Multivariate Pattern Analysis in Python
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This content refers to the previous stable release of PyMVPA. Please visit
www.pymvpa.org
for the most recent version of PyMVPA and its documentation.
PyMVPA Documentation Contents
ΒΆ
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.libsvmc.svmc
Module:
clfs.libsvmc.svmc
Classes
svm_model
svm_parameter
svm_problem
Functions
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
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