/**
* The results of the {@link SR_EELS_CharacterisationPlugin} plugin are parsed.
*
* <p>This function extracts the values that describe the pathway of the borders of a spectrum.
*
* @return a polynomial that fits the given data points
*/
private SR_EELS_Polynomial_2D getFunctionBorders() {
final double[][] vals = new double[3 * importer.size()][3];
int i = 0;
for (final float[] point : importer) {
for (int j = 0; j < 3; j++) {
// y coordinate of the fit function at the centre of the
// image/camera ->
// z value
vals[i + j][0] = point[2 + 2 * j] - CameraSetup.getFullWidth() / 2;
// Coordinate on the energy dispersive axis -> x value
// The same value for top, centre and bottom.
vals[i + j][1] = point[0] - CameraSetup.getFullHeight() / 2;
// coordinate on the lateral axis -> y value
// The indices for centre, top and bottom are 2, 4 and 6.
vals[i + j][2] =
importer.getYInterceptPoint(i / 3)[11 + j] - CameraSetup.getFullHeight() / 2;
}
i += 3;
}
/*
* Define the orders of the 2D polynomial.
*/
final int m = 3;
final int n = 2;
final SR_EELS_Polynomial_2D func = new SR_EELS_Polynomial_2D(m, n);
final double[] a_fit = new double[(m + 1) * (n + 1)];
Arrays.fill(a_fit, 1.);
final LMA lma = new LMA(func, a_fit, vals);
lma.fit();
/*
* TODO: Output information about the fit using IJ.log
*/
return new SR_EELS_Polynomial_2D(m, n, a_fit);
}
@SuppressWarnings("unchecked")
private void addFields(
DataConfig.Entity entity, DocWrapper doc, Map<String, Object> arow, VariableResolver vr) {
for (Map.Entry<String, Object> entry : arow.entrySet()) {
String key = entry.getKey();
Object value = entry.getValue();
if (value == null) continue;
if (key.startsWith("$")) continue;
List<DataConfig.Field> field = entity.colNameVsField.get(key);
if (field == null && dataImporter.getSchema() != null) {
// This can be a dynamic field or a field which does not have an entry in data-config ( an
// implicit field)
SchemaField sf = dataImporter.getSchema().getFieldOrNull(key);
if (sf == null) {
sf = dataImporter.getConfig().lowerNameVsSchemaField.get(key.toLowerCase(Locale.ENGLISH));
}
if (sf != null) {
addFieldToDoc(entry.getValue(), sf.getName(), 1.0f, sf.multiValued(), doc);
}
// else do nothing. if we add it it may fail
} else {
if (field != null) {
for (DataConfig.Field f : field) {
String name = f.getName();
if (f.dynamicName) {
name = vr.replaceTokens(name);
}
if (f.toWrite) addFieldToDoc(entry.getValue(), name, f.boost, f.multiValued, doc);
}
}
}
}
}
/**
* The results of the {@link SR_EELS_CharacterisationPlugin} plugin are parsed.
*
* <p>This function extracts the values that describe the width of a spectrum depending on its
* position on the camera.
*
* @return a polynomial that fits the given data points
*/
private SR_EELS_Polynomial_2D getFunctionWidth() {
final double[][] vals = new double[importer.size()][3];
int i = 0;
for (final float[] point : importer) {
// The width of the spectrum -> z value
vals[i][0] = point[8];
// Coordinate on the energy dispersive axis -> x value
// The same value for top, centre and bottom.
vals[i][1] = point[0] - CameraSetup.getFullWidth() / 2;
// coordinate on the lateral axis -> y value
// The indices for centre, top and bottom are 2, 4 and 6.
vals[i][2] = point[2] - CameraSetup.getFullHeight() / 2;
i++;
}
/*
* Define the orders of the 2D polynomial.
*/
final int m = 2;
final int n = 2;
final SR_EELS_Polynomial_2D func = new SR_EELS_Polynomial_2D(m, n);
final double[] b_fit = new double[(m + 1) * (n + 1)];
Arrays.fill(b_fit, 1.);
final LMA lma = new LMA(func, b_fit, vals);
lma.fit();
/*
* TODO: Output information about the fit using IJ.log
*/
return new SR_EELS_Polynomial_2D(m, n, b_fit);
}
private void invokeEventListener(String className) {
try {
EventListener listener =
(EventListener) loadClass(className, dataImporter.getCore()).newInstance();
notifyListener(listener);
} catch (Exception e) {
wrapAndThrow(SEVERE, e, "Unable to load class : " + className);
}
}
private void notifyListener(EventListener listener) {
String currentProcess;
if (dataImporter.getStatus() == DataImporter.Status.RUNNING_DELTA_DUMP) {
currentProcess = Context.DELTA_DUMP;
} else {
currentProcess = Context.FULL_DUMP;
}
listener.onEvent(
new ContextImpl(null, getVariableResolver(), null, currentProcess, session, null, this));
}
@SuppressWarnings("unchecked")
private void doFullDump() {
addStatusMessage("Full Dump Started");
if (dataImporter.getConfig().isMultiThreaded && !verboseDebug) {
try {
LOG.info("running multithreaded full-import");
new EntityRunner(root, null).run(null, Context.FULL_DUMP, null);
} catch (Exception e) {
LOG.error("error in import", e);
}
} else {
buildDocument(getVariableResolver(), null, null, root, true, null);
}
}
public VariableResolverImpl getVariableResolver() {
try {
VariableResolverImpl resolver = null;
if (dataImporter != null && dataImporter.getCore() != null) {
resolver =
new VariableResolverImpl(
dataImporter.getCore().getResourceLoader().getCoreProperties());
} else resolver = new VariableResolverImpl();
Map<String, Object> indexerNamespace = new HashMap<String, Object>();
if (persistedProperties.getProperty(LAST_INDEX_TIME) != null) {
indexerNamespace.put(LAST_INDEX_TIME, persistedProperties.getProperty(LAST_INDEX_TIME));
} else {
// set epoch
indexerNamespace.put(LAST_INDEX_TIME, DataImporter.DATE_TIME_FORMAT.get().format(EPOCH));
}
indexerNamespace.put(INDEX_START_TIME, dataImporter.getIndexStartTime());
indexerNamespace.put("request", requestParameters.requestParams);
indexerNamespace.put("functions", functionsNamespace);
for (DataConfig.Entity entity : dataImporter.getConfig().document.entities) {
String key = entity.name + "." + SolrWriter.LAST_INDEX_KEY;
String lastIndex = persistedProperties.getProperty(key);
if (lastIndex != null) {
indexerNamespace.put(key, lastIndex);
} else {
indexerNamespace.put(key, DataImporter.DATE_TIME_FORMAT.get().format(EPOCH));
}
}
resolver.addNamespace(DataConfig.IMPORTER_NS_SHORT, indexerNamespace);
resolver.addNamespace(DataConfig.IMPORTER_NS, indexerNamespace);
return resolver;
} catch (Exception e) {
wrapAndThrow(SEVERE, e);
// unreachable statement
return null;
}
}
private EntityProcessorWrapper getEntityProcessor(DataConfig.Entity entity) {
if (entity.processor != null) return entity.processor;
EntityProcessor entityProcessor = null;
if (entity.proc == null) {
entityProcessor = new SqlEntityProcessor();
} else {
try {
entityProcessor =
(EntityProcessor) loadClass(entity.proc, dataImporter.getCore()).newInstance();
} catch (Exception e) {
wrapAndThrow(
SEVERE, e, "Unable to load EntityProcessor implementation for entity:" + entity.name);
}
}
return entity.processor = new EntityProcessorWrapper(entityProcessor, this);
}
@SuppressWarnings("unchecked")
public void execute() {
dataImporter.store(DataImporter.STATUS_MSGS, statusMessages);
document = dataImporter.getConfig().document;
final AtomicLong startTime = new AtomicLong(System.currentTimeMillis());
statusMessages.put(
TIME_ELAPSED,
new Object() {
public String toString() {
return getTimeElapsedSince(startTime.get());
}
});
statusMessages.put(DataImporter.MSG.TOTAL_QUERIES_EXECUTED, importStatistics.queryCount);
statusMessages.put(DataImporter.MSG.TOTAL_ROWS_EXECUTED, importStatistics.rowsCount);
statusMessages.put(DataImporter.MSG.TOTAL_DOC_PROCESSED, importStatistics.docCount);
statusMessages.put(DataImporter.MSG.TOTAL_DOCS_SKIPPED, importStatistics.skipDocCount);
List<String> entities = requestParameters.entities;
// Trigger onImportStart
if (document.onImportStart != null) {
invokeEventListener(document.onImportStart);
}
AtomicBoolean fullCleanDone = new AtomicBoolean(false);
// we must not do a delete of *:* multiple times if there are multiple root entities to be run
Properties lastIndexTimeProps = new Properties();
lastIndexTimeProps.setProperty(
LAST_INDEX_KEY,
DataImporter.DATE_TIME_FORMAT.get().format(dataImporter.getIndexStartTime()));
for (DataConfig.Entity e : document.entities) {
if (entities != null && !entities.contains(e.name)) continue;
lastIndexTimeProps.setProperty(
e.name + "." + LAST_INDEX_KEY, DataImporter.DATE_TIME_FORMAT.get().format(new Date()));
root = e;
String delQuery = e.allAttributes.get("preImportDeleteQuery");
if (dataImporter.getStatus() == DataImporter.Status.RUNNING_DELTA_DUMP) {
cleanByQuery(delQuery, fullCleanDone);
doDelta();
delQuery = e.allAttributes.get("postImportDeleteQuery");
if (delQuery != null) {
fullCleanDone.set(false);
cleanByQuery(delQuery, fullCleanDone);
}
} else {
cleanByQuery(delQuery, fullCleanDone);
doFullDump();
delQuery = e.allAttributes.get("postImportDeleteQuery");
if (delQuery != null) {
fullCleanDone.set(false);
cleanByQuery(delQuery, fullCleanDone);
}
}
statusMessages.remove(DataImporter.MSG.TOTAL_DOC_PROCESSED);
}
if (stop.get()) {
// Dont commit if aborted using command=abort
statusMessages.put("Aborted", DataImporter.DATE_TIME_FORMAT.get().format(new Date()));
rollback();
} else {
// Do not commit unnecessarily if this is a delta-import and no documents were created or
// deleted
if (!requestParameters.clean) {
if (importStatistics.docCount.get() > 0 || importStatistics.deletedDocCount.get() > 0) {
finish(lastIndexTimeProps);
}
} else {
// Finished operation normally, commit now
finish(lastIndexTimeProps);
}
if (writer != null) {
writer.finish();
}
if (document.onImportEnd != null) {
invokeEventListener(document.onImportEnd);
}
}
statusMessages.remove(TIME_ELAPSED);
statusMessages.put(DataImporter.MSG.TOTAL_DOC_PROCESSED, "" + importStatistics.docCount.get());
if (importStatistics.failedDocCount.get() > 0)
statusMessages.put(
DataImporter.MSG.TOTAL_FAILED_DOCS, "" + importStatistics.failedDocCount.get());
statusMessages.put("Time taken ", getTimeElapsedSince(startTime.get()));
LOG.info("Time taken = " + getTimeElapsedSince(startTime.get()));
}