public void a(DataInput datainput) {
this.e = datainput.readUnsignedByte();
this.a = datainput.readInt();
this.b = datainput.readUnsignedByte();
this.c = datainput.readInt();
this.face = datainput.readUnsignedByte();
}
public static final void copyString(DataInput in, DataOutput out) throws IOException {
int len = in.readUnsignedByte();
out.writeByte(len);
if (len >= HIGH_BIT) {
int shift = 7;
int curr;
len = len & 0x7f;
while ((curr = in.readUnsignedByte()) >= HIGH_BIT) {
out.writeByte(curr);
len |= (curr & 0x7f) << shift;
shift += 7;
}
out.writeByte(curr);
len |= curr << shift;
}
// note that the length is one larger than the actual length (length 0 is a null string, not a
// zero length string)
len--;
for (int i = 0; i < len; i++) {
int c = in.readUnsignedByte();
out.writeByte(c);
while (c >= HIGH_BIT) {
c = in.readUnsignedByte();
out.writeByte(c);
}
}
}
public void readFrom(DataInput din) throws IOException {
if (!isHeadless()) {
setTransactionID(din.readUnsignedShort());
setProtocolID(din.readUnsignedShort());
m_DataLength = din.readUnsignedShort();
}
setUnitID(din.readUnsignedByte());
setFunctionCode(din.readUnsignedByte());
readData(din);
} // readFrom
/**
* Reads in a string from the specified data input stream. The string has been encoded using a
* modified UTF-8 format.
*
* <p>The first two bytes are read as if by <code>readUnsignedShort</code>. This value gives the
* number of following bytes that are in the encoded string, not the length of the resulting
* string. The following bytes are then interpreted as bytes encoding characters in the UTF-8
* format and are converted into characters.
*
* <p>This method blocks until all the bytes are read, the end of the stream is detected, or an
* exception is thrown.
*
* @param in a data input stream.
* @return a Unicode string.
* @exception EOFException if the input stream reaches the end before all the bytes.
* @exception IOException if an I/O error occurs.
* @exception UTFDataFormatException if the bytes do not represent a valid UTF-8 encoding of a
* Unicode string.
* @see java.io.DataInputStream#readUnsignedShort()
*/
public static final char[] readUTF(DataInput in) throws IOException {
int utflen = in.readUnsignedShort();
char str[] = new char[utflen];
int count = 0;
int strlen = 0;
while (count < utflen) {
int c = in.readUnsignedByte();
int char2, char3;
switch (c >> 4) {
case 0:
case 1:
case 2:
case 3:
case 4:
case 5:
case 6:
case 7:
// 0xxxxxxx
count++;
str[strlen++] = (char) c;
break;
case 12:
case 13:
// 110x xxxx 10xx xxxx
count += 2;
if (count > utflen) throw new UTFDataFormatException();
char2 = in.readUnsignedByte();
if ((char2 & 0xC0) != 0x80) throw new UTFDataFormatException();
str[strlen++] = (char) (((c & 0x1F) << 6) | (char2 & 0x3F));
break;
case 14:
// 1110 xxxx 10xx xxxx 10xx xxxx
count += 3;
if (count > utflen) throw new UTFDataFormatException();
char2 = in.readUnsignedByte();
char3 = in.readUnsignedByte();
if (((char2 & 0xC0) != 0x80) || ((char3 & 0xC0) != 0x80))
throw new UTFDataFormatException();
str[strlen++] =
(char) (((c & 0x0F) << 12) | ((char2 & 0x3F) << 6) | ((char3 & 0x3F) << 0));
break;
default:
// 10xx xxxx, 1111 xxxx
throw new UTFDataFormatException();
}
}
if (strlen < utflen) {
System.arraycopy(str, 0, str = new char[strlen], 0, strlen);
}
return str;
}
/**
* Read a long previously written by writeLong().
*
* @exception IOException an exception was thrown by a method on in.
*/
public static final long readLong(DataInput in) throws IOException {
int int_value = in.readUnsignedByte();
if ((int_value & ~0x3f) == 0) {
// test for small case first - assuming this is usual case.
// this is stored in 2 bytes.
return ((int_value << 8) | in.readUnsignedByte());
} else if ((int_value & 0x80) == 0) {
// value is stored in 4 bytes. only use low 6 bits from 1st byte.
return (((int_value & 0x3f) << 24)
| (in.readUnsignedByte() << 16)
| (in.readUnsignedByte() << 8)
| (in.readUnsignedByte()));
} else {
// value is stored in 8 bytes. only use low 7 bits from 1st byte.
return ((((long) (int_value & 0x7f)) << 56)
| (((long) in.readUnsignedByte()) << 48)
| (((long) in.readUnsignedByte()) << 40)
| (((long) in.readUnsignedByte()) << 32)
| (((long) in.readUnsignedByte()) << 24)
| (((long) in.readUnsignedByte()) << 16)
| (((long) in.readUnsignedByte()) << 8)
| (((long) in.readUnsignedByte())));
}
}
public InodeEntry readData(DataInput in) throws Exception {
if (length != null) {
byte[] buf = new byte[getReadSize()];
in.readFully(buf);
name = new String(buf);
int i = name.indexOf('\0');
if (i >= 0) name = name.substring(0, i);
} else {
fsid = Utils.getUnsigned(in.readInt());
length = in.readUnsignedByte();
type = InodeType.fromInt(in.readUnsignedByte());
}
return this;
}
/** Creates new PostTable */
protected PostTable(final DirectoryEntry de, final DataInput di) throws IOException {
this.de = (DirectoryEntry) de.clone();
version = di.readInt();
italicAngle = di.readInt();
underlinePosition = di.readShort();
underlineThickness = di.readShort();
isFixedPitch = di.readInt();
minMemType42 = di.readInt();
maxMemType42 = di.readInt();
minMemType1 = di.readInt();
maxMemType1 = di.readInt();
if (version == 0x00020000) {
numGlyphs = di.readUnsignedShort();
glyphNameIndex = new int[numGlyphs];
for (int i = 0; i < numGlyphs; i++) {
glyphNameIndex[i] = di.readUnsignedShort();
}
int h = highestGlyphNameIndex();
if (h > 257) {
h -= 257;
psGlyphName = new String[h];
for (int i = 0; i < h; i++) {
final int len = di.readUnsignedByte();
final byte[] buf = new byte[len];
di.readFully(buf);
psGlyphName[i] = new String(buf);
}
}
// } else if (version == 0x00025000) {
// } else if (version == 0x00030000) {
}
}
private static Node deserializeNode(DataInput input) throws IOException {
int level = input.readUnsignedByte();
long value = input.readLong();
double weight = input.readDouble();
return new Node(value, level, weight);
}
/** Return {@code true} if a double slot is read (in case of Double or Long constant). */
private boolean readConstantPoolEntry(final DataInput di, final int index) throws IOException {
final int tag = di.readUnsignedByte();
switch (tag) {
case CP_METHOD_TYPE:
di.skipBytes(2); // readUnsignedShort()
return false;
case CP_METHOD_HANDLE:
di.skipBytes(3);
return false;
case CP_INTEGER:
case CP_FLOAT:
case CP_REF_FIELD:
case CP_REF_METHOD:
case CP_REF_INTERFACE:
case CP_NAME_AND_TYPE:
case CP_INVOKE_DYNAMIC:
di.skipBytes(4); // readInt() / readFloat() / readUnsignedShort() * 2
return false;
case CP_LONG:
case CP_DOUBLE:
di.skipBytes(8); // readLong() / readDouble()
return true;
case CP_UTF8:
constantPool[index] = di.readUTF();
return false;
case CP_CLASS:
case CP_STRING:
// reference to CP_UTF8 entry. The referenced index can have a higher number!
constantPool[index] = di.readUnsignedShort();
return false;
default:
throw new ClassFormatError("Unkown tag value for constant pool entry: " + tag);
}
}
@Override
public int readUnsignedByte() {
try {
return input.readUnsignedByte();
} catch (IOException e) {
throw new IllegalStateException(e);
}
}
/**
* Read an integer previously written by writeInt().
*
* @exception IOException an exception was thrown by a method on in.
*/
public static final int readInt(DataInput in) throws IOException {
int value = in.readUnsignedByte();
if ((value & ~0x3f) == 0) {
// length is stored in this byte, we also know that the 0x80 bit
// was not set, so no need to mask off the sign extension from
// the byte to int conversion.
// account for 1 byte stored length of field + 1 for all returns
return (value);
} else if ((value & 0x80) == 0) {
// length is stored in 2 bytes. only use low 6 bits from 1st byte.
if (SanityManager.DEBUG) {
SanityManager.ASSERT((value & 0x40) == 0x40);
}
// top 8 bits of 2 byte length is stored in this byte, we also
// know that the 0x80 bit was not set, so no need to mask off the
// sign extension from the 1st byte to int conversion. Need to
// mask the byte in data[offset + 1] to account for possible sign
// extension.
return (((value & 0x3f) << 8) | in.readUnsignedByte());
} else {
// length is stored in 4 bytes. only use low 7 bits from 1st byte.
if (SanityManager.DEBUG) {
SanityManager.ASSERT((value & 0x80) == 0x80);
}
// top 8 bits of 4 byte length is stored in this byte, we also
// know that the 0x80 bit was set, so need to mask off the
// sign extension from the 1st byte to int conversion. Need to
// mask the bytes from the next 3 bytes data[offset + 1,2,3] to
// account for possible sign extension.
//
return (((value & 0x7f) << 24)
| (in.readUnsignedByte() << 16)
| (in.readUnsignedByte() << 8)
| (in.readUnsignedByte()));
}
}
public static String readString(DataInput in) throws IOException {
// the length we read is offset by one, because a length of zero indicates a null value
int len = in.readUnsignedByte();
if (len == 0) {
return null;
}
if (len >= HIGH_BIT) {
int shift = 7;
int curr;
len = len & 0x7f;
while ((curr = in.readUnsignedByte()) >= HIGH_BIT) {
len |= (curr & 0x7f) << shift;
shift += 7;
}
len |= curr << shift;
}
// subtract one for the null length
len -= 1;
final char[] data = new char[len];
for (int i = 0; i < len; i++) {
int c = in.readUnsignedByte();
if (c < HIGH_BIT) {
data[i] = (char) c;
} else {
int shift = 7;
int curr;
c = c & 0x7f;
while ((curr = in.readUnsignedByte()) >= HIGH_BIT) {
c |= (curr & 0x7f) << shift;
shift += 7;
}
c |= curr << shift;
data[i] = (char) c;
}
}
return new String(data, 0, len);
}
MethodParameters(int name_index, int length, DataInput input, ConstantPool constant_pool)
throws IOException {
super(Constants.ATTR_METHOD_PARAMETERS, name_index, length, constant_pool);
System.out.println("new MethodParameters");
int parameters_count = input.readUnsignedByte();
parameters = new MethodParameter[parameters_count];
for (int i = 0; i < parameters_count; i++) {
parameters[i] = new MethodParameter(input);
}
}
static String readPascalString(final DataInput pInput) throws IOException {
int length = pInput.readUnsignedByte();
if (length == 0) {
return "";
}
byte[] bytes = new byte[length];
pInput.readFully(bytes);
return StringUtil.decode(bytes, 0, bytes.length, "ASCII");
}
public UnsignedByteArray(DataInput in, int length) throws IOException {
if (length == -1) {
throw new RuntimeException("variable length " + getClass() + " not implemented");
} else {
this.length = length;
data = new short[length];
for (int i = 0; i < length; i++) {
data[i] = (short) in.readUnsignedByte();
}
this.offset = 0;
}
}
public void readData(DataInput din) throws IOException {
setByteCount(din.readUnsignedByte());
InputRegister[] registers = new InputRegister[getWordCount()];
ProcessImageFactory pimf = ModbusCoupler.getReference().getProcessImageFactory();
for (int k = 0; k < getWordCount(); k++) {
registers[k] = pimf.createInputRegister(din.readByte(), din.readByte());
}
m_Registers = registers;
// update data length
setDataLength(getByteCount() + 1);
} // readData
public void read(DataInput in) throws InvalidByteCodeException, IOException {
int numberOfEntries = in.readUnsignedByte();
entries = new MethodParametersEntry[numberOfEntries];
for (int i = 0; i < numberOfEntries; i++) {
entries[i] = MethodParametersEntry.create(in, classFile);
}
if (debug) {
debug("read ");
}
}
public void readData(DataInput din) throws IOException {
m_Reference = din.readShort();
// read lengths
int wc = din.readUnsignedShort();
int bc = din.readUnsignedByte();
// read values
if (m_NonWordDataHandler == null) {
m_Registers = new Register[wc];
ProcessImageFactory pimf = ModbusCoupler.getReference().getProcessImageFactory();
for (int i = 0; i < wc; i++) {
m_Registers[i] = pimf.createRegister(din.readByte(), din.readByte());
}
} else {
m_NonWordDataHandler.readData(din, m_Reference, wc);
}
} // readData
private static AbstractConfigValue readValueData(DataInput in, SimpleConfigOrigin origin)
throws IOException {
int stb = in.readUnsignedByte();
SerializedValueType st = SerializedValueType.forInt(stb);
if (st == null) throw new IOException("Unknown serialized value type: " + stb);
switch (st) {
case BOOLEAN:
return new ConfigBoolean(origin, in.readBoolean());
case NULL:
return new ConfigNull(origin);
case INT:
int vi = in.readInt();
String si = in.readUTF();
return new ConfigInt(origin, vi, si);
case LONG:
long vl = in.readLong();
String sl = in.readUTF();
return new ConfigLong(origin, vl, sl);
case DOUBLE:
double vd = in.readDouble();
String sd = in.readUTF();
return new ConfigDouble(origin, vd, sd);
case STRING:
return new ConfigString.Quoted(origin, in.readUTF());
case LIST:
int listSize = in.readInt();
List<AbstractConfigValue> list = new ArrayList<AbstractConfigValue>(listSize);
for (int i = 0; i < listSize; ++i) {
AbstractConfigValue v = readValue(in, origin);
list.add(v);
}
return new SimpleConfigList(origin, list);
case OBJECT:
int mapSize = in.readInt();
Map<String, AbstractConfigValue> map = new HashMap<String, AbstractConfigValue>(mapSize);
for (int i = 0; i < mapSize; ++i) {
String key = in.readUTF();
AbstractConfigValue v = readValue(in, origin);
map.put(key, v);
}
return new SimpleConfigObject(origin, map);
}
throw new IOException("Unhandled serialized value type: " + st);
}
public static RNASequence readRNASequence(DataInput in) throws IOException {
int size = in.readInt();
char[] chars = new char[size];
int completed = 0;
while (completed < size) {
int value = in.readUnsignedByte();
chars[completed++] = getUnserializedRNABase((value >> 6));
if (completed < size) {
chars[completed++] = getUnserializedRNABase(((value >> 4) - ((value >> 6) << 2)));
}
if (completed < size) {
chars[completed++] = getUnserializedRNABase(((value >> 2) - ((value >> 4) << 2)));
}
if (completed < size) {
chars[completed++] = getUnserializedRNABase(((value) - ((value >> 2) << 2)));
}
}
return new RNASequence(new String(chars));
}
private void readAnnotationElementValue(final DataInput di) throws IOException {
final int tag = di.readUnsignedByte();
if (DEBUG) {
print("tag='%c'", (char) tag);
}
switch (tag) {
case BYTE:
case CHAR:
case DOUBLE:
case FLOAT:
case INT:
case LONG:
case SHORT:
case BOOLEAN:
case STRING:
di.skipBytes(2);
break;
case ENUM:
di.skipBytes(4); // 2 * u2
break;
case CLASS:
di.skipBytes(2);
break;
case ANNOTATION:
readAnnotation(di);
break;
case ARRAY:
final int count = di.readUnsignedShort();
for (int i = 0; i < count; ++i) {
readAnnotationElementValue(di);
}
break;
default:
throw new ClassFormatError(
"Not a valid annotation element type tag: 0x" + Integer.toHexString(tag));
}
}
private static SerializedField readCode(DataInput in) throws IOException {
int c = in.readUnsignedByte();
if (c == SerializedField.UNKNOWN.ordinal())
throw new IOException("field code " + c + " is not supposed to be on the wire");
return SerializedField.forInt(c);
}
// not private because we use it to deserialize ConfigException
static SimpleConfigOrigin readOrigin(DataInput in, SimpleConfigOrigin baseOrigin)
throws IOException {
Map<SerializedField, Object> m = new EnumMap<SerializedField, Object>(SerializedField.class);
while (true) {
Object v = null;
SerializedField field = readCode(in);
switch (field) {
case END_MARKER:
return SimpleConfigOrigin.fromBase(baseOrigin, m);
case ORIGIN_DESCRIPTION:
in.readInt(); // discard length
v = in.readUTF();
break;
case ORIGIN_LINE_NUMBER:
in.readInt(); // discard length
v = in.readInt();
break;
case ORIGIN_END_LINE_NUMBER:
in.readInt(); // discard length
v = in.readInt();
break;
case ORIGIN_TYPE:
in.readInt(); // discard length
v = in.readUnsignedByte();
break;
case ORIGIN_URL:
in.readInt(); // discard length
v = in.readUTF();
break;
case ORIGIN_RESOURCE:
in.readInt(); // discard length
v = in.readUTF();
break;
case ORIGIN_COMMENTS:
in.readInt(); // discard length
int size = in.readInt();
List<String> list = new ArrayList<String>(size);
for (int i = 0; i < size; ++i) {
list.add(in.readUTF());
}
v = list;
break;
case ORIGIN_NULL_URL: // FALL THRU
case ORIGIN_NULL_RESOURCE: // FALL THRU
case ORIGIN_NULL_COMMENTS:
// nothing to read besides code and length
in.readInt(); // discard length
v = ""; // just something non-null to put in the map
break;
case ROOT_VALUE:
case ROOT_WAS_CONFIG:
case VALUE_DATA:
case VALUE_ORIGIN:
throw new IOException("Not expecting this field here: " + field);
case UNKNOWN:
// skip unknown field
skipField(in);
break;
}
if (v != null) m.put(field, v);
}
}
public static NiftiHeader read(String fn) throws IOException {
DataInput di;
boolean le = littleEndian(fn);
InputStream is = new FileInputStream(fn);
if (fn.endsWith(".gz")) is = new GZIPInputStream(is);
if (le) di = new LEDataInputStream(is);
else di = new DataInputStream(is);
NiftiHeader ds = new NiftiHeader();
ds.filename = fn;
ds.little_endian = le;
ds.sizeof_hdr = di.readInt();
byte[] bb = new byte[10];
di.readFully(bb, 0, 10);
ds.data_type_string = new StringBuffer(new String(bb));
bb = new byte[18];
di.readFully(bb, 0, 18);
ds.db_name = new StringBuffer(new String(bb));
ds.extents = di.readInt();
ds.session_error = di.readShort();
ds.regular = new StringBuffer();
ds.regular.append((char) (di.readUnsignedByte()));
ds.dim_info = new StringBuffer();
ds.dim_info.append((char) (di.readUnsignedByte()));
int fps_dim = (int) ds.dim_info.charAt(0);
ds.freq_dim = (short) (fps_dim & 3);
ds.phase_dim = (short) ((fps_dim >>> 2) & 3);
ds.slice_dim = (short) ((fps_dim >>> 4) & 3);
for (int i = 0; i < 8; i++) ds.dim[i] = di.readShort();
if (ds.dim[0] > 0) ds.dim[1] = ds.dim[1];
if (ds.dim[0] > 1) ds.dim[2] = ds.dim[2];
if (ds.dim[0] > 2) ds.dim[3] = ds.dim[3];
if (ds.dim[0] > 3) ds.dim[4] = ds.dim[4];
for (int i = 0; i < 3; i++) ds.intent[i] = di.readFloat();
ds.intent_code = di.readShort();
ds.datatype = di.readShort();
ds.bitpix = di.readShort();
ds.slice_start = di.readShort();
for (int i = 0; i < 8; i++) ds.pixdim[i] = di.readFloat();
ds.qfac = (short) Math.floor((double) (ds.pixdim[0]));
ds.vox_offset = di.readFloat();
ds.scl_slope = di.readFloat();
ds.scl_inter = di.readFloat();
ds.slice_end = di.readShort();
ds.slice_code = (byte) di.readUnsignedByte();
ds.xyzt_units = (byte) di.readUnsignedByte();
int unit_codes = (int) ds.xyzt_units;
ds.xyz_unit_code = (short) (unit_codes & 007);
ds.t_unit_code = (short) (unit_codes & 070);
ds.cal_max = di.readFloat();
ds.cal_min = di.readFloat();
ds.slice_duration = di.readFloat();
ds.toffset = di.readFloat();
ds.glmax = di.readInt();
ds.glmin = di.readInt();
bb = new byte[80];
di.readFully(bb, 0, 80);
ds.descrip = new StringBuffer(new String(bb));
bb = new byte[24];
di.readFully(bb, 0, 24);
ds.aux_file = new StringBuffer(new String(bb));
ds.qform_code = di.readShort();
ds.sform_code = di.readShort();
for (int i = 0; i < 3; i++) ds.quatern[i] = di.readFloat();
for (int i = 0; i < 3; i++) ds.qoffset[i] = di.readFloat();
for (int i = 0; i < 4; i++) ds.srow_x[i] = di.readFloat();
for (int i = 0; i < 4; i++) ds.srow_y[i] = di.readFloat();
for (int i = 0; i < 4; i++) ds.srow_z[i] = di.readFloat();
bb = new byte[16];
di.readFully(bb, 0, 16);
ds.intent_name = new StringBuffer(new String(bb));
bb = new byte[4];
di.readFully(bb, 0, 4);
ds.magic = new StringBuffer(new String(bb));
di.readFully(ds.extension, 0, 4);
if (ds.extension[0] != (byte) 0) {
int start_addr = NiftiHeader.ANZ_HDR_SIZE + 4;
while (start_addr < (int) ds.vox_offset) {
int[] size_code = new int[2];
size_code[0] = di.readInt();
size_code[1] = di.readInt();
int nb = size_code[0] - NiftiHeader.EXT_KEY_SIZE;
byte[] eblob = new byte[nb];
di.readFully(eblob, 0, nb);
ds.extension_blobs.add(eblob);
ds.extensions_list.add(size_code);
start_addr += (size_code[0]);
if (start_addr > (int) ds.vox_offset)
throw new IOException(
"Error: Data for extension "
+ (ds.extensions_list.size())
+ " appears to overrun start of image data.");
}
}
return ds;
}
public int readUnsignedByte() throws IOException {
return dataInput.readUnsignedByte();
}
protected void readPayload(final DataInput input) throws IOException {
setTeamId(input.readUnsignedByte());
}