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← Revision 42 as of 2019-12-16 14:01:02 ⇥
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| = 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. * Probability Density Functions: http://www.scs.fsu.edu/~burkardt/cpp_src/prob/prob.html * Cumulative Density Functions: http://www.scs.fsu.edu/~burkardt/cpp_src/dcdflib/dcdflib.html == Other Useful Links == * http://www.gnu.org/software/gsl/manual/html_node/Function-Index.html |
- Diff for "GSLReplacement"