[mlpack] 03/11: Merge tag 'upstream/1.0.4'
Barak A. Pearlmutter
barak+git at cs.nuim.ie
Sat Apr 5 13:03:06 UTC 2014
This is an automated email from the git hooks/post-receive script.
bap pushed a commit to branch master
in repository mlpack.
commit f8e218ae3c7e01ea54f748215bd7e579d0318e90
Merge: 318b5be 290ba84
Author: Barak A. Pearlmutter <barak+git at cs.nuim.ie>
Date: Fri Apr 4 22:35:34 2014 +0100
Merge tag 'upstream/1.0.4'
Upstream version 1.0.4
CMake/FindMatlabMex.cmake | 110 ++++++
CMake/GenerateDoxyfile.cmake | 6 -
CMake/ModifyMatlabPathdef.cmake | 25 ++
CMakeLists.txt | 34 +-
COPYRIGHT.txt | 1 +
Doxyfile | 2 +-
HISTORY.txt | 67 ++++
doc/guide/build.hpp | 26 +-
doc/guide/sample.hpp | 3 +-
src/mlpack/core.hpp | 6 +-
src/mlpack/core/arma_extend/CMakeLists.txt | 4 +-
src/mlpack/core/arma_extend/Col_extra_bones.hpp | 10 +
src/mlpack/core/arma_extend/Col_extra_meat.hpp | 21 ++
src/mlpack/core/arma_extend/Row_extra_bones.hpp | 10 +
src/mlpack/core/arma_extend/Row_extra_meat.hpp | 21 ++
src/mlpack/core/arma_extend/arma_extend.hpp | 14 +-
src/mlpack/core/arma_extend/fn_inplace_reshape.hpp | 49 +++
src/mlpack/core/arma_extend/hdf5_misc.hpp | 23 ++
src/mlpack/core/arma_extend/promote_type.hpp | 152 +++-----
src/mlpack/core/arma_extend/restrictors.hpp | 22 ++
src/mlpack/core/arma_extend/traits.hpp | 76 ++--
src/mlpack/core/arma_extend/typedef.hpp | 79 +---
src/mlpack/core/data/CMakeLists.txt | 2 -
src/mlpack/core/data/load.hpp | 3 +-
src/mlpack/core/data/load_impl.hpp | 33 +-
src/mlpack/core/data/save.hpp | 3 +-
src/mlpack/core/data/save_impl.hpp | 21 +-
src/mlpack/core/dists/CMakeLists.txt | 2 -
src/mlpack/core/dists/discrete_distribution.cpp | 14 +-
src/mlpack/core/dists/discrete_distribution.hpp | 7 +-
src/mlpack/core/dists/gaussian_distribution.cpp | 15 +-
src/mlpack/core/dists/gaussian_distribution.hpp | 13 +-
src/mlpack/core/kernels/CMakeLists.txt | 2 -
src/mlpack/core/kernels/cosine_distance.hpp | 2 +-
src/mlpack/core/kernels/cosine_distance_impl.hpp | 2 +-
src/mlpack/core/kernels/epanechnikov_kernel.cpp | 2 +-
src/mlpack/core/kernels/epanechnikov_kernel.hpp | 2 +-
.../core/kernels/epanechnikov_kernel_impl.hpp | 2 +-
src/mlpack/core/kernels/example_kernel.hpp | 2 +-
src/mlpack/core/kernels/gaussian_kernel.hpp | 2 +-
.../core/kernels/hyperbolic_tangent_kernel.hpp | 2 +-
src/mlpack/core/kernels/laplacian_kernel.hpp | 2 +-
src/mlpack/core/kernels/linear_kernel.hpp | 2 +-
src/mlpack/core/kernels/polynomial_kernel.hpp | 2 +-
.../core/kernels/pspectrum_string_kernel.cpp | 2 +-
.../core/kernels/pspectrum_string_kernel.hpp | 2 +-
.../core/kernels/pspectrum_string_kernel_impl.hpp | 2 +-
src/mlpack/core/kernels/spherical_kernel.hpp | 2 +-
src/mlpack/core/kernels/triangular_kernel.hpp | 2 +-
src/mlpack/core/math/CMakeLists.txt | 2 -
src/mlpack/core/math/clamp.hpp | 14 +-
src/mlpack/core/math/lin_alg.cpp | 2 +-
src/mlpack/core/math/lin_alg.hpp | 2 +-
src/mlpack/core/math/random.cpp | 2 +-
src/mlpack/core/math/random.hpp | 2 +-
src/mlpack/core/math/range.hpp | 7 +-
src/mlpack/core/math/range_impl.hpp | 12 +-
src/mlpack/core/math/round.hpp | 2 +-
src/mlpack/core/metrics/CMakeLists.txt | 2 -
src/mlpack/core/metrics/lmetric.hpp | 24 +-
src/mlpack/core/metrics/lmetric_impl.hpp | 12 +-
src/mlpack/core/metrics/mahalanobis_distance.hpp | 20 +-
.../core/metrics/mahalanobis_distance_impl.hpp | 6 +-
src/mlpack/core/optimizers/CMakeLists.txt | 3 +-
.../core/optimizers/aug_lagrangian/CMakeLists.txt | 2 -
.../optimizers/aug_lagrangian/aug_lagrangian.hpp | 2 +-
.../aug_lagrangian/aug_lagrangian_function.hpp | 2 +-
.../aug_lagrangian_function_impl.hpp | 2 +-
.../aug_lagrangian/aug_lagrangian_impl.hpp | 2 +-
.../aug_lagrangian_test_functions.cpp | 2 +-
.../aug_lagrangian_test_functions.hpp | 2 +-
src/mlpack/core/optimizers/lbfgs/CMakeLists.txt | 2 -
src/mlpack/core/optimizers/lbfgs/lbfgs.hpp | 28 +-
src/mlpack/core/optimizers/lbfgs/lbfgs_impl.hpp | 2 +-
.../core/optimizers/lbfgs/test_functions.cpp | 25 +-
.../core/optimizers/lbfgs/test_functions.hpp | 19 +-
src/mlpack/core/optimizers/lrsdp/lrsdp.hpp | 2 +-
src/mlpack/core/optimizers/lrsdp/lrsdp_impl.hpp | 2 +-
.../core/optimizers/{lbfgs => sgd}/CMakeLists.txt | 10 +-
src/mlpack/core/optimizers/sgd/sgd.hpp | 163 ++++++++
src/mlpack/core/optimizers/sgd/sgd_impl.hpp | 118 ++++++
src/mlpack/core/optimizers/sgd/test_function.cpp | 70 ++++
src/mlpack/core/optimizers/sgd/test_function.hpp | 60 +++
src/mlpack/core/tree/CMakeLists.txt | 4 +-
src/mlpack/core/tree/ballbound.hpp | 2 +-
src/mlpack/core/tree/ballbound_impl.hpp | 2 +-
src/mlpack/core/tree/binary_space_tree.hpp | 2 +-
.../tree/binary_space_tree/binary_space_tree.hpp | 11 +-
.../binary_space_tree/binary_space_tree_impl.hpp | 18 +-
.../tree/binary_space_tree/dual_tree_traverser.hpp | 2 +-
.../binary_space_tree/dual_tree_traverser_impl.hpp | 5 +-
.../binary_space_tree/single_tree_traverser.hpp | 2 +-
.../single_tree_traverser_impl.hpp | 2 +-
src/mlpack/core/tree/bounds.hpp | 2 +-
src/mlpack/core/tree/cover_tree.hpp | 2 +-
src/mlpack/core/tree/cover_tree/cover_tree.hpp | 39 +-
.../core/tree/cover_tree/cover_tree_impl.hpp | 21 +-
.../core/tree/cover_tree/dual_tree_traverser.hpp | 2 +-
.../tree/cover_tree/dual_tree_traverser_impl.hpp | 74 ++--
.../core/tree/cover_tree/first_point_is_root.hpp | 2 +-
.../core/tree/cover_tree/single_tree_traverser.hpp | 2 +-
.../tree/cover_tree/single_tree_traverser_impl.hpp | 2 +-
src/mlpack/core/tree/hrectbound.hpp | 42 ++-
src/mlpack/core/tree/hrectbound_impl.hpp | 184 +++++----
src/mlpack/core/tree/mrkd_statistic.cpp | 43 +++
src/mlpack/core/tree/mrkd_statistic.hpp | 206 +++++------
src/mlpack/core/tree/mrkd_statistic_impl.hpp | 99 +++++
src/mlpack/core/tree/periodichrectbound.hpp | 2 +-
src/mlpack/core/tree/periodichrectbound_impl.hpp | 2 +-
src/mlpack/core/tree/statistic.hpp | 2 +-
src/mlpack/core/util/CMakeLists.txt | 5 +-
src/mlpack/core/util/cli.cpp | 9 +-
src/mlpack/core/util/cli.hpp | 62 ++--
src/mlpack/core/util/cli_deleter.cpp | 8 +-
src/mlpack/core/util/cli_deleter.hpp | 8 +-
src/mlpack/core/util/cli_impl.hpp | 12 +-
src/mlpack/core/util/log.cpp | 4 +-
src/mlpack/core/util/log.hpp | 15 +-
src/mlpack/core/util/nulloutstream.hpp | 14 +-
src/mlpack/core/util/option.cpp | 4 +-
src/mlpack/core/util/option.hpp | 6 +-
src/mlpack/core/util/option_impl.hpp | 21 +-
src/mlpack/core/util/prefixedoutstream.cpp | 6 +-
src/mlpack/core/util/prefixedoutstream.hpp | 50 ++-
src/mlpack/core/util/prefixedoutstream_impl.hpp | 50 ++-
src/mlpack/core/util/save_restore_utility.cpp | 10 +-
src/mlpack/core/util/save_restore_utility.hpp | 11 +-
src/mlpack/core/util/save_restore_utility_impl.hpp | 6 +-
src/mlpack/core/util/sfinae_utility.hpp | 61 +++
src/mlpack/core/util/string_util.cpp | 45 +++
.../mlpack_test.cpp => core/util/string_util.hpp} | 28 +-
src/mlpack/core/util/timers.cpp | 2 +-
src/mlpack/core/util/timers.hpp | 2 +-
src/mlpack/methods/CMakeLists.txt | 4 +-
src/mlpack/methods/det/CMakeLists.txt | 2 -
src/mlpack/methods/det/det_main.cpp | 2 +-
src/mlpack/methods/det/dt_utils.cpp | 2 +-
src/mlpack/methods/det/dt_utils.hpp | 2 +-
src/mlpack/methods/det/dtree.cpp | 2 +-
src/mlpack/methods/det/dtree.hpp | 2 +-
src/mlpack/methods/emst/CMakeLists.txt | 4 +-
src/mlpack/methods/emst/dtb.hpp | 31 +-
src/mlpack/methods/emst/dtb_impl.hpp | 227 ++----------
.../dtb_rules.hpp} | 124 ++++---
src/mlpack/methods/emst/dtb_rules_impl.hpp | 260 +++++++++++++
src/mlpack/methods/emst/edge_pair.hpp | 2 +-
src/mlpack/methods/emst/emst_main.cpp | 2 +-
src/mlpack/methods/emst/union_find.hpp | 2 +-
src/mlpack/methods/gmm/CMakeLists.txt | 2 -
src/mlpack/methods/gmm/em_fit.hpp | 2 +-
src/mlpack/methods/gmm/em_fit_impl.hpp | 2 +-
src/mlpack/methods/gmm/gmm.hpp | 18 +-
src/mlpack/methods/gmm/gmm_impl.hpp | 22 +-
src/mlpack/methods/gmm/gmm_main.cpp | 10 +-
src/mlpack/methods/gmm/phi.hpp | 2 +-
src/mlpack/methods/hmm/CMakeLists.txt | 2 -
src/mlpack/methods/hmm/hmm.hpp | 2 +-
src/mlpack/methods/hmm/hmm_generate_main.cpp | 4 +-
src/mlpack/methods/hmm/hmm_impl.hpp | 2 +-
src/mlpack/methods/hmm/hmm_loglik_main.cpp | 4 +-
src/mlpack/methods/hmm/hmm_train_main.cpp | 4 +-
src/mlpack/methods/hmm/hmm_util.hpp | 6 +-
src/mlpack/methods/hmm/hmm_util_impl.hpp | 18 +-
src/mlpack/methods/hmm/hmm_viterbi_main.cpp | 4 +-
src/mlpack/methods/kernel_pca/CMakeLists.txt | 2 -
src/mlpack/methods/kernel_pca/kernel_pca.hpp | 2 +-
src/mlpack/methods/kernel_pca/kernel_pca_impl.hpp | 2 +-
src/mlpack/methods/kernel_pca/kernel_pca_main.cpp | 2 +-
src/mlpack/methods/kmeans/CMakeLists.txt | 2 -
src/mlpack/methods/kmeans/allow_empty_clusters.hpp | 2 +-
src/mlpack/methods/kmeans/kmeans.hpp | 2 +-
src/mlpack/methods/kmeans/kmeans_impl.hpp | 147 ++++----
src/mlpack/methods/kmeans/kmeans_main.cpp | 18 +-
.../methods/kmeans/max_variance_new_cluster.hpp | 2 +-
.../kmeans/max_variance_new_cluster_impl.hpp | 6 +-
src/mlpack/methods/kmeans/random_partition.hpp | 2 +-
src/mlpack/methods/lars/CMakeLists.txt | 2 -
src/mlpack/methods/lars/lars.cpp | 2 +-
src/mlpack/methods/lars/lars.hpp | 2 +-
src/mlpack/methods/lars/lars_main.cpp | 2 +-
.../methods/linear_regression/CMakeLists.txt | 2 -
.../linear_regression/linear_regression.cpp | 2 +-
.../linear_regression/linear_regression.hpp | 2 +-
.../linear_regression/linear_regression_main.cpp | 2 +-
.../methods/local_coordinate_coding/CMakeLists.txt | 2 -
src/mlpack/methods/local_coordinate_coding/lcc.hpp | 2 +-
.../methods/local_coordinate_coding/lcc_impl.hpp | 4 +-
.../methods/local_coordinate_coding/lcc_main.cpp | 4 +-
src/mlpack/methods/{gmm => lsh}/CMakeLists.txt | 25 +-
src/mlpack/methods/lsh/lsh_main.cpp | 169 +++++++++
src/mlpack/methods/lsh/lsh_search.hpp | 254 +++++++++++++
src/mlpack/methods/lsh/lsh_search_impl.hpp | 409 +++++++++++++++++++++
src/mlpack/methods/mvu/CMakeLists.txt | 2 -
src/mlpack/methods/mvu/mvu.cpp | 2 +-
src/mlpack/methods/mvu/mvu.hpp | 2 +-
src/mlpack/methods/mvu/mvu_main.cpp | 2 +-
src/mlpack/methods/naive_bayes/CMakeLists.txt | 2 -
.../methods/naive_bayes/naive_bayes_classifier.hpp | 2 +-
.../naive_bayes/naive_bayes_classifier_impl.hpp | 2 +-
src/mlpack/methods/naive_bayes/nbc_main.cpp | 2 +-
src/mlpack/methods/nca/CMakeLists.txt | 2 -
src/mlpack/methods/nca/nca.hpp | 48 ++-
src/mlpack/methods/nca/nca_impl.hpp | 43 +--
src/mlpack/methods/nca/nca_main.cpp | 183 ++++++++-
.../methods/nca/nca_softmax_error_function.hpp | 83 ++++-
.../nca/nca_softmax_error_function_impl.hpp | 229 +++++++++---
src/mlpack/methods/neighbor_search/CMakeLists.txt | 2 -
src/mlpack/methods/neighbor_search/allkfn_main.cpp | 2 +-
src/mlpack/methods/neighbor_search/allknn_main.cpp | 2 +-
.../methods/neighbor_search/neighbor_search.hpp | 2 +-
.../neighbor_search/neighbor_search_impl.hpp | 4 +-
.../neighbor_search/neighbor_search_rules.hpp | 17 +-
.../neighbor_search/neighbor_search_rules_impl.hpp | 140 +++++--
.../sort_policies/furthest_neighbor_sort.cpp | 2 +-
.../sort_policies/furthest_neighbor_sort.hpp | 20 +-
.../sort_policies/furthest_neighbor_sort_impl.hpp | 13 +-
.../sort_policies/nearest_neighbor_sort.cpp | 2 +-
.../sort_policies/nearest_neighbor_sort.hpp | 20 +-
.../sort_policies/nearest_neighbor_sort_impl.hpp | 13 +-
src/mlpack/methods/neighbor_search/typedef.hpp | 2 +-
src/mlpack/methods/nmf/CMakeLists.txt | 2 -
src/mlpack/methods/nmf/als_update_rules.hpp | 2 +-
src/mlpack/methods/nmf/mult_dist_update_rules.hpp | 2 +-
src/mlpack/methods/nmf/mult_div_update_rules.hpp | 2 +-
src/mlpack/methods/nmf/nmf.hpp | 4 +-
src/mlpack/methods/nmf/nmf_impl.hpp | 6 +-
src/mlpack/methods/nmf/nmf_main.cpp | 2 +-
src/mlpack/methods/nmf/random_acol_init.hpp | 2 +-
src/mlpack/methods/nmf/random_init.hpp | 2 +-
src/mlpack/methods/pca/CMakeLists.txt | 2 -
src/mlpack/methods/pca/pca.cpp | 2 +-
src/mlpack/methods/pca/pca.hpp | 2 +-
src/mlpack/methods/pca/pca_main.cpp | 2 +-
src/mlpack/methods/radical/CMakeLists.txt | 2 -
src/mlpack/methods/radical/radical.cpp | 177 ++++-----
src/mlpack/methods/radical/radical.hpp | 117 +++---
src/mlpack/methods/radical/radical_main.cpp | 37 +-
src/mlpack/methods/range_search/CMakeLists.txt | 2 -
src/mlpack/methods/range_search/range_search.hpp | 2 +-
.../methods/range_search/range_search_impl.hpp | 2 +-
.../methods/range_search/range_search_main.cpp | 2 +-
src/mlpack/methods/sparse_coding/CMakeLists.txt | 2 -
.../data_dependent_random_initializer.hpp | 2 +-
.../methods/sparse_coding/nothing_initializer.hpp | 2 +-
.../methods/sparse_coding/random_initializer.hpp | 2 +-
src/mlpack/methods/sparse_coding/sparse_coding.hpp | 2 +-
.../methods/sparse_coding/sparse_coding_impl.hpp | 2 +-
.../methods/sparse_coding/sparse_coding_main.cpp | 2 +-
src/mlpack/tests/CMakeLists.txt | 4 +-
src/mlpack/tests/allkfn_test.cpp | 2 +-
src/mlpack/tests/allknn_test.cpp | 2 +-
src/mlpack/tests/arma_extend_test.cpp | 50 +++
src/mlpack/tests/aug_lagrangian_test.cpp | 2 +-
src/mlpack/tests/cli_test.cpp | 4 +-
src/mlpack/tests/det_test.cpp | 2 +-
src/mlpack/tests/distribution_test.cpp | 2 +-
src/mlpack/tests/emst_test.cpp | 2 +-
src/mlpack/tests/gmm_test.cpp | 12 +-
src/mlpack/tests/hmm_test.cpp | 2 +-
src/mlpack/tests/kernel_pca_test.cpp | 2 +-
src/mlpack/tests/kernel_test.cpp | 39 +-
src/mlpack/tests/kmeans_test.cpp | 11 +-
src/mlpack/tests/lars_test.cpp | 2 +-
src/mlpack/tests/lbfgs_test.cpp | 2 +-
src/mlpack/tests/lin_alg_test.cpp | 2 +-
src/mlpack/tests/linear_regression_test.cpp | 2 +-
src/mlpack/tests/load_save_test.cpp | 131 ++++++-
src/mlpack/tests/local_coordinate_coding_test.cpp | 2 +-
src/mlpack/tests/lrsdp_test.cpp | 2 +-
src/mlpack/tests/math_test.cpp | 2 +-
src/mlpack/tests/mlpack_test.cpp | 2 +-
src/mlpack/tests/nbc_test.cpp | 2 +-
src/mlpack/tests/nca_test.cpp | 151 +++++++-
src/mlpack/tests/nmf_test.cpp | 2 +-
src/mlpack/tests/old_boost_test_definitions.hpp | 2 +-
src/mlpack/tests/pca_test.cpp | 2 +-
src/mlpack/tests/radical_test.cpp | 42 +--
src/mlpack/tests/range_search_test.cpp | 2 +-
src/mlpack/tests/save_restore_utility_test.cpp | 4 +-
src/mlpack/tests/sgd_test.cpp | 71 ++++
src/mlpack/tests/sort_policy_test.cpp | 2 +-
src/mlpack/tests/sparse_coding_test.cpp | 2 +-
src/mlpack/tests/tree_test.cpp | 364 +++++++++++++++++-
src/mlpack/tests/union_find_test.cpp | 2 +-
284 files changed, 5159 insertions(+), 1600 deletions(-)
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