• GSLReplacement

GSL Replacement

GPL is bad and we're going to replace GSL.

Stub library located at: /usr/pubsw/packages/gsl/stub/include/

See also NumericalRecipesReplacement

Files with GSL

• randomfields.h
• mri_cht2p.c
• optseq2.c
• fmriutils.c
• fsglm.c
• matrix.c -- lots of matrix functionality that we can replace with vxl
• randomfields.c
• volcluster.c

GSL Function Stack Trace

• gsl_matrix
  • matrix.c::MatrixToGSL
    • matrix.c::MatrixSVDPseudoInverse
      • gcamorph.c::gcamComputeOptimalTargetLinearTransform
        • gcamorph.c::GCAMreinitWithLTA
          • mri_ca_register.c::main
  • matrix.c::MatrixFromGSL
    • matrix.c::MatrixSVDPseudoInverse
      • ...
• gsl_matrix_alloc
  • matrix.c::MatrixToGSL
    • ...
  • matrix.c::MatrixSVDPseudoInverse
    • ...
• gsl_matrix_calloc
  • optseq2.c::AR1WhitenMatrix
    • optseq2.c::main
• gsl_matrix_free
  • optseq2.c::AR1WhitenMatrix
    • ...
  • matrix.c::MatrixSVDPseudoInverse
    • ...
• gsl_matrix_get
  • optseq2.c::AR1WhitenMatrix
    • ...
  • matrix.c::MatrixFromGSL
    • ...
• gsl_matrix_set
  • optseq2.c::AR1WhitenMatrix
    • ...
  • matrix.c::MatrixFromGSL
    • ...
• gsl_vector
  • matrix.c::VectorFromGSL
    • matrix.c::MatrixSVDPseudoInverse
      • ...
  • matrix.c::MatrixSVDPseudoInverse
    • ...
• gsl_vector_alloc
  • matrix.c::MatrixSVDPseudoInverse
    • ...
• gsl_vector_free
  • matrix.c::MatrixSVDPseudoInverse
    • ...
• gsl_vector_get
  • matrix.c::VectorFromGSL
    • matrix.c::MatrixSVDPseudoInverse
      • ...
• gsl_vector_set -- never used
• gsl_cdf_fdist_Q
  • fmriutils.c::fMRIsigF
    • mris_glm.c::main
  • fsglm.c::GLMtest
    • fsglm.c::GLManalyze -- never used
    • fsglm.c::GLMprofile
      • mri_glmfit::parse_commandline
        • mri_glmfit::main
    • fsglm.c::GLMsynth -- never used
  • randomfields.c::RFstat2PVal
    • randomfields.c::RFstat2P
      • randomfields.c::RFstat2Stat -- never used
• gsl_cdf_flat_Q
  • randomfields.c::RFstat2PVal
    • ... -- never used
• gsl_cdf_gaussian_Q
  • randomfields.c::RFstat2PVal
    • ... -- never used
• gsl_cdf_tdist_Q
  • randomfields.c::RFstat2PVal
    • ... -- never used
• gsl_cdf_chisq_Q
  • randomfields.c::RFstat2PVal
    • ... -- never used
• gsl_cdf_flat_Qinv
  • randomfields.c::RFp2StatVal
    • randomfields.c::RFp2Stat
      • randomfields.c::RFstat2Stat -- never used
• gsl_cdf_gaussian_Qinv
  • randomfields.c::RFp2StatVal
    • ...
• gsl_cdf_tdist_Qinv
  • randomfields.c::RFp2StatVal
    • ... -- never used
• gsl_cdf_chisq_Qinv
  • randomfields.c::RFp2StatVal
    • ... -- never used
• gsl_linalg_SV_decomp
  • matrix.c::MatrixSVDPseudoInverse
    • ...
• gsl_linalg_cholesky_decomp
  • optseq2.c::AR1WhitenMatrix
    • ...
• gsl_rng_type
  • RANDOM_FIELD_SPEC, RFS
    • used everywhere in randomfied.c
  • randomfields.c::RFspecInit
    • mri_glmfit.c::main
    • mri_mcsim.c::main
    • mri_volsynth.c::main
• gsl_rng
  • RANDOM_FIELD_SPEC, RFS
• gsl_rng_alloc
  • randomfields.c::RFspecInit
    • ...
• gsl_rng_free
  • randomfields.c::RFspecFree
    • RFspecFree -- never used
• gsl_rng_set
  • randomfields.c::RFspecSetSeed
    • randomfields.c::RFspecInit
      • ...
• gsl_ran_flat
  • randomfields.c::RFdrawVal
    • randomfields.c::RFsynth
      • mri_glmfit.c::main
      • mri_mcsim.c::main
      • mri_volsynth.c::main
• gsl_ran_gaussian
  • randomfields.c::RFdrawVal
    • ...
• gsl_ran_fdist
  • randomfields.c::RFdrawVal
    • ...
• gsl_ran_tdist
  • randomfields.c::RFdrawVal
    • ...
• gsl_ran_chisq
  • randomfields.c::RFdrawVal
    • ...
• gsl_ran_binomial_pdf
  • mri_cht2p.c::main
• gsl_ran_binomial_pdf
  • volcluster.c::CSDpvalClustSize
    • mri_surfcluster.c::main

GSL Types and Functions Used

• gsl_matrix
  • optseq2.c::AR1WhitenMatrix
  • matrix.c::MatrixToGSL
  • matrix.c::MatrixFromGSL
  • matrix.c::MatrixSVDPseudoInverse
• gsl_matrix_alloc
  • matrix.c::MatrixToGSL
  • matrix.c::MatrixSVDPseudoInverse
• gsl_matrix_calloc
  • optseq2.c::AR1WhitenMatrix
• gsl_matrix_free
  • optseq2.c::AR1WhitenMatrix
  • matrix.c::MatrixSVDPseudoInverse
• gsl_matrix_get
  • optseq2.c::AR1WhitenMatrix
  • matrix.c::MatrixFromGSL
• gsl_matrix_set
  • optseq2.c::AR1WhitenMatrix
  • matrix.c::MatrixFromGSL
• gsl_vector
  • matrix.c::MatrixSVDPseudoInverse
  • matrix.c::VectorFromGSL
• gsl_vector_alloc
  • matrix.c::MatrixSVDPseudoInverse
• gsl_vector_free
  • matrix.c::MatrixSVDPseudoInverse
• gsl_vector_get
  • matrix.c::VectorFromGSL
• gsl_vector_set -- not used
• gsl_cdf_fdist_Q
  • fmriutils.c::fMRIsigF
  • fsglm.c::GLMtest
  • randomfields.c::RFstat2PVal
• gsl_cdf_flat_Q
  • randomfields.c::RFstat2PVal
• gsl_cdf_gaussian_Q
  • randomfields.c::RFstat2PVal
• gsl_cdf_tdist_Q
  • randomfields.c::RFstat2PVal
  • sig.c::sigt -- only used if MGH_GSL is defined and it never is
• gsl_cdf_chisq_Q
  • randomfields.c::RFstat2PVal
• gsl_cdf_flat_Qinv
  • randomfields.c::RFp2StatVal
• gsl_cdf_gaussian_Qinv
  • randomfields.c::RFp2StatVal
• gsl_cdf_tdist_Qinv
  • randomfields.c::RFp2StatVal
• gsl_cdf_chisq_Qinv
  • randomfields.c::RFp2StatVal
• gsl_linalg_SV_decomp
  • matrix.c::MatrixSVDPseudoInverse
• gsl_linalg_cholesky_decomp
  • optseq2.c::AR1WhitenMatrix
• gsl_rng_type
  • randomfields.h::RANDOM_FIELD_SPEC, RFS
  • randomfields.h::RFspecInit
  • randomfields.c::RFspecInit
• gsl_rng_ranlux389
  • randomfields.c::RFspecInit
• gsl_rng
  • randomfields.h::RANDOM_FIELD_SPEC, RFS
• gsl_rng_alloc
  • randomfields.c::RFspecInit
• gsl_rng_free
  • randomfields.c::RFspecFree
• gsl_rng_set
  • randomfields.c::RFspecSetSeed
• gsl_ran_flat
  • randomfields.c::RFdrawVal
• gsl_ran_gaussian
  • randomfields.c::RFdrawVal
• gsl_ran_fdist
  • randomfields.c::RFdrawVal
• gsl_ran_tdist
  • randomfields.c::RFdrawVal
• gsl_ran_chisq
  • randomfields.c::RFdrawVal
• gsl_ran_binomial_pdf
  • mri_cht2p.c::main
  • volcluster.c::CSDpvalClustSize

Possible Replacements

• http://netlib.org/ -- BLAS, CBLAS, CLAPACK, ATLAS. maybe?

  • Advantages: gold standard for matrix software (used by matlab), real and complex, BSD, possible to optimize for individual platforms, parallel version available.
  • Disads: poorly documented (and I mean *poorly*), routines are low-level and would require work up-front to get going, no statistics.

• http://math.nist.gov/MatrixMarket/ -- no

  • doesn't have the stat functions we need

• http://www.oonumerics.org/oon/ -- no

  • a long list of stuff we can't use

• http://rac.uits.iu.edu/hpc/numerics.shtml -- no

  • long list of libraries

• http://osl.iu.edu/research/mtl/ -- no

  • doesn't have the stat functions we need

• http://math.nist.gov/tnt/ -- no

  • doesn't have the stat functions we need

• http://www.gnu.org/software/goose/goose.html

  • LGPL
  • has CDF
• VXL/VNL for SV Decomposition
• ITK for some of the distribution functions?

• http://cran.us.r-project.org R statistics package. Probably has all the stats we need. Don't know about the matrix stuff. Oops, I think it's GPL though. Yes, it is under GPL.

Other Useful Links

• http://www.gnu.org/software/gsl/manual/html_node/Function-Index.html