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Merged
merged 5 commits into from
Oct 13, 2018
Merged

Datahandle test improvements and Endianness fixes #337

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3e72152
DataHandle: use Bytes helper methods for correct endian coding
gab1one Sep 28, 2018
64f6419
DataHandle#readLine() use StringBuilder instead of StringBuffer
gab1one Sep 28, 2018
5835b94
FileHandle: use DataHandle methods for all endianness affected IO
gab1one Sep 28, 2018
e1290fa
DataHandleTest: extend to cover all methods in DataHandle
gab1one Sep 28, 2018
e9f820a
DataHandle: Use persistent buffer for conversions.
gab1one Oct 4, 2018
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7 changes: 7 additions & 0 deletions src/main/java/org/scijava/io/handle/AbstractDataHandle.java
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,13 @@ public abstract class AbstractDataHandle<L extends Location> extends
AbstractWrapperPlugin<L> implements DataHandle<L>
{

private byte[] conversionBuffer = new byte[8];

@Override
public byte[] conversionBuffer() {
return conversionBuffer;
}

// -- Fields --

private ByteOrder order = ByteOrder.BIG_ENDIAN;
Expand Down
158 changes: 36 additions & 122 deletions src/main/java/org/scijava/io/handle/DataHandle.java
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@

import org.scijava.io.location.Location;
import org.scijava.plugin.WrapperPlugin;
import org.scijava.util.Bytes;

/**
* A <em>data handle</em> is a plugin which provides both streaming and random
Expand Down Expand Up @@ -249,6 +250,11 @@ default void setLittleEndian(final boolean little) {
/** Sets the native encoding of the stream. */
void setEncoding(String encoding);

/**
* @return a 8 byte long buffer array used for type conversions
*/
byte[] conversionBuffer();

/** Reads a string of arbitrary length, terminated by a null char. */
default String readCString() throws IOException {
final String line = findString("\0");
Expand Down Expand Up @@ -514,18 +520,10 @@ default int readUnsignedByte() throws IOException {

@Override
default short readShort() throws IOException {
final int ch0;
final int ch1;
if (isBigEndian()) {
ch0 = read();
ch1 = read();
}
else {
ch1 = read();
ch0 = read();
}
if ((ch0 | ch1) < 0) throw new EOFException();
return (short) ((ch0 << 8) + (ch1 << 0));
final byte[] buf = conversionBuffer();
final int read = read(buf, 0, 2);
if (read < 2) throw new EOFException();
return Bytes.toShort(buf, isLittleEndian());
}

@Override
Expand All @@ -540,68 +538,20 @@ default char readChar() throws IOException {

@Override
default int readInt() throws IOException {
final int ch0;
final int ch1;
final int ch2;
final int ch3;
if (isBigEndian()) {
ch0 = read();
ch1 = read();
ch2 = read();
ch3 = read();
}
else {
ch3 = read();
ch2 = read();
ch1 = read();
ch0 = read();
}
if ((ch0 | ch1 | ch2 | ch3) < 0) throw new EOFException();
return ((ch0 << 24) + (ch1 << 16) + (ch2 << 8) + (ch3 << 0));
final byte[] buf = conversionBuffer();
final int read = read(buf, 0, 4);
if (read < 4) throw new EOFException();
return Bytes.toInt(buf, isLittleEndian());
}

@Override
default long readLong() throws IOException {
final int ch0;
final int ch1;
final int ch2;
final int ch3;
final int ch4;
final int ch5;
final int ch6;
final int ch7;
if (isBigEndian()) {
ch0 = read();
ch1 = read();
ch2 = read();
ch3 = read();
ch4 = read();
ch5 = read();
ch6 = read();
ch7 = read();
}
else {
ch7 = read();
ch6 = read();
ch5 = read();
ch4 = read();
ch3 = read();
ch2 = read();
ch1 = read();
ch0 = read();
}
if ((ch0 | ch1 | ch2 | ch3 | ch4 | ch5 | ch6 | ch7) < 0) {
final byte[] buf = conversionBuffer();
final int read = read(buf, 0, 8);
if (read < 8) {
throw new EOFException();
}
// TODO: Double check this inconsistent code.
return ((long) ch0 << 56) + //
((long) (ch1 & 255) << 48) + //
((long) (ch2 & 255) << 40) + //
((long) (ch3 & 255) << 32) + //
((long) (ch4 & 255) << 24) + //
((ch5 & 255) << 16) + //
((ch6 & 255) << 8) + //
((ch7 & 255) << 0);
return Bytes.toLong(buf, isLittleEndian());
}

@Override
Expand All @@ -618,7 +568,7 @@ default double readDouble() throws IOException {
default String readLine() throws IOException {
// NB: Adapted from java.io.RandomAccessFile.readLine().

final StringBuffer input = new StringBuffer();
final StringBuilder input = new StringBuilder();
int c = -1;
boolean eol = false;

Expand Down Expand Up @@ -669,76 +619,42 @@ default void writeByte(final int v) throws IOException {

@Override
default void writeShort(final int v) throws IOException {
if (isBigEndian()) {
write((v >>> 8) & 0xFF);
write((v >>> 0) & 0xFF);
}
else {
write((v >>> 0) & 0xFF);
write((v >>> 8) & 0xFF);
}
final byte[] buf = conversionBuffer();
Bytes.unpack(v, buf, 0, 2, isLittleEndian());
write(buf, 0, 2);
}

@Override
default void writeChar(final int v) throws IOException {
if (isBigEndian()) {
write((v >>> 8) & 0xFF);
write((v >>> 0) & 0xFF);
}
else {
write((v >>> 0) & 0xFF);
write((v >>> 8) & 0xFF);
}
writeShort(v);
}

@Override
default void writeInt(final int v) throws IOException {
if (isBigEndian()) {
write((v >>> 24) & 0xFF);
write((v >>> 16) & 0xFF);
write((v >>> 8) & 0xFF);
write((v >>> 0) & 0xFF);
}
else {
write((v >>> 0) & 0xFF);
write((v >>> 8) & 0xFF);
write((v >>> 16) & 0xFF);
write((v >>> 24) & 0xFF);
}
final byte[] buf = conversionBuffer();
Bytes.unpack(v, buf, 0, 4, isLittleEndian());
write(buf, 0, 4);
}

@Override
default void writeLong(final long v) throws IOException {
if (isBigEndian()) {
write((byte) (v >>> 56));
write((byte) (v >>> 48));
write((byte) (v >>> 40));
write((byte) (v >>> 32));
write((byte) (v >>> 24));
write((byte) (v >>> 16));
write((byte) (v >>> 8));
write((byte) (v >>> 0));
}
else {
write((byte) (v >>> 0));
write((byte) (v >>> 8));
write((byte) (v >>> 16));
write((byte) (v >>> 24));
write((byte) (v >>> 32));
write((byte) (v >>> 40));
write((byte) (v >>> 48));
write((byte) (v >>> 56));
}
final byte[] buf = conversionBuffer();
Bytes.unpack(v, buf, 0, 8, isLittleEndian());
write(buf, 0, 8);
}

@Override
default void writeFloat(final float v) throws IOException {
writeInt(Float.floatToIntBits(v));
final byte[] buf = conversionBuffer();
Bytes.unpack(Float.floatToIntBits(v), buf, 0, 4, isLittleEndian());
write(buf, 0, 4);
}

@Override
default void writeDouble(final double v) throws IOException {
writeLong(Double.doubleToLongBits(v));
final byte[] buf = conversionBuffer();
Bytes.unpack(Double.doubleToLongBits(v), buf, 0, 8, isLittleEndian());
write(buf, 0, 8);
}

@Override
Expand All @@ -750,9 +666,7 @@ default void writeBytes(final String s) throws IOException {
default void writeChars(final String s) throws IOException {
final int len = s.length();
for (int i = 0; i < len; i++) {
final int v = s.charAt(i);
write((v >>> 8) & 0xFF);
write((v >>> 0) & 0xFF);
writeChar(s.charAt(i));
}
}

Expand Down
65 changes: 0 additions & 65 deletions src/main/java/org/scijava/io/handle/FileHandle.java
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Original file line number Diff line number Diff line change
Expand Up @@ -151,21 +151,6 @@ public byte readByte() throws IOException {
return reader().readByte();
}

@Override
public char readChar() throws IOException {
return reader().readChar();
}

@Override
public double readDouble() throws IOException {
return reader().readDouble();
}

@Override
public float readFloat() throws IOException {
return reader().readFloat();
}

@Override
public void readFully(final byte[] b) throws IOException {
reader().readFully(b);
Expand All @@ -178,36 +163,16 @@ public void readFully(final byte[] b, final int off, final int len)
reader().readFully(b, off, len);
}

@Override
public int readInt() throws IOException {
return reader().readInt();
}

@Override
public String readLine() throws IOException {
return reader().readLine();
}

@Override
public long readLong() throws IOException {
return reader().readLong();
}

@Override
public short readShort() throws IOException {
return reader().readShort();
}

@Override
public int readUnsignedByte() throws IOException {
return reader().readUnsignedByte();
}

@Override
public int readUnsignedShort() throws IOException {
return reader().readUnsignedShort();
}

@Override
public String readUTF() throws IOException {
return reader().readUTF();
Expand Down Expand Up @@ -252,41 +217,11 @@ public void writeBytes(final String s) throws IOException {
writer().writeBytes(s);
}

@Override
public void writeChar(final int v) throws IOException {
writer().writeChar(v);
}

@Override
public void writeChars(final String s) throws IOException {
writer().writeChars(s);
}

@Override
public void writeDouble(final double v) throws IOException {
writer().writeDouble(v);
}

@Override
public void writeFloat(final float v) throws IOException {
writer().writeFloat(v);
}

@Override
public void writeInt(final int v) throws IOException {
writer().writeInt(v);
}

@Override
public void writeLong(final long v) throws IOException {
writer().writeLong(v);
}

@Override
public void writeShort(final int v) throws IOException {
writer().writeShort(v);
}

@Override
public void writeUTF(final String str) throws IOException {
writer().writeUTF(str);
Expand Down
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