X-Git-Url: http://git.nguyen.vg/gitweb/?a=blobdiff_plain;f=incbwt%2Fbits%2Fbitvector.cpp;fp=incbwt%2Fbits%2Fbitvector.cpp;h=b76fa9d1b82cd0dcf00dd4d65e0d4dc7faa9587a;hb=40ddf9aca842bdc081b6350a4ebfe36b066c94c9;hp=0000000000000000000000000000000000000000;hpb=af8938dbee21244687184dd0502a84ce1af70c50;p=SXSI%2FTextCollection.git

diff --git a/incbwt/bits/bitvector.cpp b/incbwt/bits/bitvector.cpp
new file mode 100644
index 0000000..b76fa9d
--- /dev/null
+++ b/incbwt/bits/bitvector.cpp
@@ -0,0 +1,270 @@
+#include <cstdlib>
+
+#include "bitvector.h"
+
+
+namespace CSA
+{
+
+
+BitVector::BitVector(std::ifstream& file) :
+  rank_index(0), select_index(0)
+{
+  file.read((char*)&(this->size), sizeof(this->size));
+  file.read((char*)&(this->items), sizeof(this->items));
+  file.read((char*)&(this->number_of_blocks), sizeof(this->number_of_blocks));
+  file.read((char*)&(this->block_size), sizeof(this->block_size));
+
+  this->array = new usint[this->block_size * this->number_of_blocks];
+  file.read((char*)(this->array), this->block_size * this->number_of_blocks * sizeof(usint));
+  this->buffer = new FastBitBuffer(this->array, this->block_size);
+
+  this->integer_bits = length(this->size);
+  this->samples = new FastBitBuffer(file, 2 * (this->number_of_blocks + 1), this->integer_bits);
+
+  this->indexForRank();
+  this->indexForSelect();
+}
+
+BitVector::BitVector(VectorEncoder& encoder, usint universe_size) :
+  size(universe_size), items(encoder.items),
+  block_size(encoder.block_size),
+  number_of_blocks(encoder.blocks),
+  rank_index(0), select_index(0)
+{
+  this->array = new usint[this->block_size * this->number_of_blocks];
+  this->buffer = new FastBitBuffer(this->array, this->block_size);
+
+  this->integer_bits = length(this->size);
+  this->samples = new FastBitBuffer(2 * (this->number_of_blocks + 1), this->integer_bits);
+
+  // Copy & linearize the array.
+  usint pos = 0;
+  for(std::list<usint*>::iterator iter = encoder.array_blocks.begin(); iter != encoder.array_blocks.end(); iter++)
+  {
+    memcpy(this->array + pos, *iter, encoder.superblock_bytes);
+    pos += encoder.block_size * encoder.blocks_in_superblock;
+  }
+  memcpy(this->array + pos, encoder.array, encoder.current_blocks * encoder.block_size * sizeof(usint));
+
+  // Compress the samples.
+  for(std::list<usint*>::iterator iter = encoder.sample_blocks.begin(); iter != encoder.sample_blocks.end(); iter++)
+  {
+    usint* buf = *iter;
+    for(usint i = 0; i < 2 * encoder.samples_in_superblock; i++)
+    {
+      this->samples->writeItem(buf[i]);
+    }
+  }
+  for(usint i = 0; i < 2 * encoder.current_samples; i++)
+  {
+    this->samples->writeItem(encoder.samples[i]);
+  }
+  this->samples->writeItem(this->items);
+  this->samples->writeItem(this->size);
+
+  this->indexForRank();
+  this->indexForSelect();
+}
+
+BitVector::~BitVector()
+{
+  delete[] this->array;
+  delete   this->buffer;
+  delete   this->samples;
+  delete   this->rank_index;
+  delete   this->select_index;
+}
+
+void
+BitVector::writeTo(std::ofstream& file)
+{
+  file.write((char*)&(this->size), sizeof(this->size));
+  file.write((char*)&(this->items), sizeof(this->items));
+  file.write((char*)&(this->number_of_blocks), sizeof(this->number_of_blocks));
+  file.write((char*)&(this->block_size), sizeof(this->block_size));
+  file.write((char*)(this->array), this->block_size * this->number_of_blocks * sizeof(usint));
+  this->samples->writeBuffer(file, false);
+}
+
+//--------------------------------------------------------------------------
+
+usint
+BitVector::reportSize()
+{
+  usint bytes = this->buffer->reportSize();
+  bytes += this->block_size * this->number_of_blocks * sizeof(usint);
+  bytes += this->samples->reportSize();
+  bytes += this->rank_index->reportSize();
+  bytes += this->select_index->reportSize();
+  return bytes;
+}
+
+//--------------------------------------------------------------------------
+
+usint
+BitVector::sampleForIndex(usint index)
+{
+  usint low = this->select_index->readItem(index / this->select_rate);
+  usint high = this->select_index->readItem(index / this->select_rate + 1);
+
+  this->samples->goToItem(2 * low + 2);
+  for(; low < high; low++)
+  {
+    if(this->samples->readItem() > index) { return low; }
+    this->samples->skipItem();
+  }
+
+  return low;
+}
+
+usint
+BitVector::sampleForValue(usint value)
+{
+  usint low = this->rank_index->readItem(value / this->rank_rate);
+  usint high = this->rank_index->readItem(value / this->rank_rate + 1);
+
+  this->samples->goToItem(2 * low + 3);
+  for(; low < high; low++)
+  {
+    if(this->samples->readItem() > value) { return low; }
+    this->samples->skipItem();
+  }
+
+  return low;
+}
+
+//--------------------------------------------------------------------------
+
+void
+BitVector::indexForRank()
+{
+  delete this->rank_index;
+
+  usint value_samples = (this->number_of_blocks + BitVector::INDEX_RATE - 1) / BitVector::INDEX_RATE;
+  this->rank_rate = (this->size + value_samples - 1) / value_samples;
+  value_samples = (this->size + this->rank_rate - 1) / this->rank_rate + 1;
+  this->rank_index = new FastBitBuffer(value_samples, length(this->number_of_blocks - 1));
+
+  usint current = 0, pointer = 0;
+  this->samples->goToItem(2);
+  while(this->samples->hasNextItem())
+  {
+    this->samples->skipItem();
+    usint limit = this->samples->readItem();
+    while(current < limit)
+    {
+      this->rank_index->writeItem(pointer);
+      current += this->rank_rate;
+    }
+    pointer++;
+  }
+  this->rank_index->writeItem(this->number_of_blocks - 1);
+}
+
+void
+BitVector::indexForSelect()
+{
+  delete this->select_index;
+
+  usint index_samples = (this->number_of_blocks + BitVector::INDEX_RATE - 1) / BitVector::INDEX_RATE;
+  this->select_rate = (this->items + index_samples - 1) / index_samples;
+  index_samples = (this->items + this->select_rate - 1) / this->select_rate + 1;
+  this->select_index = new FastBitBuffer(index_samples, length(this->number_of_blocks - 1));
+
+  usint current = 0, pointer = 0;
+  this->samples->goToItem(2);
+  while(this->samples->hasNextItem())
+  {
+    usint limit = this->samples->readItem();
+    this->samples->skipItem();
+    while(current < limit)
+    {
+      this->select_index->writeItem(pointer);
+      current += this->select_rate;
+    }
+    pointer++;
+  }
+  this->select_index->writeItem(this->number_of_blocks - 1);
+}
+
+//--------------------------------------------------------------------------
+
+VectorEncoder::VectorEncoder(usint block_bytes, usint superblock_size) :
+  size(0), items(0), blocks(0),
+  block_size(BYTES_TO_WORDS(block_bytes)),
+  superblock_bytes(superblock_size)
+{
+  this->array = new usint[this->superblock_bytes / sizeof(usint)];
+  memset(this->array, 0, this->superblock_bytes);
+  this->blocks_in_superblock = this->superblock_bytes / (sizeof(usint) * this->block_size);
+  this->current_blocks = 0;
+
+  this->samples = new usint[this->superblock_bytes / sizeof(usint)];
+  this->samples_in_superblock = this->superblock_bytes / (2 * sizeof(usint));
+  this->current_samples = 0;
+
+  this->buffer = new FastBitBuffer(this->array, this->block_size);
+}
+
+VectorEncoder::~VectorEncoder()
+{
+  delete[] this->array;
+
+  delete this->buffer;
+  for(std::list<usint*>::iterator iter = this->array_blocks.begin(); iter != this->array_blocks.end(); iter++)
+  {
+    delete[] *iter;
+  }
+
+  delete[] this->samples;
+  for(std::list<usint*>::iterator iter = this->sample_blocks.begin(); iter != this->sample_blocks.end(); iter++)
+  {
+    delete[] *iter;
+  }
+}
+
+void
+VectorEncoder::addNewBlock()
+{
+  this->blocks++;
+  this->current_blocks++;
+  this->current_samples++;
+
+  // Do we need a new superblock for the block?
+  if(this->current_blocks > this->blocks_in_superblock)
+  {
+    this->array_blocks.push_back(this->array);
+    this->array = new usint[this->superblock_bytes / sizeof(usint)];
+    memset(this->array, 0, this->superblock_bytes);
+    this->current_blocks = 1;
+  }
+  this->buffer->moveBuffer(this->array + (this->block_size * (this->current_blocks - 1)));
+
+  // Do we need a new superblock for the sample?
+  if(this->current_samples > this->samples_in_superblock)
+  {
+    this->sample_blocks.push_back(this->samples);
+    this->samples = new usint[this->superblock_bytes / sizeof(usint)];
+    this->current_samples = 1;
+  }
+  this->samples[2 * this->current_samples - 2] = this->items - 1;
+  this->samples[2 * this->current_samples - 1] = this->size - 1;
+}
+
+void
+VectorEncoder::setFirstBit(usint value)
+{
+  this->samples[0] = 0;
+  this->samples[1] = value;
+
+  this->size = value + 1;
+  this->items = 1;
+  this->blocks = 1;
+
+  this->current_blocks = 1;
+  this->current_samples = 1;
+}
+
+
+} // namespace CSA