List of usage examples for java.io DataInputStream readDouble
public final double readDouble() throws IOException
readDouble method of DataInput. From source file:ch.unil.genescore.vegas.Snp.java
/** * Read this snp from the binary file. Format is: * 1. genotypes_.length/*from www .j a va 2 s. c om*/ * 2. genotypes_ * 3. maf_ * 4. alleleSd_ * 5. alleleMean_ * @throws IOException */ public void readGenotype(DataInputStream is) throws IOException { // id_ is already read genotypes_ = new byte[genotypeLength_]; for (int i = 0; i < genotypeLength_; i++) genotypes_[i] = is.readByte(); maf_ = is.readDouble(); alleleMean_ = is.readDouble(); alleleSd_ = is.readDouble(); }
From source file:darks.learning.word2vec.Word2Vec.java
/** * Load model file/*from www . j a v a2s . c om*/ * * @param file Model file */ public void loadModel(File file) { DataInputStream dis = null; try { log.info("Reading word2vec model from " + file); dis = new DataInputStream(new BufferedInputStream(new FileInputStream(file))); int wordSize = dis.readInt(); int featureSize = dis.readInt(); wordNodes.clear(); for (int i = 0; i < wordSize; i++) { DoubleMatrix feature = new DoubleMatrix(featureSize); int nameLen = dis.readInt(); byte[] bits = new byte[nameLen]; dis.read(bits, 0, nameLen); String name = new String(bits); double len = 0; for (int f = 0; f < featureSize; f++) { double w = dis.readDouble(); feature.put(f, w); len += w * w; } len = FastMath.sqrt(len); // feature.divi(len); wordNodes.put(name, new WordNode(name, feature)); } log.info("Succeed to read word2vec model. Word dictionary size " + wordNodes.size()); } catch (Exception e) { log.error(e.getMessage(), e); } finally { IOUtils.closeStream(dis); } }
From source file:MersenneTwisterFast.java
/** Reads the entire state of the MersenneTwister RNG from the stream * @param stream input stream//from w w w. java 2 s .com * @throws IOException exception from stream reading */ public void readState(DataInputStream stream) throws IOException { int len = mt.length; for (int x = 0; x < len; x++) mt[x] = stream.readInt(); len = mag01.length; for (int x = 0; x < len; x++) mag01[x] = stream.readInt(); mti = stream.readInt(); __nextNextGaussian = stream.readDouble(); __haveNextNextGaussian = stream.readBoolean(); }
From source file:org.nd4j.linalg.util.ArrayUtil.java
public static double[] read(int length, DataInputStream dis) throws IOException { double[] ret = new double[length]; for (int i = 0; i < length; i++) ret[i] = dis.readDouble(); return ret;//from w w w . j a va 2 s.c om }
From source file:org.nd4j.linalg.util.ArrayUtil.java
public static double[] readDouble(int length, DataInputStream dis) throws IOException { double[] ret = new double[length]; for (int i = 0; i < length; i++) ret[i] = dis.readDouble(); return ret;/*w ww .java 2 s . c o m*/ }
From source file:org.openmrs.module.odkconnector.serialization.serializer.ListSerializerTest.java
@Test public void serialize_shouldSerializePatientInformation() throws Exception { File file = File.createTempFile("PatientSerialization", "Example"); GZIPOutputStream outputStream = new GZIPOutputStream(new BufferedOutputStream(new FileOutputStream(file))); log.info("Writing to: " + file.getAbsolutePath()); Cohort cohort = new Cohort(); cohort.addMember(6);//from w w w . j a v a 2 s.c o m cohort.addMember(7); cohort.addMember(8); List<Patient> patients = new ArrayList<Patient>(); List<Obs> observations = new ArrayList<Obs>(); List<Form> forms = new ArrayList<Form>(); for (Integer patientId : cohort.getMemberIds()) { Patient patient = Context.getPatientService().getPatient(patientId); observations.addAll(Context.getObsService().getObservationsByPerson(patient)); patients.add(patient); } Serializer serializer = HandlerUtil.getPreferredHandler(Serializer.class, List.class); serializer.write(outputStream, patients); serializer.write(outputStream, observations); serializer.write(outputStream, forms); outputStream.close(); GZIPInputStream inputStream = new GZIPInputStream(new BufferedInputStream(new FileInputStream(file))); DataInputStream dataInputStream = new DataInputStream(inputStream); // total number of patients Integer patientCounter = dataInputStream.readInt(); System.out.println("Patient Counter: " + patientCounter); for (int i = 0; i < patientCounter; i++) { System.out.println("=================Patient====================="); System.out.println("Patient Id: " + dataInputStream.readInt()); System.out.println("Family Name: " + dataInputStream.readUTF()); System.out.println("Middle Name: " + dataInputStream.readUTF()); System.out.println("Last Name: " + dataInputStream.readUTF()); System.out.println("Gender: " + dataInputStream.readUTF()); System.out.println("Birth Date: " + dataInputStream.readLong()); System.out.println("Identifier" + dataInputStream.readUTF()); } Integer obsCounter = dataInputStream.readInt(); for (int j = 0; j < obsCounter; j++) { System.out.println("==================Observation================="); System.out.println("Patient Id: " + dataInputStream.readInt()); System.out.println("Concept Name: " + dataInputStream.readUTF()); byte type = dataInputStream.readByte(); if (type == ObsSerializer.TYPE_STRING) System.out.println("Value: " + dataInputStream.readUTF()); else if (type == ObsSerializer.TYPE_INT) System.out.println("Value: " + dataInputStream.readInt()); else if (type == ObsSerializer.TYPE_DOUBLE) System.out.println("Value: " + dataInputStream.readDouble()); else if (type == ObsSerializer.TYPE_DATE) System.out.println("Value: " + dataInputStream.readLong()); System.out.println("Time: " + dataInputStream.readLong()); } Integer formCounter = dataInputStream.readInt(); for (int j = 0; j < formCounter; j++) { System.out.println("==================Form================="); System.out.println("Form Id: " + dataInputStream.readInt()); } System.out.println(); inputStream.close(); }
From source file:org.openmrs.module.odkconnector.serialization.serializer.openmrs.PatientSerializerTest.java
@Test public void serialize_shouldSerializePatientInformation() throws Exception { File file = File.createTempFile("PatientSerialization", "Example"); GZIPOutputStream outputStream = new GZIPOutputStream(new BufferedOutputStream(new FileOutputStream(file))); log.info("Writing to: " + file.getAbsolutePath()); Cohort cohort = new Cohort(); cohort.addMember(6);/* w w w. j a v a2 s . co m*/ cohort.addMember(7); cohort.addMember(8); List<Patient> patients = new ArrayList<Patient>(); List<Obs> observations = new ArrayList<Obs>(); List<Form> forms = new ArrayList<Form>(); for (Integer patientId : cohort.getMemberIds()) { Patient patient = Context.getPatientService().getPatient(patientId); observations.addAll(Context.getObsService().getObservationsByPerson(patient)); patients.add(patient); } Serializer serializer = HandlerUtil.getPreferredHandler(Serializer.class, List.class); serializer.write(outputStream, patients); serializer.write(outputStream, observations); serializer.write(outputStream, forms); outputStream.close(); GZIPInputStream inputStream = new GZIPInputStream(new BufferedInputStream(new FileInputStream(file))); DataInputStream dataInputStream = new DataInputStream(inputStream); // total number of patients Integer patientCounter = dataInputStream.readInt(); System.out.println("Patient Counter: " + patientCounter); for (int i = 0; i < patientCounter; i++) { System.out.println("=================Patient====================="); System.out.println("Patient Id: " + dataInputStream.readInt()); System.out.println("Family Name: " + dataInputStream.readUTF()); System.out.println("Middle Name: " + dataInputStream.readUTF()); System.out.println("Last Name: " + dataInputStream.readUTF()); System.out.println("Gender: " + dataInputStream.readUTF()); System.out.println("Birth Date: " + dataInputStream.readUTF()); System.out.println("Identifier" + dataInputStream.readUTF()); } Integer obsCounter = dataInputStream.readInt(); for (int j = 0; j < obsCounter; j++) { System.out.println("==================Observation================="); System.out.println("Patient Id: " + dataInputStream.readInt()); System.out.println("Concept Name: " + dataInputStream.readUTF()); byte type = dataInputStream.readByte(); if (type == ObsSerializer.TYPE_STRING) System.out.println("Value: " + dataInputStream.readUTF()); else if (type == ObsSerializer.TYPE_INT) System.out.println("Value: " + dataInputStream.readInt()); else if (type == ObsSerializer.TYPE_DOUBLE) System.out.println("Value: " + dataInputStream.readDouble()); else if (type == ObsSerializer.TYPE_DATE) System.out.println("Value: " + dataInputStream.readUTF()); System.out.println("Time: " + dataInputStream.readUTF()); } Integer formCounter = dataInputStream.readInt(); for (int j = 0; j < formCounter; j++) { System.out.println("==================Form================="); System.out.println("Form Id: " + dataInputStream.readInt()); } System.out.println(); inputStream.close(); }
From source file:org.bdval.cache.TableCache.java
/** * Retrieve a cached table from the cache. isTableCached should be called * before calling this to verify that the table is cached. Null will * be returned if the table wasn't in the cache or there was a problem * reading the table./*from w w w . ja v a 2 s.c om*/ * * @param splitId The split id * @param splitType The Split type * @param datasetName The dataset name * @param geneListFilter A gene list. If not null, the gene list is queried with each double * column identifier to determine if the identifier is contained in the gene list. Columns * that do not match the gene list are not loaded. * @return the table read from the cache (or null if it could not be read) */ public Table getCachedTable(final int splitId, final String splitType, final String datasetName, final GeneList geneListFilter) { final File cachedTableFile = getCachedTableFile(splitId, splitType, datasetName); if (geneListFilter != null && !(geneListFilter instanceof FullGeneList)) { final ObjectSet<CharSequence> tableColumnIds = getTableColumnIds(splitId, splitType, datasetName); geneListFilter.calculateProbeSetSelection(tableColumnIds); } DataInputStream dataInput = null; try { dataInput = new DataInputStream(new FastBufferedInputStream(new FileInputStream(cachedTableFile))); final ArrayTable result = new ArrayTable(); final int numberOfColumns = dataInput.readInt(); LOG.info("Reading cached table with " + numberOfColumns + " columns"); for (int i = 0; i < numberOfColumns; i++) { final String colType = dataInput.readUTF(); final String colId = dataInput.readUTF(); if ("s".equals(colType)) { final int numStrings = dataInput.readInt(); resize(result, numStrings); final int columnIndex = result.addColumn(colId, String.class); for (int j = 0; j < numStrings; j++) { result.appendObject(columnIndex, dataInput.readUTF()); } } else if ("d".equals(colType)) { final int numDoubles = dataInput.readInt(); resize(result, numDoubles); if (geneListFilter != null && !geneListFilter.isProbesetInList(colId)) { // the column does not match the gene list. Skip this column // we don't need to read these doubles, just skip them; final int numBytes = Double.SIZE * numDoubles / 8; final int actualBytes = dataInput.skipBytes(numBytes); if (actualBytes != numBytes) { LOG.warn("actual bytes skipped (" + actualBytes + ") does" + "not equal expected of " + numBytes); } continue; } final int columnIndex = result.addColumn(colId, double.class); for (int j = 0; j < numDoubles; j++) { result.appendDoubleValue(columnIndex, dataInput.readDouble()); } } else { LOG.error("UNKNOWN COLUMN TYPE " + colType + " cannot read cached table from file " + filenameOf(cachedTableFile)); return null; } } return result; } catch (IOException e) { LOG.error(e); return null; } catch (TypeMismatchException e) { LOG.error("TypeMismatchException adding data to Table " + filenameOf(cachedTableFile), e); return null; } finally { IOUtils.closeQuietly(dataInput); } }
From source file:com.alphabetbloc.accessmrs.services.SyncManager.java
private void insertPatientForms(final DataInputStream zdis) throws Exception { long start = System.currentTimeMillis(); SimpleDateFormat output = new SimpleDateFormat("MMM dd, yyyy"); SimpleDateFormat input = new SimpleDateFormat("yyyy-MM-dd"); SQLiteDatabase db = DbProvider.getDb(); InsertHelper ih = new InsertHelper(db, DataModel.OBSERVATIONS_TABLE); int ptIdIndex = ih.getColumnIndex(DataModel.KEY_PATIENT_ID); int obsTextIndex = ih.getColumnIndex(DataModel.KEY_VALUE_TEXT); int obsNumIndex = ih.getColumnIndex(DataModel.KEY_VALUE_NUMERIC); int obsDateIndex = ih.getColumnIndex(DataModel.KEY_VALUE_DATE); int obsIntIndex = ih.getColumnIndex(DataModel.KEY_VALUE_INT); int obsFieldIndex = ih.getColumnIndex(DataModel.KEY_FIELD_NAME); int obsTypeIndex = ih.getColumnIndex(DataModel.KEY_DATA_TYPE); int obsEncDateIndex = ih.getColumnIndex(DataModel.KEY_ENCOUNTER_DATE); db.beginTransaction();/*from ww w . j a v a 2s . co m*/ sLoopProgress.set(0); try { sLoopCount.set(zdis.readInt()); if (App.DEBUG) Log.v(TAG, "insertPatientForms icount: " + sLoopCount); for (int i = 1; i < sLoopCount.get() + 1; i++) { ih.prepareForInsert(); ih.bind(ptIdIndex, zdis.readInt()); ih.bind(obsFieldIndex, zdis.readUTF()); byte dataType = zdis.readByte(); if (dataType == DataModel.TYPE_STRING) { ih.bind(obsTextIndex, zdis.readUTF()); } else if (dataType == DataModel.TYPE_INT) { ih.bind(obsIntIndex, zdis.readInt()); } else if (dataType == DataModel.TYPE_DOUBLE) { ih.bind(obsNumIndex, zdis.readDouble()); } else if (dataType == DataModel.TYPE_DATE) { ih.bind(obsDateIndex, parseDate(input, output, zdis.readUTF())); } ih.bind(obsTypeIndex, dataType); ih.bind(obsEncDateIndex, parseDate(input, output, zdis.readUTF())); ih.execute(); sLoopProgress.getAndIncrement(); } db.setTransactionSuccessful(); } finally { ih.close(); db.endTransaction(); } long end = System.currentTimeMillis(); if (App.DEBUG) Log.v("SYNC BENCHMARK", String.format("Total Patient-Forms: \n%d\nTotal Time: \n%d\nRecords per second: \n%.2f", sLoopCount.get(), (int) (end - start), 1000 * (double) sLoopCount.get() / (double) (end - start))); }
From source file:org.apache.pulsar.testclient.LoadSimulationClient.java
private void handle(final byte command, final DataInputStream inputStream, final DataOutputStream outputStream) throws Exception { final TradeConfiguration tradeConf = new TradeConfiguration(); tradeConf.command = command;//from ww w . jav a2s .c o m switch (command) { case CHANGE_COMMAND: // Change the topic's settings if it exists. decodeProducerOptions(tradeConf, inputStream); if (topicsToTradeUnits.containsKey(tradeConf.topic)) { topicsToTradeUnits.get(tradeConf.topic).change(tradeConf); } break; case STOP_COMMAND: // Stop the topic if it exists. tradeConf.topic = inputStream.readUTF(); if (topicsToTradeUnits.containsKey(tradeConf.topic)) { topicsToTradeUnits.get(tradeConf.topic).stop.set(true); } break; case TRADE_COMMAND: // Create the topic. It is assumed that the topic does not already exist. decodeProducerOptions(tradeConf, inputStream); final TradeUnit tradeUnit = new TradeUnit(tradeConf, client, producerConf, consumerConf, payloadCache); topicsToTradeUnits.put(tradeConf.topic, tradeUnit); executor.submit(() -> { try { final String topic = tradeConf.topic; final String namespace = topic.substring("persistent://".length(), topic.lastIndexOf('/')); try { admin.namespaces().createNamespace(namespace); } catch (PulsarAdminException.ConflictException e) { // Ignore, already created namespace. } tradeUnit.start(); } catch (Exception ex) { throw new RuntimeException(ex); } }); break; case CHANGE_GROUP_COMMAND: // Change the settings of all topics belonging to a group. decodeGroupOptions(tradeConf, inputStream); tradeConf.size = inputStream.readInt(); tradeConf.rate = inputStream.readDouble(); // See if a topic belongs to this tenant and group using this regex. final String groupRegex = ".*://" + tradeConf.tenant + "/.*/" + tradeConf.group + "-.*/.*"; for (Map.Entry<String, TradeUnit> entry : topicsToTradeUnits.entrySet()) { final String destination = entry.getKey(); final TradeUnit unit = entry.getValue(); if (destination.matches(groupRegex)) { unit.change(tradeConf); } } break; case STOP_GROUP_COMMAND: // Stop all topics belonging to a group. decodeGroupOptions(tradeConf, inputStream); // See if a topic belongs to this tenant and group using this regex. final String regex = ".*://" + tradeConf.tenant + "/.*/" + tradeConf.group + "-.*/.*"; for (Map.Entry<String, TradeUnit> entry : topicsToTradeUnits.entrySet()) { final String destination = entry.getKey(); final TradeUnit unit = entry.getValue(); if (destination.matches(regex)) { unit.stop.set(true); } } break; case FIND_COMMAND: // Write a single boolean indicating if the topic was found. outputStream.writeBoolean(topicsToTradeUnits.containsKey(inputStream.readUTF())); outputStream.flush(); break; default: throw new IllegalArgumentException("Unrecognized command code received: " + command); } }