/**
* Determine the ideal fields.
*
* @param headerList The headers.
* @return The indexes of the ideal fields.
*/
private int[] determineIdealFields(final CSVHeaders headerList) {
int[] result;
final String type = getProp().getPropertyString(ScriptProperties.ML_CONFIG_TYPE);
// is it non-supervised?
if (type.equals(MLMethodFactory.TYPE_SOM)) {
result = new int[0];
return result;
}
final List<Integer> fields = new ArrayList<Integer>();
for (int currentIndex = 0; currentIndex < headerList.size(); currentIndex++) {
final String baseName = headerList.getBaseHeader(currentIndex);
final int slice = headerList.getSlice(currentIndex);
final AnalystField field = getAnalyst().getScript().findNormalizedField(baseName, slice);
if (field != null && field.isOutput()) {
fields.add(currentIndex);
}
}
// allocate result array
result = new int[fields.size()];
for (int i = 0; i < result.length; i++) {
result[i] = fields.get(i);
}
return result;
}
/**
* Extract fields from a file into a numeric array for machine learning.
*
* @param analyst The analyst to use.
* @param headers The headers for the input data.
* @param csv The CSV that holds the input data.
* @param outputLength The length of the returned array.
* @param skipOutput True if the output should be skipped.
* @return The encoded data.
*/
public static final double[] extractFields(
final EncogAnalyst analyst,
final CSVHeaders headers,
final ReadCSV csv,
final int outputLength,
final boolean skipOutput) {
final double[] output = new double[outputLength];
int outputIndex = 0;
for (final AnalystField stat : analyst.getScript().getNormalize().getNormalizedFields()) {
stat.init();
if (stat.getAction() == NormalizationAction.Ignore) {
continue;
}
if (stat.isOutput() && skipOutput) {
continue;
}
int index = headers.find(stat.getName());
final String str = csv.get(index).trim();
// is this an unknown value?
if (str.equals("?") || str.length() == 0) {
HandleMissingValues handler = analyst.getScript().getNormalize().getMissingValues();
double[] d = handler.handleMissing(analyst, stat);
// should we skip the entire row
if (d == null) {
return null;
}
// copy the returned values in place of the missing values
for (int i = 0; i < d.length; i++) {
output[outputIndex++] = d[i];
}
} else {
// known value
if (stat.getAction() == NormalizationAction.Normalize) {
double d = csv.getFormat().parse(str);
d = stat.normalize(d);
output[outputIndex++] = d;
} else if (stat.getAction() == NormalizationAction.PassThrough) {
double d = csv.getFormat().parse(str);
output[outputIndex++] = d;
} else {
final double[] d = stat.encode(str);
for (final double element : d) {
output[outputIndex++] = element;
}
}
}
}
return output;
}
/**
* Determine the input fields.
*
* @param headerList The headers.
* @return The indexes of the input fields.
*/
private int[] determineInputFields(final CSVHeaders headerList) {
final List<Integer> fields = new ArrayList<Integer>();
for (int currentIndex = 0; currentIndex < headerList.size(); currentIndex++) {
final String baseName = headerList.getBaseHeader(currentIndex);
final int slice = headerList.getSlice(currentIndex);
final AnalystField field = getAnalyst().getScript().findNormalizedField(baseName, slice);
if (field != null && field.isInput()) {
fields.add(currentIndex);
}
}
// allocate result array
final int[] result = new int[fields.size()];
for (int i = 0; i < result.length; i++) {
result[i] = fields.get(i);
}
return result;
}
/**
* Write the headers.
*
* @param tw The output stream.
*/
private void writeHeaders(final PrintWriter tw) {
final StringBuilder line = new StringBuilder();
for (final AnalystField stat : this.analyst.getScript().getNormalize().getNormalizedFields()) {
final int needed = stat.getColumnsNeeded();
for (int i = 0; i < needed; i++) {
BasicFile.appendSeparator(line, getFormat());
line.append('\"');
line.append(CSVHeaders.tagColumn(stat.getName(), i, stat.getTimeSlice(), needed > 1));
line.append('\"');
}
}
tw.println(line.toString());
}
/**
* Add headings for a raw file.
*
* @param line The line to write the raw headings to.
* @param prefix The prefix to place.
* @param format The format to use.
*/
public final void addRawHeadings(
final StringBuilder line, final String prefix, final CSVFormat format) {
final int subFields = getColumnsNeeded();
for (int i = 0; i < subFields; i++) {
final String str = CSVHeaders.tagColumn(this.name, i, this.timeSlice, subFields > 1);
BasicFile.appendSeparator(line, format);
line.append('\"');
if (prefix != null) {
line.append(prefix);
}
line.append(str);
line.append('\"');
}
}
