Dear all,
I am trying to understand why a RFE will not work with a CustomPartitioner of
mine.
The RFE snippet is:
--------------------------------------------------------------------------------
## Define RFE FractionTailSelector:
clf = LinearCSVMC()
rfe = RFE(clf.get_sensitivity_analyzer(postproc=maxofabs_sample()),
CrossValidation(clf, partitioner, errorfx=mean_mismatch_error,
postproc=mean_sample()), Repeater(2), fselector=FractionTailSelector(0.50,
mode='select', tail='upper'),
stopping_criterion=NBackHistoryStopCrit(BestDetector(), 10),
train_pmeasure=False, update_sensitivity=True)
## Run crossvalidation:
fclf = FeatureSelectionClassifier(clf, rfe)
rfecvte = CrossValidation(fclf, partitioner, errorfx=lambda p, t:np.mean(p ==
t), postproc=mean_sample(), enable_ca=['confusion', 'stats'])
rfe_res=rfecvte(fds)
--------------------------------------------------------------------------------
The snippet works smoothly if:
partitioner=NFoldPartitioner()
If however:
partitioner =
CustomPartitioner(([([0,1,2,3,4],[5]),([0,1,2,3,5],[4]),([0,1,2,4,5],[3]),([0,1,3,4,5],[2]),([0,2,3,4,5],[1]),([1,2,3,4,5],[0])]),
attr='chunks') ## Note: fds contains 6 chunks
I get the error message:
"ValueError: Got empty testing dataset from splitting in TransferMeasure. Unique
values of input split attribute are: [1])"
Originally, I wanted to use different custom parititions, but I ended up
implementing the above CustomPartitioner, which in my intentions should be
equivalent to NFoldPartitioner (leave-one-chunk-out). Apparently, no matter how
CustomPartitioner is defined, rfe will terminate with an error.
With a larger dataset, I also seem to get an error using:
partitioner=HalfPartitioner()
but again not using:
partitioner=NFoldPartitioner()
Below is the output of my mvpa2.wtf().
Thank you a lot for any help!
Marco
In [17]: mvpa2.wtf()
Out[17]:
Current date: 2013-11-20 16:48
PyMVPA:
Version: 2.2.0
Hash: $Format:%H$
Path: /usr/local/PyMVPA/mvpa2/__init__.pyc
Version control (GIT):
Status:
# On branch master
# Changes not staged for commit:
# (use "git add <file>..." to update what will be committed)
# (use "git checkout -- <file>..." to discard changes in working directory)
#
# modified: .gitattributes
# modified: .gitignore
# modified: .mailmap
# modified: .travis.yml
# modified: .travis_coveragerc
# modified: 3rd/libsvm/COPYRIGHT
# modified: 3rd/libsvm/Makefile
# modified: 3rd/libsvm/Makefile.win
# modified: 3rd/libsvm/README
# modified: 3rd/libsvm/svm.cpp
# modified: 3rd/libsvm/svm.h
# modified: AUTHOR
# modified: COPYING
# modified: MANIFEST.in
# modified: Makefile
# modified: Makefile.win
# modified: README.rst
# modified: TODO
# modified: doc/Makefile
# modified: doc/examples/eyemovements.py
# modified: doc/examples/hyperalignment.py
# modified: doc/examples/hyperplane_demo.py
# modified: doc/examples/pymvpa2.cfg
# modified: doc/misc/asciiart.txt
# modified: doc/misc/codeswarm.config
# modified: doc/misc/emacs
# modified: doc/misc/epydoc.conf
# modified: doc/misc/flexds_transition_status.txt
# modified: doc/misc/header.py
# modified: doc/misc/ipy_profile_pymvpa.py
# modified: doc/misc/kernels.tex
# modified: doc/misc/pylintrc
# modified: doc/misc/references.bib
# modified: doc/misc/references.in
# modified: doc/pics/.gitignore
# modified: doc/pics/Makefile
# modified: doc/pics/ex_curvefitting_bold.svg
# modified: doc/pics/ex_curvefitting_searchlight.svg
# modified: doc/pics/ex_eventrelated.svg
# modified: doc/pics/ex_eyemovements.svg
# modified: doc/pics/ex_mdp_fda.svg
# modified: doc/pics/ex_plot_lightbox.svg
# modified: doc/pics/ex_searchlight_vt_r0.svg
# modified: doc/pics/ex_searchlight_vt_r1.svg
# modified: doc/pics/ex_searchlight_vt_r3.svg
# modified: doc/pics/ex_sensanas.svg
# modified: doc/pics/ex_svm_margin.svg
# modified: doc/pics/pymvpa_icons.svg
# modified: doc/pics/pymvpa_logo.svg
# modified: doc/source/_static/.gitignore
# modified: doc/source/_static/neurodebian.png
# modified: doc/source/_static/nitrc.jpg
# modified: doc/source/_static/robots.txt
# modified: doc/source/_themes/pymvpa_offline/indexsidebar.html
# modified: doc/source/_themes/pymvpa_offline/layout.html
# modified: doc/source/_themes/pymvpa_offline/static/pymvpa.css_t
# modified: doc/source/_themes/pymvpa_offline/theme.conf
# modified: doc/source/_themes/pymvpa_online/indexsidebar.html
# modified: doc/source/_themes/pymvpa_online/layout.html
# modified: doc/source/_themes/pymvpa_online/page.html
# modified: doc/source/_themes/pymvpa_online/static/pymvpa.css_t
# modified: doc/source/_themes/pymvpa_online/theme.conf
# modified: doc/source/classifiers.txt
# modified: doc/source/conf.py
# modified: doc/source/contributors.txt
# modified: doc/source/datadb.rst
# modified: doc/source/datadb/face_inversion_demo.rst
# modified: doc/source/datadb/haxby2001.rst
# modified: doc/source/datadb/hyperalignment_tutorial_data.rst
# modified: doc/source/datadb/mnist.rst
# modified: doc/source/datadb/tutorial_data.rst
# modified: doc/source/datasets.txt
# modified: doc/source/devguide.rst
# modified: doc/source/docoverview.rst
# modified: doc/source/download.rst
# modified: doc/source/examples.rst
# modified: doc/source/faq.rst
# modified: doc/source/featsel.txt
# modified: doc/source/glossary.rst
# modified: doc/source/history.rst
# modified: doc/source/howtocite.txt
# modified: doc/source/index.rst
# modified: doc/source/installation.rst
# modified: doc/source/intro.rst
# modified: doc/source/link_names.txt
# modified: doc/source/manual.rst
# modified: doc/source/mappers.txt
# modified: doc/source/measures.txt
# modified: doc/source/misc.rst
# modified: doc/source/modref.rst
# modified: doc/source/mvpa_guidelines.rst
# modified: doc/source/overview.rst
# modified: doc/source/pdfmanual.rst
# modified: doc/source/pics/.gitignore
# modified: doc/source/pics/classifier_comparison_plot.png
# modified: doc/source/pics/confusion_matrix.png
# modified: doc/source/pics/design.pdf
# modified: doc/source/pics/design.png
# modified: doc/source/pics/ex_curvefitting.pdf
# modified: doc/source/pics/ex_curvefitting.png
# modified: doc/source/pics/ex_erp_plot.pdf
# modified: doc/source/pics/ex_erp_plot.png
# modified: doc/source/pics/ex_hyperalignment_alphasweep.png
# modified: doc/source/pics/ex_hyperalignment_similarity.png
# modified: doc/source/pics/ex_match_distribution.pdf
# modified: doc/source/pics/ex_match_distribution.png
# modified: doc/source/pics/ex_projections.pdf
# modified: doc/source/pics/ex_projections.png
# modified: doc/source/pics/ex_smellit2.png
# modified: doc/source/pics/ex_smellit3.png
# modified: doc/source/pics/ex_som.pdf
# modified: doc/source/pics/ex_som.png
# modified: doc/source/pics/ex_svdclf.pdf
# modified: doc/source/pics/ex_svdclf.png
# modified: doc/source/pics/ex_topo_plot.pdf
# modified: doc/source/pics/ex_topo_plot.png
# modified: doc/source/pics/extravaganza-dc09.jpg
# modified: doc/source/pics/favicon.png
# modified: doc/source/pics/history_splash.png
# modified: doc/source/pics/logo.bmp
# modified: doc/source/pics/pymvpa_on_phone.jpg
# modified: doc/source/references.rst
# modified: doc/source/release_notes_0.5.rst
# modified: doc/source/release_notes_0.6.rst
# modified: doc/source/sitemap.rst
# modified: doc/source/support.rst
# modified: doc/source/tutorial.rst
# modified: doc/source/tutorial_classifiers.rst
# modified: doc/source/tutorial_datasets.rst
# modified: doc/source/tutorial_eventrelated.rst
# modified: doc/source/tutorial_mappers.rst
# modified: doc/source/tutorial_multiclass_hyp.rst
# modified: doc/source/tutorial_prerequisites.rst
# modified: doc/source/tutorial_searchlight.rst
# modified: doc/source/tutorial_sensitivity.rst
# modified: doc/source/tutorial_significance.rst
# modified: doc/source/tutorial_start.rst
# modified: doc/source/whoisusingit.rst
# modified: doc/source/workshops/2009-fall.rst
# modified: doc/sphinxext/__init__.py
# modified: doc/sphinxext/autosummary/__init__.py
# modified: doc/sphinxext/autosummary/generate.py
# modified: doc/sphinxext/docscrape.py
# modified: doc/sphinxext/docscrape_sphinx.py
# modified: doc/sphinxext/exercise_directive.py
# modified: doc/sphinxext/numpydoc.py
# modified: doc/templates/autosummary/base.rst
# modified: doc/templates/autosummary/class.rst
# modified: doc/templates/autosummary/module.rst
# modified: mvpa2/COMMIT_HASH
# modified: mvpa2/__init__.py
# modified: mvpa2/_random.py
# modified: mvpa2/algorithms/__init__.py
# modified: mvpa2/algorithms/hyperalignment.py
# modified: mvpa2/atlases/__init__.py
# modified: mvpa2/atlases/base.py
# modified: mvpa2/atlases/fsl.py
# modified: mvpa2/atlases/transformation.py
# modified: mvpa2/atlases/warehouse.py
# modified: mvpa2/base/__init__.py
# modified: mvpa2/base/attributes.py
# modified: mvpa2/base/collections.py
# modified: mvpa2/base/config.py
# modified: mvpa2/base/dataset.py
# modified: mvpa2/base/dochelpers.py
# modified: mvpa2/base/externals.py
# modified: mvpa2/base/hdf5.py
# modified: mvpa2/base/info.py
# modified: mvpa2/base/learner.py
# modified: mvpa2/base/node.py
# modified: mvpa2/base/param.py
# modified: mvpa2/base/report.py
# modified: mvpa2/base/report_dummy.py
# modified: mvpa2/base/state.py
# modified: mvpa2/base/types.py
# modified: mvpa2/base/verbosity.py
# modified: mvpa2/clfs/__init__.py
# modified: mvpa2/clfs/_svmbase.py
# modified: mvpa2/clfs/base.py
# modified: mvpa2/clfs/blr.py
# modified: mvpa2/clfs/distance.py
# modified: mvpa2/clfs/enet.py
# modified: mvpa2/clfs/gda.py
# modified: mvpa2/clfs/glmnet.py
# modified: mvpa2/clfs/gnb.py
# modified: mvpa2/clfs/gpr.py
# modified: mvpa2/clfs/knn.py
# modified: mvpa2/clfs/lars.py
# modified: mvpa2/clfs/libsmlrc/__init__.py
# modified: mvpa2/clfs/libsmlrc/ctypes_helper.py
# modified: mvpa2/clfs/libsmlrc/smlr.c
# modified: mvpa2/clfs/libsvmc/.gitignore
# modified: mvpa2/clfs/libsvmc/__init__.py
# modified: mvpa2/clfs/libsvmc/_svm.py
# modified: mvpa2/clfs/libsvmc/sens.py
# modified: mvpa2/clfs/libsvmc/svm.py
# modified: mvpa2/clfs/libsvmc/svmc.i
# modified: mvpa2/clfs/mass.py
# modified: mvpa2/clfs/meta.py
# modified: mvpa2/clfs/model_selector.py
# modified: mvpa2/clfs/plr.py
# modified: mvpa2/clfs/ridge.py
# modified: mvpa2/clfs/sg/__init__.py
# modified: mvpa2/clfs/sg/sens.py
# modified: mvpa2/clfs/sg/svm.py
# modified: mvpa2/clfs/similarity.py
# modified: mvpa2/clfs/skl/__init__.py
# modified: mvpa2/clfs/skl/base.py
# modified: mvpa2/clfs/smlr.py
# modified: mvpa2/clfs/stats.py
# modified: mvpa2/clfs/svm.py
# modified: mvpa2/clfs/transerror.py
# modified: mvpa2/clfs/warehouse.py
# modified: mvpa2/data/README
# modified: mvpa2/data/attributes.txt
# modified: mvpa2/data/attributes_literal.txt
# modified: mvpa2/data/bold.nii.gz
# modified: mvpa2/data/bold_mc.par
# modified: mvpa2/data/bv/smpl_model.rtc
# modified: mvpa2/data/eep.bin
# modified: mvpa2/data/example4d.nii.gz
# modified: mvpa2/data/fslev3.txt
# modified: mvpa2/data/glm.mat
# modified: mvpa2/data/mask.nii.gz
# modified: mvpa2/data/sample_design.fsf
# modified: mvpa2/data/smpl_attr.txt
# modified: mvpa2/data/tueb_meg.dat.gz
# modified: mvpa2/data/tueb_meg_coord.xyz
# modified: mvpa2/data/v73.mat
# modified: mvpa2/data/xavr1010.dat
# modified: mvpa2/datasets/__init__.py
# modified: mvpa2/datasets/base.py
# modified: mvpa2/datasets/channel.py
# modified: mvpa2/datasets/eeglab.py
# modified: mvpa2/datasets/eep.py
# modified: mvpa2/datasets/eventrelated.py
# modified: mvpa2/datasets/formats.py
# modified: mvpa2/datasets/miscfx.py
# modified: mvpa2/datasets/mri.py
# modified: mvpa2/datasets/niml.py
# modified: mvpa2/datasets/sources/__init__.py
# modified: mvpa2/datasets/sources/sklearn_data.py
# modified: mvpa2/featsel/__init__.py
# modified: mvpa2/featsel/base.py
# modified: mvpa2/featsel/helpers.py
# modified: mvpa2/featsel/ifs.py
# modified: mvpa2/featsel/rfe.py
# modified: mvpa2/generators/__init__.py
# modified: mvpa2/generators/base.py
# modified: mvpa2/generators/partition.py
# modified: mvpa2/generators/permutation.py
# modified: mvpa2/generators/resampling.py
# modified: mvpa2/generators/splitters.py
# modified: mvpa2/kernels/__init__.py
# modified: mvpa2/kernels/base.py
# modified: mvpa2/kernels/libsvm.py
# modified: mvpa2/kernels/np.py
# modified: mvpa2/kernels/sg.py
# modified: mvpa2/mappers/__init__.py
# modified: mvpa2/mappers/base.py
# modified: mvpa2/mappers/boxcar.py
# modified: mvpa2/mappers/detrend.py
# modified: mvpa2/mappers/filters.py
# modified: mvpa2/mappers/flatten.py
# modified: mvpa2/mappers/fx.py
# modified: mvpa2/mappers/fxy.py
# modified: mvpa2/mappers/lle.py
# modified: mvpa2/mappers/mdp_adaptor.py
# modified: mvpa2/mappers/procrustean.py
# modified: mvpa2/mappers/projection.py
# modified: mvpa2/mappers/prototype.py
# modified: mvpa2/mappers/shape.py
# modified: mvpa2/mappers/slicing.py
# modified: mvpa2/mappers/som.py
# modified: mvpa2/mappers/staticprojection.py
# modified: mvpa2/mappers/svd.py
# modified: mvpa2/mappers/wavelet.py
# modified: mvpa2/mappers/zscore.py
# modified: mvpa2/measures/__init__.py
# modified: mvpa2/measures/adhocsearchlightbase.py
# modified: mvpa2/measures/anova.py
# modified: mvpa2/measures/base.py
# modified: mvpa2/measures/corrcoef.py
# modified: mvpa2/measures/corrstability.py
# modified: mvpa2/measures/ds.py
# modified: mvpa2/measures/gnbsearchlight.py
# modified: mvpa2/measures/irelief.py
# modified: mvpa2/measures/ismooth.py
# modified: mvpa2/measures/nnsearchlight.py
# modified: mvpa2/measures/noiseperturbation.py
# modified: mvpa2/measures/pls.py
# modified: mvpa2/measures/rsm.py
# modified: mvpa2/measures/searchlight.py
# modified: mvpa2/measures/statsmodels_adaptor.py
# modified: mvpa2/measures/winner.py
# modified: mvpa2/misc/__init__.py
# modified: mvpa2/misc/args.py
# modified: mvpa2/misc/attrmap.py
# modified: mvpa2/misc/bv/__init__.py
# modified: mvpa2/misc/bv/base.py
# modified: mvpa2/misc/cmdline.py
# modified: mvpa2/misc/data_generators.py
# modified: mvpa2/misc/dcov.py
# modified: mvpa2/misc/errorfx.py
# modified: mvpa2/misc/exceptions.py
# modified: mvpa2/misc/fsl/__init__.py
# modified: mvpa2/misc/fsl/base.py
# modified: mvpa2/misc/fsl/flobs.py
# modified: mvpa2/misc/fsl/melodic.py
# modified: mvpa2/misc/fx.py
# modified: mvpa2/misc/io/__init__.py
# modified: mvpa2/misc/io/base.py
# modified: mvpa2/misc/io/hamster.py
# modified: mvpa2/misc/io/meg.py
# modified: mvpa2/misc/neighborhood.py
# modified: mvpa2/misc/plot/__init__.py
# modified: mvpa2/misc/plot/base.py
# modified: mvpa2/misc/plot/erp.py
# modified: mvpa2/misc/plot/flat_surf.py
# modified: mvpa2/misc/plot/lightbox.py
# modified: mvpa2/misc/plot/tools.py
# modified: mvpa2/misc/plot/topo.py
# modified: mvpa2/misc/sampleslookup.py
# modified: mvpa2/misc/stats.py
# modified: mvpa2/misc/support.py
# modified: mvpa2/misc/surfing/COPYRIGHT
# modified: mvpa2/misc/surfing/__init__.py
# modified: mvpa2/misc/surfing/queryengine.py
# modified: mvpa2/misc/surfing/surf_voxel_selection.py
# modified: mvpa2/misc/surfing/volgeom.py
# modified: mvpa2/misc/surfing/volsurf.py
# modified: mvpa2/misc/surfing/volume_mask_dict.py
# modified: mvpa2/misc/transformers.py
# modified: mvpa2/misc/vproperty.py
# modified: mvpa2/sandbox/__init__.py
# modified: mvpa2/sandbox/multiclass.py
# modified: mvpa2/support/__init__.py
# modified: mvpa2/support/_copy.py
# modified: mvpa2/support/_emp_null.py
# modified: mvpa2/support/afni/__init__.py
# modified: mvpa2/support/afni/afni_utils.py
# modified: mvpa2/support/afni/lib_prep_afni_surf.py
# modified: mvpa2/support/afni/suma_setup_instacorr.py
# modified: mvpa2/support/bayes/__init__.py
# modified: mvpa2/support/bayes/multivariate_polya.py
# modified: mvpa2/support/bayes/partial_independence.py
# modified: mvpa2/support/bayes/partitioner.py
# modified: mvpa2/support/copy.py
# modified: mvpa2/support/griddata.py
# modified: mvpa2/support/ipython/__init__.py
# modified: mvpa2/support/ipython/ipy_pymvpa_completer.py
# modified: mvpa2/support/lapack_svd.py
# modified: mvpa2/support/nibabel/__init__.py
# modified: mvpa2/support/nibabel/afni_niml.py
# modified: mvpa2/support/nibabel/afni_niml_annot.py
# modified: mvpa2/support/nibabel/afni_niml_dset.py
# modified: mvpa2/support/nibabel/afni_niml_roi.py
# modified: mvpa2/support/nibabel/afni_niml_types.py
# modified: mvpa2/support/nibabel/afni_suma_1d.py
# modified: mvpa2/support/nibabel/afni_suma_spec.py
# modified: mvpa2/support/nibabel/surf.py
# modified: mvpa2/support/nibabel/surf_caret.py
# modified: mvpa2/support/nibabel/surf_fs_asc.py
# modified: mvpa2/support/nipy/__init__.py
# modified: mvpa2/support/pylab.py
# modified: mvpa2/support/rpy2_addons.py
# modified: mvpa2/support/stats.py
# modified: mvpa2/support/utils.py
# modified: mvpa2/testing/__init__.py
# modified: mvpa2/testing/clfs.py
# modified: mvpa2/testing/datasets.py
# modified: mvpa2/testing/sweepargs.py
# modified: mvpa2/testing/tools.py
# modified: mvpa2/tests/__init__.py
# modified: mvpa2/tests/badexternals/cPickle_disabled.py
# modified: mvpa2/tests/badexternals/ctypes.py
# modified: mvpa2/tests/badexternals/griddata.py
# modified: mvpa2/tests/badexternals/gzip.py
# modified: mvpa2/tests/badexternals/h5py.py
# modified: mvpa2/tests/badexternals/hcluster.py
# modified: mvpa2/tests/badexternals/libsvm.py
# modified: mvpa2/tests/badexternals/lxml.py
# modified: mvpa2/tests/badexternals/mdp.py
# modified: mvpa2/tests/badexternals/nibabel.py
# modified: mvpa2/tests/badexternals/nifti.py
# modified: mvpa2/tests/badexternals/nipy.py
# modified: mvpa2/tests/badexternals/openopt.py
# modified: mvpa2/tests/badexternals/pandas.py
# modified: mvpa2/tests/badexternals/psutil.py
# modified: mvpa2/tests/badexternals/pylab.py
# modified: mvpa2/tests/badexternals/pywt.py
# modified: mvpa2/tests/badexternals/reportlab.py
# modified: mvpa2/tests/badexternals/rpy.py
# modified: mvpa2/tests/badexternals/rpy2.py
# modified: mvpa2/tests/badexternals/scikits/__init__.py
# modified: mvpa2/tests/badexternals/scikits/learn/__init__.py
# modified: mvpa2/tests/badexternals/scipy.py
# modified: mvpa2/tests/badexternals/shogun.py
# modified: mvpa2/tests/badexternals/skimage.py
# modified: mvpa2/tests/badexternals/sklearn.py
# modified: mvpa2/tests/badexternals/statsmodels.py
# modified: mvpa2/tests/badexternals/weave.py
# modified: mvpa2/tests/runner.py
# modified: mvpa2/tests/test_args.py
# modified: mvpa2/tests/test_arraymapper.py
# modified: mvpa2/tests/test_atlases.py
# modified: mvpa2/tests/test_attrmap.py
# modified: mvpa2/tests/test_base.py
# modified: mvpa2/tests/test_boxcarmapper.py
# modified: mvpa2/tests/test_clf.py
# modified: mvpa2/tests/test_clfcrossval.py
# modified: mvpa2/tests/test_cmdline.py
# modified: mvpa2/tests/test_collections.py
# modified: mvpa2/tests/test_config.py
# modified: mvpa2/tests/test_datameasure.py
# modified: mvpa2/tests/test_dataset_formats.py
# modified: mvpa2/tests/test_datasetfx.py
# modified: mvpa2/tests/test_datasetng.py
# modified: mvpa2/tests/test_datasrcs.py
# modified: mvpa2/tests/test_dcov.py
# modified: mvpa2/tests/test_dochelpers.py
# modified: mvpa2/tests/test_eeglab.py
# modified: mvpa2/tests/test_eepdataset.py
# modified: mvpa2/tests/test_emp_null.py
# modified: mvpa2/tests/test_enet.py
# modified: mvpa2/tests/test_erdataset.py
# modified: mvpa2/tests/test_errorfx.py
# modified: mvpa2/tests/test_externals.py
# modified: mvpa2/tests/test_filters.py
# modified: mvpa2/tests/test_fxmapper.py
# modified: mvpa2/tests/test_generators.py
# modified: mvpa2/tests/test_glmnet.py
# modified: mvpa2/tests/test_gnb.py
# modified: mvpa2/tests/test_gpr.py
# modified: mvpa2/tests/test_hamster.py
# modified: mvpa2/tests/test_hdf5.py
# modified: mvpa2/tests/test_hdf5_clf.py
# modified: mvpa2/tests/test_hyperalignment.py
# modified: mvpa2/tests/test_ifs.py
# modified: mvpa2/tests/test_iohelpers.py
# modified: mvpa2/tests/test_kernel.py
# modified: mvpa2/tests/test_knn.py
# modified: mvpa2/tests/test_lars.py
# modified: mvpa2/tests/test_mapper.py
# modified: mvpa2/tests/test_mapper_sp.py
# modified: mvpa2/tests/test_mdp.py
# modified: mvpa2/tests/test_meg.py
# modified: mvpa2/tests/test_misc.py
# modified: mvpa2/tests/test_multiclf.py
# modified: mvpa2/tests/test_neighborhood.py
# modified: mvpa2/tests/test_niftidataset.py
# modified: mvpa2/tests/test_params.py
# modified: mvpa2/tests/test_perturbsensana.py
# modified: mvpa2/tests/test_plr.py
# modified: mvpa2/tests/test_procrust.py
# modified: mvpa2/tests/test_prototypemapper.py
# modified: mvpa2/tests/test_regr.py
# modified: mvpa2/tests/test_report.py
# modified: mvpa2/tests/test_rfe.py
# modified: mvpa2/tests/test_ridge.py
# modified: mvpa2/tests/test_searchlight.py
# modified: mvpa2/tests/test_senses.py
# modified: mvpa2/tests/test_smlr.py
# modified: mvpa2/tests/test_som.py
# modified: mvpa2/tests/test_spam.py
# modified: mvpa2/tests/test_splitter.py
# modified: mvpa2/tests/test_state.py
# modified: mvpa2/tests/test_staticprojection.py
# modified: mvpa2/tests/test_stats.py
# modified: mvpa2/tests/test_stats_sp.py
# modified: mvpa2/tests/test_suite.py
# modified: mvpa2/tests/test_support.py
# modified: mvpa2/tests/test_surfing.py
# modified: mvpa2/tests/test_surfing_afni.py
# modified: mvpa2/tests/test_surfing_voxelselection.py
# modified: mvpa2/tests/test_svdmapper.py
# modified: mvpa2/tests/test_svm.py
# modified: mvpa2/tests/test_svmkernels.py
# modified: mvpa2/tests/test_testing.py
# modified: mvpa2/tests/test_transerror.py
# modified: mvpa2/tests/test_transformers.py
# modified: mvpa2/tests/test_usecases.py
# modified: mvpa2/tests/test_verbosity.py
# modified: mvpa2/tests/test_waveletmapper.py
# modified: mvpa2/tests/test_winner.py
# modified: mvpa2/tests/test_zscoremapper.py
# modified: py3tool.py
# modified: setup.cfg.win
# modified: tools/Makefile
# modified: tools/apigen.py
# modified: tools/mpkg_wrapper.py
# modified: tools/pdfbook.c
# modified: tools/valgrind-python.supp
#
no changes added to commit (use "git add" and/or "git commit -a")
Reference:
c67827abe179baf19bf2bd6040a2b8711871e478 HEAD
c67827abe179baf19bf2bd6040a2b8711871e478 refs/remotes/origin/HEAD
Difference from last release 2.2.0:
160 files changed, 18050 insertions(+), 882 deletions(-)
SYSTEM:
OS: posix Linux 3.10-3-amd64 #1 SMP Debian 3.10.11-1 (2013-09-10)
Distribution: debian/jessie/sid
EXTERNALS:
Present: atlas_fsl, cPickle, ctypes, good scipy.stats.rdist, good
scipy.stats.rv_continuous._reduce_func(floc,fscale), good
scipy.stats.rv_discrete.ppf, griddata, gzip, h5py, ipython, liblapack.so,
libsvm, libsvm verbosity control, lxml, matplotlib, mdp, mdp ge 2.4, nibabel,
nose, numpy, numpy_correct_unique, pprocess, pylab, pylab plottable, pywt, pywt
wp reconstruct, reportlab, running ipython env, scipy, skl, weave
Absent: atlas_pymvpa, cran-energy, elasticnet, glmnet, hcluster, lars,
mass, nipy, nipy.neurospin, numpydoc, openopt, pywt wp reconstruct fixed, rpy2,
sg ge 0.6.4, sg ge 0.6.5, sg_fixedcachesize, shogun, shogun.krr,
shogun.lightsvm, shogun.mpd, shogun.svmocas, shogun.svrlight, statsmodels
Versions of critical externals:
ctypes : 1.1.0
h5py : 2.0.1
ipython : 0.13.2
lxml : 3.2.0
matplotlib : 1.3.1
mdp : 3.4
nibabel : 1.3.0
numpy : 1.7.1
pprocess : 0.5
reportlab : 2.5
scipy : 0.12.0
skl : 0.14.1
Matplotlib backend: TkAgg
RUNTIME:
PyMVPA Environment Variables:
PYTHONPATH :
":/usr/lib/python2.7/lib-old:/usr/local/lib/python2.7/dist-packages:/usr/local/PyMVPA:/usr/lib/python2.7/plat-x86_64-linux-gnu:/usr/lib/python2.7/lib-tk:/usr/lib/python2.7/lib-dynload:/home/marco/data/bll/abstrasomat_pymvpa/negsomloc6s_abssom6s_pymvpa:/usr/bin:/usr/local/PyMVPA/:/usr/lib/python2.7/dist-packages:/usr/lib/pymodules/python2.7:/usr/lib/python2.7/dist-packages/IPython/extensions:/usr/lib/python2.7:/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode:/home/marco/.python27_compiled:/usr/lib/python2.7/dist-packages/gtk-2.0:/usr/lib/python2.7/dist-packages/PIL"
PyMVPA Runtime Configuration:
[general]
verbose = 1
[externals]
have running ipython env = yes
have ipython = yes
have numpy = yes
have scipy = yes
have matplotlib = yes
have h5py = yes
have reportlab = yes
have weave = yes
have good scipy.stats.rdist = yes
have good scipy.stats.rv_discrete.ppf = yes
have good scipy.stats.rv_continuous._reduce_func(floc,fscale) = yes
have pylab = yes
have lars = no
have elasticnet = no
have glmnet = no
have skl = yes
have ctypes = yes
have libsvm = yes
have shogun = no
have openopt = no
have nibabel = yes
have mdp = yes
have mdp ge 2.4 = yes
have statsmodels = no
have pywt = yes
have cpickle = yes
have gzip = yes
have cran-energy = no
have griddata = yes
have nipy.neurospin = no
have lxml = yes
have atlas_fsl = yes
have atlas_pymvpa = no
have hcluster = no
have liblapack.so = yes
have libsvm verbosity control = yes
have mass = no
have nipy = no
have nose = yes
have numpy_correct_unique = yes
have numpydoc = no
have pprocess = yes
have pylab plottable = yes
have pywt wp reconstruct = yes
have pywt wp reconstruct fixed = no
have rpy2 = no
have sg ge 0.6.4 = no
have sg ge 0.6.5 = no
have sg_fixedcachesize = no
have shogun.krr = no
have shogun.lightsvm = no
have shogun.mpd = no
have shogun.svmocas = no
have shogun.svrlight = no
Process Information:
Name: ipython
State: R (running)
Tgid: 7966
Pid: 7966
PPid: 4220
TracerPid: 0
Uid: 1000 1000 1000 1000
Gid: 1000 1000 1000 1000
FDSize: 256
Groups: 6 7 20 24 25 27 29 30 44 46 100 104 113 114 116 999 1000
VmPeak: 1156192 kB
VmSize: 786244 kB
VmLck: 0 kB
VmPin: 0 kB
VmHWM: 538160 kB
VmRSS: 165008 kB
VmData: 296740 kB
VmStk: 136 kB
VmExe: 2792 kB
VmLib: 55308 kB
VmPTE: 1232 kB
VmSwap: 0 kB
Threads: 3
SigQ: 0/254507
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000001001000
SigCgt: 0000000180000002
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: 0000001fffffffff
Seccomp: 0
Cpus_allowed: ff
Cpus_allowed_list: 0-7
Mems_allowed: 00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 62667
nonvoluntary_ctxt_switches: 788
--
Marco Tettamanti, Ph.D.
Nuclear Medicine Department & Division of Neuroscience
San Raffaele Scientific Institute
Via Olgettina 58
I-20132 Milano, Italy
Phone ++39-02-26434888
Fax ++39-02-26434892
Email: [email protected]
Skype: mtettamanti
_______________________________________________
Pkg-ExpPsy-PyMVPA mailing list
[email protected]
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
