Multivariate Pattern Analysis in Python
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PDF version of the PyMVPA Manual
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The PDF version of the manual is available for
download
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Introduction
What this Manual is NOT
A bit of History
Authors & Contributors
How to cite 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
Additional Little Helpers
Random Number Generation
Unittests at a Grasp
Others
FSL Bindings
Full Examples
Example fMRI Dataset
Preprocessing
Simple preprocessing of event-related data using FSL EV3 design files
Visualization of Data Projection Methods
Simple Data-Exploration
Analysis
Tiny Example of a Full Cross-Validation
Compare SMLR to Linear SVM Classifier
Classifier Sweep
Minimal Searchlight Example
Searchlight on fMRI data
Sensitivity Measure
Classification of SVD-mapped Datasets
Monte-Carlo testing of Classifier-based Analyses
Determine the Distribution of some Variable
Visualization
ERP/ERF-Plots
Simple Plotting of Classifier Behavior
Generating Topography plots
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
Module Reference
Global Facilities
mvpa
Package Organization
Datasets: Input, Output, Storage and Preprocessing
mvpa.datasets
Module Description
Module Organization
mvpa.datasets.base
Dataset
mvpa.datasets.channel
ChannelDataset
mvpa.datasets.eep
EEPDataset
mvpa.datasets.event
EventDataset
mvpa.datasets.mapped
MappedDataset
mvpa.datasets.masked
MaskedDataset
mvpa.datasets.meta
MetaDataset
mvpa.datasets.miscfx
Functions
mvpa.datasets.miscfx_sp
mvpa.datasets.nifti
Classes
ERNiftiDataset
NiftiDataset
Functions
mvpa.datasets.splitter
Classes
CustomSplitter
HalfSplitter
NFoldSplitter
NoneSplitter
OddEvenSplitter
Splitter
Mappers: Data Transformations
mvpa.mappers
mvpa.mappers.array
DenseArrayMapper
mvpa.mappers.base
Classes
ChainMapper
CombinedMapper
Mapper
ProjectionMapper
mvpa.mappers.boxcar
BoxcarMapper
mvpa.mappers.ica
ICAMapper
mvpa.mappers.mask
MaskMapper
mvpa.mappers.metric
Classes
DescreteMetric
Metric
mvpa.mappers.pca
PCAMapper
mvpa.mappers.samplegroup
SampleGroupMapper
mvpa.mappers.svd
SVDMapper
mvpa.mappers.wavelet
Classes
WaveletPacketMapper
WaveletTransformationMapper
Classifiers and Errors
mvpa.clfs
Module Organization
mvpa.clfs.base
Classes
BinaryClassifier
BoostedClassifier
Classifier
ClassifierCombiner
CombinedClassifier
FeatureSelectionClassifier
MappedClassifier
MaximalVote
MeanPrediction
MulticlassClassifier
PredictionsCombiner
ProxyClassifier
SplitClassifier
mvpa.clfs.blr
BLR
mvpa.clfs.distance
Functions
mvpa.clfs.gpr
Classes
GPR
GPRLinearWeights
mvpa.clfs.kernel
Classes
Kernel
KernelConstant
KernelExponential
KernelLinear
KernelMatern_3_2
KernelMatern_5_2
KernelRationalQuadratic
KernelSquaredExponential
mvpa.clfs.knn
kNN
mvpa.clfs.lars
Classes
LARS
LARSWeights
mvpa.clfs.libsmlrc
mvpa.clfs.libsmlrc.ctypes_helper
Functions
mvpa.clfs.libsvmc
mvpa.clfs.libsvmc.sens
LinearSVMWeights
mvpa.clfs.libsvmc.svm
Classes
LinearSVMWeights
SVM
mvpa.clfs.model_selector
ModelSelector
mvpa.clfs.plr
PLR
mvpa.clfs.ridge
RidgeReg
mvpa.clfs.sg
mvpa.clfs.sg.sens
LinearSVMWeights
mvpa.clfs.sg.svm
SVM
mvpa.clfs.smlr
Classes
SMLR
SMLRWeights
mvpa.clfs.stats
Classes
AdaptiveNormal
AdaptiveNullDist
AdaptiveRDist
FixedNullDist
MCNullDist
Nonparametric
NullDist
Functions
mvpa.clfs.svm
mvpa.clfs.transerror
Classes
ClassifierError
ConfusionBasedError
ConfusionMatrix
ROCCurve
RegressionStatistics
SummaryStatistics
TransferError
mvpa.clfs.warehouse
Warehouse
Measures: Searchlights and Sensitivties
mvpa.measures
mvpa.measures.anova
OneWayAnova
mvpa.measures.base
Classes
BoostedClassifierSensitivityAnalyzer
CombinedFeaturewiseDatasetMeasure
DatasetMeasure
FeaturewiseDatasetMeasure
MappedClassifierSensitivityAnalyzer
ProxyClassifierSensitivityAnalyzer
Sensitivity
StaticDatasetMeasure
mvpa.measures.corrcoef
CorrCoef
mvpa.measures.irelief
Classes
IterativeRelief
IterativeReliefOnline
IterativeReliefOnline_Devel
IterativeRelief_Devel
mvpa.measures.noiseperturbation
NoisePerturbationSensitivity
mvpa.measures.pls
Classes
PLS
TaskPLS
mvpa.measures.searchlight
Searchlight
mvpa.measures.splitmeasure
SplitFeaturewiseMeasure
Feature Selection
mvpa.featsel
mvpa.featsel.base
Classes
FeatureSelection
FeatureSelectionPipeline
SensitivityBasedFeatureSelection
mvpa.featsel.helpers
Classes
BestDetector
ElementSelector
FixedErrorThresholdStopCrit
FixedNElementTailSelector
FractionTailSelector
MultiStopCrit
NBackHistoryStopCrit
NStepsStopCrit
RangeElementSelector
StoppingCriterion
TailSelector
mvpa.featsel.ifs
IFS
mvpa.featsel.rfe
RFE
Additional Algorithms
mvpa.algorithms
mvpa.algorithms.cvtranserror
CrossValidatedTransferError
Common Facilities
mvpa.base
Module Organization
WarningLog
mvpa.base.config
ConfigManager
mvpa.base.dochelpers
Functions
mvpa.base.externals
Functions
mvpa.base.verbosity
Classes
LevelLogger
Logger
OnceLogger
SetLogger
Miscellaneous
mvpa.misc
mvpa.misc.args
Functions
mvpa.misc.bv
mvpa.misc.bv.base
BrainVoyagerRTC
mvpa.misc.cmdline
Classes
OptionGroups
Options
mvpa.misc.data_generators
Functions
mvpa.misc.errorfx
Classes
AUCErrorFx
MeanMismatchErrorFx
RMSErrorFx
RelativeRMSErrorFx
Variance1SVFx
Functions
mvpa.misc.exceptions
Classes
ConvergenceError
DatasetError
InvalidHyperparameterError
UnknownStateError
mvpa.misc.fsl
mvpa.misc.fsl.base
Classes
FslEV3
McFlirtParams
mvpa.misc.fsl.flobs
mvpa.misc.fsl.melodic
MelodicResults
mvpa.misc.fx
Functions
mvpa.misc.io
mvpa.misc.io.base
Classes
ColumnData
DataReader
SampleAttributes
SensorLocations
TuebingenMEGSensorLocations
XAVRSensorLocations
Functions
mvpa.misc.io.eepbin
EEPBin
mvpa.misc.io.hamster
Hamster
mvpa.misc.io.meg
TuebingenMEG
mvpa.misc.param
Classes
KernelParameter
Parameter
mvpa.misc.plot
mvpa.misc.plot.base
Functions
mvpa.misc.plot.erp
Functions
mvpa.misc.plot.topo
Functions
mvpa.misc.state
Classes
AttributeWithUnique
AttributesCollector
ClassWithCollections
CollectableAttribute
Collection
DatasetAttribute
FeatureAttribute
Harvestable
ParameterCollection
SampleAttribute
SampleAttributesCollection
StateCollection
StateVariable
mvpa.misc.stats
mvpa.misc.support
Classes
Event
Harvester
HarvesterCall
MapOverlap
Functions
mvpa.misc.transformers
Class
OverAxis
Functions
mvpa.misc.vproperty
VProperty
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