@Override
public Map<String, Object> saveMap(Map<String, Object> object, Class clazz) throws Exception {
StringBuilder sql = new StringBuilder();
EntityInfo entityInfo = ClassUtils.getEntityInfoByClazz(clazz);
sql.append("INSERT INTO ");
sql.append(entityInfo.getTableName());
sql.append("(");
List<String> columns = new ArrayList<String>();
List<Object> values = new ArrayList<Object>();
Map<String, String> ptcMap = ClassUtils.propToColumnMap.get(entityInfo.getClazzName());
for (Map.Entry<String, Object> entry : object.entrySet()) {
columns.add(ptcMap.get(entry.getKey()));
values.add(entry.getValue());
}
sql.append(StringUtils.join(columns, ","));
sql.append(") VALUES(");
String[] params = new String[values.size()];
Arrays.fill(params, "?");
sql.append(StringUtils.join(params, ","));
sql.append(")");
if (entityInfo.getStrategy().equals(GenerationType.IDENTITY)) {
Long id = addReutrnId(sql.toString(), values);
if (id != null) {
object.put(entityInfo.getPkName(), id);
}
} else {
add(sql.toString(), values);
}
return object;
}
public void setSwingDataCollection(Collection<ICFSecurityISOCountryObj> value) {
final String S_ProcName = "setSwingDataCollection";
swingDataCollection = value;
if (swingDataCollection == null) {
arrayOfISOCountry = new ICFSecurityISOCountryObj[0];
} else {
int len = value.size();
arrayOfISOCountry = new ICFSecurityISOCountryObj[len];
Iterator<ICFSecurityISOCountryObj> iter = swingDataCollection.iterator();
int idx = 0;
while (iter.hasNext() && (idx < len)) {
arrayOfISOCountry[idx++] = iter.next();
}
if (idx < len) {
throw CFLib.getDefaultExceptionFactory()
.newRuntimeException(
getClass(),
S_ProcName,
"Collection iterator did not fully populate the array copy");
}
if (iter.hasNext()) {
throw CFLib.getDefaultExceptionFactory()
.newRuntimeException(
getClass(),
S_ProcName,
"Collection iterator had left over items when done populating array copy");
}
Arrays.sort(arrayOfISOCountry, compareISOCountryByQualName);
}
PickerTableModel tblDataModel = getDataModel();
if (tblDataModel != null) {
tblDataModel.fireTableDataChanged();
}
}
@Override
public boolean removeMetadataBlob(
UserPublicKey owner, byte[] encodedWritingPublicKey, byte[] writingKeySignedMapKeyPlusBlob) {
UserPublicKey writingKey = new UserPublicKey(encodedWritingPublicKey);
try {
byte[] payload = writingKey.unsignMessage(writingKeySignedMapKeyPlusBlob);
byte[] mapKey = Arrays.copyOfRange(payload, 0, 32);
byte[] metadataBlob =
Arrays.copyOfRange(
payload,
32,
payload
.length); // will be zero length for now // TODO change to the current blob hash
MetadataBlob blob = new MetadataBlob(writingKey.getPublicKeys(), mapKey, metadataBlob);
return blob.delete();
} catch (TweetNaCl.InvalidSignatureException e) {
System.err.println(
"Invalid signature during removeMetadataBlob for owner: "
+ owner
+ " and sharer: "
+ writingKey);
return false;
}
}
public List<ICFAccTaxObj> readAllTax(boolean forceRead) {
final String S_ProcName = "readAllTax";
if ((allTax == null) || forceRead) {
Map<CFAccTaxPKey, ICFAccTaxObj> map = new HashMap<CFAccTaxPKey, ICFAccTaxObj>();
allTax = map;
CFAccTaxBuff[] buffList =
((ICFAccSchema) schema.getBackingStore())
.getTableTax()
.readAllDerived(schema.getAuthorization());
CFAccTaxBuff buff;
ICFAccTaxObj obj;
for (int idx = 0; idx < buffList.length; idx++) {
buff = buffList[idx];
obj = newInstance();
obj.setPKey(((ICFAccSchema) schema.getBackingStore()).getFactoryTax().newPKey());
obj.setBuff(buff);
ICFAccTaxObj realized = (ICFAccTaxObj) obj.realize();
}
}
Comparator<ICFAccTaxObj> cmp =
new Comparator<ICFAccTaxObj>() {
public int compare(ICFAccTaxObj lhs, ICFAccTaxObj rhs) {
if (lhs == null) {
if (rhs == null) {
return (0);
} else {
return (-1);
}
} else if (rhs == null) {
return (1);
} else {
CFAccTaxPKey lhsPKey = lhs.getPKey();
CFAccTaxPKey rhsPKey = rhs.getPKey();
int ret = lhsPKey.compareTo(rhsPKey);
return (ret);
}
}
};
int len = allTax.size();
ICFAccTaxObj arr[] = new ICFAccTaxObj[len];
Iterator<ICFAccTaxObj> valIter = allTax.values().iterator();
int idx = 0;
while ((idx < len) && valIter.hasNext()) {
arr[idx++] = valIter.next();
}
if (idx < len) {
throw CFLib.getDefaultExceptionFactory()
.newArgumentUnderflowException(getClass(), S_ProcName, 0, "idx", idx, len);
} else if (valIter.hasNext()) {
throw CFLib.getDefaultExceptionFactory()
.newArgumentOverflowException(getClass(), S_ProcName, 0, "idx", idx, len);
}
Arrays.sort(arr, cmp);
ArrayList<ICFAccTaxObj> arrayList = new ArrayList<ICFAccTaxObj>(len);
for (idx = 0; idx < len; idx++) {
arrayList.add(arr[idx]);
}
List<ICFAccTaxObj> sortedList = arrayList;
return (sortedList);
}
private LogisticRegressionModel instantiateSparkModel() {
Configuration conf = new Configuration();
conf.set("fs.defaultFS", topologyConfig.getProperty("hdfs.url"));
double[] sparkModelInfo = null;
try {
sparkModelInfo =
getSparkModelInfoFromHDFS(
new Path(topologyConfig.getProperty("hdfs.url") + "/tmp/sparkML_weights"), conf);
} catch (Exception e) {
LOG.error("Couldn't instantiate Spark model in prediction bolt: " + e.getMessage());
e.printStackTrace();
throw new RuntimeException(e);
}
// all numbers besides the last value are the weights
double[] weights = Arrays.copyOfRange(sparkModelInfo, 0, sparkModelInfo.length - 1);
// the last number in the array is the intercept
double intercept = sparkModelInfo[sparkModelInfo.length - 1];
org.apache.spark.mllib.linalg.Vector weightsV = (Vectors.dense(weights));
return new LogisticRegressionModel(weightsV, intercept);
}
SqlDialect get(DataSource dataSource) {
Connection connection = null;
try {
connection = dataSource.getConnection();
DatabaseMetaData metaData = connection.getMetaData();
String productName = metaData.getDatabaseProductName();
String productVersion = metaData.getDatabaseProductVersion();
List key = Arrays.asList(productName, productVersion);
SqlDialect dialect = map.get(key);
if (dialect == null) {
final SqlDialect.DatabaseProduct product =
SqlDialect.getProduct(productName, productVersion);
dialect = new SqlDialect(product, productName, metaData.getIdentifierQuoteString());
map.put(key, dialect);
}
connection.close();
connection = null;
return dialect;
} catch (SQLException e) {
throw new RuntimeException(e);
} finally {
if (connection != null) {
try {
connection.close();
} catch (SQLException e) {
// ignore
}
}
}
}
public void loadData(boolean forceReload) {
ICFFreeSwitchSchemaObj schemaObj = swingSchema.getSchema();
if ((containingCluster == null) || forceReload) {
CFSecurityAuthorization auth = schemaObj.getAuthorization();
long containingClusterId = auth.getSecClusterId();
containingCluster = schemaObj.getClusterTableObj().readClusterByIdIdx(containingClusterId);
}
if ((listOfTenant == null) || forceReload) {
arrayOfTenant = null;
listOfTenant =
schemaObj
.getTenantTableObj()
.readTenantByClusterIdx(containingCluster.getRequiredId(), swingIsInitializing);
if (listOfTenant != null) {
Object objArray[] = listOfTenant.toArray();
if (objArray != null) {
int len = objArray.length;
arrayOfTenant = new ICFSecurityTenantObj[len];
for (int i = 0; i < len; i++) {
arrayOfTenant[i] = (ICFSecurityTenantObj) objArray[i];
}
Arrays.sort(arrayOfTenant, compareTenantByQualName);
}
}
}
}
/**
* Return Regions as Array
*
* @param ctx context
* @return MCountry Array
*/
public static MRegion[] getRegions(Ctx ctx) {
if (s_regions.isEmpty()) loadAllRegions(ctx);
MRegion[] retValue = new MRegion[s_regions.size()];
s_regions.values().toArray(retValue);
Arrays.sort(retValue, new MRegion(ctx, 0, null));
return retValue;
} // getRegions
@Parameterized.Parameters(name = "{index} - {4}")
public static Collection<Object[]> getData() {
return Arrays.asList(
new Object[][] {
{null, "jdbc:h2:mem:test;DB_CLOSE_DELAY=-1", "sa", "", "H2 test"},
{new jdbcDriver(), "jdbc:hsqldb:mem:testmemdb", "SA", "", "HyperSQL DB test"}
});
}
@BeforeClass
public static void doTestSuiteSetup() throws Exception {
/* List all of the object names being used in this entire class.
* The objects are dropped with errors ignored, so it is OK if the
* object does not exist for a particular test.
*/
objDropList = new ArrayList<String>(Arrays.asList("table " + ATABLE_NAME));
doBaseTestSuiteSetup();
}
private static Collection<?> foreach(
ScanRanges scanRanges, int[] widths, KeyRange[] expectedSplits) {
SkipScanFilter filter = new SkipScanFilter(scanRanges.getRanges(), buildSchema(widths));
Scan scan =
new Scan().setFilter(filter).setStartRow(KeyRange.UNBOUND).setStopRow(KeyRange.UNBOUND);
List<Object> ret = Lists.newArrayList();
ret.add(new Object[] {scan, scanRanges, Arrays.<KeyRange>asList(expectedSplits)});
return ret;
}
protected void maybeCreateTables(boolean dropTables) {
boolean createTables = false;
try {
size();
} catch (DataAccessException e) {
createTables = true;
}
Connection connection = getConnection();
try {
startTransaction(connection);
if (dropTables && !createTables) {
// TODO: Logging....
System.err.println("--- dropping tables:");
List<String> tables = new ArrayList<String>(Arrays.asList(TABLES));
Collections.reverse(tables);
for (String table : tables) {
System.err.print("Dropping table " + table);
dropTable(table, connection);
System.err.println("ok!");
}
createTables = true;
}
if (createTables) {
System.err.println("--- creating " + TABLES.length + " tables:");
for (String table : TABLES) {
System.err.print("--- creating table " + table + "...");
InputStream inputStream =
getClass().getClassLoader().getResourceAsStream("ddl/" + table + ".ddl");
if (inputStream == null) {
System.err.println("Could not find DDL file for table " + table + "!");
return;
}
try {
String sql = IOUtils.toString(inputStream);
createTable(sql, connection);
} catch (IOException e) {
System.err.println("Failed!");
e.printStackTrace();
return;
} finally {
IOUtils.closeQuietly(inputStream);
}
System.err.println("ok");
}
}
} catch (DataAccessException e) {
rollback(connection);
} finally {
endTransaction(connection);
close(connection);
}
}
@Override
public boolean setMetadataBlob(
UserPublicKey owner, byte[] encodedWritingPublicKey, byte[] writingKeySignedMapKey) {
UserPublicKey writingKey = new UserPublicKey(encodedWritingPublicKey);
try {
byte[] payload = writingKey.unsignMessage(writingKeySignedMapKey);
byte[] mapKey = Arrays.copyOfRange(payload, 0, 32);
byte[] metadataBlob = Arrays.copyOfRange(payload, 32, payload.length);
MetadataBlob blob = new MetadataBlob(writingKey.getPublicKeys(), mapKey, metadataBlob);
return blob.insert();
} catch (TweetNaCl.InvalidSignatureException e) {
System.err.println(
"Invalid signature during setMetadataBlob for owner: "
+ owner
+ " and sharer: "
+ writingKey);
return false;
}
}
/**
* Return Array of Regions of Country
*
* @param ctx context
* @param C_Country_ID country
* @return MRegion Array
*/
public static MRegion[] getRegions(Ctx ctx, int C_Country_ID) {
if (s_regions.isEmpty()) loadAllRegions(ctx);
ArrayList<MRegion> list = new ArrayList<MRegion>();
Iterator<MRegion> it = s_regions.values().iterator();
while (it.hasNext()) {
MRegion r = it.next();
if (r.getC_Country_ID() == C_Country_ID) list.add(r);
}
// Sort it
MRegion[] retValue = new MRegion[list.size()];
list.toArray(retValue);
Arrays.sort(retValue, new MRegion(ctx, 0, null));
return retValue;
} // getRegions
private static Collection<?> foreach(
KeyRange[][] ranges, int[] widths, KeyRange[] expectedSplits) {
RowKeySchema schema = buildSchema(widths);
List<List<KeyRange>> slots = Lists.transform(Lists.newArrayList(ranges), ARRAY_TO_LIST);
SkipScanFilter filter = new SkipScanFilter(slots, schema);
// Always set start and stop key to max to verify we are using the information in skipscan
// filter over the scan's KMIN and KMAX.
Scan scan =
new Scan().setFilter(filter).setStartRow(KeyRange.UNBOUND).setStopRow(KeyRange.UNBOUND);
ScanRanges scanRanges = ScanRanges.create(slots, schema);
List<Object> ret = Lists.newArrayList();
ret.add(new Object[] {scan, scanRanges, Arrays.<KeyRange>asList(expectedSplits)});
return ret;
}
@Override
public void batchDel(List<Object> ids, Class clazz) throws Exception {
EntityInfo entityInfo = ClassUtils.getEntityInfoByClazz(clazz);
if (entityInfo == null) {
throw new DaoException("无效的实体类class");
}
Object[] objects = new Object[ids.size()];
Arrays.fill(objects, "?");
SqlHelper sqlHelper = SqlHelper.getDeleteHelper(clazz);
sqlHelper
.append(" WHERE ")
.append(entityInfo.getPkClumnName())
.append(" IN (")
.append(StringUtils.join(objects, ","))
.append(")");
update(sqlHelper.getSql(), ids);
}
@Test
public void testSearch_Has() throws SQLException {
Connection connection = null;
ResultSet resultSet = null;
try {
ConnectionManager connectionManager = temporaryFileDatabase.getConnectionManager(true);
initWithTestData(connectionManager);
connection = connectionManager.getConnection(null);
resultSet = DBQueries.search(has(self(Car.class)), NAME, connection);
assertResultSetObjectKeysOrderAgnostic(resultSet, Arrays.asList(1, 2, 3));
} finally {
DBUtils.closeQuietly(connection);
DBUtils.closeQuietly(resultSet);
}
}
//
// Return the methods of an interface in a deterministic
// order. Class.getMethods() does not do us this favor.
//
private Method[] sortMethods(Class iface) throws Exception {
Method[] raw = iface.getMethods();
int count = raw.length;
Method[] cooked = new Method[count];
MethodSortable[] sortables = new MethodSortable[count];
for (int i = 0; i < count; i++) {
sortables[i] = new MethodSortable(raw[i]);
}
Arrays.sort(sortables);
for (int i = 0; i < count; i++) {
cooked[i] = sortables[i].getMethod();
}
return cooked;
}
// debug print the list of methods which throw SQLFeatureNotSupportedException
private void printUnsupportedList(HashSet<String> unsupportedList) {
int count = unsupportedList.size();
if (count == 0) {
return;
}
println("--------------- UNSUPPORTED METHODS ------------------");
println("--");
String[] result = new String[count];
unsupportedList.toArray(result);
Arrays.sort(result);
for (int i = 0; i < count; i++) {
println(result[i]);
}
}
// debug print the list of methods which have disappeared from the SQL interface
private void printVanishedMethodList(HashSet<String> vanishedMethodList) {
int count = vanishedMethodList.size();
if (count == 0) {
return;
}
println("--------------- VANISHED METHODS ------------------");
println("--");
String[] result = new String[count];
vanishedMethodList.toArray(result);
Arrays.sort(result);
for (int i = 0; i < count; i++) {
println(result[i]);
}
}
public void loadData(boolean forceReload) {
ICFBamSchemaObj schemaObj = swingSchema.getSchema();
if ((listOfAccessFrequency == null) || forceReload) {
arrayOfAccessFrequency = null;
listOfAccessFrequency =
schemaObj.getAccessFrequencyTableObj().readAllAccessFrequency(swingIsInitializing);
if (listOfAccessFrequency != null) {
Object objArray[] = listOfAccessFrequency.toArray();
if (objArray != null) {
int len = objArray.length;
arrayOfAccessFrequency = new ICFBamAccessFrequencyObj[len];
for (int i = 0; i < len; i++) {
arrayOfAccessFrequency[i] = (ICFBamAccessFrequencyObj) objArray[i];
}
Arrays.sort(arrayOfAccessFrequency, compareAccessFrequencyByQualName);
}
}
}
}
@Test
public void testSearch_StringStartsWith() throws SQLException {
Connection connection = null;
ResultSet resultSet = null;
try {
ConnectionManager connectionManager = temporaryFileDatabase.getConnectionManager(true);
initWithTestData(connectionManager);
StringStartsWith<Car, String> startsWith = startsWith(Car.FEATURES, "ab");
connection = connectionManager.getConnection(null);
resultSet = DBQueries.search(startsWith, NAME, connection);
assertResultSetObjectKeysOrderAgnostic(resultSet, Arrays.asList(1, 3));
} finally {
DBUtils.closeQuietly(connection);
DBUtils.closeQuietly(resultSet);
}
}
public void loadData(boolean forceReload) {
ICFSecuritySchemaObj schemaObj = swingSchema.getSchema();
if ((listOfISOTimezone == null) || forceReload) {
arrayOfISOTimezone = null;
listOfISOTimezone =
schemaObj.getISOTimezoneTableObj().readAllISOTimezone(swingIsInitializing);
if (listOfISOTimezone != null) {
Object objArray[] = listOfISOTimezone.toArray();
if (objArray != null) {
int len = objArray.length;
arrayOfISOTimezone = new ICFSecurityISOTimezoneObj[len];
for (int i = 0; i < len; i++) {
arrayOfISOTimezone[i] = (ICFSecurityISOTimezoneObj) objArray[i];
}
Arrays.sort(arrayOfISOTimezone, compareISOTimezoneByQualName);
}
}
}
}
// Debug print the list of method failures which we don't understand
private void printNotUnderstoodList(HashSet<String> notUnderstoodList) {
int count = notUnderstoodList.size();
if (count == 0) {
return;
}
println("\n\n");
println("--------------- NOT UNDERSTOOD METHODS ------------------");
println("--");
String[] result = new String[count];
notUnderstoodList.toArray(result);
Arrays.sort(result);
for (int i = 0; i < count; i++) {
println(result[i]);
}
}
public void writePredictionToHDFS(Tuple input, double[] params, double prediction)
throws Exception {
try {
Configuration conf = new Configuration();
conf.set("fs.defaultFS", topologyConfig.getProperty("hdfs.url"));
FileSystem fs = FileSystem.get(conf);
Path pt =
new Path(
topologyConfig.getProperty("hdfs.url")
+ "/tmp/predictions/"
+ System.currentTimeMillis());
BufferedWriter br = new BufferedWriter(new OutputStreamWriter(fs.create(pt, true)));
br.write("Original Event: " + input + "\n");
br.write("\n");
br.write("Certification status (from HBase): " + (params[0] == 1 ? "Y" : "N") + "\n");
br.write("Wage plan (from HBase): " + (params[1] == 1 ? "Miles" : "Hours" + "\n"));
br.write("Hours logged (from HBase): " + params[2] * 100 + "\n");
br.write("Miles logged (from HBase): " + params[3] * 1000 + "\n");
br.write("\n");
br.write("Is Foggy? (from weather API): " + (params[4] == 1 ? "Y" : "N" + "\n"));
br.write("Is Rainy? (from weather API): " + (params[5] == 1 ? "Y" : "N" + "\n"));
br.write("Is Windy? (from weather API): " + (params[6] == 1 ? "Y" : "N" + "\n"));
br.write("\n");
br.write("\n");
br.write("Input to Spark ML model: " + Arrays.toString(params) + "\n");
br.write("\n");
br.write("Prediction from Spark ML model: " + prediction + "\n");
br.flush();
br.close();
} catch (Exception e) {
e.printStackTrace();
}
}
public static void showCSVFileOpenDialog(
String tablename, String parentTable, int parentKeyColumn, int passwordField)
throws FileNotFoundException, IOException, SQLException, NoSuchAlgorithmException {
JFileChooser fopen = new JFileChooser();
javax.swing.filechooser.FileFilter filter =
new FileNameExtensionFilter("Comma Separated Values(CSV) Files", "csv");
fopen.addChoosableFileFilter(filter);
int ret = fopen.showDialog(null, "Open File");
if (ret == JFileChooser.APPROVE_OPTION) {
CSVRead loginCSV = new CSVRead();
String[] deptCheckTables = {"equipment", "user", "class", "subject"};
if (Arrays.asList(deptCheckTables).contains(tablename) && !LoginForm.userRole.equals("sa")) {
loginCSV.setDeptCheck(true);
}
loginCSV.setFilename(fopen.getSelectedFile().toString());
loginCSV.setTablename(tablename);
if (parentTable != null) {
loginCSV.setParentTable(parentTable);
}
if (parentKeyColumn != 0) {
loginCSV.setParentKeyColumn(parentKeyColumn);
}
if (passwordField != 0) {
loginCSV.setPasswordField(passwordField);
}
try {
loginCSV.insertRows();
} catch (FileNotFoundException ex) {
JOptionPane.showMessageDialog(null, "Invalid File");
} catch (IOException ex) {
JOptionPane.showMessageDialog(null, "Invalid Data");
}
} else {
fopen.setVisible(false);
}
}
static {
try {
CON_PROXY_CTOR = createProxyConstructor(ProxyConnection.class);
Class[] argClasses = new Class[0];
RS_CLOSE_METHOD = ResultSet.class.getMethod("close", argClasses);
STMT_CLOSE_METHOD = Statement.class.getMethod("close", argClasses);
CLOSE_ARGS = new Object[0];
OBJECT_METHODS =
Collections.unmodifiableSet(new HashSet(Arrays.asList(Object.class.getMethods())));
} catch (Exception e) {
// e.printStackTrace();
logger.log(
MLevel.SEVERE,
"An Exception occurred in static initializer of" + C3P0PooledConnection.class.getName(),
e);
throw new InternalError(
"Something is very wrong, or this is a pre 1.3 JVM."
+ "We cannot set up dynamic proxies and/or methods!");
}
}
public static int[] getMSPIDs(MSPLocator loc, Connection c) throws SQLException {
Statement s = c.createStatement();
String name = loc.getNameVersion().name;
String version = loc.getNameVersion().version;
ResultSet rs =
s.executeQuery(
"select id from rosettaanalysis where name='"
+ name
+ "' and "
+ "version = '"
+ version
+ "'");
Vector<Integer> values = new Vector<Integer>();
while (rs.next()) {
values.add(rs.getInt(1));
}
s.close();
int[] array = new int[values.size()];
for (int i = 0; i < values.size(); i++) {
array[i] = values.get(i);
}
Arrays.sort(array);
return array;
}
public static void main(String[] args) {
//////////////////////////
// The values in following 4 lines should be user input
int startPos = 200;
int endPos = 1000;
int totalNumPixel = 1044;
double threshhold = 0.0001;
/////////////////////////
int numPixel = endPos - startPos;
double wavelength[] = new double[totalNumPixel];
double photonCount[] = new double[totalNumPixel];
double SpecNoBk[] = new double[numPixel];
double ThisSpectrum[] = new double[numPixel];
double ThisXaxis[] = new double[numPixel];
double Po[] = new double[numPixel];
double Re[] = new double[numPixel];
double P[] = new double[6];
double Re2[] = new double[numPixel - 1];
double mySUM[] = new double[numPixel];
int ind[];
double DEV;
double prevDEV;
Connection connection = null;
Statement stmt = null;
String pattern = "##.##";
try {
Scanner in = new Scanner(new FileReader(args[0]));
int i = 0;
while (in.hasNextDouble()) {
wavelength[i] = in.nextDouble();
photonCount[i] = in.nextDouble();
++i;
}
} catch (FileNotFoundException e) {
e.printStackTrace();
}
ThisSpectrum = Arrays.copyOfRange(photonCount, startPos, endPos);
ThisXaxis = Arrays.copyOfRange(wavelength, startPos, endPos);
final WeightedObservedPoints obs = new WeightedObservedPoints();
for (int i = 0; i < numPixel; i++) {
obs.add(ThisXaxis[i], ThisSpectrum[i]);
}
final PolynomialCurveFitter fitter = PolynomialCurveFitter.create(5);
P = fitter.fit(obs.toList());
Polyval pVal = new Polyval(P, ThisXaxis, numPixel);
Po = pVal.evl();
for (int i = 0; i < numPixel; i++) {
Re[i] = ThisSpectrum[i] - Po[i];
}
for (int i = 0; i < numPixel - 1; i++) {
Re2[i] = Re[i + 1] - Re[i];
}
DEV = Math.sqrt(StatUtils.populationVariance(Re2, 0, Re2.length));
for (int i = 0; i < numPixel; i++) {
mySUM[i] = Po[i] + DEV;
}
int jj = 0; // jj is the length of points to be removed
for (int i = 0; i < numPixel; i++) {
if (ThisSpectrum[i] > mySUM[i]) {
jj++;
;
}
}
ind = new int[jj];
int jjj = 0;
for (int i = 0; i < numPixel; i++) {
if (ThisSpectrum[i] > mySUM[i]) {
ind[jjj] = i;
jjj++;
}
}
int indKeepLength = numPixel - ind.length;
int indKeep[] = new int[indKeepLength];
int k = 0;
for (int i = 0; i < numPixel; i++) {
if (!ArrayUtils.contains(ind, i)) {
indKeep[k] = i;
k++;
}
}
double ThisSpectrumKeep[] = new double[indKeepLength];
double ThisXaxisKeep[] = new double[indKeepLength];
double PoKeep[] = new double[indKeepLength];
double ReKeep[] = new double[indKeepLength];
double Re2Keep[] = new double[indKeepLength - 1];
double mySUMKeep[] = new double[indKeepLength];
for (int i = 0; i < indKeepLength; i++) {
ThisSpectrumKeep[i] = ThisSpectrum[indKeep[i]];
ThisXaxisKeep[i] = ThisXaxis[indKeep[i]];
}
prevDEV = DEV;
// at the point, ThisSpectrum and ThisXaxis should have reduced size
final WeightedObservedPoints obs1 = new WeightedObservedPoints();
for (int i = 0; i < indKeepLength; i++) {
obs1.add(ThisXaxisKeep[i], ThisSpectrumKeep[i]);
}
while (true) {
final PolynomialCurveFitter fitter1 = PolynomialCurveFitter.create(5);
P = fitter1.fit(obs1.toList());
Polyval pVal1 = new Polyval(P, ThisXaxisKeep, indKeepLength);
PoKeep = pVal1.evl();
for (int i = 0; i < indKeepLength; i++) {
ReKeep[i] = ThisSpectrumKeep[i] - PoKeep[i];
}
for (int i = 0; i < indKeepLength - 1; i++) {
Re2Keep[i] = ReKeep[i + 1] - ReKeep[i];
}
DEV = Math.sqrt(StatUtils.populationVariance(Re2Keep, 0, Re2Keep.length));
for (int i = 0; i < indKeepLength; i++) {
mySUMKeep[i] = PoKeep[i] + DEV;
}
for (int i = 0; i < indKeepLength; i++) {
if (ThisSpectrumKeep[i] > mySUMKeep[i]) ThisSpectrumKeep[i] = mySUMKeep[i];
}
if ((Math.abs(DEV - prevDEV) / DEV) < threshhold) break;
prevDEV = DEV;
obs1.clear();
for (int i = 0; i < indKeepLength; i++) {
obs1.add(ThisXaxisKeep[i], ThisSpectrumKeep[i]);
}
}
Polyval pVal2 = new Polyval(P, ThisXaxis, numPixel);
double FLbk[] = pVal2.evl();
for (int i = 0; i < ThisXaxis.length; i++) {
SpecNoBk[i] = ThisSpectrum[i] - FLbk[i];
}
// the write-to-file part is only for testing purpose, ThisXaxis and SpecNoBk are two outputs
try {
FileWriter fr = new FileWriter(args[1]);
BufferedWriter br = new BufferedWriter(fr);
PrintWriter out = new PrintWriter(br);
DecimalFormat df = new DecimalFormat(pattern);
for (int j = 0; j < ThisXaxis.length; j++) {
if (Double.toString(wavelength[j]) != null) out.write(ThisXaxis[j] + "\t" + SpecNoBk[j]);
out.write("\r\n");
}
out.close();
} catch (IOException e) {
System.out.println(e);
}
}
public List<ICFAccTaxObj> readTaxByTenantIdx(long TenantId, boolean forceRead) {
final String S_ProcName = "readTaxByTenantIdx";
CFAccTaxByTenantIdxKey key =
((ICFAccSchema) schema.getBackingStore()).getFactoryTax().newTenantIdxKey();
key.setRequiredTenantId(TenantId);
Map<CFAccTaxPKey, ICFAccTaxObj> dict;
if (indexByTenantIdx == null) {
indexByTenantIdx = new HashMap<CFAccTaxByTenantIdxKey, Map<CFAccTaxPKey, ICFAccTaxObj>>();
}
if ((!forceRead) && indexByTenantIdx.containsKey(key)) {
dict = indexByTenantIdx.get(key);
} else {
dict = new HashMap<CFAccTaxPKey, ICFAccTaxObj>();
// Allow other threads to dirty-read while we're loading
indexByTenantIdx.put(key, dict);
ICFAccTaxObj obj;
CFAccTaxBuff[] buffList =
((ICFAccSchema) schema.getBackingStore())
.getTableTax()
.readDerivedByTenantIdx(schema.getAuthorization(), TenantId);
CFAccTaxBuff buff;
for (int idx = 0; idx < buffList.length; idx++) {
buff = buffList[idx];
obj = schema.getTaxTableObj().newInstance();
obj.setPKey(((ICFAccSchema) schema.getBackingStore()).getFactoryTax().newPKey());
obj.setBuff(buff);
ICFAccTaxObj realized = (ICFAccTaxObj) obj.realize();
}
}
Comparator<ICFAccTaxObj> cmp =
new Comparator<ICFAccTaxObj>() {
public int compare(ICFAccTaxObj lhs, ICFAccTaxObj rhs) {
if (lhs == null) {
if (rhs == null) {
return (0);
} else {
return (-1);
}
} else if (rhs == null) {
return (1);
} else {
CFAccTaxPKey lhsPKey = lhs.getPKey();
CFAccTaxPKey rhsPKey = rhs.getPKey();
int ret = lhsPKey.compareTo(rhsPKey);
return (ret);
}
}
};
int len = dict.size();
ICFAccTaxObj arr[] = new ICFAccTaxObj[len];
Iterator<ICFAccTaxObj> valIter = dict.values().iterator();
int idx = 0;
while ((idx < len) && valIter.hasNext()) {
arr[idx++] = valIter.next();
}
if (idx < len) {
throw CFLib.getDefaultExceptionFactory()
.newArgumentUnderflowException(getClass(), S_ProcName, 0, "idx", idx, len);
} else if (valIter.hasNext()) {
throw CFLib.getDefaultExceptionFactory()
.newArgumentOverflowException(getClass(), S_ProcName, 0, "idx", idx, len);
}
Arrays.sort(arr, cmp);
ArrayList<ICFAccTaxObj> arrayList = new ArrayList<ICFAccTaxObj>(len);
for (idx = 0; idx < len; idx++) {
arrayList.add(arr[idx]);
}
List<ICFAccTaxObj> sortedList = arrayList;
return (sortedList);
}