List of usage examples for java.nio ByteBuffer get
public abstract byte get();
From source file:edu.harvard.iq.dvn.ingest.statdataio.impl.plugins.por.PORFileReader.java
private File decodeHeader(BufferedInputStream stream) throws IOException { File tempPORfile = null;//from w w w . j a v a 2 s . c o m if (stream == null) { throw new IllegalArgumentException("file == null!"); } byte[] headerByes = new byte[POR_HEADER_SIZE]; if (stream.markSupported()) { stream.mark(1000); } int nbytes = stream.read(headerByes, 0, POR_HEADER_SIZE); //printHexDump(headerByes, "hex dump of the byte-array"); if (nbytes == 0) { throw new IOException("decodeHeader: reading failure"); } else if (nbytes < 491) { // Size test: by defnition, it must have at least // 491-byte header, i.e., the file size less than this threshold // is not a POR file dbgLog.fine("this file is NOT spss-por type"); throw new IllegalArgumentException("file is not spss-por type"); } // rewind the current reading position back to the beginning if (stream.markSupported()) { stream.reset(); } // line-terminating characters are usually one or two by defnition // however, a POR file saved by a genuine SPSS for Windows // had a three-character line terminator, i.e., failed to remove the // original file's one-character terminator when it was opened, and // saved it with the default two-character terminator without // removing original terminators. So we have to expect such a rare // case // // terminator // windows [0D0A]=> [1310] = [CR/LF] // unix [0A] => [10] // mac [0D] => [13] // 3char [0D0D0A]=> [131310] spss for windows rel 15 // // terminating characters should be found at the following // column positions[counting from 0]: // unix case: [0A] : [80], [161], [242], [323], [404], [485] // windows case: [0D0A] : [81], [163], [245], [327], [409], [491] // : [0D0D0A] : [82], [165], [248], [331], [414], [495] // convert b into a ByteBuffer ByteBuffer buff = ByteBuffer.wrap(headerByes); byte[] nlch = new byte[36]; int pos1; int pos2; int pos3; int ucase = 0; int wcase = 0; int mcase = 0; int three = 0; int nolines = 6; int nocols = 80; for (int i = 0; i < nolines; ++i) { int baseBias = nocols * (i + 1); // 1-char case pos1 = baseBias + i; buff.position(pos1); dbgLog.finer("\tposition(1)=" + buff.position()); int j = 6 * i; nlch[j] = buff.get(); if (nlch[j] == 10) { ucase++; } else if (nlch[j] == 13) { mcase++; } // 2-char case pos2 = baseBias + 2 * i; buff.position(pos2); dbgLog.finer("\tposition(2)=" + buff.position()); nlch[j + 1] = buff.get(); nlch[j + 2] = buff.get(); // 3-char case pos3 = baseBias + 3 * i; buff.position(pos3); dbgLog.finer("\tposition(3)=" + buff.position()); nlch[j + 3] = buff.get(); nlch[j + 4] = buff.get(); nlch[j + 5] = buff.get(); dbgLog.finer(i + "-th iteration position =" + nlch[j] + "\t" + nlch[j + 1] + "\t" + nlch[j + 2]); dbgLog.finer(i + "-th iteration position =" + nlch[j + 3] + "\t" + nlch[j + 4] + "\t" + nlch[j + 5]); if ((nlch[j + 3] == 13) && (nlch[j + 4] == 13) && (nlch[j + 5] == 10)) { three++; } else if ((nlch[j + 1] == 13) && (nlch[j + 2] == 10)) { wcase++; } buff.rewind(); } boolean windowsNewLine = true; if (three == nolines) { windowsNewLine = false; // lineTerminator = "0D0D0A" } else if ((ucase == nolines) && (wcase < nolines)) { windowsNewLine = false; // lineTerminator = "0A" } else if ((ucase < nolines) && (wcase == nolines)) { windowsNewLine = true; //lineTerminator = "0D0A" } else if ((mcase == nolines) && (wcase < nolines)) { windowsNewLine = false; //lineTerminator = "0D" } buff.rewind(); int PORmarkPosition = POR_MARK_POSITION_DEFAULT; if (windowsNewLine) { PORmarkPosition = PORmarkPosition + 5; } else if (three == nolines) { PORmarkPosition = PORmarkPosition + 10; } byte[] pormark = new byte[8]; buff.position(PORmarkPosition); buff.get(pormark, 0, 8); String pormarks = new String(pormark); //dbgLog.fine("pormark =>" + pormarks + "<-"); dbgLog.fine( "pormark[hex: 53 50 53 53 50 4F 52 54 == SPSSPORT] =>" + new String(Hex.encodeHex(pormark)) + "<-"); if (pormarks.equals(POR_MARK)) { dbgLog.fine("POR ID toke test: Passed"); init(); smd.getFileInformation().put("mimeType", MIME_TYPE); smd.getFileInformation().put("fileFormat", MIME_TYPE); } else { dbgLog.fine("this file is NOT spss-por type"); throw new IllegalArgumentException("decodeHeader: POR ID token was not found"); } // save the POR file without new line characters FileOutputStream fileOutPOR = null; Writer fileWriter = null; // Scanner class can handle three-character line-terminator Scanner porScanner = null; try { tempPORfile = File.createTempFile("tempPORfile.", ".por"); fileOutPOR = new FileOutputStream(tempPORfile); fileWriter = new BufferedWriter(new OutputStreamWriter(fileOutPOR, "utf8")); porScanner = new Scanner(stream); // Because 64-bit and 32-bit machines decode POR's first 40-byte // sequence differently, the first 5 leader lines are skipped from // the new-line-stripped file int lineCounter = 0; while (porScanner.hasNextLine()) { lineCounter++; if (lineCounter <= 5) { String line = porScanner.nextLine().toString(); dbgLog.fine("line=" + lineCounter + ":" + line.length() + ":" + line); } else { fileWriter.write(porScanner.nextLine().toString()); } } } finally { try { if (fileWriter != null) { fileWriter.close(); } } catch (IOException ex) { ex.printStackTrace(); } if (porScanner != null) { porScanner.close(); } } return tempPORfile; }
From source file:edu.harvard.iq.dataverse.ingest.tabulardata.impl.plugins.por.PORFileReader.java
private File decodeHeader(BufferedInputStream stream) throws IOException { dbgLog.fine("decodeHeader(): start"); File tempPORfile = null;// w w w . ja v a2s. c om if (stream == null) { throw new IllegalArgumentException("file == null!"); } byte[] headerByes = new byte[POR_HEADER_SIZE]; if (stream.markSupported()) { stream.mark(1000); } int nbytes = stream.read(headerByes, 0, POR_HEADER_SIZE); //printHexDump(headerByes, "hex dump of the byte-array"); if (nbytes == 0) { throw new IOException("decodeHeader: reading failure"); } else if (nbytes < 491) { // Size test: by defnition, it must have at least // 491-byte header, i.e., the file size less than this threshold // is not a POR file dbgLog.fine("this file is NOT spss-por type"); throw new IllegalArgumentException("file is not spss-por type"); } // rewind the current reading position back to the beginning if (stream.markSupported()) { stream.reset(); } // line-terminating characters are usually one or two by defnition // however, a POR file saved by a genuine SPSS for Windows // had a three-character line terminator, i.e., failed to remove the // original file's one-character terminator when it was opened, and // saved it with the default two-character terminator without // removing original terminators. So we have to expect such a rare // case // // terminator // windows [0D0A]=> [1310] = [CR/LF] // unix [0A] => [10] // mac [0D] => [13] // 3char [0D0D0A]=> [131310] spss for windows rel 15 // // terminating characters should be found at the following // column positions[counting from 0]: // unix case: [0A] : [80], [161], [242], [323], [404], [485] // windows case: [0D0A] : [81], [163], [245], [327], [409], [491] // : [0D0D0A] : [82], [165], [248], [331], [414], [495] // convert b into a ByteBuffer ByteBuffer buff = ByteBuffer.wrap(headerByes); byte[] nlch = new byte[36]; int pos1; int pos2; int pos3; int ucase = 0; int wcase = 0; int mcase = 0; int three = 0; int nolines = 6; int nocols = 80; for (int i = 0; i < nolines; ++i) { int baseBias = nocols * (i + 1); // 1-char case pos1 = baseBias + i; buff.position(pos1); dbgLog.finer("\tposition(1)=" + buff.position()); int j = 6 * i; nlch[j] = buff.get(); if (nlch[j] == 10) { ucase++; } else if (nlch[j] == 13) { mcase++; } // 2-char case pos2 = baseBias + 2 * i; buff.position(pos2); dbgLog.finer("\tposition(2)=" + buff.position()); nlch[j + 1] = buff.get(); nlch[j + 2] = buff.get(); // 3-char case pos3 = baseBias + 3 * i; buff.position(pos3); dbgLog.finer("\tposition(3)=" + buff.position()); nlch[j + 3] = buff.get(); nlch[j + 4] = buff.get(); nlch[j + 5] = buff.get(); dbgLog.finer(i + "-th iteration position =" + nlch[j] + "\t" + nlch[j + 1] + "\t" + nlch[j + 2]); dbgLog.finer(i + "-th iteration position =" + nlch[j + 3] + "\t" + nlch[j + 4] + "\t" + nlch[j + 5]); if ((nlch[j + 3] == 13) && (nlch[j + 4] == 13) && (nlch[j + 5] == 10)) { three++; } else if ((nlch[j + 1] == 13) && (nlch[j + 2] == 10)) { wcase++; } buff.rewind(); } boolean windowsNewLine = true; if (three == nolines) { windowsNewLine = false; // lineTerminator = "0D0D0A" } else if ((ucase == nolines) && (wcase < nolines)) { windowsNewLine = false; // lineTerminator = "0A" } else if ((ucase < nolines) && (wcase == nolines)) { windowsNewLine = true; //lineTerminator = "0D0A" } else if ((mcase == nolines) && (wcase < nolines)) { windowsNewLine = false; //lineTerminator = "0D" } buff.rewind(); int PORmarkPosition = POR_MARK_POSITION_DEFAULT; if (windowsNewLine) { PORmarkPosition = PORmarkPosition + 5; } else if (three == nolines) { PORmarkPosition = PORmarkPosition + 10; } byte[] pormark = new byte[8]; buff.position(PORmarkPosition); buff.get(pormark, 0, 8); String pormarks = new String(pormark); //dbgLog.fine("pormark =>" + pormarks + "<-"); dbgLog.fine( "pormark[hex: 53 50 53 53 50 4F 52 54 == SPSSPORT] =>" + new String(Hex.encodeHex(pormark)) + "<-"); if (pormarks.equals(POR_MARK)) { dbgLog.fine("POR ID toke test: Passed"); init(); dataTable.setOriginalFileFormat(MIME_TYPE); dataTable.setUnf("UNF:6:NOTCALCULATED"); } else { dbgLog.fine("this file is NOT spss-por type"); throw new IllegalArgumentException("decodeHeader: POR ID token was not found"); } // save the POR file without new line characters FileOutputStream fileOutPOR = null; Writer fileWriter = null; // Scanner class can handle three-character line-terminator Scanner porScanner = null; try { tempPORfile = File.createTempFile("tempPORfile.", ".por"); fileOutPOR = new FileOutputStream(tempPORfile); fileWriter = new BufferedWriter(new OutputStreamWriter(fileOutPOR, "utf8")); porScanner = new Scanner(stream); // Because 64-bit and 32-bit machines decode POR's first 40-byte // sequence differently, the first 5 leader lines are skipped from // the new-line-stripped file int lineCounter = 0; while (porScanner.hasNextLine()) { lineCounter++; if (lineCounter <= 5) { String line = porScanner.nextLine(); dbgLog.fine("line=" + lineCounter + ":" + line.length() + ":" + line); } else { fileWriter.write(porScanner.nextLine()); } } } finally { try { if (fileWriter != null) { fileWriter.close(); } } catch (IOException ex) { ex.printStackTrace(); } if (porScanner != null) { porScanner.close(); } } return tempPORfile; }
From source file:com.healthmarketscience.jackcess.IndexData.java
/** * Read the rest of the index info from a tableBuffer * @param tableBuffer table definition buffer to read from initial info * @param availableColumns Columns that this index may use */// ww w.j av a 2 s . c o m public void read(ByteBuffer tableBuffer, List<Column> availableColumns) throws IOException { ByteUtil.forward(tableBuffer, getFormat().SKIP_BEFORE_INDEX); //Forward past Unknown for (int i = 0; i < MAX_COLUMNS; i++) { short columnNumber = tableBuffer.getShort(); byte colFlags = tableBuffer.get(); if (columnNumber != COLUMN_UNUSED) { // find the desired column by column number (which is not necessarily // the same as the column index) Column idxCol = null; for (Column col : availableColumns) { if (col.getColumnNumber() == columnNumber) { idxCol = col; break; } } if (idxCol == null) { throw new IOException("Could not find column with number " + columnNumber + " for index"); } _columns.add(newColumnDescriptor(idxCol, colFlags)); } } int umapRowNum = tableBuffer.get(); int umapPageNum = ByteUtil.get3ByteInt(tableBuffer); _ownedPages = UsageMap.read(getTable().getDatabase(), umapPageNum, umapRowNum, false); _rootPageNumber = tableBuffer.getInt(); ByteUtil.forward(tableBuffer, getFormat().SKIP_BEFORE_INDEX_FLAGS); //Forward past Unknown _indexFlags = tableBuffer.get(); ByteUtil.forward(tableBuffer, getFormat().SKIP_AFTER_INDEX_FLAGS); //Forward past other stuff }
From source file:com.healthmarketscience.jackcess.Column.java
/** * Deserialize a raw byte value for this column into an Object * @param data The raw byte value/*from ww w . j av a 2 s. co m*/ * @param order Byte order in which the raw value is stored * @return The deserialized Object * @usage _advanced_method_ */ public Object read(byte[] data, ByteOrder order) throws IOException { ByteBuffer buffer = ByteBuffer.wrap(data); buffer.order(order); if (_type == DataType.BOOLEAN) { throw new IOException("Tried to read a boolean from data instead of null mask."); } else if (_type == DataType.BYTE) { return Byte.valueOf(buffer.get()); } else if (_type == DataType.INT) { return Short.valueOf(buffer.getShort()); } else if (_type == DataType.LONG) { return Integer.valueOf(buffer.getInt()); } else if (_type == DataType.DOUBLE) { return Double.valueOf(buffer.getDouble()); } else if (_type == DataType.FLOAT) { return Float.valueOf(buffer.getFloat()); } else if (_type == DataType.SHORT_DATE_TIME) { return readDateValue(buffer); } else if (_type == DataType.BINARY) { return data; } else if (_type == DataType.TEXT) { return decodeTextValue(data); } else if (_type == DataType.MONEY) { return readCurrencyValue(buffer); } else if (_type == DataType.OLE) { if (data.length > 0) { return readLongValue(data); } return null; } else if (_type == DataType.MEMO) { if (data.length > 0) { return readLongStringValue(data); } return null; } else if (_type == DataType.NUMERIC) { return readNumericValue(buffer); } else if (_type == DataType.GUID) { return readGUIDValue(buffer, order); } else if ((_type == DataType.UNKNOWN_0D) || (_type == DataType.UNKNOWN_11)) { // treat like "binary" data return data; } else if (_type == DataType.COMPLEX_TYPE) { return new ComplexValueForeignKey(this, buffer.getInt()); } else if (_type.isUnsupported()) { return rawDataWrapper(data); } else { throw new IOException("Unrecognized data type: " + _type); } }
From source file:au.org.ala.layers.intersect.Grid.java
public void getClassInfo(Map<Float, float[]> info) { long length = ((long) nrows) * ((long) ncols); RandomAccessFile afile = null; File f2 = new File(filename + ".GRI"); try { //read of random access file can throw an exception if (!f2.exists()) { afile = new RandomAccessFile(filename + ".gri", "r"); } else {//w w w .ja v a 2 s .c o m afile = new RandomAccessFile(filename + ".GRI", "r"); } byte[] b = new byte[65536]; long i = 0; long max = 0; long len; float v; float ndv = (float) nodatavalue; while ((len = afile.read(b)) > 0) { ByteBuffer bb = ByteBuffer.wrap(b); if (byteorderLSB) { bb.order(ByteOrder.LITTLE_ENDIAN); } if (datatype.equalsIgnoreCase("UBYTE")) { max += len; max = Math.min(max, length); for (; i < max; i++) { v = bb.get(); if (v < 0) v += 256; if (v != ndv) updatesStats(info, i, v * rescale); } } else if (datatype.equalsIgnoreCase("BYTE")) { max += len; max = Math.min(max, length); for (; i < max; i++) { v = bb.get(); if (v != ndv) updatesStats(info, i, v * rescale); } } else if (datatype.equalsIgnoreCase("SHORT")) { max += len / 2; max = Math.min(max, length); for (; i < max; i++) { v = bb.getShort(); if (v != ndv) updatesStats(info, i, v * rescale); } } else if (datatype.equalsIgnoreCase("INT")) { max += len / 4; max = Math.min(max, length); for (; i < max; i++) { v = bb.getInt(); if (v != ndv) updatesStats(info, i, v * rescale); } } else if (datatype.equalsIgnoreCase("LONG")) { max += len / 8; max = Math.min(max, length); for (; i < max; i++) { v = bb.getLong(); if (v != ndv) updatesStats(info, i, v * rescale); } } else if (datatype.equalsIgnoreCase("FLOAT")) { max += len / 4; max = Math.min(max, length); for (; i < max; i++) { v = bb.getFloat(); if (v != ndv) updatesStats(info, i, v * rescale); } } else if (datatype.equalsIgnoreCase("DOUBLE")) { max += len / 8; max = Math.min(max, length); for (; i < max; i++) { v = (float) bb.getDouble(); if (v != ndv) updatesStats(info, i, v * rescale); } } else { max += len / 4; for (; i < max; i++) { // should not happen; catch anyway... } } } } catch (Exception e) { logger.error("An error has occurred getting grid class stats", e); } finally { if (afile != null) { try { afile.close(); } catch (Exception e) { logger.error(e.getMessage(), e); } } } }
From source file:edu.hawaii.soest.kilonalu.ctd.SBE37Source.java
/** * A method that executes the streaming of data from the source to the RBNB * server after all configuration of settings, connections to hosts, and * thread initiatizing occurs. This method contains the detailed code for * streaming the data and interpreting the stream. *///www .j av a2 s . c o m protected boolean execute() { logger.debug("SBE37Source.execute() called."); // do not execute the stream if there is no connection if (!isConnected()) return false; boolean failed = false; // while data are being sent, read them into the buffer try { this.socketChannel = getSocketConnection(); // create four byte placeholders used to evaluate up to a four-byte // window. The FIFO layout looks like: // ------------------------- // in ---> | One | Two |Three|Four | ---> out // ------------------------- byte byteOne = 0x00, // set initial placeholder values byteTwo = 0x00, byteThree = 0x00, byteFour = 0x00; // Create a buffer that will store the sample bytes as they are read ByteBuffer sampleBuffer = ByteBuffer.allocate(getBufferSize()); // create a byte buffer to store bytes from the TCP stream ByteBuffer buffer = ByteBuffer.allocateDirect(getBufferSize()); // create a character string to store characters from the TCP stream StringBuilder responseString = new StringBuilder(); // add a channel of data that will be pushed to the server. // Each sample will be sent to the Data Turbine as an rbnb frame. ChannelMap rbnbChannelMap = new ChannelMap(); int channelIndex = rbnbChannelMap.Add(getRBNBChannelName()); // wake the instrument with an initial take sample command this.command = this.commandPrefix + getInstrumentID() + "TS" + this.commandSuffix; this.sentCommand = queryInstrument(this.command); // verify the instrument ID is correct while (getInstrumentID() == null) { // allow time for the instrument response streamingThread.sleep(2000); buffer.clear(); // send the command and update the sentCommand status this.sentCommand = queryInstrument(this.command); // read the response into the buffer. Note that the streamed bytes // are 8-bit, not 16-bit Unicode characters. Use the US-ASCII // encoding instead. while (this.socketChannel.read(buffer) != -1 || buffer.position() > 0) { buffer.flip(); while (buffer.hasRemaining()) { String nextCharacter = new String(new byte[] { buffer.get() }, "US-ASCII"); responseString.append(nextCharacter); } // look for the command line ending if (responseString.toString().indexOf("S>") > 0) { // parse the ID from the idCommand response int idStartIndex = responseString.indexOf("=") + 2; int idStopIndex = responseString.indexOf("=") + 4; String idString = responseString.substring(idStartIndex, idStopIndex); // test that the ID is a valid number and set the instrument ID if ((new Integer(idString)).intValue() > 0) { setInstrumentID(idString); buffer.clear(); logger.debug("Instrument ID is " + getInstrumentID() + "."); break; } else { logger.debug("Instrument ID \"" + idString + "\" was not set."); } } else { break; } buffer.compact(); if (getInstrumentID() != null) { break; } } } // instrumentID is set // allow time for the instrument response streamingThread.sleep(5000); this.command = this.commandPrefix + getInstrumentID() + this.takeSampleCommand + this.commandSuffix; this.sentCommand = queryInstrument(command); // while there are bytes to read from the socket ... while (this.socketChannel.read(buffer) != -1 || buffer.position() > 0) { // prepare the buffer for reading buffer.flip(); // while there are unread bytes in the ByteBuffer while (buffer.hasRemaining()) { byteOne = buffer.get(); //logger.debug("b1: " + new String(Hex.encodeHex((new byte[]{byteOne}))) + "\t" + // "b2: " + new String(Hex.encodeHex((new byte[]{byteTwo}))) + "\t" + // "b3: " + new String(Hex.encodeHex((new byte[]{byteThree}))) + "\t" + // "b4: " + new String(Hex.encodeHex((new byte[]{byteFour}))) + "\t" + // "sample pos: " + sampleBuffer.position() + "\t" + // "sample rem: " + sampleBuffer.remaining() + "\t" + // "sample cnt: " + sampleByteCount + "\t" + // "buffer pos: " + buffer.position() + "\t" + // "buffer rem: " + buffer.remaining() + "\t" + // "state: " + state //); // Use a State Machine to process the byte stream. // Start building an rbnb frame for the entire sample, first by // inserting a timestamp into the channelMap. This time is merely // the time of insert into the data turbine, not the time of // observations of the measurements. That time should be parsed out // of the sample in the Sink client code switch (state) { case 0: // sample line is begun by S> // note bytes are in reverse order in the FIFO window if (byteOne == 0x3E && byteTwo == 0x53) { // we've found the beginning of a sample, move on state = 1; break; } else { break; } case 1: // read the rest of the bytes to the next EOL characters // sample line is terminated by S> // note bytes are in reverse order in the FIFO window if (byteOne == 0x3E && byteTwo == 0x53) { sampleByteCount++; // add the last byte found to the count // add the last byte found to the sample buffer if (sampleBuffer.remaining() > 0) { sampleBuffer.put(byteOne); } else { sampleBuffer.compact(); sampleBuffer.put(byteOne); } // extract just the length of the sample bytes (less 2 bytes // to exclude the 'S>' prompt characters) out of the // sample buffer, and place it in the channel map as a // byte array. Then, send it to the data turbine. byte[] sampleArray = new byte[sampleByteCount - 2]; sampleBuffer.flip(); sampleBuffer.get(sampleArray); // send the sample to the data turbine rbnbChannelMap.PutTimeAuto("server"); String sampleString = new String(sampleArray, "US-ASCII"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, sampleString); getSource().Flush(rbnbChannelMap); logger.info("Sample: " + sampleString); logger.info("flushed data to the DataTurbine. "); byteOne = 0x00; byteTwo = 0x00; byteThree = 0x00; byteFour = 0x00; sampleBuffer.clear(); sampleByteCount = 0; //rbnbChannelMap.Clear(); //logger.debug("Cleared b1,b2,b3,b4. Cleared sampleBuffer. Cleared rbnbChannelMap."); //state = 0; // Once the sample is flushed, take a new sample if (getInstrumentID() != null) { // allow time for the instrument response streamingThread.sleep(2000); this.command = this.commandPrefix + getInstrumentID() + this.takeSampleCommand + this.commandSuffix; this.sentCommand = queryInstrument(command); } } else { // not 0x0A0D // still in the middle of the sample, keep adding bytes sampleByteCount++; // add each byte found if (sampleBuffer.remaining() > 0) { sampleBuffer.put(byteOne); } else { sampleBuffer.compact(); logger.debug("Compacting sampleBuffer ..."); sampleBuffer.put(byteOne); } break; } // end if for 0x0A0D EOL } // end switch statement // shift the bytes in the FIFO window byteFour = byteThree; byteThree = byteTwo; byteTwo = byteOne; } //end while (more unread bytes) // prepare the buffer to read in more bytes from the stream buffer.compact(); } // end while (more socket bytes to read) this.socketChannel.close(); } catch (IOException e) { // handle exceptions // In the event of an i/o exception, log the exception, and allow execute() // to return false, which will prompt a retry. failed = true; e.printStackTrace(); return !failed; } catch (SAPIException sapie) { // In the event of an RBNB communication exception, log the exception, // and allow execute() to return false, which will prompt a retry. failed = true; sapie.printStackTrace(); return !failed; } catch (java.lang.InterruptedException ie) { ie.printStackTrace(); } return !failed; }
From source file:au.org.ala.layers.intersect.Grid.java
public float[] getGrid() { int maxArrayLength = Integer.MAX_VALUE - 10; if (grid_data != null) { return grid_data; }/*from w ww. java2 s.c o m*/ Grid loadedAlready = getLoadedGrid(filename); if (loadedAlready != null && loadedAlready.grid_data != null) { return loadedAlready.grid_data; } int length = nrows * ncols; float[] ret = new float[length]; RandomAccessFile afile = null; File f2 = new File(filename + ".GRI"); try { //read of random access file can throw an exception if (!f2.exists()) { afile = new RandomAccessFile(filename + ".gri", "r"); } else { afile = new RandomAccessFile(filename + ".GRI", "r"); } byte[] b = new byte[(int) Math.min(afile.length(), maxArrayLength)]; int i = 0; int max = 0; int len; while ((len = afile.read(b)) > 0) { ByteBuffer bb = ByteBuffer.wrap(b); if (byteorderLSB) { bb.order(ByteOrder.LITTLE_ENDIAN); } if (datatype.equalsIgnoreCase("UBYTE")) { max += len; max = Math.min(max, ret.length); for (; i < max; i++) { ret[i] = bb.get(); if (ret[i] < 0) { ret[i] += 256; } } } else if (datatype.equalsIgnoreCase("BYTE")) { max += len; max = Math.min(max, ret.length); for (; i < max; i++) { ret[i] = bb.get(); } } else if (datatype.equalsIgnoreCase("SHORT")) { max += len / 2; max = Math.min(max, ret.length); for (; i < max; i++) { ret[i] = bb.getShort(); } } else if (datatype.equalsIgnoreCase("INT")) { max += len / 4; max = Math.min(max, ret.length); for (; i < max; i++) { ret[i] = bb.getInt(); } } else if (datatype.equalsIgnoreCase("LONG")) { max += len / 8; max = Math.min(max, ret.length); for (; i < max; i++) { ret[i] = bb.getLong(); } } else if (datatype.equalsIgnoreCase("FLOAT")) { max += len / 4; max = Math.min(max, ret.length); for (; i < max; i++) { ret[i] = bb.getFloat(); } } else if (datatype.equalsIgnoreCase("DOUBLE")) { max += len / 8; max = Math.min(max, ret.length); for (; i < max; i++) { ret[i] = (float) bb.getDouble(); } } else { // / should not happen; catch anyway... max += len / 4; for (; i < max; i++) { ret[i] = Float.NaN; } } } //replace not a number for (i = 0; i < length; i++) { if ((float) ret[i] == (float) nodatavalue) { ret[i] = Float.NaN; } else { ret[i] *= rescale; } } } catch (Exception e) { logger.error("An error has occurred - probably a file error", e); } finally { if (afile != null) { try { afile.close(); } catch (Exception e) { logger.error(e.getMessage(), e); } } } grid_data = ret; return ret; }
From source file:au.org.ala.layers.intersect.Grid.java
float[] getGrid(double xmin, double ymin, double xmax, double ymax) { //expects largest y at the top //expects input ranges inside of grid ranges int width = (int) ((xmax - xmin) / xres); int height = (int) ((ymax - ymin) / yres); int startx = (int) ((xmin - this.xmin) / xres); int endx = startx + width; int starty = (int) ((ymin - this.ymin) / yres); //int endy = starty + height; int length = width * height; float[] ret = new float[length]; int pos = 0;//w ww . j ava2 s .c om int i; RandomAccessFile afile = null; File f2 = new File(filename + ".GRI"); int size = 4; if (datatype.equals("BYTE") || datatype.equals("UBYTE")) { size = 1; } else if (datatype.equals("SHORT")) { size = 2; } else if (datatype.equals("INT")) { size = 4; } else if (datatype.equals("LONG")) { size = 8; } else if (datatype.equals("FLOAT")) { size = 4; } else if (datatype.equals("DOUBLE")) { size = 8; } try { //read of random access file can throw an exception if (!f2.exists()) { afile = new RandomAccessFile(filename + ".gri", "r"); } else { afile = new RandomAccessFile(filename + ".GRI", "r"); } //seek to first raster afile.seek(((long) this.ncols) * starty * size); //read relevant rasters int readSize = this.ncols * height * size; int readLen = this.ncols * height; byte[] b = new byte[readSize]; afile.read(b); ByteBuffer bb = ByteBuffer.wrap(b); if (byteorderLSB) { bb.order(ByteOrder.LITTLE_ENDIAN); } if (datatype.equalsIgnoreCase("BYTE")) { for (i = 0; i < readLen; i++) { int x = i % this.ncols; if (x < startx || x >= endx) { bb.get(); } else { ret[pos++] = bb.get(); } } } else if (datatype.equalsIgnoreCase("UBYTE")) { for (i = 0; i < readLen; i++) { int x = i % this.ncols; if (x < startx || x >= endx) { bb.get(); } else { ret[pos] = bb.get(); if (ret[pos] < 0) { ret[pos] += 256; } pos++; } } } else if (datatype.equalsIgnoreCase("SHORT")) { for (i = 0; i < readLen; i++) { int x = i % this.ncols; if (x < startx || x >= endx) { bb.getShort(); } else { ret[pos++] = bb.getShort(); } } } else if (datatype.equalsIgnoreCase("INT")) { for (i = 0; i < readLen; i++) { int x = i % this.ncols; if (x < startx || x >= endx) { bb.getInt(); } else { ret[pos++] = bb.getInt(); } } } else if (datatype.equalsIgnoreCase("LONG")) { for (i = 0; i < readLen; i++) { int x = i % this.ncols; if (x < startx || x >= endx) { bb.getLong(); } else { ret[pos++] = bb.getLong(); } } } else if (datatype.equalsIgnoreCase("FLOAT")) { for (i = 0; i < readLen; i++) { int x = i % this.ncols; if (x < startx || x >= endx) { bb.getFloat(); } else { ret[pos++] = bb.getFloat(); } } } else if (datatype.equalsIgnoreCase("DOUBLE")) { for (i = 0; i < readLen; i++) { int x = i % this.ncols; if (x < startx || x >= endx) { bb.getDouble(); } else { ret[pos++] = (float) bb.getDouble(); } } } else { // / should not happen; catch anyway... for (i = 0; i < length; i++) { ret[i] = Float.NaN; } } //replace not a number for (i = 0; i < length; i++) { if ((float) ret[i] == (float) nodatavalue) { ret[i] = Float.NaN; } else { ret[i] *= rescale; } } } catch (Exception e) { logger.error("GRID: " + e.toString(), e); } finally { if (afile != null) { try { afile.close(); } catch (Exception e) { logger.error(e.getMessage(), e); } } } grid_data = ret; return ret; }
From source file:au.org.ala.layers.intersect.Grid.java
/** * Increase sampleEveryNthPoint to return a smaller grid. * * Grid max and min values may be skipped. * * This does not used previously cached data. * * @param sampleEveryNthPoint//from ww w . j av a 2 s . com * @return */ public float[] getGrid(int sampleEveryNthPoint) { int maxArrayLength = Integer.MAX_VALUE - 10; if (subgrids != null) { //sample points int size = 1000; double[][] points = new double[size * size][2]; int pos = 0; for (int i = 0; i < 1000; i++) { for (int j = 0; j < 1000; j++) { points[pos][0] = xmin + (xmax - xmin) * j / (double) size; points[pos][1] = ymax - (ymax - ymin) * i / (double) size; pos++; } } return getValues3(points, 64); } int length = (nrows / sampleEveryNthPoint) * (ncols); float[] ret = new float[length]; RandomAccessFile afile = null; File f2 = new File(filename + ".GRI"); try { //read of random access file can throw an exception if (!f2.exists()) { afile = new RandomAccessFile(filename + ".gri", "r"); } else { afile = new RandomAccessFile(filename + ".GRI", "r"); } int sz = (int) Math.min(afile.length() / sampleEveryNthPoint / sampleEveryNthPoint, maxArrayLength); sz += 8 - sz % 8; byte[] b = new byte[sz]; long i = 0; long max = 0; int len; while ((len = afile.read(b)) > 0) { ByteBuffer bb = ByteBuffer.wrap(b); if (byteorderLSB) { bb.order(ByteOrder.LITTLE_ENDIAN); } if (datatype.equalsIgnoreCase("UBYTE")) { max += len; max = Math.min(max, ret.length * (long) sampleEveryNthPoint); for (; i < max; i++) { ret[(int) (i / sampleEveryNthPoint)] = bb.get(); if (ret[(int) (i / sampleEveryNthPoint)] < 0) { ret[(int) (i / sampleEveryNthPoint)] += 256; } } } else if (datatype.equalsIgnoreCase("BYTE")) { max += len; max = Math.min(max, ret.length * (long) sampleEveryNthPoint); for (; i < max; i++) { ret[(int) (i / sampleEveryNthPoint)] = bb.get(); } } else if (datatype.equalsIgnoreCase("SHORT")) { max += len / 2; max = Math.min(max, ret.length * (long) sampleEveryNthPoint); for (; i < max; i++) { ret[(int) (i / sampleEveryNthPoint)] = bb.getShort(); } } else if (datatype.equalsIgnoreCase("INT")) { max += len / 4; max = Math.min(max, ret.length * (long) sampleEveryNthPoint); for (; i < max; i++) { ret[(int) (i / sampleEveryNthPoint)] = bb.getInt(); } } else if (datatype.equalsIgnoreCase("LONG")) { max += len / 8; max = Math.min(max, ret.length * (long) sampleEveryNthPoint); for (; i < max; i++) { ret[(int) (i / sampleEveryNthPoint)] = bb.getLong(); } } else if (datatype.equalsIgnoreCase("FLOAT")) { max += len / 4; max = Math.min(max, ret.length * (long) sampleEveryNthPoint); for (; i < max; i++) { ret[(int) (i / sampleEveryNthPoint)] = bb.getFloat(); } } else if (datatype.equalsIgnoreCase("DOUBLE")) { max += len / 8; max = Math.min(max, ret.length * (long) sampleEveryNthPoint); for (; i < max; i++) { ret[(int) (i / (long) sampleEveryNthPoint)] = (float) bb.getDouble(); } } else { // / should not happen; catch anyway... max += len / 4; for (; i < max; i++) { ret[(int) (i / (long) sampleEveryNthPoint)] = Float.NaN; } } } //replace not a number for (i = 0; i < length; i++) { if ((float) ret[(int) i] == (float) nodatavalue) { ret[(int) i] = Float.NaN; } else { ret[(int) i] *= rescale; } } } catch (Exception e) { logger.error("An error has occurred - probably a file error", e); } finally { if (afile != null) { try { afile.close(); } catch (Exception e) { logger.error(e.getMessage(), e); } } } grid_data = ret; return ret; }
From source file:com.healthmarketscience.jackcess.impl.IndexData.java
/** * Read the rest of the index info from a tableBuffer * @param tableBuffer table definition buffer to read from initial info * @param availableColumns Columns that this index may use *///ww w.j a v a 2 s . c o m public void read(ByteBuffer tableBuffer, List<ColumnImpl> availableColumns) throws IOException { ByteUtil.forward(tableBuffer, getFormat().SKIP_BEFORE_INDEX); //Forward past Unknown for (int i = 0; i < MAX_COLUMNS; i++) { short columnNumber = tableBuffer.getShort(); byte colFlags = tableBuffer.get(); if (columnNumber != COLUMN_UNUSED) { // find the desired column by column number (which is not necessarily // the same as the column index) ColumnImpl idxCol = null; for (ColumnImpl col : availableColumns) { if (col.getColumnNumber() == columnNumber) { idxCol = col; break; } } if (idxCol == null) { throw new IOException("Could not find column with number " + columnNumber + " for index"); } _columns.add(newColumnDescriptor(idxCol, colFlags)); } } _ownedPages = UsageMap.read(getTable().getDatabase(), tableBuffer, false); _rootPageNumber = tableBuffer.getInt(); ByteUtil.forward(tableBuffer, getFormat().SKIP_BEFORE_INDEX_FLAGS); //Forward past Unknown _indexFlags = tableBuffer.get(); ByteUtil.forward(tableBuffer, getFormat().SKIP_AFTER_INDEX_FLAGS); //Forward past other stuff }