Yeti is a Yorick extension
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README.md

Yeti-logo: a Yorick extension

[News] [License]

Yeti is an extension of Yorick (a fast interpreted interactive data processing language written by David Munro) which implements (see "Quick Reference" below for a list of additional functions):

  • hash table objects
  • regular expressions
  • complex, real-complex and complex-real FFT by FFTW (the Fastest Fourier Transform in the West -- version 2)
  • wavelet filtering ("à trou" method)
  • fast convolution along a chosen dimension with various border conditions
  • more string functions
  • memory hacking routines
  • more math functions (sinc, round, arc)
  • generalized matrix-vector multiplication (with possibly sparse matrix)
  • routines to query/check Yorick's symbols
  • support for reading TIFF images
  • morpho-math operators
  • ...

This distribution of Yeti may come with several extensions (depending whether corresponding directories exist or not):

  • fftw ..... support for FFTW
  • regex .... support for POSIX regular expressions
  • tiff ..... support for reading TIFF images

Compilation and Installation

Starting with version 6.0.0, Yeti is built as a regular Yorick plugin and some of the Yeti extensions are built as standalone Yorick plugins (they do not require Yeti to be used). The installation of Yeti depends on that of Yorick which must have been installed prior to Yeti. You'll need at least version 2.2 of Yorick (for Yorick version 1.5, you can install Yeti 5.3 and for Yorick 1.6 to 2.1 you can install Yeti 6.2).

The first installation step consists in the configuration of Yeti software suite. This is done via the "configure" script (1). In order to figure out the different options (and their default values), you can just do:

./configure --help

At least version 2.2 of Yorick is required to configure/build this version of Yeti.

By default, the script tries to find an axecutable named "yorick" in your path (according to your environment variable PATH). You can however specify a different Yorick executable with option:

./configure [...] --yorick=PATH_TO_YORICK_EXECUTABLE [...]

with PATH_TO_YORICK_EXECUTABLE the full path to Yorick executable.

If you want Yeti plugin for extended regular support, you'll have the choice to use a system provided POSIX REGEX library or the GNU REGEX library which can be built into the plugin. This is achieved by defining the preprocessor macro HAVE_REGEX to true if you trust your system REGEX library. To use the POSIX REGEX library of your system:

./configure [...] --with-regex-defs='-DHAVE_REGEX=1' [...]

and to build the GNU REGEX library into the plugin (this is the default behaviour):

./configure [...] --with-regex-defs='-DHAVE_REGEX=0' [...]

For instance, here is how to call the configure script to use builtin REGEX support and to enable plugins for FFTW (installed in /usr/local) and TIFF (installed in standard locations):

./configure --with-regex \
    --with-fftw --with-fftw-defs="-I/usr/local/include" \
    --with-fftw-libs="-L/usr/local/lib -lrfftw -lfftw" \
    --with-tiff --with-tiff-libs="-ltiff"

In order to check your configuration settings, you can add --help as the last argument of the call to ./configure.

After configuration, you can build Yeti and all related plugins by just doing:

make

In order to install Yeti files into Yorick installation directories, you simply do:

make install

Note that the configure script is actually a wrapper around the command:

yorick -batch ./config.i [...]

with [...] the arguments passed to configure.

Quick Reference

h_cleanup ............ delete void members of hash table object
h_clone .............. clone a hash table
h_copy ............... duplicate hash table object
h_delete ............. delete members from a hash table
h_first .............. get name of first hash table member
h_functor ............ create "functor" object
h_get ................ get value of hash table member
h_has ................ check existence of hash table member
h_info ............... list contents of hash table
h_keys ............... get member names of a hash table object
h_list ............... make a hash table into a list
h_new. ............... create a new hash table object
h_next ............... get name of next hash table member
h_pop ................ pop member out of an hash table object
h_restore_builtin .... restore builtin functions
h_save ............... save variables in a hash table
h_save_symbols ....... save builtin functions
h_set................. set member of hash table object
h_set_copy............ set member of hash table object
h_show ............... display a hash table as an expanded tree
h_stat ............... get statistics of hash table object

Yeti Hierarchical Data (YHD) files:

#include "yeti_yhdf.i"

yhd_check ............ check version of YHD file
yhd_info ............. print some information about an YHD file
yhd_restore .......... restore a hash table object from an YHD file
yhd_save ............. save a hash table object into an YHD file

Regular Expressions:

#include "yeti_regex.i"

regcomp ............... compile regular expression
regmatch .............. match a regular expression against an array of strings
regmatch_part ......... peek substrings given indices returned by regmatch
regsub ................ substitute regular expression into an array of strings

Miscellaneous:

anonymous ............. create anonymous (lambda) functions
expand_path ........... expand directory names to absolute paths
heapsort............... sort an array by heap-sort method
insure_temporary ...... make sure a variable is not referenced
is_hash ............... check if an object is a hash table
is_sparse_matrix ...... check if an object is a sparse matrix
quick_select .......... find K-th smallest element in an array
quick_median .......... find median value (faster than median function)
quick_interquartile_range
 ...................... compute inter-quartile range of values
yeti_init setup ....... setup Yeti internals and query version

Memory Hacking:

mem_base .............. get base address of an array object
mem_copy .............. copy array data at a given address
mem_info .............. print memory information
mem_peek .............. make a new array from a base address, type and
                        dimension list
native_byte_order ..... compute native byte order

Binary Encoding of Data:

get_encoding .......... get description of binary encoding for various
                        machines
install_encoding ...... install binary description into a binary stream
same_encoding ......... compare two encodings

Math/Numerical:

arc ................... lengh of arc in radians
cost_l2 ............... cost function and gradient for l2 norm
cost_l2l0 ............. cost function and gradient for l2-l0 norm
cost_l2l1 ............. cost function and gradient for l2-l1 norm
machine_constant ...... get machine dependent constant (such as EPSILON)
mvmult ................ (sparse)matrix-vector multiplication
round ................. round to nearest integer
sinc .................. cardinal sine: sinc(x) = sin(pi*x)/(pi*x)
smooth3 ............... smooth an array by 3-element convolution
sparse_expand ......... convert a sparse matrix array into a regular array
sparse_grow ........... augment a sparse array
sparse_matrix ......... create a new sparse matrix
sparse_squeeze ........ convert a regular array into a sparse one
yeti_convolve ......... convolution along a given dimension
yeti_wavelet .......... "à trou" wavelet decomposition

Strings:

strlower .............. convert array of strings to lower case
strtrimleft ........... remove leading spaces from an array of strings
strtrimright .......... remove trailing spaces from an array of strings
strupper .............. convert array of strings to upper case

Yorick Internals:

memory_info ........... display memory used by Yorick symbols
symbol_info ........... get some information about existing Yorick symbols
nrefsof ............... get number of references of an object

Morpho-math operations:

morph_black_top_hat ... perform valley detection
morph_closing ......... perform morpho-math closing operation
morph_dilation ........ perform morpho-math dilation operation
morph_erosion ......... perform morpho-math erosion operation
morph_opening ......... perform morpho-math opening operation
morph_white_top_hat ... perform summit detection

TIFF images:

#include "yeti_tiff.i"

tiff_open ............. open TIFF file
tiff_debug ............ control printing of TIFF warning messages
tiff_read_pixels ...... read pixel values in a TIFF file
tiff_read_image ....... read image in a TIFF file
tiff_read_directory ... move to next TIFF "directory"
tiff_read ............. read image/pixels in a TIFF file
tiff_check ............ check if a file is a readable TIFF file.

FFTW:

#include "yeti_fftw.i"

fftw_plan ............. setup a plan for FFTW
fftw .................. computes FFT of an array according to a plan
cfftw ................. computes complex FFT of an array
fftw_indgen ........... generates FFT indices
fftw_dist ............. computes length of spatial frequencies
fftw_smooth ........... smooths an array
fftw_convolve ......... fast convolution of two arrays

Copyright and Warranty

(See file LICENSE for details.)

Copyright (C), 1996-2015: Éric Thiébaut thiebaut@obs.univ-lyon1.fr

This software is governed by the CeCILL-C license under French law and abiding by the rules of distribution of free software. You can use, modify and/or redistribute the software under the terms of the CeCILL-C license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info".

As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability.

In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security.

The fact that you are presently reading this means that you have had knowledge of the CeCILL-C license and that you accept its terms.

References and notes

  1. Yorick is an interpreted programming language for scientific simulations or calculations, postprocessing or steering large simulation codes, interactive scientific graphics, and reading, writing, or translating large files of numbers.

  2. FFTW is the Fastest Fourier Transform in the West. Please note that since FFTW API has changed with FFTW version 3, only FFTW version 2 (latest is 2.1.5) is supported in Yeti. A new plug-in XFFT will be soon available for FFTW3 in Yorick.

  3. To use some special functions of GSL (the GNU Scientific Library) in Yorick, yeti_gsl has been abandoned in favor of a separate plugin YGSL.

  4. LibTIFF is a free TIFF library which provides support for the Tag Image File Format (TIFF), a widely used format for storing image data.