PyMVPA Documentation Contents

• Introduction
  • What this Manual is NOT
  • A bit of History
  • Authors & Contributors
  • How to cite PyMVPA
    • Peer-reviewed publications
    • Posters
    • Studies employing PyMVPA
  • Acknowledgements

• Installation
  • Dependencies
    • Must Have
    • Strong Recommendations
    • Suggestions
  • Installing Binary Packages
    • Debian
    • Debian backports and inofficial Ubuntu packages
    • Windows
    • MacOS X
    • RPM-based GNU/Linux Distributions
  • Building from Source
    • Three Ways to Obtain the Sources
    • Build it (General instructions)
    • Build with enabled LIBSVM bindings
    • Alternative build procedure
    • Windows
    • OpenSUSE
    • Fedora
    • MacOS X

• Getting Started
  • For the Impatient
  • Module Overview

• Datasets
  • The Basic Concepts
  • Data Mapping
  • Data Access Sugaring
  • Data Formats
  • Data Splitting

• Classifiers
  • Stateful objects
  • Error Calculation
    • Cross-validated Transfer Error
  • Error Reporting
  • Basic Supervised Learning Methods
    • Gaussian Process Regression
    • k-Nearest-Neighbour
    • Least Angle Regression
    • Penalized Logistic Regression
    • Ridge Regression
    • Sparse Multinomial Logistic Regression
    • Support Vector Machines
  • Meta-Classifiers
    • Examples of Meta-Classifiers
    • Implementation Examples
  • Retrainable Classifiers
  • Classifiers “Warehouse”

• Measures
  • Sensitivity Measures
    • Basic Sensitivity (and related Measures)
      • ANOVA
      • Linear SVM Weights
      • Other linear Classifier Weights
      • Noise Perturbation
    • Meta Sensitivity Measures
      • Splitting Measures

• Feature Selection
  • Recursive Feature Elimination
  • Incremental Feature Search

• Miscellaneous
  • Managing (Custom) Configurations
  • Progress Tracking
    • Redirecting Output
    • Verbose Messages
    • Warning Messages
    • Debug Messages
    • PyMVPA Status Summary
  • Additional Little Helpers
    • Random Number Generation
    • Unittests at a Grasp
    • Others
  • FSL Bindings

• Full Examples
  • Example fMRI Dataset
  • Preprocessing
    • Visualization of Data Projection Methods
    • Simple Data-Exploration
  • Analysis
    • Tiny Example of a Full Cross-Validation
    • Compare SMLR to Linear SVM Classifier
    • Classifier Sweep
    • The effect of different hyperparameters in GPR
    • Minimal Searchlight Example
    • Searchlight on fMRI data
    • A searchlight computing a dissimilarity matrix measure
    • Sensitivity Measure
    • Classification of SVD-mapped Datasets
    • Monte-Carlo testing of Classifier-based Analyses
    • Determine the Distribution of some Variable
    • Spatio-temporal Analysis of event-related fMRI data
  • Visualization
    • ERP/ERF-Plots
    • Simple Plotting of Classifier Behavior
    • Generating Topography plots
    • Self-organizing Maps
  • Miscellaneous
    • Kernel-Demo
    • Curve-Fitting

• PyMVPA for Matlab Users

• Frequently Asked Questions
  • General
    • It is sloooooow. What can I do?
    • I am tired of writing these endless import blocks. Any alternative?
    • I feel like I want to contribute something, do you mind?
    • I want to develop a new feature for PyMVPA. How can I do it efficiently?
    • The manual is quite insufficient. When will you improve it?
  • Data import, export and storage
    • What file formats are understood by PyMVPA?
    • What if there is no special file format for some particular datatype?
  • Data preprocessing
    • Is there an easy way to remove invariant features from a dataset?
    • How can I do block-averaging of my block-design fMRI dataset?
  • Data analysis
    • How do I know which features were finally selected by a classifier doing feature selection?
    • How do I extract sensitivities from a classifier used within a cross-validation?
    • Can PyMVPA deal with literal class labels?

• Glossary

• References

• License

• PyMVPA Development Changelog
  • Releases

• PyMVPA - The Movie

• TODO

• Module Reference
  • Global Facilities
    • mvpa
      • mvpa
        • Package Organization
  • Datasets: Input, Output, Storage and Preprocessing
    • datasets.base
      • Module: datasets.base
      • Dataset
    • datasets.channel
      • Module: datasets.channel
      • ChannelDataset
    • datasets.eep
      • Module: datasets.eep
      • EEPDataset
    • datasets.event
      • Module: datasets.event
      • EventDataset
    • datasets.mapped
      • Module: datasets.mapped
      • MappedDataset
    • datasets.masked
      • Module: datasets.masked
      • MaskedDataset
    • datasets.meta
      • Module: datasets.meta
      • MetaDataset
    • datasets.miscfx
      • Module: datasets.miscfx
      • Class
      • SequenceStats
      • Functions
    • datasets.miscfx_sp
      • Module: datasets.miscfx_sp
    • datasets.nifti
      • Module: datasets.nifti
      • Classes
        • ERNiftiDataset
        • NiftiDataset
      • Functions
    • datasets.splitters
      • Module: datasets.splitters
        • Module Description
        • Brief Description of Available Splitters
        • Module Organization
      • Classes
        • CustomSplitter
        • HalfSplitter
        • NFoldSplitter
        • NGroupSplitter
        • NoneSplitter
        • OddEvenSplitter
        • Splitter
  • Mappers: Data Transformations
    • mappers.array
      • Module: mappers.array
      • DenseArrayMapper
    • mappers.base
      • Module: mappers.base
      • Classes
        • ChainMapper
        • CombinedMapper
        • Mapper
        • ProjectionMapper
    • mappers.boxcar
      • Module: mappers.boxcar
      • BoxcarMapper
    • mappers.ica
      • Module: mappers.ica
      • ICAMapper
    • mappers.lle
      • Module: mappers.lle
      • LLEMapper
    • mappers.mask
      • Module: mappers.mask
      • MaskMapper
    • mappers.metric
      • Module: mappers.metric
      • Classes
        • DescreteMetric
        • Metric
    • mappers.pca
      • Module: mappers.pca
      • PCAMapper
    • mappers.procrustean
      • Module: mappers.procrustean
      • ProcrusteanMapper
    • mappers.samplegroup
      • Module: mappers.samplegroup
      • SampleGroupMapper
    • mappers.som
      • Module: mappers.som
      • SimpleSOMMapper
    • mappers.svd
      • Module: mappers.svd
      • SVDMapper
    • mappers.wavelet
      • Module: mappers.wavelet
      • Classes
        • WaveletPacketMapper
        • WaveletTransformationMapper
    • mappers.zscore
      • Module: mappers.zscore
      • ZScoreMapper
  • Classifiers and Errors
    • clfs.base
      • Module: clfs.base
      • Classes
        • Classifier
        • DegenerateInputError
        • FailedToPredictError
        • FailedToTrainError
        • LearnerError
    • clfs.blr
      • Module: clfs.blr
      • BLR
    • clfs.distance
      • Module: clfs.distance
      • Functions
    • clfs.enet
      • Module: clfs.enet
      • Classes
        • ENET
        • ENETWeights
    • clfs.glmnet
      • Module: clfs.glmnet
      • Classes
        • GLMNETWeights
        • GLMNET_C
        • GLMNET_R
    • clfs.gnb
      • Module: clfs.gnb
      • GNB
    • clfs.gpr
      • Module: clfs.gpr
      • Classes
        • GPR
        • GPRLinearWeights
    • clfs.kernel
      • Module: clfs.kernel
      • Classes
        • Kernel
        • KernelConstant
        • KernelExponential
        • KernelLinear
        • KernelMatern_3_2
        • KernelMatern_5_2
        • KernelRationalQuadratic
        • KernelSquaredExponential
    • clfs.knn
      • Module: clfs.knn
      • kNN
    • clfs.lars
      • Module: clfs.lars
      • Classes
        • LARS
        • LARSWeights
    • clfs.libsmlrc
      • Module: clfs.libsmlrc
    • clfs.libsmlrc.ctypes_helper
      • Module: clfs.libsmlrc.ctypes_helper
      • Functions
    • clfs.libsvmc.sens
      • Module: clfs.libsvmc.sens
      • LinearSVMWeights
    • clfs.libsvmc.svm
      • Module: clfs.libsvmc.svm
      • SVM
    • clfs.meta
      • Module: clfs.meta
      • Classes
        • BinaryClassifier
        • BoostedClassifier
        • ClassifierCombiner
        • CombinedClassifier
        • FeatureSelectionClassifier
        • MappedClassifier
        • MaximalVote
        • MeanPrediction
        • MulticlassClassifier
        • PredictionsCombiner
        • ProxyClassifier
        • SplitClassifier
        • TreeClassifier
    • clfs.model_selector
      • Module: clfs.model_selector
      • ModelSelector
    • clfs.plr
      • Module: clfs.plr
      • PLR
    • clfs.ridge
      • Module: clfs.ridge
      • RidgeReg
    • clfs.sg.sens
      • Module: clfs.sg.sens
      • LinearSVMWeights
    • clfs.sg.svm
      • Module: clfs.sg.svm
      • SVM
    • clfs.smlr
      • Module: clfs.smlr
      • Classes
        • SMLR
        • SMLRWeights
    • clfs.stats
      • Module: clfs.stats
      • Classes
        • AdaptiveNormal
        • AdaptiveNullDist
        • AdaptiveRDist
        • FixedNullDist
        • MCNullDist
        • Nonparametric
        • NullDist
      • Functions
    • clfs.transerror
      • Module: clfs.transerror
      • Classes
        • ClassifierError
        • ConfusionBasedError
        • ConfusionMatrix
        • ROCCurve
        • RegressionStatistics
        • SummaryStatistics
        • TransferError
    • clfs.warehouse
      • Module: clfs.warehouse
      • Warehouse
  • Measures: Searchlights and Sensitivties
    • measures.anova
      • Module: measures.anova
      • Classes
        • CompoundOneWayAnova
        • OneWayAnova
    • measures.base
      • Module: measures.base
      • Classes
        • BoostedClassifierSensitivityAnalyzer
        • CombinedFeaturewiseDatasetMeasure
        • DatasetMeasure
        • FeatureSelectionClassifierSensitivityAnalyzer
        • FeaturewiseDatasetMeasure
        • MappedClassifierSensitivityAnalyzer
        • ProxyClassifierSensitivityAnalyzer
        • Sensitivity
        • SplitFeaturewiseDatasetMeasure
        • StaticDatasetMeasure
    • measures.corrcoef
      • Module: measures.corrcoef
      • CorrCoef
    • measures.corrstability
      • Module: measures.corrstability
      • CorrStability
    • measures.ds
      • Module: measures.ds
      • DSMDatasetMeasure
    • measures.glm
      • Module: measures.glm
      • GLM
    • measures.irelief
      • Module: measures.irelief
      • Classes
        • IterativeRelief
        • IterativeReliefOnline
        • IterativeReliefOnline_Devel
        • IterativeRelief_Devel
    • measures.noiseperturbation
      • Module: measures.noiseperturbation
      • NoisePerturbationSensitivity
    • measures.pls
      • Module: measures.pls
      • Classes
        • PLS
        • TaskPLS
    • measures.searchlight
      • Module: measures.searchlight
      • Searchlight
    • measures.splitmeasure
      • Module: measures.splitmeasure
      • Classes
        • SplitFeaturewiseMeasure
        • TScoredFeaturewiseMeasure
  • Feature Selection
    • featsel.base
      • Module: featsel.base
      • Classes
        • CombinedFeatureSelection
        • FeatureSelection
        • FeatureSelectionPipeline
        • SensitivityBasedFeatureSelection
    • featsel.helpers
      • Module: featsel.helpers
      • Classes
        • BestDetector
        • ElementSelector
        • FixedErrorThresholdStopCrit
        • FixedNElementTailSelector
        • FractionTailSelector
        • MultiStopCrit
        • NBackHistoryStopCrit
        • NStepsStopCrit
        • RangeElementSelector
        • StoppingCriterion
        • TailSelector
    • featsel.ifs
      • Module: featsel.ifs
      • IFS
    • featsel.rfe
      • Module: featsel.rfe
      • RFE
  • Additional Algorithms
    • algorithms.cvtranserror
      • Module: algorithms.cvtranserror
      • CrossValidatedTransferError
    • algorithms.hyperalignment
      • Module: algorithms.hyperalignment
      • Hyperalignment
  • Common Facilities
    • base
      • Module: base
        • Module Organization
      • WarningLog
    • base.config
      • Module: base.config
      • ConfigManager
    • base.dochelpers
      • Module: base.dochelpers
      • Functions
    • base.externals
      • Module: base.externals
      • Functions
    • base.info
      • Module: base.info
      • WTF
    • base.report
      • Module: base.report
      • Report
    • base.report_dummy
      • Module: base.report_dummy
      • Report
    • base.verbosity
      • Module: base.verbosity
      • Classes
        • LevelLogger
        • Logger
        • OnceLogger
        • SetLogger
  • Miscellaneous
    • misc.args
      • Module: misc.args
      • Functions
    • misc.attributes
      • Module: misc.attributes
      • Classes
        • AttributeWithUnique
        • CollectableAttribute
        • DatasetAttribute
        • FeatureAttribute
        • SampleAttribute
        • StateVariable
    • misc.bv.base
      • Module: misc.bv.base
      • BrainVoyagerRTC
    • misc.cmdline
      • Module: misc.cmdline
      • Classes
        • OptionGroups
        • Options
    • misc.data_generators
      • Module: misc.data_generators
      • Functions
    • misc.errorfx
      • Module: misc.errorfx
      • Classes
        • AUCErrorFx
        • MeanMismatchErrorFx
        • RMSErrorFx
        • RelativeRMSErrorFx
        • Variance1SVFx
      • Functions
    • misc.exceptions
      • Module: misc.exceptions
      • Classes
        • ConvergenceError
        • DatasetError
        • InvalidHyperparameterError
        • UnknownStateError
    • misc.fsl.base
      • Module: misc.fsl.base
      • Classes
        • FslEV3
        • FslGLMDesign
        • McFlirtParams
      • Function
    • misc.fsl.flobs
      • Module: misc.fsl.flobs
    • misc.fsl.melodic
      • Module: misc.fsl.melodic
      • MelodicResults
    • misc.fx
      • Module: misc.fx
      • Functions
    • misc.io.base
      • Module: misc.io.base
      • Classes
        • ColumnData
        • DataReader
        • SampleAttributes
        • SensorLocations
        • TuebingenMEGSensorLocations
        • XAVRSensorLocations
      • Functions
    • misc.io.eepbin
      • Module: misc.io.eepbin
      • EEPBin
    • misc.io.hamster
      • Module: misc.io.hamster
      • Hamster
    • misc.io.meg
      • Module: misc.io.meg
      • TuebingenMEG
    • misc.param
      • Module: misc.param
      • Classes
        • KernelParameter
        • Parameter
    • misc.plot.base
      • Module: misc.plot.base
      • Functions
    • misc.plot.erp
      • Module: misc.plot.erp
      • Functions
    • misc.plot.mri
      • Module: misc.plot.mri
    • misc.plot.topo
      • Module: misc.plot.topo
      • Functions
    • misc.state
      • Module: misc.state
      • Classes
        • AttributesCollector
        • ClassWithCollections
        • Collection
        • Harvestable
        • ParameterCollection
        • SampleAttributesCollection
        • StateCollection
    • misc.stats
      • Module: misc.stats
      • DSMatrix
    • misc.support
      • Module: misc.support
      • Classes
        • Event
        • Harvester
        • HarvesterCall
        • MapOverlap
        • SmartVersion
      • Functions
    • misc.transformers
      • Module: misc.transformers
      • Classes
        • DistPValue
        • OverAxis
      • Functions
    • misc.vproperty
      • Module: misc.vproperty
      • VProperty
    • atlases.base
      • Module: atlases.base
        • TODOs:
        • Module Organization
      • Classes
        • BaseAtlas
        • Label
        • LabelsAtlas
        • LabelsLevel
        • Level
        • PyMVPAAtlas
        • ReferencesAtlas
        • ReferencesLevel
        • XMLAtlasException
        • XMLBasedAtlas
      • Function
    • atlases.fsl
      • Module: atlases.fsl
      • Classes
        • FSLAtlas
        • FSLLabelsAtlas
        • FSLProbabilisticAtlas
    • atlases.transformation
      • Module: atlases.transformation
      • Classes
        • Linear
        • MNI2Tal_MatthewBrett
        • SpaceTransformation
        • TransformationBase
        • TypeProxy
      • Functions
    • atlases.warehouse
      • Module: atlases.warehouse