plugins.nherve.toolbox.PersistenceToolbox Maven / Gradle / Ivy
/*
* Copyright 2010, 2011 Institut Pasteur.
* Copyright 2012 Institut National de l'Audiovisuel.
*
* This file is part of NHerveTools.
*
* NHerveTools is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* NHerveTools is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with NHerveTools. If not, see > HOOKS_BY_TYPE = new HashMap>();
public final static Map, SignaturePersistenceHook> HOOKS_BY_CLASS = new HashMap, SignaturePersistenceHook>();
/**
* Dump bag of signatures.
*
* @param fc
* the fc
* @param s
* the s
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static void dumpBagOfSignatures(FileChannel fc, BagOfSignatures s) throws IOException {
dumpInt(fc, s.size());
for (DefaultVectorSignature vs : s) {
dumpSignature(fc, vs);
}
}
/**
* Dump boolean.
*
* @param fc
* the fc
* @param b
* the b
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static void dumpBoolean(FileChannel fc, boolean b) throws IOException {
if (b) {
dumpInt(fc, 1);
} else {
dumpInt(fc, 0);
}
}
/**
* Dump dense vector signature.
*
* @param fc
* the fc
* @param s
* the s
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static void dumpDenseVectorSignature(FileChannel fc, DenseVectorSignature s) throws IOException {
dumpInt(fc, s.getSize());
ByteBuffer bb = ByteBuffer.allocate(DOUBLE_NB_BYTES * s.getSize());
DoubleBuffer db = bb.asDoubleBuffer();
db.put(s.getData());
db.flip();
fc.write(bb);
}
/**
* Dump double.
*
* @param fc
* the fc
* @param d
* the d
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static void dumpDouble(FileChannel fc, double d) throws IOException {
ByteBuffer bb = ByteBuffer.allocate(DOUBLE_NB_BYTES);
DoubleBuffer db = bb.asDoubleBuffer();
db.put(d);
db.flip();
fc.write(bb);
}
/**
* Dump float.
*
* @param fc
* the fc
* @param f
* the f
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static void dumpFloat(FileChannel fc, float f) throws IOException {
ByteBuffer bb = ByteBuffer.allocate(FLOAT_NB_BYTES);
FloatBuffer db = bb.asFloatBuffer();
db.put(f);
db.flip();
fc.write(bb);
}
public static void dumpFullIntArray(FileChannel fc, int[] i) throws IOException {
dumpInt(fc, i.length);
dumpIntArray(fc, i);
}
public static void dumpFullLongArray(FileChannel fc, long[] i) throws IOException {
dumpInt(fc, i.length);
dumpLongArray(fc, i);
}
public static void dumpIndexSignature(FileChannel fc, IndexSignature s) throws IOException {
dumpInt(fc, s.getSize());
ByteBuffer bb = ByteBuffer.allocate(INT_NB_BYTES * s.getSize());
IntBuffer db = bb.asIntBuffer();
db.put(s.getData());
db.flip();
fc.write(bb);
}
/**
* Dump int.
*
* @param fc
* the fc
* @param i
* the i
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static void dumpInt(FileChannel fc, int i) throws IOException {
ByteBuffer bb = ByteBuffer.allocate(INT_NB_BYTES);
IntBuffer ib = bb.asIntBuffer();
ib.put(i);
ib.flip();
fc.write(bb);
}
/**
* Dump int array.
*
* @param fc
* the fc
* @param i
* the i
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static void dumpIntArray(FileChannel fc, int[] i) throws IOException {
ByteBuffer bb = ByteBuffer.allocate(i.length * INT_NB_BYTES);
IntBuffer ib = bb.asIntBuffer();
ib.put(i);
ib.flip();
fc.write(bb);
}
public static void dumpLong(FileChannel fc, long l) throws IOException {
ByteBuffer bb = ByteBuffer.allocate(LONG_NB_BYTES);
LongBuffer lb = bb.asLongBuffer();
lb.put(l);
lb.flip();
fc.write(bb);
}
public static void dumpLongArray(FileChannel fc, long[] i) throws IOException {
ByteBuffer bb = ByteBuffer.allocate(i.length * LONG_NB_BYTES);
LongBuffer ib = bb.asLongBuffer();
ib.put(i);
ib.flip();
fc.write(bb);
}
/**
* Dump signature.
*
* @param fc
* the fc
* @param s
* the s
* @throws IOException
* Signals that an I/O exception has occurred.
*/
@SuppressWarnings("unchecked")
public static void dumpSignature(FileChannel fc, Signature s) throws IOException {
if (s == null) {
dumpInt(fc, NULL_TYPE);
} else if (s instanceof DenseVectorSignature) {
dumpInt(fc, DENSE_TYPE);
dumpDenseVectorSignature(fc, (DenseVectorSignature) s);
} else if (s instanceof IndexSignature) {
dumpInt(fc, INDEX_TYPE);
dumpIndexSignature(fc, (IndexSignature) s);
} else if (s instanceof SparseVectorSignature) {
dumpInt(fc, SPARSE_TYPE);
dumpSparseVectorSignature(fc, (SparseVectorSignature) s);
} else if (s instanceof BagOfSignatures) {
dumpInt(fc, BAG_TYPE);
dumpBagOfSignatures(fc, (BagOfSignatures) s);
} else if (HOOKS_BY_CLASS.containsKey(s.getClass())) {
SignaturePersistenceHook hook = HOOKS_BY_CLASS.get(s.getClass());
dumpInt(fc, hook.getTypeCode());
hook.dumpSignature(fc, (DefaultVectorSignature)s);
} else {
throw new IOException("dumpSignature(" + s.getClass().getName() + ") not yet implemented");
}
}
/**
* Dump sparse vector signature.
*
* @param fc
* the fc
* @param s
* the s
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static void dumpSparseVectorSignature(FileChannel fc, SparseVectorSignature s) throws IOException {
try {
int nzb = s.getNonZeroBins();
int[] i = new int[nzb];
double[] d = new double[nzb];
int n = 0;
for (int c : s) {
i[n] = c;
d[n] = s.get(c);
n++;
}
dumpInt(fc, s.getSize());
dumpInt(fc, nzb);
ByteBuffer bb1 = ByteBuffer.allocate(INT_NB_BYTES * nzb);
IntBuffer ib = bb1.asIntBuffer();
ib.put(i);
ib.flip();
fc.write(bb1);
ByteBuffer bb2 = ByteBuffer.allocate(DOUBLE_NB_BYTES * nzb);
DoubleBuffer db = bb2.asDoubleBuffer();
db.put(d);
db.flip();
fc.write(bb2);
} catch (SignatureException e) {
throw new IOException(e);
}
}
/**
* Dump string.
*
* @param fc
* the fc
* @param s
* the s
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static void dumpString(FileChannel fc, String s) throws IOException {
CharBuffer cb = CharBuffer.allocate(s.length());
cb.put(s);
cb.flip();
ByteBuffer buff = cse.encode(cb);
dumpInt(fc, buff.limit());
fc.write(buff);
}
/**
* Gets the file.
*
* @param f
* the f
* @param write
* the write
* @return the file
* @throws FileNotFoundException
* the file not found exception
*/
public static RandomAccessFile getFile(File f, boolean write) throws FileNotFoundException {
if (write) {
if (f.exists()) {
f.delete();
}
f.getParentFile().mkdirs();
return new RandomAccessFile(f, "rw");
} else {
return new RandomAccessFile(f, "r");
}
}
/**
* Load bag of signatures.
*
* @param fc
* the fc
* @return the bag of signatures
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static BagOfSignatures loadBagOfSignatures(FileChannel fc) throws IOException {
int type = loadInt(fc);
if (type == NULL_TYPE) {
return null;
}
if (type != BAG_TYPE) {
throw new IOException("Unknown BagOfSignatures type (" + type + ")");
}
int sz = loadInt(fc);
BagOfSignatures bag = new BagOfSignatures();
for (int i = 0; i < sz; i++) {
bag.add(loadVectorSignature(fc));
}
return bag;
}
/**
* Load boolean.
*
* @param fc
* the fc
* @return true, if successful
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static boolean loadBoolean(FileChannel fc) throws IOException {
return loadInt(fc) == 1;
}
/**
* Load dense vector signature.
*
* @param fc
* the fc
* @return the dense vector signature
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static DenseVectorSignature loadDenseVectorSignature(FileChannel fc) throws IOException {
int sz = loadInt(fc);
ByteBuffer bb = ByteBuffer.allocate(DOUBLE_NB_BYTES * sz);
fc.read(bb);
bb.flip();
DoubleBuffer db = bb.asDoubleBuffer();
double[] data = new double[sz];
db.get(data);
DenseVectorSignature v = new DenseVectorSignature(data);
return v;
}
/**
* Load double.
*
* @param fc
* the fc
* @return the double
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static double loadDouble(FileChannel fc) throws IOException {
ByteBuffer bb = ByteBuffer.allocate(DOUBLE_NB_BYTES);
fc.read(bb);
bb.flip();
DoubleBuffer db = bb.asDoubleBuffer();
return db.get();
}
/**
* Load float.
*
* @param fc
* the fc
* @return the float
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static float loadFloat(FileChannel fc) throws IOException {
ByteBuffer bb = ByteBuffer.allocate(FLOAT_NB_BYTES);
fc.read(bb);
bb.flip();
FloatBuffer db = bb.asFloatBuffer();
return db.get();
}
public static int[] loadFullIntArray(FileChannel fc) throws IOException {
int sz = loadInt(fc);
return loadIntArray(fc, sz);
}
public static long[] loadFullLongArray(FileChannel fc) throws IOException {
int sz = loadInt(fc);
return loadLongArray(fc, sz);
}
public static IndexSignature loadIndexSignature(FileChannel fc) throws IOException {
int sz = loadInt(fc);
ByteBuffer bb = ByteBuffer.allocate(INT_NB_BYTES * sz);
fc.read(bb);
bb.flip();
IntBuffer db = bb.asIntBuffer();
int[] data = new int[sz];
db.get(data);
IndexSignature v = new IndexSignature(data);
return v;
}
/**
* Load int.
*
* @param fc
* the fc
* @return the int
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static int loadInt(FileChannel fc) throws IOException {
ByteBuffer bb = ByteBuffer.allocate(INT_NB_BYTES);
fc.read(bb);
bb.flip();
IntBuffer ib = bb.asIntBuffer();
return ib.get();
}
public static int[] loadIntArray(FileChannel fc, int sz) throws IOException {
ByteBuffer bb = ByteBuffer.allocate(PersistenceToolbox.INT_NB_BYTES * sz);
fc.read(bb);
bb.flip();
IntBuffer ib = bb.asIntBuffer();
int[] res = new int[sz];
ib.get(res);
return res;
}
public static long loadLong(FileChannel fc) throws IOException {
ByteBuffer bb = ByteBuffer.allocate(LONG_NB_BYTES);
fc.read(bb);
bb.flip();
LongBuffer ib = bb.asLongBuffer();
return ib.get();
}
public static long[] loadLongArray(FileChannel fc, int sz) throws IOException {
ByteBuffer bb = ByteBuffer.allocate(PersistenceToolbox.LONG_NB_BYTES * sz);
fc.read(bb);
bb.flip();
LongBuffer ib = bb.asLongBuffer();
long[] res = new long[sz];
ib.get(res);
return res;
}
/**
* Load sparse vector signature.
*
* @param fc
* the fc
* @return the sparse vector signature
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static SparseVectorSignature loadSparseVectorSignature(FileChannel fc) throws IOException {
try {
int sz = loadInt(fc);
int nzb = loadInt(fc);
SparseVectorSignature v = new SparseVectorSignature(sz);
ByteBuffer bb1 = ByteBuffer.allocate(INT_NB_BYTES * nzb);
fc.read(bb1);
bb1.flip();
IntBuffer ib = bb1.asIntBuffer();
ib.rewind();
ByteBuffer bb2 = ByteBuffer.allocate(DOUBLE_NB_BYTES * nzb);
fc.read(bb2);
bb2.flip();
DoubleBuffer db = bb2.asDoubleBuffer();
db.rewind();
while (db.hasRemaining() && ib.hasRemaining()) {
v.set(ib.get(), db.get());
}
if (db.hasRemaining() || ib.hasRemaining()) {
throw new IOException("IntBuffer and DoubleBuffer sizes mismatch");
}
return v;
} catch (SignatureException e) {
throw new IOException(e);
}
}
/**
* Load string.
*
* @param fc
* the fc
* @return the string
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static String loadString(FileChannel fc) throws IOException {
int sz = loadInt(fc);
ByteBuffer bb = ByteBuffer.allocate(sz);
fc.read(bb);
bb.flip();
CharBuffer cb = csd.decode(bb);
return cb.toString();
}
/**
* Load vector signature.
*
* @param fc
* the fc
* @return the vector signature
* @throws IOException
* Signals that an I/O exception has occurred.
*/
public static DefaultVectorSignature loadVectorSignature(FileChannel fc) throws IOException {
int type = loadInt(fc);
switch (type) {
case NULL_TYPE:
return null;
case DENSE_TYPE:
return loadDenseVectorSignature(fc);
case SPARSE_TYPE:
return loadSparseVectorSignature(fc);
}
if (HOOKS_BY_TYPE.containsKey(type)) {
return HOOKS_BY_TYPE.get(type).loadSignature(fc);
}
throw new IOException("Unknown VectorSignature type (" + type + ")");
}
public static void registerSignaturePersistenceHook(SignaturePersistenceHook hook) {
HOOKS_BY_TYPE.put(hook.getTypeCode(), hook);
HOOKS_BY_CLASS.put(hook.getSignatureClass(), hook);
}
}
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