http://cia.vc/stats/author/swaroopgj143 CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276189321 swaroopgj d3ff78b doc/examples/cachedkernel.py D: Adding a simple example on how to use cached kernel CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276189319 swaroopgj 48f1801 doc/source/modref.rst mvpa/base/hdf5.py mvpa/mappers/base.py mvpa/tests/test_hdf5.py mvpa/tests/test_mapper.py tools/daily_tests.sh Merge branch 'mh/master' of git://github.com/hanke/PyMVPA * 'mh/master' of git://github.com/hanke/PyMVPA: RF+BIG: Heavy refactoring of HDF5 code. NF: Support for recursive references in HDF5 IO BF: Simplify object detection in h5load() DOC: adding gnbsearchlight to modref RF: not running daily tests for mh/master upon mh request ;-) ENH: provide "filler" argument to FeatureSliceMapper which could be used instead of 0 upon reverse call. Close gh-28 CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276189314 swaroopgj 4772dbb Makefile bin/atlaslabeler doc/examples/eventrelated.py doc/misc/asciiart.txt doc/pics/.gitignore doc/pics/ex_sensanas.svg doc/source/_static/.gitignore doc/source/_static/nitrc.jpg doc/source/_themes/pymvpa_offline/layout.html doc/source/_themes/pymvpa_online/indexsidebar.html doc/source/_themes/pymvpa_online/layout.html doc/source/datadb.rst doc/source/datadb/demo_blockfmri.rst doc/source/datadb/tutorial_data.rst doc/source/pics/.gitignore doc/source/pics/ex_sensanas.pdf doc/source/pics/ex_sensanas.png doc/source/tutorial.rst doc/source/tutorial_prerequisites.rst mvpa/atlases/base.py mvpa/atlases/fsl.py mvpa/base/__init__.py mvpa/base/hdf5.py mvpa/datasets/splitters.py mvpa/featsel/base.py mvpa/kernels/base.py mvpa/misc/data_generators.py mvpa/misc/plot/lightbox.py mvpa/misc/sampleslookup.py mvpa/misc/support.py mvpa/tests/__init__.py mvpa/tests/test_atlases.py mvpa/tests/test_hdf5.py mvpa/tests/test_hyperalignment.py mvpa/tests/test_support.py mvpa/tests/test_svmkernels.py tools/daily_tests.sh tools/refactor_0.5.sh tools/tutorial_lib.py Merge branch 'mh/master' of git://github.com/hanke/PyMVPA * 'mh/master' of git://github.com/hanke/PyMVPA: (27 commits) DOC: Update sensanas example output figure. BF: HDF5 can handle single 0d array(object) BF: test_svmkernels ValueError should be raised only in __debug__ mode BF: order voxels for xyz order now in eventrelated example RF: 2nd wave of deprecating demo_blocfmri RF: deprecating demo_blockfmri -- we use tutorial_data -- 1st step --renaming NF: oops -- forgotten to commit asciiart -- what if comes useful BF: provide exit=False for nose whenever ran from cmdline RF: deprecating get_unique_length_n_combinations in favor of (x)unique_combinations BF: removed duplicate get_unique_length_n_combinations DOC: extended Emanuele's comment on returned datasets in feature selection BF: removed duplicate *getUniqueLengthNCombinations -- appeared due to cherry pick and later merge BF: provide output of git describe not within action so it could be seen actually DOC: documenting unexpected sharing of .labels and .chunks. ENH: option to enforce recaching of CachedKernel in compute() BF(RF): use init_origids in SamplesLookup, and assure that all those are unique ENH: atlaslabeler -- enhanced statistics + reporting coordinates via qform OPT: using np.ix_ in selecting a subkernel in CachedKernel ENH: debug messages for CachedKernel + unittest which hoped to ring the bell for Swaroop's issue (it didn't) ENH: debug messages for SamplesLookup ... CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276189199 swaroopgj 22ccacf .gitignore COPYING Changelog Makefile bin/atlaslabeler doc/examples/clfs_examples.py doc/examples/curvefitting.py doc/examples/kerneldemo.py doc/examples/match_distribution.py doc/examples/mri_plot.py doc/examples/projections.py doc/examples/searchlight.py doc/examples/searchlight_app.py doc/examples/searchlight_minimal.py doc/examples/sensanas.py doc/examples/start_easy.py doc/examples/svdclf.py doc/misc/references.bib doc/source/datadb/demo_blockfmri.rst doc/source/devguide.rst doc/source/docoverview.rst doc/source/examples.rst doc/source/glossary.rst doc/source/modref.rst doc/source/mvpa_guidelines.rst doc/source/references.rst doc/source/release_notes_0.5.rst doc/source/sitemap.rst doc/source/support.rst doc/source/tutorial_classifiers.rst doc/source/tutorial_datasets.rst doc/source/tutorial_eventrelated.rst doc/source/tutorial_mappers.rst doc/source/tutorial_prerequisites.rst doc/source/tutorial_significance.rst doc/source/whoisusingit.rst mvpa/__init__.py mvpa/atlases/base.py mvpa/atlases/fsl.py mvpa/base/__init__.py mvpa/base/dataset.py mvpa/base/externals.py mvpa/base/info.py mvpa/base/verbosity.py mvpa/clfs/_svmbase.py mvpa/clfs/base.py mvpa/clfs/distance.py mvpa/clfs/enet.py mvpa/clfs/glmnet.py mvpa/clfs/gnb.py mvpa/clfs/gpr.py mvpa/clfs/lars.py mvpa/clfs/libsvmc/sens.py mvpa/clfs/meta.py mvpa/clfs/sg/svm.py mvpa/clfs/similarity.py mvpa/clfs/smlr.py mvpa/clfs/stats.py mvpa/clfs/warehouse.py mvpa/datasets/miscfx.py mvpa/datasets/splitters.py mvpa/featsel/base.py mvpa/kernels/base.py mvpa/kernels/libsvm.py mvpa/kernels/np.py mvpa/kernels/sg.py mvpa/mappers/base.py mvpa/mappers/prototype.py mvpa/mappers/svd.py mvpa/mappers/wavelet.py mvpa/mappers/zscore.py mvpa/measures/anova.py mvpa/measures/base.py mvpa/measures/gnbsearchlight.py mvpa/measures/searchlight.py mvpa/misc/attrmap.py mvpa/misc/errorfx.py mvpa/misc/neighborhood.py mvpa/misc/plot/base.py mvpa/misc/plot/erp.py mvpa/misc/support.py mvpa/suite.py mvpa/support/ipython/__init__.py mvpa/support/ipython/ipy_pymvpa_completer.py mvpa/support/pylab.py mvpa/testing/datasets.py mvpa/testing/sweepargs.py mvpa/tests/__init__.py mvpa/tests/main.py mvpa/tests/test_atlases.py mvpa/tests/test_attrmap.py mvpa/tests/test_clf.py mvpa/tests/test_clfcrossval.py mvpa/tests/test_datameasure.py mvpa/tests/test_datasetng.py mvpa/tests/test_enet.py mvpa/tests/test_hdf5_clf.py mvpa/tests/test_neighborhood.py mvpa/tests/test_regr.py mvpa/tests/test_searchlight.py mvpa/tests/test_spam.py mvpa/tests/test_stats_sp.py mvpa/tests/test_transerror.py mvpa/tests/test_zscoremapper.py setup.py tools/daily_tests.sh tools/refactor_0.5.sh Merge branch 'mh/master' of git://github.com/hanke/PyMVPA * 'mh/master' of git://github.com/hanke/PyMVPA: (150 commits) DOC: More references. BF: in-place (before it would operate on copy) zscoring of ndarrays. . Close gh-27 BF: moving scipy-dependent statement in gnbsearchlight BF+RF: apparently epsilon is tube_epsilon for sg.LibSVR + sg.svm.seed DOC: Restructure paper listing. DOC: Note new users with Nature Neuroscience paper ;-) BF: workaround for shogun -- epsilon in constructor for regressions has no effect NF: mvpa.support.ipython + ipy_pymvpa_completer BF: import debug for kernels.sg ENH: complement CorrErrorFx with just CorrFx ENH: fslatlas.get_maps -- accepts now 'key_attr' defining on what to use for keys ENH: more debugging for sg kernels and svm BF+DOC: Wrong link to tutorial. RF: atlas.levels now corresponds to previous atlas.levels_dict RF/ENH: atlaslabeler -- ability to provide a stream of voxels indices RF: atlases __getitem__ for queries by voxel indices, __call__ -- by coordinates BF: actually fail (error exist status) whenever unittest-debug fails (uff) BF: access selected_ids from .ca BF: unittest-debug -- do not rely on MVPA_SEED or OK being in the tail -- just go to the end ;) BF: nr_class can be None, so just use %s in debug printout ... CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276188890 swaroopgj 69d5918 COPYING Makefile doc/examples/clfs_examples.py doc/examples/permutation_test.py doc/misc/pylintrc doc/source/classifiers.rst doc/source/conf.py doc/source/devguide.rst doc/source/faq.rst doc/source/featsel.rst doc/source/glossary.rst doc/source/tutorial.rst doc/source/tutorial_classifiers.rst doc/source/tutorial_datasets.rst doc/source/tutorial_searchlight.rst doc/source/tutorial_sensitivity.rst doc/source/tutorial_significance.rst doc/source/tutorial_start.rst mvpa/__init__.py mvpa/algorithms/cvtranserror.py mvpa/algorithms/hyperalignment.py mvpa/base/dochelpers.py mvpa/base/externals.py mvpa/base/hdf5.py mvpa/clfs/_svmbase.py mvpa/clfs/base.py mvpa/clfs/blr.py mvpa/clfs/gnb.py mvpa/clfs/gpr.py mvpa/clfs/knn.py mvpa/clfs/libsvmc/sens.py mvpa/clfs/libsvmc/svm.py mvpa/clfs/meta.py mvpa/clfs/sg/sens.py mvpa/clfs/sg/svm.py mvpa/clfs/smlr.py mvpa/clfs/stats.py mvpa/clfs/transerror.py mvpa/datasets/miscfx.py mvpa/datasets/mri.py mvpa/datasets/splitters.py mvpa/featsel/base.py mvpa/featsel/helpers.py mvpa/featsel/ifs.py mvpa/featsel/rfe.py mvpa/kernels/np.py mvpa/mappers/fx.py mvpa/measures/base.py mvpa/measures/glm.py mvpa/measures/searchlight.py mvpa/misc/attributes.py mvpa/misc/neighborhood.py mvpa/misc/param.py mvpa/misc/plot/base.py mvpa/misc/state.py mvpa/misc/stats.py mvpa/misc/transformers.py mvpa/suite.py mvpa/testing/datasets.py mvpa/tests/__init__.py mvpa/tests/test_datameasure.py mvpa/tests/test_dataset.py mvpa/tests/test_datasetfx.py mvpa/tests/test_datasetng.py mvpa/tests/test_dochelpers.py mvpa/tests/test_fxmapper.py mvpa/tests/test_hdf5.py mvpa/tests/test_hdf5_clf.py mvpa/tests/test_niftidataset.py mvpa/tests/test_params.py mvpa/tests/test_regr.py mvpa/tests/test_searchlight.py mvpa/tests/test_spam.py mvpa/tests/test_splitter.py mvpa/tests/test_state.py mvpa/tests/test_stats_sp.py mvpa/tests/test_transerror.py tools/fillin_states tools/refactor_0.5.sh tools/refactor_camel_case.sh tools/state_refactor.sh Merge branch 'mh/master' of git://github.com/hanke/PyMVPA * 'mh/master' of git://github.com/hanke/PyMVPA: (61 commits) DOC: Note NiBabel as alternative MRI IO backend. Close gh-18 BF: Remove print statements; allow hdf5 tests also for nibabel. BF: fixed up or RF a bit magical parameters/docstrings handling RF+BIG: Allow loading MRI data with nibabel. RF: searchlights -- consistent prefix roi_ (instead of roi in roisizes) and roi_ids instead of center_ids (which is still used in sphere_searchlight) RF: minimal RF of searchlight.py so we could have subclasses with specific implementations RF: taking larger dataset for test_hdf5_clf so error is more stable RF: Allow for nibabel as alternative storage backend for MRI. RF+BIG: Change fMRI samples from z,y,x to x,y,z PL: minor in searchlight DOCstrings: Default: in params descriptions gets repr, no unneeded indent for ca listing DOC (+BF): GNB -- just minor touches removing test_dataset.py -- if want to look at old code -- checkout maint/0.4 ;-) RF: explicitly call suppress warnings for scipy if scipy is known to be present RF: Prep for an alternative MRI IO backend. NF: additional testing for storing/restoring/training of classifier minor: for convenience bind sim_modulated to sin_modulated_train as well NF+BF: obj2hdf to puke when trying to store lambdas, hdf2obj handle types, HDF5ConversionError new refactor_0.5.sh to reflect the fact that those were deprecated RF: second_axis_*_of_abs transformers deprecated into favor of *_of_abs ... CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276188749 swaroopgj 4cc32b6 .gitignore Makefile doc/examples/tutorial_lib.py doc/pics/ex_eventrelated.svg doc/source/index.rst doc/source/support.rst doc/source/tutorial_classifiers.rst doc/source/tutorial_datasets.rst doc/source/tutorial_eventrelated.rst doc/source/tutorial_mappers.rst doc/source/tutorial_searchlight.rst doc/source/tutorial_sensitivity.rst doc/source/tutorial_start.rst mvpa/base/__init__.py mvpa/clfs/meta.py mvpa/featsel/base.py mvpa/featsel/ifs.py mvpa/featsel/rfe.py mvpa/measures/searchlight.py mvpa/misc/neighborhood.py mvpa/misc/plot/base.py mvpa/tests/__init__.py mvpa/tests/test_datameasure.py mvpa/tests/test_erdataset.py mvpa/tests/test_searchlight.py setup.py tools/tutorial_lib.py Merge branch 'mh/master' of git://github.com/hanke/PyMVPA * 'mh/master' of git://github.com/hanke/PyMVPA: DOC: Typos DOC: Add comments about tutorial results and 'alt' hints Put tutorial_lib.py into tools/ BF: fixed support text link + removed Freenode for IRC DOC+RF: Tutorial data now in separate location. DOC+BK: Complete draft of event-related tutorial; mapper bug pending BF: Unittest for 1D multispace searchlights. RF: FeatureSelection returns a single dataset if possible. RF+NF: chunk -> block within searchlight (confusing with chunks) + SLC_ debug target BF: make Sphere to deal with scalars as coordinates (i.e. degenerate 1D ;-)) DOC: Bits for the event-related tutorial. BK: IndexQueryEngine is broken. BF: Unbelievable -- erdataset tests never ran. RF: plot_err_line() returns line objects for later modification. DOC: Updated event-related figure. RF: Reuse as much as we can. BF: include mvpa.support.nipy into distribution CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276188733 swaroopgj 2e418c4 doc/source/tutorial_eventrelated.rst DOC: Typos CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276188685 swaroopgj 90dc99e COPYING Makefile bin/atlaslabeler bin/mvpa-prep-fmri doc/examples/clfs_examples.py doc/examples/curvefitting.py doc/examples/erp_plot.py doc/examples/eventrelated.py doc/examples/gpr.py doc/examples/gpr_model_selection0.py doc/examples/hyperplane_demo.py doc/examples/kerneldemo.py doc/examples/knn_plot.py doc/examples/match_distribution.py doc/examples/mdp_mnist.py doc/examples/mri_plot.py doc/examples/projections.py doc/examples/pylab_2d.py doc/examples/searchlight.py doc/examples/searchlight_app.py doc/examples/searchlight_dsm.py doc/examples/sensanas.py doc/examples/smellit.py doc/examples/smlr.py doc/examples/som.py doc/examples/start_easy.py doc/examples/svdclf.py doc/examples/topo_plot.py doc/examples/tutorial_lib.py doc/misc/references.bib doc/pics/.gitignore doc/pics/Makefile doc/pics/ex_eventrelated.svg doc/source/_static/.gitignore doc/source/_static/pymvpa_logo.jpg doc/source/_themes/pymvpa_online/page.html doc/source/classifiers.rst doc/source/conf.py doc/source/datadb.rst doc/source/datadb/demo_blockfmri.rst doc/source/datasets.rst doc/source/devguide.rst doc/source/docoverview.rst doc/source/index.rst doc/source/intro.rst doc/source/misc.rst doc/source/modref.rst doc/source/overview.rst doc/source/pics/.gitignore doc/source/references.rst doc/source/release_notes_0.5.rst doc/source/support.rst doc/source/tutorial.rst doc/source/tutorial_classifiers.rst doc/source/tutorial_datasets.rst doc/source/tutorial_mappers.rst doc/source/tutorial_searchlight.rst doc/source/tutorial_sensitivity.rst doc/source/tutorial_significance.rst doc/source/tutorial_start.rst mvpa/__init__.py mvpa/algorithms/cvtranserror.py mvpa/algorithms/hyperalignment.py mvpa/atlases/base.py mvpa/atlases/fsl.py mvpa/atlases/transformation.py mvpa/base/__init__.py mvpa/base/collections.py mvpa/base/dataset.py mvpa/base/dochelpers.py mvpa/base/externals.py mvpa/base/hdf5.py mvpa/base/report.py mvpa/base/types.py mvpa/clfs/_svmbase.py mvpa/clfs/base.py mvpa/clfs/blr.py mvpa/clfs/distance.py mvpa/clfs/enet.py mvpa/clfs/glmnet.py mvpa/clfs/gnb.py mvpa/clfs/gpr.py mvpa/clfs/knn.py mvpa/clfs/lars.py mvpa/clfs/libsmlrc/__init__.py mvpa/clfs/libsmlrc/ctypes_helper.py mvpa/clfs/libsvmc/_svm.py mvpa/clfs/libsvmc/sens.py mvpa/clfs/libsvmc/svm.py mvpa/clfs/meta.py mvpa/clfs/model_selector.py mvpa/clfs/plr.py mvpa/clfs/ridge.py mvpa/clfs/sg/sens.py mvpa/clfs/sg/svm.py mvpa/clfs/similarity.py mvpa/clfs/smlr.py mvpa/clfs/stats.py mvpa/clfs/transerror.py mvpa/data/v73.mat mvpa/datasets/__init__.py mvpa/datasets/base.py mvpa/datasets/channel.py mvpa/datasets/eep.py mvpa/datasets/eventrelated.py mvpa/datasets/miscfx.py mvpa/datasets/mri.py mvpa/datasets/splitters.py mvpa/featsel/helpers.py mvpa/featsel/ifs.py mvpa/kernels/base.py mvpa/kernels/np.py mvpa/kernels/sg.py mvpa/mappers/base.py mvpa/mappers/boxcar.py mvpa/mappers/detrend.py mvpa/mappers/filter.py mvpa/mappers/flatten.py mvpa/mappers/fx.py mvpa/mappers/lle.py mvpa/mappers/mdp_adaptor.py mvpa/mappers/procrustean.py mvpa/mappers/projection.py mvpa/mappers/prototype.py mvpa/mappers/som.py mvpa/mappers/svd.py mvpa/mappers/wavelet.py mvpa/mappers/zscore.py mvpa/measures/anova.py mvpa/measures/base.py mvpa/measures/corrcoef.py mvpa/measures/corrstability.py mvpa/measures/ds.py mvpa/measures/glm.py mvpa/measures/irelief.py mvpa/measures/noiseperturbation.py mvpa/measures/pls.py mvpa/measures/searchlight.py mvpa/misc/attributes.py mvpa/misc/attrmap.py mvpa/misc/bv/base.py mvpa/misc/data_generators.py mvpa/misc/errorfx.py mvpa/misc/fsl/base.py mvpa/misc/fsl/flobs.py mvpa/misc/fsl/melodic.py mvpa/misc/fx.py mvpa/misc/io/base.py mvpa/misc/io/hamster.py mvpa/misc/io/meg.py mvpa/misc/neighborhood.py mvpa/misc/param.py mvpa/misc/plot/__init__.py mvpa/misc/plot/base.py mvpa/misc/plot/erp.py mvpa/misc/plot/lightbox.py mvpa/misc/plot/tools.py mvpa/misc/plot/topo.py mvpa/misc/sampleslookup.py mvpa/misc/stats.py mvpa/misc/support.py mvpa/misc/transformers.py mvpa/suite.py mvpa/support/griddata.py mvpa/support/nipy/__init__.py mvpa/support/nipy/_emp_null.py mvpa/support/rpy2_addons.py mvpa/support/stats.py mvpa/testing/__init__.py mvpa/testing/clfs.py mvpa/testing/datasets.py mvpa/testing/sweepargs.py mvpa/testing/tools.py mvpa/tests/__init__.py mvpa/tests/badexternals/lxml.py mvpa/tests/badexternals/nipy.py mvpa/tests/badexternals/openopt.py mvpa/tests/badexternals/reportlab.py mvpa/tests/badexternals/rpy2.py mvpa/tests/main.py mvpa/tests/test_arraymapper.py mvpa/tests/test_atlases.py mvpa/tests/test_attrmap.py mvpa/tests/test_boxcarmapper.py mvpa/tests/test_clf.py mvpa/tests/test_clfcrossval.py mvpa/tests/test_collections.py mvpa/tests/test_datameasure.py mvpa/tests/test_dataset.py mvpa/tests/test_datasetfx.py mvpa/tests/test_datasetng.py mvpa/tests/test_eepdataset.py mvpa/tests/test_emp_null.py mvpa/tests/test_enet.py mvpa/tests/test_erdataset.py mvpa/tests/test_fxmapper.py mvpa/tests/test_glmnet.py mvpa/tests/test_gnb.py mvpa/tests/test_gpr.py mvpa/tests/test_hamster.py mvpa/tests/test_hdf5.py mvpa/tests/test_hyperalignment.py mvpa/tests/test_ifs.py mvpa/tests/test_iohelpers.py mvpa/tests/test_kernel.py mvpa/tests/test_knn.py mvpa/tests/test_lars.py mvpa/tests/test_mapper.py mvpa/tests/test_mapper_sp.py mvpa/tests/test_mdp.py mvpa/tests/test_meg.py mvpa/tests/test_neighborhood.py mvpa/tests/test_niftidataset.py mvpa/tests/test_params.py mvpa/tests/test_perturbsensana.py mvpa/tests/test_plr.py mvpa/tests/test_procrust.py mvpa/tests/test_prototypemapper.py mvpa/tests/test_regr.py mvpa/tests/test_report.py mvpa/tests/test_rfe.py mvpa/tests/test_ridge.py mvpa/tests/test_searchlight.py mvpa/tests/test_smlr.py mvpa/tests/test_som.py mvpa/tests/test_splitter.py mvpa/tests/test_state.py mvpa/tests/test_stats.py mvpa/tests/test_stats_sp.py mvpa/tests/test_support.py mvpa/tests/test_svdmapper.py mvpa/tests/test_svm.py mvpa/tests/test_svmkernels.py mvpa/tests/test_transerror.py mvpa/tests/test_transformers.py mvpa/tests/test_waveletmapper.py mvpa/tests/test_zscoremapper.py mvpa/tests/tests_warehouse.py mvpa/tests/tests_warehouse_clfs.py tools/daily_tests.sh tools/sitemap.sh Merge branch 'mh/master' of git://github.com/hanke/PyMVPA * 'mh/master' of git://github.com/hanke/PyMVPA: (131 commits) DOC: Complete draft of the sensitivity tutorial. DOC: tiny adjustment to TreeClassifier docstring RF: tune up ipython completion only when importing mvpa.suite NF: by default in ipython do not complete protected/private DOC: First half of the sensitivity tutorial. print meaningful msg for knn plot example DOC: minor RF: raiseException -> raise_ (following PEP) DOC: Note in release notes about N -> np RF (HUGE): 3nd wave -- import numpy/pylab as np/pl correspondingly to be inline with most of other python projects RF: minor -- commented out imports * in easy-to-debug code within plot_samples_distance to please Python RF: 2nd wave -- perchunk -> chunks_attr + some places added targets_attr argument (e.g. permute_labels) RF: 1st wave -- chunks='chunks' -> chunks_attr='chunks' NF: Splitter now perform basic slicing by default if possible. DOC: minor in tutorial_significance -- so that I could proceed with refactorings BF: temporary to assign versions upon request (if no external checking was done before, like if their presence was loaded from a config file) DOC: adjustments to significance testing blurb DOC: put licenses/copyrights for 3rd party code into COPYING "enabling" nipy"s emp_null within PyMVPA (adjusting unittest/ adding tosuite) Borrowing emp_null NiPy to be carried within PyMVPA to avoid evil 'reinvent the wheel' ... CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276188625 swaroopgj 175ff8c doc/source/classifiers.rst doc/source/tutorial_searchlight.rst mvpa/misc/plot/base.py mvpa/tests/__init__.py DOC: Typos CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276188353 swaroopgj d3ff78b doc/examples/cachedkernel.py D: Adding a simple example on how to use cached kernel CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276188342 swaroopgj 48f1801 doc/source/modref.rst mvpa/base/hdf5.py mvpa/mappers/base.py mvpa/tests/test_hdf5.py mvpa/tests/test_mapper.py tools/daily_tests.sh Merge branch 'mh/master' of git://github.com/hanke/PyMVPA * 'mh/master' of git://github.com/hanke/PyMVPA: RF+BIG: Heavy refactoring of HDF5 code. NF: Support for recursive references in HDF5 IO BF: Simplify object detection in h5load() DOC: adding gnbsearchlight to modref RF: not running daily tests for mh/master upon mh request ;-) ENH: provide "filler" argument to FeatureSliceMapper which could be used instead of 0 upon reverse call. Close gh-28 CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276188319 swaroopgj 4772dbb Makefile bin/atlaslabeler doc/examples/eventrelated.py doc/misc/asciiart.txt doc/pics/.gitignore doc/pics/ex_sensanas.svg doc/source/_static/.gitignore doc/source/_static/nitrc.jpg doc/source/_themes/pymvpa_offline/layout.html doc/source/_themes/pymvpa_online/indexsidebar.html doc/source/_themes/pymvpa_online/layout.html doc/source/datadb.rst doc/source/datadb/demo_blockfmri.rst doc/source/datadb/tutorial_data.rst doc/source/pics/.gitignore doc/source/pics/ex_sensanas.pdf doc/source/pics/ex_sensanas.png doc/source/tutorial.rst doc/source/tutorial_prerequisites.rst mvpa/atlases/base.py mvpa/atlases/fsl.py mvpa/base/__init__.py mvpa/base/hdf5.py mvpa/datasets/splitters.py mvpa/featsel/base.py mvpa/kernels/base.py mvpa/misc/data_generators.py mvpa/misc/plot/lightbox.py mvpa/misc/sampleslookup.py mvpa/misc/support.py mvpa/tests/__init__.py mvpa/tests/test_atlases.py mvpa/tests/test_hdf5.py mvpa/tests/test_hyperalignment.py mvpa/tests/test_support.py mvpa/tests/test_svmkernels.py tools/daily_tests.sh tools/refactor_0.5.sh tools/tutorial_lib.py Merge branch 'mh/master' of git://github.com/hanke/PyMVPA * 'mh/master' of git://github.com/hanke/PyMVPA: (27 commits) DOC: Update sensanas example output figure. BF: HDF5 can handle single 0d array(object) BF: test_svmkernels ValueError should be raised only in __debug__ mode BF: order voxels for xyz order now in eventrelated example RF: 2nd wave of deprecating demo_blocfmri RF: deprecating demo_blockfmri -- we use tutorial_data -- 1st step --renaming NF: oops -- forgotten to commit asciiart -- what if comes useful BF: provide exit=False for nose whenever ran from cmdline RF: deprecating get_unique_length_n_combinations in favor of (x)unique_combinations BF: removed duplicate get_unique_length_n_combinations DOC: extended Emanuele's comment on returned datasets in feature selection BF: removed duplicate *getUniqueLengthNCombinations -- appeared due to cherry pick and later merge BF: provide output of git describe not within action so it could be seen actually DOC: documenting unexpected sharing of .labels and .chunks. ENH: option to enforce recaching of CachedKernel in compute() BF(RF): use init_origids in SamplesLookup, and assure that all those are unique ENH: atlaslabeler -- enhanced statistics + reporting coordinates via qform OPT: using np.ix_ in selecting a subkernel in CachedKernel ENH: debug messages for CachedKernel + unittest which hoped to ring the bell for Swaroop's issue (it didn't) ENH: debug messages for SamplesLookup ... CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276188008 swaroopgj 22ccacf .gitignore COPYING Changelog Makefile bin/atlaslabeler doc/examples/clfs_examples.py doc/examples/curvefitting.py doc/examples/kerneldemo.py doc/examples/match_distribution.py doc/examples/mri_plot.py doc/examples/projections.py doc/examples/searchlight.py doc/examples/searchlight_app.py doc/examples/searchlight_minimal.py doc/examples/sensanas.py doc/examples/start_easy.py doc/examples/svdclf.py doc/misc/references.bib doc/source/datadb/demo_blockfmri.rst doc/source/devguide.rst doc/source/docoverview.rst doc/source/examples.rst doc/source/glossary.rst doc/source/modref.rst doc/source/mvpa_guidelines.rst doc/source/references.rst doc/source/release_notes_0.5.rst doc/source/sitemap.rst doc/source/support.rst doc/source/tutorial_classifiers.rst doc/source/tutorial_datasets.rst doc/source/tutorial_eventrelated.rst doc/source/tutorial_mappers.rst doc/source/tutorial_prerequisites.rst doc/source/tutorial_significance.rst doc/source/whoisusingit.rst mvpa/__init__.py mvpa/atlases/base.py mvpa/atlases/fsl.py mvpa/base/__init__.py mvpa/base/dataset.py mvpa/base/externals.py mvpa/base/info.py mvpa/base/verbosity.py mvpa/clfs/_svmbase.py mvpa/clfs/base.py mvpa/clfs/distance.py mvpa/clfs/enet.py mvpa/clfs/glmnet.py mvpa/clfs/gnb.py mvpa/clfs/gpr.py mvpa/clfs/lars.py mvpa/clfs/libsvmc/sens.py mvpa/clfs/meta.py mvpa/clfs/sg/svm.py mvpa/clfs/similarity.py mvpa/clfs/smlr.py mvpa/clfs/stats.py mvpa/clfs/warehouse.py mvpa/datasets/miscfx.py mvpa/datasets/splitters.py mvpa/featsel/base.py mvpa/kernels/base.py mvpa/kernels/libsvm.py mvpa/kernels/np.py mvpa/kernels/sg.py mvpa/mappers/base.py mvpa/mappers/prototype.py mvpa/mappers/svd.py mvpa/mappers/wavelet.py mvpa/mappers/zscore.py mvpa/measures/anova.py mvpa/measures/base.py mvpa/measures/gnbsearchlight.py mvpa/measures/searchlight.py mvpa/misc/attrmap.py mvpa/misc/errorfx.py mvpa/misc/neighborhood.py mvpa/misc/plot/base.py mvpa/misc/plot/erp.py mvpa/misc/support.py mvpa/suite.py mvpa/support/ipython/__init__.py mvpa/support/ipython/ipy_pymvpa_completer.py mvpa/support/pylab.py mvpa/testing/datasets.py mvpa/testing/sweepargs.py mvpa/tests/__init__.py mvpa/tests/main.py mvpa/tests/test_atlases.py mvpa/tests/test_attrmap.py mvpa/tests/test_clf.py mvpa/tests/test_clfcrossval.py mvpa/tests/test_datameasure.py mvpa/tests/test_datasetng.py mvpa/tests/test_enet.py mvpa/tests/test_hdf5_clf.py mvpa/tests/test_neighborhood.py mvpa/tests/test_regr.py mvpa/tests/test_searchlight.py mvpa/tests/test_spam.py mvpa/tests/test_stats_sp.py mvpa/tests/test_transerror.py mvpa/tests/test_zscoremapper.py setup.py tools/daily_tests.sh tools/refactor_0.5.sh Merge branch 'mh/master' of git://github.com/hanke/PyMVPA * 'mh/master' of git://github.com/hanke/PyMVPA: (150 commits) DOC: More references. BF: in-place (before it would operate on copy) zscoring of ndarrays. . Close gh-27 BF: moving scipy-dependent statement in gnbsearchlight BF+RF: apparently epsilon is tube_epsilon for sg.LibSVR + sg.svm.seed DOC: Restructure paper listing. DOC: Note new users with Nature Neuroscience paper ;-) BF: workaround for shogun -- epsilon in constructor for regressions has no effect NF: mvpa.support.ipython + ipy_pymvpa_completer BF: import debug for kernels.sg ENH: complement CorrErrorFx with just CorrFx ENH: fslatlas.get_maps -- accepts now 'key_attr' defining on what to use for keys ENH: more debugging for sg kernels and svm BF+DOC: Wrong link to tutorial. RF: atlas.levels now corresponds to previous atlas.levels_dict RF/ENH: atlaslabeler -- ability to provide a stream of voxels indices RF: atlases __getitem__ for queries by voxel indices, __call__ -- by coordinates BF: actually fail (error exist status) whenever unittest-debug fails (uff) BF: access selected_ids from .ca BF: unittest-debug -- do not rely on MVPA_SEED or OK being in the tail -- just go to the end ;) BF: nr_class can be None, so just use %s in debug printout ... CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276187909 swaroopgj d3ff78b doc/examples/cachedkernel.py D: Adding a simple example on how to use cached kernel CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276187894 swaroopgj 48f1801 doc/source/modref.rst mvpa/base/hdf5.py mvpa/mappers/base.py mvpa/tests/test_hdf5.py mvpa/tests/test_mapper.py tools/daily_tests.sh Merge branch 'mh/master' of git://github.com/hanke/PyMVPA * 'mh/master' of git://github.com/hanke/PyMVPA: RF+BIG: Heavy refactoring of HDF5 code. NF: Support for recursive references in HDF5 IO BF: Simplify object detection in h5load() DOC: adding gnbsearchlight to modref RF: not running daily tests for mh/master upon mh request ;-) ENH: provide "filler" argument to FeatureSliceMapper which could be used instead of 0 upon reverse call. Close gh-28 CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276187867 swaroopgj 4772dbb Makefile bin/atlaslabeler doc/examples/eventrelated.py doc/misc/asciiart.txt doc/pics/.gitignore doc/pics/ex_sensanas.svg doc/source/_static/.gitignore doc/source/_static/nitrc.jpg doc/source/_themes/pymvpa_offline/layout.html doc/source/_themes/pymvpa_online/indexsidebar.html doc/source/_themes/pymvpa_online/layout.html doc/source/datadb.rst doc/source/datadb/demo_blockfmri.rst doc/source/datadb/tutorial_data.rst doc/source/pics/.gitignore doc/source/pics/ex_sensanas.pdf doc/source/pics/ex_sensanas.png doc/source/tutorial.rst doc/source/tutorial_prerequisites.rst mvpa/atlases/base.py mvpa/atlases/fsl.py mvpa/base/__init__.py mvpa/base/hdf5.py mvpa/datasets/splitters.py mvpa/featsel/base.py mvpa/kernels/base.py mvpa/misc/data_generators.py mvpa/misc/plot/lightbox.py mvpa/misc/sampleslookup.py mvpa/misc/support.py mvpa/tests/__init__.py mvpa/tests/test_atlases.py mvpa/tests/test_hdf5.py mvpa/tests/test_hyperalignment.py mvpa/tests/test_support.py mvpa/tests/test_svmkernels.py tools/daily_tests.sh tools/refactor_0.5.sh tools/tutorial_lib.py Merge branch 'mh/master' of git://github.com/hanke/PyMVPA * 'mh/master' of git://github.com/hanke/PyMVPA: (27 commits) DOC: Update sensanas example output figure. BF: HDF5 can handle single 0d array(object) BF: test_svmkernels ValueError should be raised only in __debug__ mode BF: order voxels for xyz order now in eventrelated example RF: 2nd wave of deprecating demo_blocfmri RF: deprecating demo_blockfmri -- we use tutorial_data -- 1st step --renaming NF: oops -- forgotten to commit asciiart -- what if comes useful BF: provide exit=False for nose whenever ran from cmdline RF: deprecating get_unique_length_n_combinations in favor of (x)unique_combinations BF: removed duplicate get_unique_length_n_combinations DOC: extended Emanuele's comment on returned datasets in feature selection BF: removed duplicate *getUniqueLengthNCombinations -- appeared due to cherry pick and later merge BF: provide output of git describe not within action so it could be seen actually DOC: documenting unexpected sharing of .labels and .chunks. ENH: option to enforce recaching of CachedKernel in compute() BF(RF): use init_origids in SamplesLookup, and assure that all those are unique ENH: atlaslabeler -- enhanced statistics + reporting coordinates via qform OPT: using np.ix_ in selecting a subkernel in CachedKernel ENH: debug messages for CachedKernel + unittest which hoped to ring the bell for Swaroop's issue (it didn't) ENH: debug messages for SamplesLookup ... CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276187537 swaroopgj d3ff78b doc/examples/cachedkernel.py D: Adding a simple example on how to use cached kernel CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276187537 swaroopgj d3ff78b doc/examples/cachedkernel.py D: Adding a simple example on how to use cached kernel CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276187521 swaroopgj 48f1801 doc/source/modref.rst mvpa/base/hdf5.py mvpa/mappers/base.py mvpa/tests/test_hdf5.py mvpa/tests/test_mapper.py tools/daily_tests.sh Merge branch 'mh/master' of git://github.com/hanke/PyMVPA * 'mh/master' of git://github.com/hanke/PyMVPA: RF+BIG: Heavy refactoring of HDF5 code. NF: Support for recursive references in HDF5 IO BF: Simplify object detection in h5load() DOC: adding gnbsearchlight to modref RF: not running daily tests for mh/master upon mh request ;-) ENH: provide "filler" argument to FeatureSliceMapper which could be used instead of 0 upon reverse call. Close gh-28 CIA Perl client for Git 1.0+alioth1 pymvpa pymvpa per/master 1276187521 swaroopgj 48f1801 doc/source/modref.rst mvpa/base/hdf5.py mvpa/mappers/base.py mvpa/tests/test_hdf5.py mvpa/tests/test_mapper.py tools/daily_tests.sh Merge branch 'mh/master' of git://github.com/hanke/PyMVPA * 'mh/master' of git://github.com/hanke/PyMVPA: RF+BIG: Heavy refactoring of HDF5 code. NF: Support for recursive references in HDF5 IO BF: Simplify object detection in h5load() DOC: adding gnbsearchlight to modref RF: not running daily tests for mh/master upon mh request ;-) ENH: provide "filler" argument to FeatureSliceMapper which could be used instead of 0 upon reverse call. Close gh-28