/**
* Sorts the in-memory buffer
*
* @param write whether to write the sorted buffer to a temp file
* @throws Exception if a problem occurs
*/
protected void sortBuffer(boolean write) throws Exception {
String msg = statusMessagePrefix() + "Sorting in memory buffer....";
if (m_log != null) {
m_log.statusMessage(msg);
m_log.logMessage("[" + getCustomName() + "] " + msg);
}
Collections.sort(m_incrementalBuffer, m_sortComparator);
if (!write) {
return;
}
String tmpDir = m_tempDirectory;
File tempFile = File.createTempFile("Sorter", ".tmp");
if (tmpDir != null && tmpDir.length() > 0) {
try {
tmpDir = m_env.substitute(tmpDir);
File tempDir = new File(tmpDir);
if (tempDir.exists() && tempDir.canWrite()) {
String filename = tempFile.getName();
File newFile = new File(tmpDir + File.separator + filename);
tempFile = newFile;
tempFile.deleteOnExit();
}
} catch (Exception ex) {
}
}
if (!m_stopRequested.get()) {
m_bufferFiles.add(tempFile);
FileOutputStream fos = new FileOutputStream(tempFile);
// GZIPOutputStream gzo = new GZIPOutputStream(fos);
BufferedOutputStream bos = new BufferedOutputStream(fos, 50000);
ObjectOutputStream oos = new ObjectOutputStream(bos);
msg = statusMessagePrefix() + "Writing buffer to temp file " + m_bufferFiles.size() + "...";
if (m_log != null) {
m_log.statusMessage(msg);
m_log.logMessage("[" + getCustomName() + "] " + msg);
}
for (int i = 0; i < m_incrementalBuffer.size(); i++) {
InstanceHolder temp = m_incrementalBuffer.get(i);
temp.m_instance.setDataset(null);
oos.writeObject(temp);
if (i % (m_bufferSizeI / 10) == 0) {
oos.reset();
}
}
bos.flush();
oos.close();
}
m_incrementalBuffer.clear();
}
/**
* Stops the step (and upstream ones) and then prints an error message and optional exception
* message
*
* @param error the error message to print
* @param ex the optional exception
*/
protected void stopWithErrorMessage(String error, Exception ex) {
stop();
if (m_log != null) {
m_log.statusMessage(statusMessagePrefix() + error + " - see log for details");
m_log.logMessage(statusMessagePrefix() + error + (ex != null ? " " + ex.getMessage() : ""));
}
}
/**
* Convert an <code>Instance</code> to an array of values that matches the format of the mining
* schema. First maps raw attribute values and then applies rules for missing values, outliers
* etc.
*
* @param inst the <code>Instance</code> to convert
* @param miningSchema the mining schema incoming instance attributes
* @return an array of doubles that are values from the incoming Instances, correspond to the
* format of the mining schema and have had missing values, outliers etc. dealt with.
* @throws Exception if something goes wrong
*/
public double[] instanceToSchema(Instance inst, MiningSchema miningSchema) throws Exception {
Instances miningSchemaI = miningSchema.getMiningSchemaAsInstances();
// allocate enough space for both mining schema fields and any derived fields
double[] result = new double[miningSchema.getFieldsAsInstances().numAttributes()];
// Copy over the values
for (int i = 0; i < miningSchemaI.numAttributes(); i++) {
// if (miningSchemaI.attribute(i).isNumeric()) {
result[i] = inst.value(m_fieldsMap[i]);
if (miningSchemaI.attribute(i).isNominal() || miningSchemaI.attribute(i).isString()) {
// If not missing, look up the index of this incoming categorical value in
// the mining schema
if (!Utils.isMissingValue(inst.value(m_fieldsMap[i]))) {
int[] valueMap = m_nominalValueMaps[i];
int index = valueMap[(int) inst.value(m_fieldsMap[i])];
String incomingAttValue =
inst.attribute(m_fieldsMap[i]).value((int) inst.value(m_fieldsMap[i]));
/*int index = miningSchemaI.attribute(i).indexOfValue(incomingAttValue); */
if (index >= 0) {
result[i] = index;
} else {
// set this to "unknown" (-1) for nominal valued attributes
result[i] = UNKNOWN_NOMINAL_VALUE;
String warningString =
"[MappingInfo] WARNING: Can't match nominal value " + incomingAttValue;
if (m_log != null) {
m_log.logMessage(warningString);
} else {
System.err.println(warningString);
}
}
}
}
}
// Now deal with missing values and outliers...
miningSchema.applyMissingAndOutlierTreatments(result);
// printInst(result);
// now fill in any derived values
ArrayList<DerivedFieldMetaInfo> derivedFields = miningSchema.getDerivedFields();
for (int i = 0; i < derivedFields.size(); i++) {
DerivedFieldMetaInfo temp = derivedFields.get(i);
// System.err.println("Applying : " + temp);
double r = temp.getDerivedValue(result);
result[i + miningSchemaI.numAttributes()] = r;
}
/*System.err.print("==> ");
for (int i = 0; i < result.length; i++) {
System.err.print(" " + result[i]);
}
System.err.println();*/
return result;
}
public MappingInfo(Instances dataSet, MiningSchema miningSchema, Logger log) throws Exception {
m_log = log;
// miningSchema.convertStringAttsToNominal();
Instances fieldsI = miningSchema.getMiningSchemaAsInstances();
m_fieldsMap = new int[fieldsI.numAttributes()];
m_nominalValueMaps = new int[fieldsI.numAttributes()][];
for (int i = 0; i < fieldsI.numAttributes(); i++) {
String schemaAttName = fieldsI.attribute(i).name();
boolean found = false;
for (int j = 0; j < dataSet.numAttributes(); j++) {
if (dataSet.attribute(j).name().equals(schemaAttName)) {
Attribute miningSchemaAtt = fieldsI.attribute(i);
Attribute incomingAtt = dataSet.attribute(j);
// check type match
if (miningSchemaAtt.type() != incomingAtt.type()) {
throw new Exception(
"[MappingInfo] type mismatch for field "
+ schemaAttName
+ ". Mining schema type "
+ miningSchemaAtt.toString()
+ ". Incoming type "
+ incomingAtt.toString()
+ ".");
}
// check nominal values (number, names...)
if (miningSchemaAtt.numValues() != incomingAtt.numValues()) {
String warningString =
"[MappingInfo] WARNING: incoming nominal attribute "
+ incomingAtt.name()
+ " does not have the same "
+ "number of values as the corresponding mining "
+ "schema attribute.";
if (m_log != null) {
m_log.logMessage(warningString);
} else {
System.err.println(warningString);
}
}
if (miningSchemaAtt.isNominal() || miningSchemaAtt.isString()) {
int[] valuesMap = new int[incomingAtt.numValues()];
for (int k = 0; k < incomingAtt.numValues(); k++) {
String incomingNomVal = incomingAtt.value(k);
int indexInSchema = miningSchemaAtt.indexOfValue(incomingNomVal);
if (indexInSchema < 0) {
String warningString =
"[MappingInfo] WARNING: incoming nominal attribute "
+ incomingAtt.name()
+ " has value "
+ incomingNomVal
+ " that doesn't occur in the mining schema.";
if (m_log != null) {
m_log.logMessage(warningString);
} else {
System.err.println(warningString);
}
valuesMap[k] = UNKNOWN_NOMINAL_VALUE;
} else {
valuesMap[k] = indexInSchema;
}
}
m_nominalValueMaps[i] = valuesMap;
}
/*if (miningSchemaAtt.isNominal()) {
for (int k = 0; k < miningSchemaAtt.numValues(); k++) {
if (!miningSchemaAtt.value(k).equals(incomingAtt.value(k))) {
throw new Exception("[PMMLUtils] value " + k + " (" +
miningSchemaAtt.value(k) + ") does not match " +
"incoming value (" + incomingAtt.value(k) +
") for attribute " + miningSchemaAtt.name() +
".");
}
}
}*/
found = true;
m_fieldsMap[i] = j;
}
}
if (!found) {
throw new Exception(
"[MappingInfo] Unable to find a match for mining schema "
+ "attribute "
+ schemaAttName
+ " in the "
+ "incoming instances!");
}
}
// check class attribute (if set)
if (fieldsI.classIndex() >= 0) {
if (dataSet.classIndex() < 0) {
// first see if we can find a matching class
String className = fieldsI.classAttribute().name();
Attribute classMatch = dataSet.attribute(className);
if (classMatch == null) {
throw new Exception(
"[MappingInfo] Can't find match for target field "
+ className
+ "in incoming instances!");
}
dataSet.setClass(classMatch);
} else if (!fieldsI.classAttribute().name().equals(dataSet.classAttribute().name())) {
throw new Exception(
"[MappingInfo] class attribute in mining schema does not match "
+ "class attribute in incoming instances!");
}
}
// Set up the textual description of the mapping
fieldsMappingString(fieldsI, dataSet);
}
/**
* Accept and process an instance event
*
* @param e an <code>InstanceEvent</code> value
*/
@Override
public void acceptInstance(InstanceEvent e) {
if (e.getStatus() == InstanceEvent.FORMAT_AVAILABLE) {
m_connectedFormat = e.getStructure();
m_stopRequested.set(false);
try {
init(new Instances(e.getStructure(), 0));
} catch (IllegalArgumentException ex) {
if (m_log != null) {
String message = "ERROR: There is a problem with the incoming instance structure";
// m_log.statusMessage(statusMessagePrefix() + message
// + " - see log for details");
// m_log.logMessage(statusMessagePrefix() + message + " :"
// + ex.getMessage());
stopWithErrorMessage(message, ex);
// m_busy = false;
return;
}
}
String buffSize = m_bufferSize;
try {
buffSize = m_env.substitute(buffSize);
m_bufferSizeI = Integer.parseInt(buffSize);
} catch (Exception ex) {
ex.printStackTrace();
}
m_incrementalBuffer = new ArrayList<InstanceHolder>(m_bufferSizeI);
m_bufferFiles = new ArrayList<File>();
m_streamCounter = 0;
return;
}
m_busy = true;
if (e.getInstance() != null) {
if (m_streamCounter == 0) {
if (m_log != null) {
m_log.statusMessage(statusMessagePrefix() + "Starting streaming sort...");
m_log.logMessage(
"[Sorter] "
+ statusMessagePrefix()
+ " Using streaming buffer size: "
+ m_bufferSizeI);
}
}
InstanceHolder tempH = new InstanceHolder();
tempH.m_instance = e.getInstance();
tempH.m_fileNumber = -1; // unused here
if (m_stringAttIndexes != null) {
copyStringAttVals(tempH);
}
m_incrementalBuffer.add(tempH);
m_streamCounter++;
}
if (e.getInstance() == null || e.getStatus() == InstanceEvent.BATCH_FINISHED) {
emitBufferedInstances();
// thread will set busy to false and report done status when
// complete
return;
} else if (m_incrementalBuffer.size() == m_bufferSizeI) {
// time to sort and write this to a temp file
try {
sortBuffer(true);
} catch (Exception ex) {
String msg = statusMessagePrefix() + "ERROR: unable to write to temp file.";
// if (m_log != null) {
// m_log.statusMessage(msg);
// m_log.logMessage("[" + getCustomName() + "] " + msg);
// }
stopWithErrorMessage(msg, ex);
// ex.printStackTrace();
m_busy = false;
return;
}
}
m_busy = false;
}