Examples with ByteOrder java.nio.ByteOrder used on opensource projects

Example 31 with ByteOrder

use of java.nio.ByteOrder in project ffx by mjschnie.

the class CCP4MapWriter method write.

/**
 * write data to file, does not normalize
 *
 * @param data map data to write out
 * @param norm should the data be normalized by mean/sd?
 */
public void write(double[] data, boolean norm) {
    ByteOrder b = ByteOrder.nativeOrder();
    FileOutputStream fos;
    DataOutputStream dos;
    double min = Double.POSITIVE_INFINITY;
    double max = Double.NEGATIVE_INFINITY;
    double mean = 0.0;
    double sd = 0.0;
    int n = 0;
    for (int k = 0; k < extz; k++) {
        for (int j = 0; j < exty; j++) {
            for (int i = 0; i < extx; i++) {
                int index = stride * (i + extx * (j + exty * k));
                // int index = k * (exty * (extx + 2)) + j * (extx + 2) + i;
                n++;
                if (data[index] < min) {
                    min = data[index];
                }
                if (data[index] > max) {
                    max = data[index];
                }
                mean += (data[index] - mean) / n;
            }
        }
    }
    n = 0;
    for (int k = 0; k < extz; k++) {
        for (int j = 0; j < exty; j++) {
            for (int i = 0; i < extx; i++) {
                int index = stride * (i + extx * (j + exty * k));
                // int index = k * (exty * (extx + 2)) + j * (extx + 2) + i;
                sd += pow(data[index] - mean, 2.0);
                n++;
            }
        }
    }
    sd = sqrt(sd / n);
    if (norm) {
        for (int k = 0; k < extz; k++) {
            for (int j = 0; j < exty; j++) {
                for (int i = 0; i < extx; i++) {
                    int index = stride * (i + extx * (j + exty * k));
                    data[index] = (data[index] - mean) / sd;
                }
            }
        }
        // recurse
        write(data, false);
    }
    try {
        if (logger.isLoggable(Level.INFO)) {
            StringBuilder sb = new StringBuilder();
            sb.append(String.format("\nwriting CCP4 map file: \"%s\"\n", filename));
            sb.append(String.format("map min: %g max: %g mean: %g standard dev.: %g", min, max, mean, sd));
            logger.info(sb.toString());
        }
        fos = new FileOutputStream(filename);
        dos = new DataOutputStream(fos);
        byte[] bytes = new byte[2048];
        int offset = 0;
        int imapdata;
        float fmapdata;
        String mapstr;
        // header
        ByteBuffer bb = ByteBuffer.wrap(bytes);
        bb.order(b).putInt(extx);
        bb.order(b).putInt(exty);
        bb.order(b).putInt(extz);
        // mode (2 = reals, only one we accept)
        bb.order(b).putInt(2);
        bb.order(b).putInt(orix);
        bb.order(b).putInt(oriy);
        bb.order(b).putInt(oriz);
        bb.order(b).putInt(nx);
        bb.order(b).putInt(ny);
        bb.order(b).putInt(nz);
        bb.order(b).putFloat((float) crystal.a);
        bb.order(b).putFloat((float) crystal.b);
        bb.order(b).putFloat((float) crystal.c);
        bb.order(b).putFloat((float) crystal.alpha);
        bb.order(b).putFloat((float) crystal.beta);
        bb.order(b).putFloat((float) crystal.gamma);
        bb.order(b).putInt(1);
        bb.order(b).putInt(2);
        bb.order(b).putInt(3);
        bb.order(b).putFloat((float) min);
        bb.order(b).putFloat((float) max);
        bb.order(b).putFloat((float) mean);
        bb.order(b).putInt(crystal.spaceGroup.number);
        // bb.order(b).putInt(1);
        // symmetry bytes - should set this up at some point
        // imapdata = swap ? ByteSwap.swap(320) : 320;
        bb.order(b).putInt(80);
        bb.order(b).putInt(0);
        for (int i = 0; i < 12; i++) {
            bb.order(b).putFloat(0.0f);
        }
        for (int i = 0; i < 15; i++) {
            bb.order(b).putInt(0);
        }
        dos.write(bytes, offset, 208);
        bb.rewind();
        mapstr = "MAP ";
        dos.writeBytes(mapstr);
        // 0x4441 for LE, 0x1111 for BE
        if (ByteOrder.nativeOrder().equals(ByteOrder.LITTLE_ENDIAN)) {
            imapdata = 0x4441;
        } else {
            imapdata = 0x1111;
        }
        bb.order(b).putInt(imapdata);
        bb.order(b).putFloat((float) sd);
        bb.order(b).putInt(1);
        dos.write(bytes, offset, 12);
        StringBuilder sb = new StringBuilder();
        sb.append("map data from ffx");
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dos.writeBytes(sb.toString());
        sb = new StringBuilder();
        while (sb.length() < 80) {
            sb.append(" ");
        }
        for (int i = 0; i < 9; i++) {
            dos.writeBytes(sb.toString());
        }
        sb = new StringBuilder();
        sb.append("x,y,z");
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dos.writeBytes(sb.toString());
        bb.rewind();
        for (int k = 0; k < extz; k++) {
            for (int j = 0; j < exty; j++) {
                for (int i = 0; i < extx; i++) {
                    int index = stride * (i + extx * (j + exty * k));
                    // int index = k * (exty * (extx + 2)) + j * (extx + 2) + i;
                    fmapdata = (float) data[index];
                    bb.order(b).putFloat(fmapdata);
                    if (!bb.hasRemaining()) {
                        dos.write(bytes);
                        bb.rewind();
                    }
                }
            }
        }
        if (bb.position() > 0) {
            dos.write(bytes);
            bb.rewind();
        }
        dos.close();
    } catch (Exception e) {
        String message = "Fatal exception evaluating structure factors.\n";
        logger.log(Level.SEVERE, message, e);
        System.exit(-1);
    }
}

Example 32 with ByteOrder

use of java.nio.ByteOrder in project simple-binary-encoding by real-logic.

the class CSharpGenerator method generateArrayProperty.

private CharSequence generateArrayProperty(final String propertyName, final Token token, final String indent) {
    final String typeName = cSharpTypeName(token.encoding().primitiveType());
    final String typePrefix = toUpperFirstChar(token.encoding().primitiveType().primitiveName());
    final int offset = token.offset();
    final ByteOrder byteOrder = token.encoding().byteOrder();
    final String byteOrderStr = generateByteOrder(byteOrder, token.encoding().primitiveType().size());
    final int fieldLength = token.arrayLength();
    final int typeSize = token.encoding().primitiveType().size();
    final String propName = toUpperFirstChar(propertyName);
    final StringBuilder sb = new StringBuilder();
    sb.append(String.format("\n" + indent + "public const int %sLength = %d;\n", propName, fieldLength));
    sb.append(String.format("\n" + indent + "public %1$s Get%2$s(int index)\n" + indent + "{\n" + indent + INDENT + "if (index < 0 || index >= %3$d)\n" + indent + INDENT + "{\n" + indent + INDENT + INDENT + "throw new IndexOutOfRangeException(\"index out of range: index=\" + index);\n" + indent + INDENT + "}\n\n" + "%4$s" + indent + INDENT + "return _buffer.%5$sGet%8$s(_offset + %6$d + (index * %7$d));\n" + indent + "}\n", typeName, propName, fieldLength, generateFieldNotPresentCondition(token.version(), token.encoding(), indent), typePrefix, offset, typeSize, byteOrderStr));
    sb.append(String.format("\n" + indent + "public void Set%1$s(int index, %2$s value)\n" + indent + "{\n" + indent + INDENT + "if (index < 0 || index >= %3$d)\n" + indent + INDENT + "{\n" + indent + INDENT + INDENT + "throw new IndexOutOfRangeException(\"index out of range: index=\" + index);\n" + indent + INDENT + "}\n\n" + indent + INDENT + "_buffer.%4$sPut%7$s(_offset + %5$d + (index * %6$d), value);\n" + indent + "}\n", propName, typeName, fieldLength, typePrefix, offset, typeSize, byteOrderStr));
    if (token.encoding().primitiveType() == PrimitiveType.CHAR) {
        generateCharacterEncodingMethod(sb, propertyName, token.encoding().characterEncoding(), indent);
        sb.append(String.format("\n" + indent + "public int Get%1$s(byte[] dst, int dstOffset)\n" + indent + "{\n" + indent + INDENT + "const int length = %2$d;\n" + indent + INDENT + "if (dstOffset < 0 || dstOffset > (dst.Length - length))\n" + indent + INDENT + "{\n" + indent + INDENT + INDENT + "throw new IndexOutOfRangeException(" + "\"dstOffset out of range for copy: offset=\" + dstOffset);\n" + indent + INDENT + "}\n\n" + "%3$s" + indent + INDENT + "_buffer.GetBytes(_offset + %4$d, dst, dstOffset, length);\n" + indent + INDENT + "return length;\n" + indent + "}\n", propName, fieldLength, generateArrayFieldNotPresentCondition(token.version(), indent), offset));
        sb.append(String.format("\n" + indent + "public void Set%1$s(byte[] src, int srcOffset)\n" + indent + "{\n" + indent + INDENT + "const int length = %2$d;\n" + indent + INDENT + "if (srcOffset < 0 || srcOffset > src.Length)\n" + indent + INDENT + "{\n" + indent + INDENT + INDENT + "throw new IndexOutOfRangeException(\"srcOffset out of range for copy: offset=\" + srcOffset);\n" + indent + INDENT + "}\n\n" + indent + INDENT + "if (src.Length > length)\n" + indent + INDENT + "{\n" + indent + INDENT + INDENT + "throw new ArgumentOutOfRangeException($\"src.Length={src.Length} is too large.\");\n" + indent + INDENT + "}\n\n" + indent + INDENT + "_buffer.SetBytes(_offset + %3$d, src, srcOffset, src.Length - srcOffset);\n" + indent + "}\n", propName, fieldLength, offset));
    }
    return sb;
}

Example 33 with ByteOrder

use of java.nio.ByteOrder in project simple-binary-encoding by real-logic.

the class CSharpGenerator method generateBitSetProperty.

private Object generateBitSetProperty(final String propertyName, final Token token, final String indent) {
    final StringBuilder sb = new StringBuilder();
    final String bitSetName = formatClassName(token.applicableTypeName());
    final int offset = token.offset();
    final String typePrefix = toUpperFirstChar(token.encoding().primitiveType().primitiveName());
    final ByteOrder byteOrder = token.encoding().byteOrder();
    final String byteOrderStr = generateByteOrder(byteOrder, token.encoding().primitiveType().size());
    final String typeName = cSharpTypeName(token.encoding().primitiveType());
    sb.append(String.format("\n" + indent + INDENT + "public %1$s %2$s\n" + indent + INDENT + "{\n" + indent + INDENT + INDENT + "get\n" + indent + INDENT + INDENT + "{\n" + "%3$s" + indent + INDENT + INDENT + INDENT + "return (%4$s)_buffer.%5$sGet%7$s(_offset + %6$d);\n" + indent + INDENT + INDENT + "}\n" + indent + INDENT + INDENT + "set\n" + indent + INDENT + INDENT + "{\n" + indent + INDENT + INDENT + INDENT + "_buffer.%5$sPut%7$s(_offset + %6$d, (%8$s)value);\n" + indent + INDENT + INDENT + "}\n" + indent + INDENT + "}\n", bitSetName, toUpperFirstChar(propertyName), generateTypeFieldNotPresentCondition(token.version(), indent), bitSetName, typePrefix, offset, byteOrderStr, typeName));
    return sb;
}

Example 34 with ByteOrder

use of java.nio.ByteOrder in project jedis by xetorthio.

the class MurmurHash method hash.

/**
 * Hashes the bytes in a buffer from the current position to the limit.
 * @param buf The bytes to hash.
 * @param seed The seed for the hash.
 * @return The 32 bit murmur hash of the bytes in the buffer.
 */
public static int hash(ByteBuffer buf, int seed) {
    // save byte order for later restoration
    ByteOrder byteOrder = buf.order();
    buf.order(ByteOrder.LITTLE_ENDIAN);
    int m = 0x5bd1e995;
    int r = 24;
    int h = seed ^ buf.remaining();
    int k;
    while (buf.remaining() >= 4) {
        k = buf.getInt();
        k *= m;
        k ^= k >>> r;
        k *= m;
        h *= m;
        h ^= k;
    }
    if (buf.remaining() > 0) {
        ByteBuffer finish = ByteBuffer.allocate(4).order(ByteOrder.LITTLE_ENDIAN);
        // for big-endian version, use this first:
        // finish.position(4-buf.remaining());
        finish.put(buf).rewind();
        h ^= finish.getInt();
        h *= m;
    }
    h ^= h >>> 13;
    h *= m;
    h ^= h >>> 15;
    buf.order(byteOrder);
    return h;
}

Example 35 with ByteOrder

use of java.nio.ByteOrder in project databus by linkedin.

the class TestDbusEventV2 method testDbusEventV2SerializationDeserialization.

@Test
public void testDbusEventV2SerializationDeserialization() throws Exception {
    DbusOpcode[] opcodes = new DbusOpcode[] { DbusOpcode.UPSERT, DbusOpcode.DELETE, null };
    DbusEventKey longDek = new DbusEventKey(longKey);
    DbusEventKey strDek = new DbusEventKey(strKey.getBytes(Charset.forName("UTF-8")));
    DbusEventPart schemaKeyPart = new DbusEventPart(DbusEvent.SchemaDigestType.CRC32, keySchemaCrc, keySchemaVersion, ByteBuffer.wrap(schemaKey));
    DbusEventKey schemaDek = new DbusEventKey(schemaKeyPart);
    DbusEventKey[] keys = new DbusEventKey[] { longDek, strDek, schemaDek };
    ByteOrder[] orders = new ByteOrder[] { ByteOrder.LITTLE_ENDIAN, ByteOrder.BIG_ENDIAN };
    int[] offsets = new int[] { 0, 5 };
    DbusEventPart md5Metadata = new DbusEventPart(DbusEvent.SchemaDigestType.MD5, payloadSchemaMd5, metadataSchemaVersion, ByteBuffer.wrap(metadataBytes));
    DbusEventPart crcMetadata = new DbusEventPart(DbusEvent.SchemaDigestType.CRC32, crcSignature, metadataSchemaVersion, ByteBuffer.wrap(metadataBytes));
    DbusEventPart[] metadatas = new DbusEventPart[] { null, md5Metadata, crcMetadata };
    for (DbusOpcode opcode : opcodes) {
        for (DbusEventPart metadata : metadatas) {
            DbusEventInfo evInfo = new DbusEventInfo(opcode, seq, partitionId, partitionId, timeStamp, srcId, payloadSchemaMd5, payload, // enabletracing
            false, // auto-commit
            true, DbusEventFactory.DBUS_EVENT_V2, payloadSchemaVersion, // DbusEventPart for metadataBytes
            metadata);
            for (DbusEventKey evKey : keys) {
                for (int offset : offsets) {
                    // buffer.
                    for (ByteOrder byteOrder : orders) {
                        // Replicated event
                        evInfo.setReplicated(true);
                        testSerDeser(evKey, evInfo, offset, byteOrder);
                        // Not a Replicated event
                        evInfo.setReplicated(false);
                        testSerDeser(evKey, evInfo, offset, byteOrder);
                    }
                }
            }
        }
    }
}