET, TAGS_TYPE));
}
optionString = Utils.getOption('S', options);
if (optionString.length() != 0) {
setLookupCacheSize(Integer.parseInt(optionString));
}
m_verbose = Utils.getFlag('Z', options);
}
/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -N
* Initial structure is empty (instead of Naive Bayes)</pre>
*
* <pre> -P <nr of parents>
* Maximum number of parents</pre>
*
* <pre> -R
* Random order.
* (default false)</pre>
*
* <pre> -mbc
* Applies a Markov Blanket correction to the network structure,
* after a network structure is learned. This ensures that all
* nodes in the network are part of the Markov blanket of the
* classifier node.</pre>
*
* <pre> -S [LOO-CV|k-Fold-CV|Cumulative-CV]
* Score type (LOO-CV,k-Fold-CV,Cumulative-CV)</pre>
*
* <pre> -Q
* Use probabilistic or 0/1 scoring.
* (default probabilistic scoring)</pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
setRandomOrder(Utils.getFlag('R', options));
m_bInitAsNaiveBayes = !(Utils.getFlag('N', options));
String sMaxNrOfParents = Utils.getOption('P', options);
if (sMaxNrOfParents.length() != 0) {
setMaxNrOfParents(Integer.parseInt(sMaxNrOfParents));
} else {
setMaxNrOfParents(100000);
}
super.setOptions(options);
}
/**
* Parses a given list of options. Valid options are:
*
* <p>-folds folds <br>
* the number of folds for splitting the training set into train and test set. the first fold is
* always the training set. With '-V' you can invert this, i.e., instead of 20/80 for 5 folds
* you'll get 80/20. (default 5)
*
* <p>-V <br>
* inverts the fold selection, i.e., instead of using the first fold for the training set it is
* used for test set and the remaining folds for training.
*
* <p>-verbose <br>
* whether to output some more information during improving the classifier.
*
* <p>-insight <br>
* whether to use the labels of the original test set to output more statistics.
*
* <p>Options after -- are passed to the designated classifier.
*
* <p>
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
String tmpStr;
tmpStr = Utils.getOption("folds", options);
if (tmpStr.length() != 0) setSplitFolds(Integer.parseInt(tmpStr));
else setSplitFolds(0);
setInvertSplitFolds(Utils.getFlag('V', options));
setVerbose(Utils.getFlag("verbose", options));
setUseInsight(Utils.getFlag("insight", options));
super.setOptions(options);
}
/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -D
* Enables debug output.
* (default: off)</pre>
*
* <pre> -F
* Stores the filename in an additional attribute.
* (default: off)</pre>
*
* <pre> -dir <directory>
* The directory to work on.
* (default: current directory)</pre>
*
* <pre> -charset <charset name>
* The character set to use, e.g UTF-8.
* (default: use the default character set)</pre>
*
* <pre> -R
* Retain all string attribute values when reading incrementally.</pre>
*
* <!-- options-end -->
*
* @param options the options
* @throws Exception if options cannot be set
*/
public void setOptions(String[] options) throws Exception {
setDebug(Utils.getFlag("D", options));
setOutputFilename(Utils.getFlag("F", options));
setDirectory(new File(Utils.getOption("dir", options)));
String charSet = Utils.getOption("charset", options);
m_charSet = "";
if (charSet.length() > 0) {
m_charSet = charSet;
}
setRetainStringValues(Utils.getFlag('R', options));
}
/**
* Sets the options.
*
* @param options the options
* @throws Exception if invalid option
*/
@Override
public void setOptions(String[] options) throws Exception {
String tmpStr;
super.setOptions(options);
tmpStr = Utils.getOption('a', options);
if (tmpStr.length() != 0) {
setNumAttributes(Integer.parseInt(tmpStr));
} else {
setNumAttributes(defaultNumAttributes());
}
setClassFlag(Utils.getFlag('c', options));
tmpStr = Utils.getOption('b', options);
setBooleanIndices(tmpStr);
m_booleanCols.setUpper(getNumAttributes() - 1);
tmpStr = Utils.getOption('m', options);
setNominalIndices(tmpStr);
m_nominalCols.setUpper(getNumAttributes() - 1);
// check indices
tmpStr = checkIndices();
if (tmpStr.length() > 0) {
throw new IllegalArgumentException(tmpStr);
}
}
/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -M
* Minimize expected misclassification cost. Default is to
* reweight training instances according to costs per class</pre>
*
* <pre> -C <cost file name>
* File name of a cost matrix to use. If this is not supplied,
* a cost matrix will be loaded on demand. The name of the
* on-demand file is the relation name of the training data
* plus ".cost", and the path to the on-demand file is
* specified with the -N option.</pre>
*
* <pre> -N <directory>
* Name of a directory to search for cost files when loading
* costs on demand (default current directory).</pre>
*
* <pre> -cost-matrix <matrix>
* The cost matrix in Matlab single line format.</pre>
*
* <pre> -S <num>
* Random number seed.
* (default 1)</pre>
*
* <pre> -D
* If set, classifier is run in debug mode and
* may output additional info to the console</pre>
*
* <pre> -W
* Full name of base classifier.
* (default: weka.classifiers.rules.ZeroR)</pre>
*
* <pre>
* Options specific to classifier weka.classifiers.rules.ZeroR:
* </pre>
*
* <pre> -D
* If set, classifier is run in debug mode and
* may output additional info to the console</pre>
*
* <!-- options-end -->
* Options after -- are passed to the designated classifier.
*
* <p>
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
setMinimizeExpectedCost(Utils.getFlag('M', options));
String costFile = Utils.getOption('C', options);
if (costFile.length() != 0) {
try {
setCostMatrix(new CostMatrix(new BufferedReader(new FileReader(costFile))));
} catch (Exception ex) {
// now flag as possible old format cost matrix. Delay cost matrix
// loading until buildClassifer is called
setCostMatrix(null);
}
setCostMatrixSource(new SelectedTag(MATRIX_SUPPLIED, TAGS_MATRIX_SOURCE));
m_CostFile = costFile;
} else {
setCostMatrixSource(new SelectedTag(MATRIX_ON_DEMAND, TAGS_MATRIX_SOURCE));
}
String demandDir = Utils.getOption('N', options);
if (demandDir.length() != 0) {
setOnDemandDirectory(new File(demandDir));
}
String cost_matrix = Utils.getOption("cost-matrix", options);
if (cost_matrix.length() != 0) {
StringWriter writer = new StringWriter();
CostMatrix.parseMatlab(cost_matrix).write(writer);
setCostMatrix(new CostMatrix(new StringReader(writer.toString())));
setCostMatrixSource(new SelectedTag(MATRIX_SUPPLIED, TAGS_MATRIX_SOURCE));
}
super.setOptions(options);
}
/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -B <num>
* Manual blend setting (default 20%)
* </pre>
*
* <pre> -E
* Enable entropic auto-blend setting (symbolic class only)
* </pre>
*
* <pre> -M <char>
* Specify the missing value treatment mode (default a)
* Valid options are: a(verage), d(elete), m(axdiff), n(ormal)
* </pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
String debug = "(KStar.setOptions)";
String blendStr = Utils.getOption('B', options);
if (blendStr.length() != 0) {
setGlobalBlend(Integer.parseInt(blendStr));
}
setEntropicAutoBlend(Utils.getFlag('E', options));
String missingModeStr = Utils.getOption('M', options);
if (missingModeStr.length() != 0) {
switch (missingModeStr.charAt(0)) {
case 'a':
setMissingMode(new SelectedTag(M_AVERAGE, TAGS_MISSING));
break;
case 'd':
setMissingMode(new SelectedTag(M_DELETE, TAGS_MISSING));
break;
case 'm':
setMissingMode(new SelectedTag(M_MAXDIFF, TAGS_MISSING));
break;
case 'n':
setMissingMode(new SelectedTag(M_NORMAL, TAGS_MISSING));
break;
default:
setMissingMode(new SelectedTag(M_AVERAGE, TAGS_MISSING));
}
}
Utils.checkForRemainingOptions(options);
}
/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -C <col>
* Index of the attribute to be changed
* (default last attribute)</pre>
*
* <pre> -M
* Treat missing values as an extra value
* </pre>
*
* <pre> -P <num>
* Specify the percentage of noise introduced
* to the data (default 10)</pre>
*
* <pre> -S <num>
* Specify the random number seed (default 1)</pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
String indexString = Utils.getOption('C', options);
if (indexString.length() != 0) {
setAttributeIndex(indexString);
} else {
setAttributeIndex("last");
}
if (Utils.getFlag('M', options)) {
setUseMissing(true);
}
String percentString = Utils.getOption('P', options);
if (percentString.length() != 0) {
setPercent((int) Double.valueOf(percentString).doubleValue());
} else {
setPercent(10);
}
String seedString = Utils.getOption('S', options);
if (seedString.length() != 0) {
setRandomSeed(Integer.parseInt(seedString));
} else {
setRandomSeed(1);
}
}
/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -P <start set>
* Specify a starting set of attributes.
* Eg. 1,3,5-7.</pre>
*
* <pre> -D <0 = backward | 1 = forward | 2 = bi-directional>
* Direction of search. (default = 1).</pre>
*
* <pre> -N <num>
* Number of non-improving nodes to
* consider before terminating search.</pre>
*
* <pre> -S <num>
* Size of lookup cache for evaluated subsets.
* Expressed as a multiple of the number of
* attributes in the data set. (default = 1)</pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
String optionString;
resetOptions();
optionString = Utils.getOption('P', options);
if (optionString.length() != 0) {
setStartSet(optionString);
}
optionString = Utils.getOption('D', options);
if (optionString.length() != 0) {
setDirection(new SelectedTag(Integer.parseInt(optionString), TAGS_SELECTION));
} else {
setDirection(new SelectedTag(SELECTION_FORWARD, TAGS_SELECTION));
}
optionString = Utils.getOption('N', options);
if (optionString.length() != 0) {
setSearchTermination(Integer.parseInt(optionString));
}
optionString = Utils.getOption('S', options);
if (optionString.length() != 0) {
setLookupCacheSize(Integer.parseInt(optionString));
}
m_debug = Utils.getFlag('Z', options);
}
/**
* Parses a given list of options.
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -Q <query>
* SQL query to execute.</pre>
*
* <pre> -S
* Return sparse rather than normal instances.</pre>
*
* <pre> -U <username>
* The username to use for connecting.</pre>
*
* <pre> -P <password>
* The password to use for connecting.</pre>
*
* <pre> -D
* Enables debug output.</pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
String tmpStr;
setSparseData(Utils.getFlag('S', options));
tmpStr = Utils.getOption('Q', options);
if (tmpStr.length() != 0) setQuery(tmpStr);
tmpStr = Utils.getOption('U', options);
if (tmpStr.length() != 0) setUsername(tmpStr);
tmpStr = Utils.getOption('P', options);
if (tmpStr.length() != 0) setPassword(tmpStr);
setDebug(Utils.getFlag('D', options));
}
public static void main(String[] argv) {
try {
if (Utils.getFlag('b', argv)) Filter.batchFilterFile(new Nominal(), argv);
else Filter.filterFile(new Nominal(), argv);
} catch (Exception ex) {
System.out.println(ex.getMessage());
}
}
/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre>
* -R
* Attributes to act on. Can be either a range
* string (e.g. 1,2,6-10) OR a comma-separated list of named attributes
* (default none)
* </pre>
*
* <pre>
* -V
* Invert matching sense (i.e. act on all attributes other than those specified)
* </pre>
*
* <pre>
* -N
* Nominal labels and their replacement values.
* E.g. red:blue, black:white, fred:bob
* </pre>
*
* <pre>
* -I
* Ignore case when matching nominal values
* </pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
@Override
public void setOptions(String[] options) throws Exception {
String atts = Utils.getOption('R', options);
if (atts.length() > 0) {
setSelectedAttributes(atts);
}
String replacements = Utils.getOption('N', options);
if (replacements.length() > 0) {
setValueReplacements(replacements);
}
setInvertSelection(Utils.getFlag('V', options));
setIgnoreCase(Utils.getFlag('I', options));
Utils.checkForRemainingOptions(options);
}
/**
* Parses a given list of options.
*
* @param options the list of options as an array of strings
* @exception Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
String optionString = Utils.getOption('A', options);
if (optionString.length() != 0) setAlphaStar(Double.parseDouble(optionString));
optionString = Utils.getOption('S', options);
if (optionString.length() != 0) setSigma(Double.parseDouble(optionString));
optionString = Utils.getOption('R', options);
if (optionString.length() != 0) setR(Double.parseDouble(optionString));
setUseSparseMatrix(Utils.getFlag('M', options));
}
/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -D
* Produce debugging output.
* (default no debugging output)</pre>
*
* <pre> -S <number of selection method>
* Set the attribute selection method to use. 1 = None, 2 = Greedy.
* (default 0 = M5' method)</pre>
*
* <pre> -C
* Do not try to eliminate colinear attributes.
* </pre>
*
* <pre> -R <double>
* Set ridge parameter (default 1.0e-8).
* </pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
String selectionString = Utils.getOption('S', options);
if (selectionString.length() != 0) {
setAttributeSelectionMethod(
new SelectedTag(Integer.parseInt(selectionString), TAGS_SELECTION));
} else {
setAttributeSelectionMethod(new SelectedTag(SELECTION_M5, TAGS_SELECTION));
}
String ridgeString = Utils.getOption('R', options);
if (ridgeString.length() != 0) {
setRidge(new Double(ridgeString).doubleValue());
} else {
setRidge(1.0e-8);
}
setDebug(Utils.getFlag('D', options));
setEliminateColinearAttributes(!Utils.getFlag('C', options));
}
/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -I <num>
* Number of iterations.
* (default 10)</pre>
*
* <pre> -R <num>
* Number of restarts.
* (default 10)</pre>
*
* <pre> -log
* Creates logs in the tmp directory for all kinds of internal data.
* Use only for debugging purposes!
* </pre>
*
* <pre> -U
* Updates also the labels of the training set.
* </pre>
*
* <pre> -eval <num>
* The type of evaluation to use (0 = Randomwalk/Last model used for
* prediction, 1=Randomwalk/Best model used for prediction,
* 2=Hillclimbing).
* </pre>
*
* <pre> -compare <num>
* The type of comparisong used for comparing models.
* (0=overall RMS, 1=RMS on train set, 2=RMS on test set,
* 3=Accuracy on train set)
* </pre>
*
* <pre> -flipper "<classname [parameters]>"
* The flipping algorithm (and optional parameters) to use for
* flipping labels.
* </pre>
*
* <pre> -folds <folds>
* The number of folds for splitting the training set into
* train and test set. The first fold is always the training
* set. With '-V' you can invert this, i.e., instead of 20/80
* for 5 folds you'll get 80/20.
* (default 5)</pre>
*
* <pre> -V
* Inverts the fold selection, i.e., instead of using the first
* fold for the training set it is used for test set and the
* remaining folds for training.</pre>
*
* <pre> -verbose
* Whether to print some more information during building the
* classifier.
* (default is off)</pre>
*
* <pre> -verbose
* Whether to print some more information during building the
* classifier.
* (default is off)</pre>
*
* <pre> -S <num>
* Random number seed.
* (default 1)</pre>
*
* <pre> -D
* If set, classifier is run in debug mode and
* may output additional info to the console</pre>
*
* <pre> -W
* Full name of base classifier.
* (default: weka.classifiers.trees.J48)</pre>
*
* <pre>
* Options specific to classifier weka.classifiers.trees.J48:
* </pre>
*
* <pre> -U
* Use unpruned tree.</pre>
*
* <pre> -C <pruning confidence>
* Set confidence threshold for pruning.
* (default 0.25)</pre>
*
* <pre> -M <minimum number of instances>
* Set minimum number of instances per leaf.
* (default 2)</pre>
*
* <pre> -R
* Use reduced error pruning.</pre>
*
* <pre> -N <number of folds>
* Set number of folds for reduced error
* pruning. One fold is used as pruning set.
* (default 3)</pre>
*
* <pre> -B
* Use binary splits only.</pre>
*
* <pre> -S
* Don't perform subtree raising.</pre>
*
* <pre> -L
* Do not clean up after the tree has been built.</pre>
*
* <pre> -A
* Laplace smoothing for predicted probabilities.</pre>
*
* <pre> -Q <seed>
* Seed for random data shuffling (default 1).</pre>
*
* <!-- options-end -->
* Options after -- are passed to the designated classifier.
*
* <p>
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
@Override
public void setOptions(String[] options) throws Exception {
String tmpStr;
String[] tmpOptions;
tmpStr = Utils.getOption('I', options);
if (tmpStr.length() != 0) setNumIterations(Integer.parseInt(tmpStr));
else setNumIterations(10);
tmpStr = Utils.getOption('R', options);
if (tmpStr.length() != 0) setNumRestarts(Integer.parseInt(tmpStr));
else setNumRestarts(10);
setLog(Utils.getFlag("log", options));
setUpdateTraining(Utils.getFlag('U', options));
tmpStr = Utils.getOption("eval", options);
if (tmpStr.length() != 0)
setEvaluationType(new SelectedTag(Integer.parseInt(tmpStr), CollectiveInstances.EVAL_TAGS));
else
setEvaluationType(
new SelectedTag(CollectiveInstances.EVAL_RANDOMWALK_LAST, CollectiveInstances.EVAL_TAGS));
tmpStr = Utils.getOption("compare", options);
if (tmpStr.length() != 0)
setComparisonType(
new SelectedTag(Integer.parseInt(tmpStr), CollectiveInstances.COMPARE_TAGS));
else
setComparisonType(
new SelectedTag(CollectiveInstances.COMPARE_RMS, CollectiveInstances.COMPARE_TAGS));
tmpStr = Utils.getOption("flipper", options);
if (tmpStr.length() != 0) {
tmpOptions = Utils.splitOptions(tmpStr);
tmpStr = tmpOptions[0];
tmpOptions[0] = "";
setFlipper(Flipper.forName(tmpStr, tmpOptions));
} else {
setFlipper(new TriangleFlipper());
}
super.setOptions(options);
}
/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -N <num>
* number of clusters.
* (default 2).</pre>
*
* <pre> -P
* Initialize using the k-means++ method.
* </pre>
*
* <pre> -V
* Display std. deviations for centroids.
* </pre>
*
* <pre> -M
* Replace missing values with mean/mode.
* </pre>
*
* <pre> -A <classname and options>
* Distance function to use.
* (default: weka.core.EuclideanDistance)</pre>
*
* <pre> -I <num>
* Maximum number of iterations.
* </pre>
*
* <pre> -O
* Preserve order of instances.
* </pre>
*
* <pre> -fast
* Enables faster distance calculations, using cut-off values.
* Disables the calculation/output of squared errors/distances.
* </pre>
*
* <pre> -S <num>
* Random number seed.
* (default 10)</pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
String optionString = Utils.getOption("I", options);
if (optionString.length() != 0) {
setMaxIterations(Integer.parseInt(optionString));
}
optionString = Utils.getOption("max", options);
if (optionString.length() > 0) {
setMaxNumClusters(Integer.parseInt(optionString));
}
optionString = Utils.getOption("min", options);
if (optionString.length() > 0) {
setMinNumClusters(Integer.parseInt(optionString));
}
optionString = Utils.getOption("restarts", options);
if (optionString.length() > 0) {
setRestarts(Integer.parseInt(optionString));
}
setManuallySelectNumClusters(Utils.getFlag("manual", options));
setPrintDebug(Utils.getFlag("debug", options));
initializeWithKMeansPlusPlus = Utils.getFlag('P', options);
String distFunctionClass = Utils.getOption('A', options);
if (distFunctionClass.length() != 0) {
String distFunctionClassSpec[] = Utils.splitOptions(distFunctionClass);
if (distFunctionClassSpec.length == 0) {
throw new Exception("Invalid DistanceFunction specification string.");
}
String className = distFunctionClassSpec[0];
distFunctionClassSpec[0] = "";
setDistanceFunction(
(DistanceFunction)
Utils.forName(DistanceFunction.class, className, distFunctionClassSpec));
} else {
setDistanceFunction(new EuclideanDistance());
}
super.setOptions(options);
}
/**
* Parses a given list of options.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -D
* Enables debugging output (if available) to be printed.
* (default: off)</pre>
*
* <pre> -no-checks
* Turns off all checks - use with caution!
* (default: checks on)</pre>
*
* <pre> -C <num>
* The size of the cache (a prime number), 0 for full cache and
* -1 to turn it off.
* (default: 250007)</pre>
*
* <pre> -E <num>
* The Exponent to use.
* (default: 1.0)</pre>
*
* <pre> -L
* Use lower-order terms.
* (default: no)</pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
String tmpStr;
tmpStr = Utils.getOption('E', options);
if (tmpStr.length() != 0) setExponent(Double.parseDouble(tmpStr));
else setExponent(1.0);
setUseLowerOrder(Utils.getFlag('L', options));
super.setOptions(options);
}
/**
* Main method for testing this class.
*
* @param args should contain arguments to the filter: use -h for help
*/
public static void main(String[] args) {
try {
if (Utils.getFlag('b', args)) {
Filter.batchFilterFile(new AddExpression(), args);
} else {
Filter.filterFile(new AddExpression(), args);
}
} catch (Exception ex) {
System.out.println(ex.getMessage());
}
}
/**
* Parses the options for this object.
*
* <p>
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -S <search method specification>
* Full class name of search method, followed
* by its options.
* eg: "weka.attributeSelection.BestFirst -D 1"
* (default weka.attributeSelection.BestFirst)</pre>
*
* <pre> -X <number of folds>
* Use cross validation to evaluate features.
* Use number of folds = 1 for leave one out CV.
* (Default = leave one out CV)</pre>
*
* <pre> -E <acc | rmse | mae | auc>
* Performance evaluation measure to use for selecting attributes.
* (Default = accuracy for discrete class and rmse for numeric class)</pre>
*
* <pre> -I
* Use nearest neighbour instead of global table majority.</pre>
*
* <pre> -R
* Display decision table rules.
* </pre>
*
* <pre>
* Options specific to search method weka.attributeSelection.BestFirst:
* </pre>
*
* <pre> -P <start set>
* Specify a starting set of attributes.
* Eg. 1,3,5-7.</pre>
*
* <pre> -D <0 = backward | 1 = forward | 2 = bi-directional>
* Direction of search. (default = 1).</pre>
*
* <pre> -N <num>
* Number of non-improving nodes to
* consider before terminating search.</pre>
*
* <pre> -S <num>
* Size of lookup cache for evaluated subsets.
* Expressed as a multiple of the number of
* attributes in the data set. (default = 1)</pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
String optionString;
resetOptions();
optionString = Utils.getOption('X', options);
if (optionString.length() != 0) {
m_CVFolds = Integer.parseInt(optionString);
}
m_useIBk = Utils.getFlag('I', options);
m_displayRules = Utils.getFlag('R', options);
optionString = Utils.getOption('E', options);
if (optionString.length() != 0) {
if (optionString.equals("acc")) {
setEvaluationMeasure(new SelectedTag(EVAL_ACCURACY, TAGS_EVALUATION));
} else if (optionString.equals("rmse")) {
setEvaluationMeasure(new SelectedTag(EVAL_RMSE, TAGS_EVALUATION));
} else if (optionString.equals("mae")) {
setEvaluationMeasure(new SelectedTag(EVAL_MAE, TAGS_EVALUATION));
} else if (optionString.equals("auc")) {
setEvaluationMeasure(new SelectedTag(EVAL_AUC, TAGS_EVALUATION));
} else {
throw new IllegalArgumentException("Invalid evaluation measure");
}
}
String searchString = Utils.getOption('S', options);
if (searchString.length() == 0)
searchString = weka.attributeSelection.BestFirst.class.getName();
String[] searchSpec = Utils.splitOptions(searchString);
if (searchSpec.length == 0) {
throw new IllegalArgumentException("Invalid search specification string");
}
String searchName = searchSpec[0];
searchSpec[0] = "";
setSearch(ASSearch.forName(searchName, searchSpec));
}
/**
* Parses a given list of options.
* <!-- options-start -->
* Valid options are:
*
* <p>
*
* <pre> -Q <query>
* SQL query to execute.</pre>
*
* <pre> -S
* Return sparse rather than normal instances.</pre>
*
* <pre> -U <username>
* The username to use for connecting.</pre>
*
* <pre> -P <password>
* The password to use for connecting.</pre>
*
* <pre> -D
* Enables debug output.</pre>
*
* <!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
String tmpStr;
setSparseData(Utils.getFlag('S', options));
tmpStr = Utils.getOption('Q', options);
if (tmpStr.length() != 0) setQuery(tmpStr);
tmpStr = Utils.getOption('U', options);
if (tmpStr.length() != 0) setUsername(tmpStr);
tmpStr = Utils.getOption('P', options);
if (tmpStr.length() != 0) setPassword(tmpStr);
tmpStr = Utils.getOption("custom-props", options);
if (tmpStr.length() == 0) setCustomPropsFile(null);
else setCustomPropsFile(new File(tmpStr));
setDebug(Utils.getFlag('D', options));
}
public void setOptions(String[] options) throws Exception {
String knnString = Utils.getOption('K', options);
if (knnString.length() != 0) {
classifier.setkNearest(Integer.parseInt(knnString));
} else {
classifier.setkNearest(1);
}
if (Utils.getFlag('I', options)) {
classifier.setInverseWeighting(true);
} else {
classifier.setInverseWeighting(false);
}
if (Utils.getFlag('E', options)) {
classifier.setMetric(1);
} else {
classifier.setMetric(0);
}
}