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ebremerebremer
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4 files changed

+225
-200
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‎src/main/java/com/ebremer/beakgraph/HDTish/BitPackedWriter.java‎

Lines changed: 177 additions & 177 deletions
Original file line numberDiff line numberDiff line change
@@ -1,177 +1,177 @@
1-
package com.ebremer.beakgraph.HDTish;
2-
3-
import java.io.ByteArrayOutputStream;
4-
import java.io.IOException;
5-
import java.nio.ByteBuffer;
6-
import java.nio.file.Path;
7-
import java.util.HashMap;
8-
import java.util.Map;
9-
10-
interface ByteWriter {
11-
void writeByte(byte b) throws IOException;
12-
}
13-
14-
public class BitPackedWriter implements HDF5Buffer, AutoCloseable {
15-
private final ByteWriter byteWriter;
16-
private final long width;
17-
private long bitBuffer = 0;
18-
private int bitCount = 0;
19-
private ByteArrayOutputStream os;
20-
private Path path;
21-
private long entries = 0;
22-
23-
private BitPackedWriter(Path path, ByteWriter byteWriter, long width, ByteArrayOutputStream os) {
24-
this.path = path;
25-
this.byteWriter = byteWriter;
26-
this.width = width;
27-
this.os = os;
28-
}
29-
30-
@Override
31-
public Map<String, Object> getProperties() {
32-
Map<String,Object> meta = new HashMap<>();
33-
meta.put("width", width);
34-
meta.put("numEntries", entries);
35-
return meta;
36-
}
37-
38-
@Override
39-
public Path getName() {
40-
return path;
41-
}
42-
43-
@Override
44-
public byte[] getBuffer() {
45-
return os.toByteArray();
46-
}
47-
48-
// Write the least significant n bits of the integer to the buffer
49-
public void writeInteger(int value) throws IOException {
50-
//if (width < 0 || width > 32) {
51-
// throw new IllegalArgumentException("n must be between 0 and 32 ---> "+value);
52-
// }
53-
entries++;
54-
// Extract the least significant n bits
55-
long bits = value & ((1L << width) - 1);
56-
// Shift existing bits left and append new bits
57-
bitBuffer = (bitBuffer << width) | bits;
58-
bitCount += width;
59-
// Write full bytes when possible
60-
while (bitCount >= 8) {
61-
int shift = bitCount - 8;
62-
byte b = (byte) (bitBuffer >>> shift);
63-
byteWriter.writeByte(b);
64-
// Keep the remaining bits
65-
bitBuffer = bitBuffer & ((1L << shift) - 1);
66-
bitCount -= 8;
67-
}
68-
}
69-
70-
public void writeLong(long value) throws IOException {
71-
//if (width < 0 || width > 64) {
72-
// throw new IllegalArgumentException("width must be between 0 and 64");
73-
// }
74-
entries++;
75-
long bits = value & ((1L << width) - 1);
76-
bitBuffer = (bitBuffer << width) | bits;
77-
bitCount += width;
78-
while (bitCount >= 8) {
79-
int shift = bitCount - 8;
80-
byte b = (byte) (bitBuffer >>> shift);
81-
byteWriter.writeByte(b);
82-
bitBuffer = bitBuffer & ((1L << shift) - 1);
83-
bitCount -= 8;
84-
}
85-
}
86-
87-
@Override
88-
public void close() throws IOException {
89-
if (bitCount > 0) {
90-
// Pad the remaining bits with zeros on the right
91-
byte b = (byte) (bitBuffer << (8 - bitCount));
92-
byteWriter.writeByte(b);
93-
}
94-
os.flush();
95-
os.close();
96-
}
97-
98-
public static BitPackedWriter forBuffer(Path path, long width) throws IOException {
99-
if (width < 0 || width > 64) {
100-
throw new IllegalArgumentException("n must be between 0 and 64 ---> "+width);
101-
}
102-
System.out.println(path+" ---> "+width);
103-
ByteArrayOutputStream buffer = new ByteArrayOutputStream();
104-
ByteWriter fileWriter = new ByteWriter() {
105-
@Override
106-
public void writeByte(byte b) throws IOException {
107-
buffer.write(b);
108-
}
109-
};
110-
return new BitPackedWriter(path, fileWriter, width, buffer);
111-
}
112-
113-
/*
114-
public static BitPackedWriter forFile(Path file, int width) throws IOException {
115-
BufferedOutputStream fos = new BufferedOutputStream( new FileOutputStream(file.toFile()));
116-
ByteWriter fileWriter = new ByteWriter() {
117-
@Override
118-
public void writeByte(byte b) throws IOException {
119-
fos.write(b);
120-
}
121-
};
122-
return new BitPackedWriter(fileWriter, width, fos);
123-
}*/
124-
125-
public static String toBinaryString(ByteBuffer buffer, String delimiter) {
126-
buffer.mark();
127-
StringBuilder binary = new StringBuilder();
128-
while (buffer.hasRemaining()) {
129-
byte b = buffer.get();
130-
String binaryByte = String.format("%8s", Integer.toBinaryString(b & 0xFF)).replace(' ', '0');
131-
binary.append(binaryByte);
132-
if (buffer.hasRemaining()) {
133-
binary.append(delimiter);
134-
}
135-
}
136-
buffer.reset();
137-
return binary.toString();
138-
}
139-
140-
/*
141-
public static BitPackedWriter forByteBuffer(ByteBuffer buffer, int width) {
142-
ByteWriter bufferWriter = new ByteWriter() {
143-
@Override
144-
public void writeByte(byte b) throws IOException {
145-
if (!buffer.hasRemaining()) {
146-
throw new IOException("ByteBuffer capacity exceeded");
147-
}
148-
buffer.put(b);
149-
}
150-
};
151-
return new BitPackedWriter(bufferWriter, width, fos);
152-
}*/
153-
154-
/*
155-
public static void main(String[] args) throws IOException {
156-
BitPackedWriter fileWriter = BitPackedWriter.forFile(new File("output.dat"), 3);
157-
fileWriter.writeInteger(5); // 101
158-
fileWriter.writeInteger(3); // 011
159-
fileWriter.writeInteger(7); // 111
160-
fileWriter.writeInteger(2); // 111
161-
fileWriter.writeInteger(1); // 111
162-
fileWriter.writeInteger(1); // 111
163-
fileWriter.writeInteger(4); // 111
164-
fileWriter.close();
165-
166-
167-
ByteBuffer buffer = ByteBuffer.allocate(10);
168-
BitPackedWriter bufferWriter = BitPackedWriter.forByteBuffer(buffer,3);
169-
bufferWriter.writeInteger(5);
170-
bufferWriter.writeInteger(3);
171-
bufferWriter.writeInteger(7);
172-
bufferWriter.close();
173-
174-
buffer.rewind();
175-
System.out.println(toBinaryString(buffer, " "));
176-
}*/
177-
}
1+
package com.ebremer.beakgraph.HDTish;
2+
3+
import java.io.ByteArrayOutputStream;
4+
import java.io.IOException;
5+
import java.nio.ByteBuffer;
6+
import java.nio.file.Path;
7+
import java.util.HashMap;
8+
import java.util.Map;
9+
10+
interface ByteWriter {
11+
void writeByte(byte b) throws IOException;
12+
}
13+
14+
public class BitPackedWriter implements HDF5Buffer, AutoCloseable {
15+
private final ByteWriter byteWriter;
16+
private final long width;
17+
private long bitBuffer = 0;
18+
private int bitCount = 0;
19+
private ByteArrayOutputStream os;
20+
private Path path;
21+
private long entries = 0;
22+
23+
private BitPackedWriter(Path path, ByteWriter byteWriter, long width, ByteArrayOutputStream os) {
24+
this.path = path;
25+
this.byteWriter = byteWriter;
26+
this.width = width;
27+
this.os = os;
28+
}
29+
30+
@Override
31+
public Map<String, Object> getProperties() {
32+
Map<String,Object> meta = new HashMap<>();
33+
meta.put("width", width);
34+
meta.put("numEntries", entries);
35+
return meta;
36+
}
37+
38+
@Override
39+
public Path getName() {
40+
return path;
41+
}
42+
43+
@Override
44+
public byte[] getBuffer() {
45+
return os.toByteArray();
46+
}
47+
48+
// Write the least significant n bits of the integer to the buffer
49+
public void writeInteger(int value) throws IOException {
50+
//if (width < 0 || width > 32) {
51+
// throw new IllegalArgumentException("n must be between 0 and 32 ---> "+value);
52+
// }
53+
entries++;
54+
// Extract the least significant n bits
55+
long bits = value & ((1L << width) - 1);
56+
// Shift existing bits left and append new bits
57+
bitBuffer = (bitBuffer << width) | bits;
58+
bitCount += width;
59+
// Write full bytes when possible
60+
while (bitCount >= 8) {
61+
int shift = bitCount - 8;
62+
byte b = (byte) (bitBuffer >>> shift);
63+
byteWriter.writeByte(b);
64+
// Keep the remaining bits
65+
bitBuffer = bitBuffer & ((1L << shift) - 1);
66+
bitCount -= 8;
67+
}
68+
}
69+
70+
public void writeLong(long value) throws IOException {
71+
//if (width < 0 || width > 64) {
72+
// throw new IllegalArgumentException("width must be between 0 and 64");
73+
// }
74+
entries++;
75+
long bits = value & ((1L << width) - 1);
76+
bitBuffer = (bitBuffer << width) | bits;
77+
bitCount += width;
78+
while (bitCount >= 8) {
79+
int shift = bitCount - 8;
80+
byte b = (byte) (bitBuffer >>> shift);
81+
byteWriter.writeByte(b);
82+
bitBuffer = bitBuffer & ((1L << shift) - 1);
83+
bitCount -= 8;
84+
}
85+
}
86+
87+
@Override
88+
public void close() throws IOException {
89+
if (bitCount > 0) {
90+
// Pad the remaining bits with zeros on the right
91+
byte b = (byte) (bitBuffer << (8 - bitCount));
92+
byteWriter.writeByte(b);
93+
}
94+
os.flush();
95+
os.close();
96+
}
97+
98+
public static BitPackedWriter forBuffer(Path path, long width) throws IOException {
99+
if (width < 0 || width > 64) {
100+
throw new IllegalArgumentException("n must be between 0 and 64 ---> "+width);
101+
}
102+
System.out.println(path+" ---> "+width);
103+
ByteArrayOutputStream buffer = new ByteArrayOutputStream();
104+
ByteWriter fileWriter = new ByteWriter() {
105+
@Override
106+
public void writeByte(byte b) throws IOException {
107+
buffer.write(b);
108+
}
109+
};
110+
return new BitPackedWriter(path, fileWriter, width, buffer);
111+
}
112+
113+
/*
114+
public static BitPackedWriter forFile(Path file, int width) throws IOException {
115+
BufferedOutputStream fos = new BufferedOutputStream( new FileOutputStream(file.toFile()));
116+
ByteWriter fileWriter = new ByteWriter() {
117+
@Override
118+
public void writeByte(byte b) throws IOException {
119+
fos.write(b);
120+
}
121+
};
122+
return new BitPackedWriter(fileWriter, width, fos);
123+
}*/
124+
125+
public static String toBinaryString(ByteBuffer buffer, String delimiter) {
126+
buffer.mark();
127+
StringBuilder binary = new StringBuilder();
128+
while (buffer.hasRemaining()) {
129+
byte b = buffer.get();
130+
String binaryByte = String.format("%8s", Integer.toBinaryString(b & 0xFF)).replace(' ', '0');
131+
binary.append(binaryByte);
132+
if (buffer.hasRemaining()) {
133+
binary.append(delimiter);
134+
}
135+
}
136+
buffer.reset();
137+
return binary.toString();
138+
}
139+
140+
/*
141+
public static BitPackedWriter forByteBuffer(ByteBuffer buffer, int width) {
142+
ByteWriter bufferWriter = new ByteWriter() {
143+
@Override
144+
public void writeByte(byte b) throws IOException {
145+
if (!buffer.hasRemaining()) {
146+
throw new IOException("ByteBuffer capacity exceeded");
147+
}
148+
buffer.put(b);
149+
}
150+
};
151+
return new BitPackedWriter(bufferWriter, width, fos);
152+
}*/
153+
154+
/*
155+
public static void main(String[] args) throws IOException {
156+
BitPackedWriter fileWriter = BitPackedWriter.forFile(new File("output.dat"), 3);
157+
fileWriter.writeInteger(5); // 101
158+
fileWriter.writeInteger(3); // 011
159+
fileWriter.writeInteger(7); // 111
160+
fileWriter.writeInteger(2); // 111
161+
fileWriter.writeInteger(1); // 111
162+
fileWriter.writeInteger(1); // 111
163+
fileWriter.writeInteger(4); // 111
164+
fileWriter.close();
165+
166+
167+
ByteBuffer buffer = ByteBuffer.allocate(10);
168+
BitPackedWriter bufferWriter = BitPackedWriter.forByteBuffer(buffer,3);
169+
bufferWriter.writeInteger(5);
170+
bufferWriter.writeInteger(3);
171+
bufferWriter.writeInteger(7);
172+
bufferWriter.close();
173+
174+
buffer.rewind();
175+
System.out.println(toBinaryString(buffer, " "));
176+
}*/
177+
}

‎src/main/java/com/ebremer/beakgraph/HDTish/DictionaryWriter.java‎

Lines changed: 14 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -136,25 +136,22 @@ private void Add(Node node) {
136136
}
137137
} else if (node.isLiteral()) {
138138
String dt = node.getLiteralDatatypeURI();
139-
if (dt.equals(XSD.xlong.getURI())) {
140-
if (node.getLiteralValue() instanceof Long x) {
141-
try {
142-
offsets.writeInteger(Long.BYTES);
143-
datatype.writeInteger(DataType.LONG.ordinal());
144-
longs.writeLong(x);
145-
} catch (IOException ex) {
146-
Logger.getLogger(DictionaryWriter.class.getName()).log(Level.SEVERE, null, ex);
147-
}
139+
if (dt.equals(XSD.xlong.getURI())) {
140+
try {
141+
offsets.writeInteger(Long.BYTES);
142+
datatype.writeInteger(DataType.LONG.ordinal());
143+
longs.writeLong(((Number) node.getLiteralValue()).longValue());
144+
} catch (IOException ex) {
145+
Logger.getLogger(DictionaryWriter.class.getName()).log(Level.SEVERE, null, ex);
148146
}
149147
} else if (dt.equals(XSD.xint.getURI())) {
150-
if (node.getLiteralValue() instanceof Integer x) {
151-
try {
152-
offsets.writeInteger(Integer.BYTES);
153-
integers.writeInteger(x);
154-
datatype.writeInteger(DataType.INT.ordinal());
155-
} catch (IOException ex) {
156-
Logger.getLogger(DictionaryWriter.class.getName()).log(Level.SEVERE, null, ex);
157-
}
148+
System.out.println("WRITING INTEGER =======> "+node.getLiteralValue());
149+
try {
150+
offsets.writeInteger(Integer.BYTES);
151+
integers.writeInteger(((Number) node.getLiteralValue()).intValue());
152+
datatype.writeInteger(DataType.INT.ordinal());
153+
} catch (IOException ex) {
154+
Logger.getLogger(DictionaryWriter.class.getName()).log(Level.SEVERE, null, ex);
158155
}
159156
} else if (dt.equals(XSD.xdouble.getURI())) {
160157
if (node.getLiteralValue() instanceof Double x) {

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