Wavelets:library

  Authors:
  Shane J. Neph, Michael S. Kuehn, John Stamatoyonnapoulos
  University of Washington
  Genome Sciences

Wavelets Library and Application

  o Read the license.  If you agree to those conditions then download the source, build the application, and run it by typing in a terminal:
     - tar -xzf wavelets.tgz (or tar -xf wavelets.tar)
     - cd wavelets/src
     - make
     - ../bin/wavelets --help
  o The wavelets application has no runtime dependencies.  You may move it wherever you like.
  o The library is written to be efficient in RAM and time with particular emphasis on RAM.
  o The default application provided efficiently utilizes the library.

Main Design Goals

Library

• Make it fast and memory efficient, with particular emphasis on RAM requirements.
• Build as a generic library API that can work with any number of different data types, including user-defined. The application discussed here does NOT utilize the full features of the library API, and is only a single example of how an application may utilize the library.
• Make computing wavelet values independent of the level/scale requested in terms of RAM requirements.

Application: wavelets

• Wrap many features of the library and expose as a command-line tool
• Use the library in the most efficient ways possible, even if the application itself becomes slightly cumbersome (see Output)

Application Usage

'wavelets --help' shows a lot of useful information, including available filters, boundary conditions and more.

wavelets
  [--boundary <string = periodic>]
  [--filter <string = LA8>]
  [--help]
  [--level <integer = 4>]
  [--operation <string = smooth>]
  [--prefix <string = "">]
  [--to-stdout]
  [--version]
  <file-name>

Where

  ++++++++++++
  <file-name> is required and may be '-' to indicate reading from standard input

  ++++++++++++
  --boundary
      periodic  [default]
      reflected

  ++++++++++++
  --filter
      d4, d6, d8, d10, d12, d14, d16, d18, d20 (daubechies)
      la8, la10, la12, la14, la16, la18, la20 (least asymmetric) [la8 by default]
      bl14, bl18, bl20 (best localized)
      c6, c12, c18, c24, c30 (coiflet)
      haar

  ++++++++++++
  --level
      the number of levels the program will sweep through [4 by default]

  ++++++++++++
  --operation
      all
      details
      mra
      scale (coefficients)
      smooth [default]
      wave (coefficients)
      wave-scale (coefficients)

  ++++++++++++
  --prefix
      prefix for all output files generated (may include directory path if specified)
      incompatible with --to-stdout

  ++++++++++++
  --to-stdout
    send calculations to standard output
    only available when --operation set to smooth or scale
    incompatible with --prefix


  Application option names and string values are case insensitive.

Output

  Files produced from the default application have names of the form:
    details.i: i = 1..level
    scaling-coefficients.level
    smoothing.level
    wavelet-coefficients.i: i = 1..level

  Any '--prefix' specified by the end user precedes each name shown above.
  Not all of these files are produced unless --operation is set to ALL

Open Issues, Notes and Related Items

  o Only MODWT and related items are currently available from the library.  The rest is left as an exercise for the reader.
  o The capability to feed files to the program to calculate the original series was not exposed, but the library has this functionality.
  o Files are sent to current working directory when neither --to-stdout nor --prefix option is specified.
  o The default application uses the C++ vector class for runtime flexibility.  The library also works with built-in arrays if needed.
  o The default application uses the float data type.  For more precision (likely doubles RAM requirements):
     1) Open WaveletApp.cpp and go to line 291
     2) Change 'typedef float T;' to 'typedef double T;'
     3) Build the application again