/**
* ************************************************** Convert a table to a set of instances, with
* <b>columns</b> representing individual </b>instances</b> and <b>rows</b> representing
* <b>attributes</b> (e.g. as is common with microarray data)
*/
public Instances tableColsToInstances(Table t, String relationName) {
System.err.print("Converting table cols to instances...");
// Set up attributes, which for colInstances will be the rowNames...
FastVector atts = new FastVector();
ArrayList<Boolean> isNominal = new ArrayList<Boolean>();
ArrayList<FastVector> allAttVals = new ArrayList<FastVector>(); // Save values for later...
System.err.print("creating attributes...");
for (int r = 0; r < t.numRows; r++) {
if (rowIsNumeric(t, r)) {
isNominal.add(false);
atts.addElement(new Attribute(t.rowNames[r]));
allAttVals.add(null); // No enumeration of attribute values.
} else {
// It's nominal... determine the range of values and create a nominal attribute...
isNominal.add(true);
FastVector attVals = getRowValues(t, r);
atts.addElement(new Attribute(t.rowNames[r], attVals));
// Save it for later
allAttVals.add(attVals);
}
}
System.err.print("creating instances...");
// Create Instances object..
Instances data = new Instances(relationName, atts, 0);
data.setRelationName(relationName);
/** ***** CREATE INSTANCES ************* */
// Fill the instances with data...
// For each instance...
for (int c = 0; c < t.numCols; c++) {
double[] vals =
new double[data.numAttributes()]; // Even nominal values are stored as double pointers.
// For each attribute fill in the numeric or attributeValue index...
for (int r = 0; r < t.numRows; r++) {
String val = (String) t.matrix.getQuick(r, c);
if (val == "?") vals[r] = Instance.missingValue();
else if (isNominal.get(r)) {
vals[r] = allAttVals.get(r).indexOf(val);
} else {
vals[r] = Double.parseDouble((String) val);
}
}
// Add the a newly minted instance with those attribute values...
data.add(new Instance(1.0, vals));
}
System.err.print("add feature names...");
/** ***** ADD FEATURE NAMES ************* */
// takes basically zero time... all time is in previous 2 chunks.
if (addInstanceNamesAsFeatures) {
Instances newData = new Instances(data);
newData.insertAttributeAt(new Attribute("ID", (FastVector) null), 0);
int attrIdx = newData.attribute("ID").index(); // Paranoid... should be 0
// We save the instanceNames in a list because it's handy later on...
instanceNames = new ArrayList<String>();
for (int c = 0; c < t.colNames.length; c++) {
instanceNames.add(t.colNames[c]);
newData.instance(c).setValue(attrIdx, t.colNames[c]);
}
data = newData;
}
System.err.println("done.");
return (data);
}
/**
* ************************************************** Convert a table to a set of instances, with
* <b>rows</b> representing individual </b>instances</b> and <b>columns</b> representing
* <b>attributes</b>
*/
public Instances tableRowsToNominalInstances(Table t, String relationName) {
System.err.print("Converting table rows to instances...");
// Set up attributes, which for rowInstances will be the colNames...
FastVector atts = new FastVector();
ArrayList<Boolean> isNominal = new ArrayList<Boolean>();
ArrayList<FastVector> allAttVals = new ArrayList<FastVector>(); // Save values for later...
System.err.print("creating attributes...");
for (int c = 0; c < t.numCols; c++) {
// It's nominal... determine the range of values
isNominal.add(true);
FastVector attVals = getColValues(t, c);
atts.addElement(new Attribute(t.colNames[c], attVals));
// Save it for later
allAttVals.add(attVals);
}
System.err.print("creating instances...");
// Create Instances object..
Instances data = new Instances(relationName, atts, 0);
data.setRelationName(relationName);
// Fill the instances with data...
// For each instance...
for (int r = 0; r < t.numRows; r++) {
double[] vals = new double[data.numAttributes()];
// for each attribute
for (int c = 0; c < t.numCols; c++) {
String val = (String) t.matrix.getQuick(r, c);
if (val == "?") vals[c] = Instance.missingValue();
else if (isNominal.get(c)) {
vals[c] = allAttVals.get(c).indexOf(val);
} else {
vals[c] = Double.parseDouble((String) val);
}
}
// Add the a newly minted instance with those attribute values...
data.add(new Instance(1.0, vals));
}
System.err.print("add feature names...");
if (addInstanceNamesAsFeatures) {
Instances newData = new Instances(data);
newData.insertAttributeAt(new Attribute("ID", (FastVector) null), 0);
int attrIdx = newData.attribute("ID").index(); // Paranoid... should be 0
// We save the instanceNames in a list because it's handy later on...
instanceNames = new ArrayList<String>();
for (int r = 0; r < t.rowNames.length; r++) {
instanceNames.add(t.rowNames[r]);
newData.instance(r).setValue(attrIdx, t.rowNames[r]);
}
data = newData;
}
System.err.println("done.");
return (data);
}