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Miscellaneous Utilities (Pure Java)
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/*
* Copyright (c) 2019 by Andrew Charneski.
*
* The author licenses this file to you under the
* Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance
* with the License. You may obtain a copy
* of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
* KIND, either express or implied. See the License for the
* specific language governing permissions and limitations
* under the License.
*/
package com.simiacryptus.util.binary.bitset;
import com.simiacryptus.ref.lang.RefAware;
import com.simiacryptus.ref.lang.RefUtil;
import com.simiacryptus.ref.wrappers.*;
import com.simiacryptus.ref.wrappers.RefMaps.EntryTransformer;
import com.simiacryptus.util.binary.BitInputStream;
import com.simiacryptus.util.binary.BitOutputStream;
import com.simiacryptus.util.binary.Bits;
import com.simiacryptus.util.binary.codes.Gaussian;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.util.Map;
import java.util.Map.Entry;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.concurrent.atomic.AtomicLong;
public class CountTreeBitsCollection extends BitsCollection> {
public static boolean SERIALIZATION_CHECKS = false;
private boolean useBinomials = true;
public CountTreeBitsCollection() {
super(new RefTreeMap());
}
public CountTreeBitsCollection(@Nonnull final BitInputStream bitStream) throws IOException {
this();
this.read(bitStream);
}
public CountTreeBitsCollection(@Nonnull final BitInputStream bitStream, final int bitDepth) throws IOException {
this(bitDepth);
this.read(bitStream);
}
public CountTreeBitsCollection(@Nonnull final byte[] data) throws IOException {
this(BitInputStream.toBitStream(data));
}
public CountTreeBitsCollection(@Nonnull final byte[] data, final int bitDepth) throws IOException {
this(BitInputStream.toBitStream(data), bitDepth);
}
public CountTreeBitsCollection(final int bitDepth) {
super(bitDepth, new RefTreeMap());
}
public void setUseBinomials(final boolean useBinomials) {
this.useBinomials = useBinomials;
}
public static T isNull(@Nullable final T value, final T defaultValue) {
return null == value ? defaultValue : value;
}
@Nonnull
public RefTreeMap computeSums() {
final RefTreeMap sums = new RefTreeMap();
AtomicLong total = new AtomicLong();
assert this.map != null;
RefHashSet> entries = this.map.entrySet();
entries.forEach(e -> {
RefUtil.freeRef(sums.put(e.getKey(), total.addAndGet(e.getValue().get())));
RefUtil.freeRef(e);
});
entries.freeRef();
return sums;
}
@Override
public void read(@Nonnull final BitInputStream in) throws IOException {
RefMap temp_13_0001 = this.getMap();
temp_13_0001.clear();
temp_13_0001.freeRef();
final long size = in.readVarLong();
if (0 < size) {
this.read(in, Bits.NULL, size);
}
}
public void read(@Nonnull final BitInputStream in, final int size) throws IOException {
RefMap temp_13_0002 = this.getMap();
temp_13_0002.clear();
temp_13_0002.freeRef();
if (0 < size) {
this.read(in, Bits.NULL, size);
}
}
public long sum(@Nonnull final @RefAware RefCollection values) {
long total = values.stream().mapToLong(v -> v).sum();
values.freeRef();
return total;
}
@Nonnull
public byte[] toBytes() throws IOException {
final ByteArrayOutputStream outBuffer = new ByteArrayOutputStream();
final BitOutputStream out = new BitOutputStream(outBuffer);
this.write(out);
out.flush();
return outBuffer.toByteArray();
}
public boolean useBinomials() {
return this.useBinomials;
}
@Override
public void write(@Nonnull final BitOutputStream out) throws IOException {
final RefTreeMap sums = this.computeSums();
Map.Entry temp_13_0003 = sums.lastEntry();
final long value = 0 == sums.size() ? 0 : temp_13_0003.getValue();
RefUtil.freeRef(temp_13_0003);
out.writeVarLong(value);
if (0 < value) {
this.write(out, Bits.NULL, RefUtil.addRef(sums));
}
sums.freeRef();
}
public void write(@Nonnull final BitOutputStream out, final int size) throws IOException {
final RefTreeMap sums = this.computeSums();
Map.Entry temp_13_0004 = sums.lastEntry();
final long value = 0 == sums.size() ? 0 : temp_13_0004.getValue();
RefUtil.freeRef(temp_13_0004);
if (value != size) {
sums.freeRef();
throw new RuntimeException();
}
if (0 < value) {
this.write(out, Bits.NULL, RefUtil.addRef(sums));
}
sums.freeRef();
}
public @SuppressWarnings("unused")
void _free() {
super._free();
}
@Nonnull
public @Override
@SuppressWarnings("unused")
CountTreeBitsCollection addRef() {
return (CountTreeBitsCollection) super.addRef();
}
@Nonnull
protected BranchCounts readBranchCounts(@Nonnull final BitInputStream in, @Nonnull final Bits code, final long size)
throws IOException {
final BranchCounts branchCounts = new BranchCounts(code, size);
final CodeType currentCodeType = this.getType(code);
long maximum = size;
// Get terminals
if (currentCodeType == CodeType.Unknown) {
branchCounts.terminals = this.readTerminalCount(in, maximum);
} else if (currentCodeType == CodeType.Terminal) {
branchCounts.terminals = size;
} else {
branchCounts.terminals = 0;
}
maximum -= branchCounts.terminals;
// Get zero-suffixed primary
if (maximum > 0) {
assert Thread.currentThread().getStackTrace().length < 100;
branchCounts.zeroCount = this.readZeroBranchSize(in, maximum);
}
maximum -= branchCounts.zeroCount;
branchCounts.oneCount = maximum;
return branchCounts;
}
protected long readTerminalCount(@Nonnull final BitInputStream in, final long size) throws IOException {
if (SERIALIZATION_CHECKS) {
in.expect(SerializationChecks.BeforeTerminal);
}
final long readBoundedLong = in.readBoundedLong(1 + size);
if (SERIALIZATION_CHECKS) {
in.expect(SerializationChecks.AfterTerminal);
}
return readBoundedLong;
}
protected long readZeroBranchSize(@Nonnull final BitInputStream in, final long max) throws IOException {
if (0 == max) {
return 0;
}
final long value;
if (SERIALIZATION_CHECKS) {
in.expect(SerializationChecks.BeforeCount);
}
if (this.useBinomials) {
value = Gaussian.fromBinomial(0.5, max).decode(in, max);
} else {
value = in.readBoundedLong(1 + max);
}
if (SERIALIZATION_CHECKS) {
in.expect(SerializationChecks.AfterCount);
}
return value;
}
protected void writeBranchCounts(@Nonnull final BranchCounts branch, @Nonnull final BitOutputStream out) throws IOException {
final CodeType currentCodeType = this.getType(branch.path);
long maximum = branch.size;
assert maximum >= branch.terminals;
if (currentCodeType == CodeType.Unknown) {
this.writeTerminalCount(out, branch.terminals, maximum);
} else if (currentCodeType == CodeType.Terminal) {
assert branch.size == branch.terminals;
assert 0 == branch.zeroCount;
assert 0 == branch.oneCount;
} else
assert currentCodeType != CodeType.Prefix || 0 == branch.terminals;
maximum -= branch.terminals;
assert maximum >= branch.zeroCount;
if (0 < maximum) {
this.writeZeroBranchSize(out, branch.zeroCount, maximum);
maximum -= branch.zeroCount;
} else {
assert 0 == branch.zeroCount;
}
assert maximum == branch.oneCount;
}
protected void writeTerminalCount(@Nonnull final BitOutputStream out, final long value, final long max) throws IOException {
assert 0 <= value;
assert max >= value;
if (SERIALIZATION_CHECKS) {
out.write(SerializationChecks.BeforeTerminal);
}
out.writeBoundedLong(value, 1 + max);
if (SERIALIZATION_CHECKS) {
out.write(SerializationChecks.AfterTerminal);
}
}
protected void writeZeroBranchSize(@Nonnull final BitOutputStream out, final long value, final long max)
throws IOException {
assert 0 <= value;
assert max >= value;
if (SERIALIZATION_CHECKS) {
out.write(SerializationChecks.BeforeCount);
}
if (this.useBinomials) {
Gaussian.fromBinomial(0.5, max).encode(out, value, max);
} else {
out.writeBoundedLong(value, 1 + max);
}
if (SERIALIZATION_CHECKS) {
out.write(SerializationChecks.AfterCount);
}
}
private void read(@Nonnull final BitInputStream in, @Nonnull final Bits code, final long size) throws IOException {
if (SERIALIZATION_CHECKS) {
in.expect(SerializationChecks.StartTree);
}
final BranchCounts branchCounts = this.readBranchCounts(in, code, size);
if (0 < branchCounts.terminals) {
assert this.map != null;
RefUtil.freeRef(this.map.put(code, new AtomicInteger((int) branchCounts.terminals)));
}
if (0 < branchCounts.zeroCount) {
this.read(in, code.concatenate(Bits.ZERO), branchCounts.zeroCount);
}
// Get one-suffixed primary
if (branchCounts.oneCount > 0) {
this.read(in, code.concatenate(Bits.ONE), branchCounts.oneCount);
}
if (SERIALIZATION_CHECKS) {
in.expect(SerializationChecks.EndTree);
}
}
private void write(@Nonnull final BitOutputStream out, @Nonnull final Bits currentCode,
@Nonnull final @RefAware RefNavigableMap sums) throws IOException {
final Entry firstEntry = sums.firstEntry();
final RefNavigableMap remainder = sums.tailMap(currentCode, false);
final Bits splitCode = currentCode.concatenate(Bits.ONE);
final RefNavigableMap zeroMap = remainder.headMap(splitCode, false);
final RefNavigableMap oneMap = remainder.tailMap(splitCode, true);
remainder.freeRef();
assert this.map != null;
AtomicInteger atomicInteger = this.map.get(firstEntry.getKey());
final int firstEntryCount = atomicInteger.get();
final long baseCount = firstEntry.getValue() - firstEntryCount;
Map.Entry temp_13_0005 = sums.lastEntry();
final long endCount = temp_13_0005.getValue();
RefUtil.freeRef(temp_13_0005);
final long size = endCount - baseCount;
final long terminals = firstEntry.getKey().equals(currentCode) ? firstEntryCount : 0;
RefUtil.freeRef(firstEntry);
Map.Entry temp_13_0006 = zeroMap.lastEntry();
final long zeroCount = 0 == zeroMap.size() ? 0 : temp_13_0006.getValue() - baseCount - terminals;
if (null != temp_13_0006)
RefUtil.freeRef(temp_13_0006);
final long oneCount = size - terminals - zeroCount;
final EntryTransformer transformer = new EntryTransformer() {
@Nonnull
@Override
public Long transformEntry(final @RefAware Bits key, final Long value) {
AtomicInteger atomicInteger = CountTreeBitsCollection.this.map.get(key);
return (long) atomicInteger.get();
}
};
RefMap temp_13_0007 = RefMaps.transformEntries(RefUtil.addRef(sums), transformer);
assert size == this.sum(temp_13_0007.values());
temp_13_0007.freeRef();
sums.freeRef();
RefMap temp_13_0008 = RefMaps.transformEntries(RefUtil.addRef(zeroMap), transformer);
assert zeroCount == this.sum(temp_13_0008.values());
temp_13_0008.freeRef();
RefMap temp_13_0009 = RefMaps.transformEntries(RefUtil.addRef(oneMap), transformer);
assert oneCount == this.sum(temp_13_0009.values());
temp_13_0009.freeRef();
final BranchCounts branchCounts = new BranchCounts(currentCode, size, terminals, zeroCount, oneCount);
if (SERIALIZATION_CHECKS) {
out.write(SerializationChecks.StartTree);
}
this.writeBranchCounts(branchCounts, out);
if (0 < zeroCount) {
this.write(out, currentCode.concatenate(Bits.ZERO), RefUtil.addRef(zeroMap));
}
zeroMap.freeRef();
if (0 < oneCount) {
this.write(out, currentCode.concatenate(Bits.ONE), RefUtil.addRef(oneMap));
}
oneMap.freeRef();
if (SERIALIZATION_CHECKS) {
out.write(SerializationChecks.EndTree);
}
}
public enum SerializationChecks {
StartTree, EndTree, BeforeCount, AfterCount, BeforeTerminal, AfterTerminal
}
public static class BranchCounts {
public Bits path;
public long size;
public long terminals;
public long zeroCount;
public long oneCount;
public BranchCounts(final Bits path, final long size) {
this.path = path;
this.size = size;
}
public BranchCounts(final Bits path, final long size, final long terminals, final long zeroCount,
final long oneCount) {
this.path = path;
this.size = size;
this.terminals = terminals;
this.zeroCount = zeroCount;
this.oneCount = oneCount;
}
}
}