Package it.unimi.dsi.sux4j.io

Class ChunkedHashStore<T>

java.lang.Object
it.unimi.dsi.sux4j.io.ChunkedHashStore<T>
All Implemented Interfaces:
SafelyCloseable, Closeable, Serializable, AutoCloseable, Iterable<ChunkedHashStore.Chunk>
@Deprecated public class ChunkedHashStore<T> extends Object implements Serializable, SafelyCloseable, Iterable<ChunkedHashStore.Chunk>
Deprecated.
Please use a BucketedHashStore, which provides accurate bucket sizing.
A temporary store of hash triples virtually divided into chunks.

A chunked hash store accumulates elements (objects of type T) by turning them into bit vectors (using a provided TransformationStrategy) and then hashing such vectors into a triple of longs (i.e., overall we get a hash of 192 bits). Elements can be added one by one or in batches. Elements must be distinct, or, more precisely, they must be transformed into distinct bit vectors.

Besides the hashes, we store some data associated with each element: if no data is specified, we store the rank of each element added (the first element added has rank 0, the second one has rank 1, and so on), unless you specified at construction time a nonzero hash width: in that case, the value stored by add(Object) will be given the lowest bits of the first hash of the triple associated with the object (the hash width is the number of bits stored). This feature makes it possible, for example, to implement a static dictionary using a GOV3Function.

Once all elements have been added, they can be gathered into chunks whose tentative size can be set by calling log2Chunks(int). More precisely, if the latter method is called with argument k, then each chunk will be formed by grouping triples by the k most significant bits of their first hash.

To obtain triples, one calls iterator(), which returns chunks one at a time (in their natural order); triples within each chunk are returned by increasing hash. Actually, the iterator provided by a chunk returns a quadruple whose last element is the data associated with the element that generated the triple.

It is possible (albeit very unlikely) that different elements generate the same hash. This event is detected during chunk iteration (not while accumulating hashes), and it will throw a ChunkedHashStore.DuplicateException. At that point, the caller must handle the exception by resetting the store and trying again from scratch. Note that after a few (say, three) exceptions you can safely assume that there are duplicate elements. If you need to force a check on the whole store you can call check(). If all your elements come from an Iterable, checkAndRetry(Iterable, LongIterable) will try three times to build a checked chunked hash store.

Every reset(long) changes the seed used by the store to generate triples. So, if this seed has to be stored this must happen after the last call to reset(long). To help tracking this fact, a call to seed() will lock the store; any further call to reset(long) will throw an IllegalStateException. In case the store needs to be reused, you can call clear(), that will bring back the store to after-creation state.

When you have finished using a chunked hash store, you should close() it. This class implements SafelyCloseable, and thus provides a safety-net finalizer.

Filtering

You can at any time set a predicate that will filter the triples returned by the store.

Computing frequencies

If you specify so at construction time, a chunked hash store will compute for you a a map from values to their frequency.

Implementation details

Internally, a chunked hash store has a notion of disk chunk: triples are stored on disk using a fixed number of bits. Once the user chooses a chunk size, the store exhibits the data on disk by grouping disk chunks or splitting them in a suitable way. This process is transparent to the user.

An instance of this class will save triples into DISK_CHUNKS disk chunks. Triples have to be loaded into memory only chunk by chunk, so to be sorted and tested for uniqueness. As long as DISK_CHUNKS is larger than eight, the store will need less than one bit per element of main memory. DISK_CHUNKS can be increased arbitrarily at compile time, but each store will open DISK_CHUNKS files at the same time. (For the same reason, it is strongly suggested that you close your stores as soon as you do not need them).

Intended usage

Chunked hash stores should be built by classes that need to manipulate elements in chunks of approximate given size without needing access to the elements themselves, but just to their triples, a typical example being GOV3Function, which uses the triples to compute a 3-hyperedge. Once a chunked hash store is built, it can be passed on to further substructures, reducing greatly the computation time (as the original collection need not to be scanned again).

To compute the chunk corresponding to given element, use 

 final long[] h = new long[3];
 Hashes.spooky4(transform.toBitVector(key), seed, h);
 final int chunk = chunkShift == Long.SIZE ? 0 : (int)(h[0] >>> chunkShift);
where seed is the store seed, and chunkShift is the return value of log2Chunks(int) and should be stored by the caller. Note that you do not need the chunked hash store to compute these data, but just its seed and the chunk shift.
Since:
1.0.4
Author:
Sebastiano Vigna
See Also:

  • Nested Class Summary

    Nested Classes
    Modifier and Type
    Class
    Description
    static final class 
    ChunkedHashStore.Chunk
    Deprecated.
    A chunk returned by a ChunkedHashStore.
    static class 
    ChunkedHashStore.DuplicateException
    Deprecated.
    Denotes that the chunked hash store contains a duplicate hash triple.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    BUFFER_SIZE
    Deprecated.
    The size of the output buffers.
    static final int
    DISK_CHUNKS
    Deprecated.
    The number of physical disk chunks.
    static final int
    DISK_CHUNKS_SHIFT
    Deprecated.
    The shift for physical disk chunks.
    protected long
    filteredSize
    Deprecated.
    The number of elements that pass the current filter, or -1 we it must be recomputed.
    static final int
    LOG2_DISK_CHUNKS
    Deprecated.
    The logarithm of the number of physical disk chunks.
    protected long
    seed
    Deprecated.
    The seed used to generate the hash triples.
    static final long
    serialVersionUID
    Deprecated.
     
    protected long
    size
    Deprecated.
    The number of elements ever added.

  • Constructor Summary

    Constructors
    Constructor
    Description
    ChunkedHashStore(TransformationStrategy<? super T> transform)
    Deprecated.
    Creates a chunked hash store with given transformation strategy.
    ChunkedHashStore(TransformationStrategy<? super T> transform, ProgressLogger pl)
    Deprecated.
    Creates a chunked hash store with given transformation strategy.
    ChunkedHashStore(TransformationStrategy<? super T> transform, File tempDir)
    Deprecated.
    Creates a chunked hash store with given transformation strategy and temporary file directory.
    ChunkedHashStore(TransformationStrategy<? super T> transform, File tempDir, int hashWidthOrCountValues, ProgressLogger pl)
    Deprecated.
    Creates a chunked hash store with given transformation strategy, hash width and progress logger.
    ChunkedHashStore(TransformationStrategy<? super T> transform, File tempDir, ProgressLogger pl)
    Deprecated.
    Creates a chunked hash store with given transformation strategy and progress logger.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    add(T o)
    Deprecated.
    Adds an element to this store, associating it with its ordinal position.
    void
    add(T o, long value)
    Deprecated.
    Adds an element to this store, associating it with a specified value.
    void
    addAll(Iterator<? extends T> elements)
    Deprecated.
    Adds the elements returned by an iterator to this store, associating them with their ordinal position.
    void
    addAll(Iterator<? extends T> elements, LongIterator values)
    Deprecated.
    Adds the elements returned by an iterator to this store, associating them with specified values.
    void
    addAll(Iterator<? extends T> elements, LongIterator values, boolean requiresValue2CountMap)
    Deprecated.
    Adds the elements returned by an iterator to this store, associating them with specified values, possibly building the associated value frequency map.
    void
    check()
    Deprecated.
    Checks that this store has no duplicate triples, throwing an exception if this fails to happen.
    void
    checkAndRetry(Iterable<? extends T> iterable)
    Deprecated.
    Checks that this store has no duplicate triples, and try to rebuild if this fails to happen.
    void
    checkAndRetry(Iterable<? extends T> iterable, LongIterable values)
    Deprecated.
    Checks that this store has no duplicate triples, and try to rebuild if this fails to happen.
    void
    clear()
    Deprecated.
    Clears this store.
    void
    close()
    Deprecated.
    Closes this store, disposing all associated resources.
    void
    filter(Predicate<long[]> filter)
    Deprecated.
    Sets a filter for this store.
    protected void
    finalize()
    Deprecated.
     
    Iterator<ChunkedHashStore.Chunk>
    iterator()
    Deprecated.
    Returns an iterator over the chunks of this chunked hash store.
    int
    log2Chunks(int log2chunks)
    Deprecated.
    Sets the number of chunks.
    void
    reset(long seed)
    Deprecated.
    Resets this store using a new seed.
    long
    seed()
    Deprecated.
    Return the current seed of this chunked hash store.
    LongBigList
    signatures(int signatureWidth, ProgressLogger pl)
    Deprecated.
    Generate a list of signatures using the lowest bits of the first hash in this store.
    long
    size()
    Deprecated.
    Returns the size of this store.
    File
    tempDir()
    Deprecated.
    Return the temporary directory of this chunked hash store, or null.
    TransformationStrategy<? super T>
    transform()
    Deprecated.
    Return the transformation strategy provided at construction time.
    Long2LongOpenHashMap
    value2FrequencyMap()
    Deprecated.
    Return the current value frequency map.

    Methods inherited from class java.lang.Object

    clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    Methods inherited from interface java.lang.Iterable

    forEach, spliterator

  • Field Details

    • serialVersionUID

      public static final long serialVersionUID
      Deprecated.
      See Also:

    • BUFFER_SIZE

      public static final int BUFFER_SIZE
      Deprecated.
      The size of the output buffers.
      See Also:

    • LOG2_DISK_CHUNKS

      public static final int LOG2_DISK_CHUNKS
      Deprecated.
      The logarithm of the number of physical disk chunks.
      See Also:

    • DISK_CHUNKS

      public static final int DISK_CHUNKS
      Deprecated.
      The number of physical disk chunks.
      See Also:

    • DISK_CHUNKS_SHIFT

      public static final int DISK_CHUNKS_SHIFT
      Deprecated.
      The shift for physical disk chunks.
      See Also:

    • size

      protected long size
      Deprecated.
      The number of elements ever added.

    • filteredSize

      protected long filteredSize
      Deprecated.
      The number of elements that pass the current filter, or -1 we it must be recomputed.

    • seed

      protected long seed
      Deprecated.
      The seed used to generate the hash triples.

  • Constructor Details

    • ChunkedHashStore

      public ChunkedHashStore(TransformationStrategy<? super T> transform) throws IOException
      Deprecated.
      Creates a chunked hash store with given transformation strategy.
      Parameters:
      transform - a transformation strategy for the elements.
      Throws:
      IOException

    • ChunkedHashStore

      public ChunkedHashStore(TransformationStrategy<? super T> transform, File tempDir) throws IOException
      Deprecated.
      Creates a chunked hash store with given transformation strategy and temporary file directory.
      Parameters:
      transform - a transformation strategy for the elements.
      tempDir - a temporary directory for the store files, or null for the current directory.
      Throws:
      IOException

    • ChunkedHashStore

      public ChunkedHashStore(TransformationStrategy<? super T> transform, ProgressLogger pl) throws IOException
      Deprecated.
      Creates a chunked hash store with given transformation strategy.
      Parameters:
      transform - a transformation strategy for the elements.
      pl - a progress logger, or null.
      Throws:
      IOException

    • ChunkedHashStore

      public ChunkedHashStore(TransformationStrategy<? super T> transform, File tempDir, ProgressLogger pl) throws IOException
      Deprecated.
      Creates a chunked hash store with given transformation strategy and progress logger.
      Parameters:
      transform - a transformation strategy for the elements.
      tempDir - a temporary directory for the store files, or null for the current directory.
      pl - a progress logger, or null.
      Throws:
      IOException

    • ChunkedHashStore

      public ChunkedHashStore(TransformationStrategy<? super T> transform, File tempDir, int hashWidthOrCountValues, ProgressLogger pl) throws IOException
      Deprecated.
      Creates a chunked hash store with given transformation strategy, hash width and progress logger.
      Parameters:
      transform - a transformation strategy for the elements.
      tempDir - a temporary directory for the store files, or null for the current directory.
      hashWidthOrCountValues - if positive, no associated data is saved in the store: ChunkedHashStore.Chunk.data(long) will return this many lower bits of the first of the three hashes associated with the key; zero, values are stored; if negative, values are stored and a map from values to their frequency is computed.
      pl - a progress logger, or null.
      Throws:
      IOException

  • Method Details

    • seed

      public long seed()
      Deprecated.
      Return the current seed of this chunked hash store. After calling this method, no reset(long) will be allowed (unless the store is cleared).
      Returns:
      the current seed of this chunked hash store.

    • tempDir

      public File tempDir()
      Deprecated.
      Return the temporary directory of this chunked hash store, or null.
      Returns:
      the temporary directory of this chunked hash store, or null.

    • transform

      public TransformationStrategy<? super T> transform()
      Deprecated.
      Return the transformation strategy provided at construction time.
      Returns:
      the transformation strategy provided at construction time.

    • add

      public void add(T o, long value) throws IOException
      Deprecated.
      Adds an element to this store, associating it with a specified value.
      Parameters:
      o - the element to be added.
      value - the associated value.
      Throws:
      IOException

    • add

      public void add(T o) throws IOException
      Deprecated.
      Adds an element to this store, associating it with its ordinal position.
      Parameters:
      o - the element to be added.
      Throws:
      IOException

    • addAll

      public void addAll(Iterator<? extends T> elements, LongIterator values, boolean requiresValue2CountMap) throws IOException
      Deprecated.
      Adds the elements returned by an iterator to this store, associating them with specified values, possibly building the associated value frequency map.
      Parameters:
      elements - an iterator returning elements.
      values - an iterator on values parallel to elements.
      requiresValue2CountMap - whether to build the value frequency map (associating with each value its frequency).
      Throws:
      IOException

    • addAll

      public void addAll(Iterator<? extends T> elements, LongIterator values) throws IOException
      Deprecated.
      Adds the elements returned by an iterator to this store, associating them with specified values.
      Parameters:
      elements - an iterator returning elements.
      values - an iterator on values parallel to elements.
      Throws:
      IOException

    • addAll

      public void addAll(Iterator<? extends T> elements) throws IOException
      Deprecated.
      Adds the elements returned by an iterator to this store, associating them with their ordinal position.
      Parameters:
      elements - an iterator returning elements.
      Throws:
      IOException

    • size

      public long size() throws IOException
      Deprecated.
      Returns the size of this store. Note that if you set up a filter, the first call to this method will require a scan to the whole store.
      Returns:
      the number of (possibly filtered) triples of this store.
      Throws:
      IOException

    • clear

      public void clear() throws IOException
      Deprecated.
      Clears this store. After a call to this method, the store can be reused.
      Throws:
      IOException

    • value2FrequencyMap

      public Long2LongOpenHashMap value2FrequencyMap()
      Deprecated.
      Return the current value frequency map.
      Returns:
      the current value frequency map.
      Throws:
      IllegalStateException - if this chunked hash store does not contain a value frequency map.

    • finalize

      protected void finalize() throws Throwable
      Deprecated.
      Overrides:
      finalize in class Object
      Throws:
      Throwable

    • close

      public void close() throws IOException
      Deprecated.
      Closes this store, disposing all associated resources.
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable
      Throws:
      IOException

    • reset

      public void reset(long seed) throws IOException
      Deprecated.
      Resets this store using a new seed. All accumulated data are cleared, and a new seed is reinstated.
      Parameters:
      seed - the new seed.
      Throws:
      IllegalStateException - if this store was locked by a call to seed(), and never cleared thereafter.
      IOException

    • check

      public void check() throws ChunkedHashStore.DuplicateException
      Deprecated.
      Checks that this store has no duplicate triples, throwing an exception if this fails to happen.
      Throws:
      ChunkedHashStore.DuplicateException - if this store contains duplicate triples.

    • checkAndRetry

      public void checkAndRetry(Iterable<? extends T> iterable, LongIterable values) throws IOException
      Deprecated.
      Checks that this store has no duplicate triples, and try to rebuild if this fails to happen.
      Parameters:
      iterable - the elements with which the store will be refilled if there are duplicate triples.
      values - the values that will be associated with the elements returned by iterable.
      Throws:
      IllegalArgumentException - if after a few trials the store still contains duplicate triples.
      IOException

    • checkAndRetry

      public void checkAndRetry(Iterable<? extends T> iterable) throws IOException
      Deprecated.
      Checks that this store has no duplicate triples, and try to rebuild if this fails to happen.

      Warning: the actions are executed exactly in the specified order—first check, then retry. If you invoke this method on an empty store you'll get a checked empty store.

      Parameters:
      iterable - the elements with which the store will be refilled if there are duplicate triples.
      Throws:
      IllegalArgumentException - if after a few trials the store still contains duplicate triples.
      IOException

    • signatures

      public LongBigList signatures(int signatureWidth, ProgressLogger pl) throws IOException
      Deprecated.
      Generate a list of signatures using the lowest bits of the first hash in this store.

      For this method to work, this store must contain ranks.

      Parameters:
      signatureWidth - the width in bits of the signatures.
      pl - a progress logger.
      Throws:
      IOException

    • log2Chunks

      public int log2Chunks(int log2chunks)
      Deprecated.
      Sets the number of chunks.

      Once the store is filled, you must call this method to set the number of chunks. The store will take care of merging or fragmenting disk chunks to get exactly the desired chunks.

      Parameters:
      log2chunks - the base-2 logarithm of the number of chunks.
      Returns:
      the shift to be applied to the first hash of a triple to get the chunk number (see the introduction).

    • filter

      public void filter(Predicate<long[]> filter)
      Deprecated.
      Sets a filter for this store.
      Parameters:
      filter - a predicate that will be used to filter triples.

    • iterator

      public Iterator<ChunkedHashStore.Chunk> iterator()
      Deprecated.
      Returns an iterator over the chunks of this chunked hash store.

      Note that at each iteration part of the state of this chunked hash store is reused. Thus, after each call to next() the previously returned ChunkedHashStore.Chunk will be no longer valid. Please use the provided copy constructor if you need to process in parallel several chunks.

      Specified by:
      iterator in interface Iterable<T>
      Returns:
      an iterator over the chunks of this chunked hash store.