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PyMVPA: Python MultiVariate Pattern Analysis
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Module Hierarchy
mvpa
:
MultiVariate Pattern Analysis
mvpa.algorithms
:
Import helper for PyMVPA algorithms.
mvpa.algorithms.cvtranserror
:
Cross-validate a classifier on a dataset
mvpa.atlases
:
Import helper for PyMVPA anatomical atlases
mvpa.atlases.base
:
Base classes for Anatomy atlases support
mvpa.atlases.fsl
:
FSL atlases interfaces
mvpa.atlases.transformation
:
Coordinate transformations
mvpa.atlases.warehouse
:
Collection of the known atlases
mvpa.base
:
Base functionality of PyMVPA
mvpa.base.config
:
Registry-like monster
mvpa.base.dochelpers
:
Various helpers to improve docstrings and textual output
mvpa.base.externals
:
Helper to verify presence of external libraries and modules
mvpa.base.info
:
Provide system and PyMVPA information useful while reporting bugs
mvpa.base.report
:
Creating simple PDF reports using reportlab
mvpa.base.report_dummy
:
Dummy report class, to just be there in case if reportlab is not available.
mvpa.base.verbosity
:
Verbose output and debugging facility
mvpa.clfs
:
Import helper for PyMVPA classifiers
mvpa.clfs._svmbase
:
Common to all SVM implementations functionality.
mvpa.clfs.base
:
Base class for all classifiers.
mvpa.clfs.blr
:
Bayesian Linear Regression (BLR).
mvpa.clfs.distance
:
Distance functions to be used in kernels and elsewhere
mvpa.clfs.enet
:
Elastic-Net (ENET) regression classifier.
mvpa.clfs.glmnet
:
GLM-Net (GLMNET) regression classifier.
mvpa.clfs.gpr
:
Gaussian Process Regression (GPR).
mvpa.clfs.kernel
:
Kernels for Gaussian Process Regression and Classification.
mvpa.clfs.knn
:
k-Nearest-Neighbour classifier.
mvpa.clfs.lars
:
Least angle regression (LARS) classifier.
mvpa.clfs.libsmlrc
:
Wraper for the stepwise_regression function for SMLR.
mvpa.clfs.libsmlrc.ctypes_helper
:
Helpers for wrapping C libraries with ctypes.
mvpa.clfs.libsvmc
:
Classifiers provied by LibSVM library
mvpa.clfs.libsvmc._svm
:
Python interface to the SWIG-wrapped libsvm
mvpa.clfs.libsvmc.sens
:
Provide sensitivity measures for libsvm's SVM.
mvpa.clfs.libsvmc.svm
:
Wrap the libsvm package into a very simple class interface.
mvpa.clfs.meta
:
Classes for meta classifiers -- classifiers which use other classifiers
mvpa.clfs.model_selector
:
Model selction.
mvpa.clfs.plr
:
Penalized logistic regression classifier.
mvpa.clfs.ridge
:
Ridge regression classifier.
mvpa.clfs.sg
:
Classifiers provied by shogun (sg) library
mvpa.clfs.sg.sens
:
Provide sensitivity measures for sg's SVM.
mvpa.clfs.sg.svm
:
Wrap the libsvm package into a very simple class interface.
mvpa.clfs.smlr
:
Sparse Multinomial Logistic Regression classifier.
mvpa.clfs.stats
:
Estimator for classifier error distributions.
mvpa.clfs.svm
:
Importer for the available SVM and SVR machines.
mvpa.clfs.transerror
:
Utility class to compute the transfer error of classifiers.
mvpa.clfs.warehouse
:
Collection of classifiers to ease the exploration.
mvpa.datasets
:
PyMVPA datasets and helper classes such as splitters
mvpa.datasets.base
:
Dataset container
mvpa.datasets.channel
:
Dataset handling data structured in channels.
mvpa.datasets.eep
:
Dataset that gets its samples from an EEP binary file
mvpa.datasets.event
:
Event-based dataset type
mvpa.datasets.mapped
:
Mapped dataset
mvpa.datasets.masked
:
Dataset with applied mask
mvpa.datasets.meta
:
Dataset container
mvpa.datasets.miscfx
:
Misc function performing operations on datasets.
mvpa.datasets.miscfx_sp
:
Misc function performing operations on datasets which are based on scipy
mvpa.datasets.nifti
:
Dataset that gets its samples from a NIfTI file
mvpa.datasets.splitters
:
Collection of dataset splitters.
mvpa.featsel
:
Feature selection methods.
mvpa.featsel.base
:
Feature selection base class and related stuff base classes and helpers.
mvpa.featsel.helpers
mvpa.featsel.ifs
:
Incremental feature search (IFS).
mvpa.featsel.rfe
:
Recursive feature elimination.
mvpa.mappers
:
PyMVPA mappers.
mvpa.mappers.array
:
Data mapper
mvpa.mappers.base
:
Data mapper
mvpa.mappers.boxcar
:
Data mapper
mvpa.mappers.ica
:
Data mapper
mvpa.mappers.lle
:
Local Linear Embedding Data mapper.
mvpa.mappers.mask
:
Data mapper which applies mask to the data
mvpa.mappers.metric
:
Classes and functions to provide sense of distances between sample points
mvpa.mappers.pca
:
Data mapper
mvpa.mappers.procrustean
:
Procrustean rotation mapper
mvpa.mappers.samplegroup
:
Data mapper
mvpa.mappers.som
:
Self-organizing map (SOM) mapper.
mvpa.mappers.svd
:
Singular-value decomposition mapper
mvpa.mappers.wavelet
:
Wavelet mappers
mvpa.mappers.zscore
:
Simple mapper to perform zscoring
mvpa.measures
:
PyMVPA measures.
mvpa.measures.anova
:
FeaturewiseDatasetMeasure performing a univariate ANOVA.
mvpa.measures.base
:
Base class for data measures: algorithms that quantify properties of datasets.
mvpa.measures.corrcoef
:
FeaturewiseDatasetMeasure of correlation with the labels.
mvpa.measures.corrstability
:
FeaturewiseDatasetMeasure of stability of labels across chunks based on correlation.
mvpa.measures.ds
:
Dissimilarity measure.
mvpa.measures.glm
:
The general linear model (GLM).
mvpa.measures.irelief
:
FeaturewiseDatasetMeasure performing multivariate Iterative RELIEF (I-RELIEF) algorithm.
mvpa.measures.noiseperturbation
:
This is a
FeaturewiseDatasetMeasure
that uses a scalar
DatasetMeasure
and selective noise perturbation to compute a sensitivity map.
mvpa.measures.pls
mvpa.measures.searchlight
:
Implementation of the Searchlight algorithm
mvpa.measures.splitmeasure
:
This is a
FeaturewiseDatasetMeasure
that uses another
FeaturewiseDatasetMeasure
and runs it multiple times on differents splits of a
Dataset
.
mvpa.misc
:
Import helper for PyMVPA misc modules
mvpa.misc.args
:
Helpers for arguments handling.
mvpa.misc.attributes
:
Module with some special objects to be used as magic attributes with dedicated containers aka.
mvpa.misc.bv
:
Import helper for Brain Voyager
mvpa.misc.bv.base
:
Tiny snippets to interface with FSL easily.
mvpa.misc.cmdline
:
Common functions and options definitions for command line
mvpa.misc.data_generators
:
Miscelaneous data generators for unittests and demos
mvpa.misc.errorfx
:
Error functions helpers.
mvpa.misc.exceptions
:
Exception classes which might get thrown
mvpa.misc.fsl
:
Import helper for FSL
mvpa.misc.fsl.base
:
Tiny snippets to interface with FSL easily.
mvpa.misc.fsl.flobs
:
Wrapper around FSLs halfcosbasis to generate HRF kernels
mvpa.misc.fsl.melodic
:
Wrapper around the output of MELODIC (part of FSL)
mvpa.misc.fx
:
Misc.
mvpa.misc.io
:
Import helper for IO helpers
mvpa.misc.io.base
:
Some little helper for reading (and writing) common formats from and to disk.
mvpa.misc.io.eepbin
:
Reader for binary EEP files.
mvpa.misc.io.hamster
:
Helper for simple storage facility via cPickle and optionally zlib
mvpa.misc.io.meg
:
IO helper for MEG datasets.
mvpa.misc.param
:
Parameter representation
mvpa.misc.plot
:
Import helper for miscalaneouse PyMVPA plotting functions (mvpa.misc.plot)
mvpa.misc.plot.base
:
Misc.
mvpa.misc.plot.erp
:
Basic ERP (here ERP = Event Related Plot ;-)) plotting
mvpa.misc.plot.mri
:
Basic (f)MRI plotting with ability to interactively perform thresholding
mvpa.misc.plot.topo
:
Plot parameter distributions on a head surface (topography plots).
mvpa.misc.state
:
Classes to control and store state information.
mvpa.misc.stats
:
Little statistics helper
mvpa.misc.support
:
Support function -- little helpers in everyday life
mvpa.misc.transformers
:
Simply functors that transform something.
mvpa.misc.vproperty
:
C++-like virtual properties
mvpa.suite
:
MultiVariate Pattern Analysis -- load helper
mvpa.support
:
Import helper for PyMVPA support modules
mvpa.support._copy
:
Generic (shallow and deep) copying operations.
mvpa.support.copy
:
Support for python's copy module.
mvpa.support.griddata
:
Import griddata with preference to the version from matplotlib
mvpa.support.stats
:
Fixer for rdist in scipy
mvpa.tests
:
Unit test interface for PyMVPA
mvpa.tests.main
:
Unit test console interface for PyMVPA
mvpa.tests.runner
:
Helper module to enable profiling of the testcase
mvpa.tests.test_args
:
Unit tests for PyMVPA args helpers
mvpa.tests.test_arraymapper
:
Unit tests for PyMVPA dense array mapper
mvpa.tests.test_atlases
:
Unit tests for PyMVPA atlases
mvpa.tests.test_base
:
Test some base functionality which did not make it into a separate unittests
mvpa.tests.test_boxcarmapper
:
Unit tests for PyMVPA Boxcar mapper
mvpa.tests.test_clf
:
Unit tests for PyMVPA basic Classifiers
mvpa.tests.test_clfcrossval
:
Unit tests for PyMVPA classifier cross-validation
mvpa.tests.test_cmdline
:
Unit tests for PyMVPA cmdline helpers
mvpa.tests.test_config
:
Unit tests for PyMVPA dense array mapper
mvpa.tests.test_datameasure
:
Unit tests for PyMVPA SplittingSensitivityAnalyzer
mvpa.tests.test_dataset
:
Unit tests for PyMVPA dataset handling
mvpa.tests.test_datasetfx
:
Unit tests for PyMVPA miscelaneouse functions operating on datasets
mvpa.tests.test_datasetfx_sp
:
Unit tests for PyMVPA miscelaneouse functions operating on datasets and requiring SciPy
mvpa.tests.test_datasetng
:
Tests for the dataset implementation
mvpa.tests.test_dochelpers
:
Unit tests for PyMVPA dochelpers
mvpa.tests.test_eepdataset
:
Unit tests for PyMVPA EEP dataset
mvpa.tests.test_enet
:
Unit tests for PyMVPA least angle regression (ENET) classifier
mvpa.tests.test_externals
:
Test externals checking
mvpa.tests.test_hamster
:
Unit tests for PyMVPA Hamster
mvpa.tests.test_icamapper
:
Unit tests for PyMVPA ICA mapper
mvpa.tests.test_ifs
:
Unit tests for PyMVPA incremental feature search.
mvpa.tests.test_iohelpers
:
Unit tests for PyMVPA IO helpers
mvpa.tests.test_kernel
:
Unit tests for PyMVPA kernels
mvpa.tests.test_knn
:
Unit tests for PyMVPA kNN classifier
mvpa.tests.test_lars
:
Unit tests for PyMVPA least angle regression (LARS) classifier
mvpa.tests.test_maskeddataset
:
Unit tests for PyMVPA pattern handling
mvpa.tests.test_meg
:
Unit tests for PyMVPA MEG stuff
mvpa.tests.test_metadataset
:
Unit tests for PyMVPA meta dataset handling
mvpa.tests.test_neighbor
:
Unit tests for PyMVPA metrics
mvpa.tests.test_niftidataset
:
Unit tests for PyMVPA nifti dataset
mvpa.tests.test_params
:
Unit tests for PyMVPA Parameter class.
mvpa.tests.test_pcamapper
:
Unit tests for PyMVPA PCA mapper
mvpa.tests.test_perturbsensana
:
Unit tests for PyMVPA perturbation sensitivity analyzer.
mvpa.tests.test_plr
:
Unit tests for PyMVPA logistic regression classifier
mvpa.tests.test_pls
:
Unit tests for Partial Least Squares measures.
mvpa.tests.test_procrust
:
Unit tests for PyMVPA Procrustean mapper
mvpa.tests.test_regr
:
Unit tests for PyMVPA Regressions
mvpa.tests.test_report
:
Unit tests for PyMVPA simple report facility
mvpa.tests.test_rfe
:
Unit tests for PyMVPA recursive feature elimination
mvpa.tests.test_ridge
:
Unit tests for PyMVPA ridge regression classifier
mvpa.tests.test_samplegroupmapper
:
Unit tests for PyMVPA SampleGroup mapper
mvpa.tests.test_searchlight
:
Unit tests for PyMVPA searchlight algorithm
mvpa.tests.test_smlr
:
Unit tests for PyMVPA sparse multinomial logistic regression classifier
mvpa.tests.test_som
:
Unit tests for PyMVPA SOM mapper
mvpa.tests.test_splitsensana
:
Unit tests for PyMVPA SplittingSensitivityAnalyzer
mvpa.tests.test_splitter
:
Unit tests for PyMVPA pattern handling
mvpa.tests.test_state
:
Unit tests for PyMVPA State parent class
mvpa.tests.test_stats
:
Unit tests for PyMVPA stats helpers
mvpa.tests.test_stats_sp
:
Unit tests for PyMVPA stats helpers -- those requiring scipy
mvpa.tests.test_suite
:
Unit test for PyMVPA mvpa.suite() of being loading ok
mvpa.tests.test_support
:
Unit tests for PyMVPA serial feature inclusion algorithm
mvpa.tests.test_svdmapper
:
Unit tests for PyMVPA SVD mapper
mvpa.tests.test_svm
:
Unit tests for SVM classifier
mvpa.tests.test_transerror
:
Unit tests for PyMVPA classifier cross-validation
mvpa.tests.test_transformers
:
Unit tests for PyMVPA transformers.
mvpa.tests.test_verbosity
:
Unit tests for PyMVPA verbose and debug output
mvpa.tests.test_waveletmapper
:
Unit tests for PyMVPA Wavelet mappers
mvpa.tests.test_zscoremapper
:
Unit tests for PyMVPA ZScore mapper
mvpa.tests.tests_warehouse
:
Miscelaneous functions/datasets to be used in the unit tests
mvpa.tests.tests_warehouse_clfs
:
Provides
clfs
dictionary with instances of all available classifiers.
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PyMVPA: Python MultiVariate Pattern Analysis
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