API

Release:0.1 Date:September 08, 2010

• algorithms.diagnostics.screens
  • Module: algorithms.diagnostics.screens
  • Functions
• algorithms.diagnostics.timediff
  • Module: algorithms.diagnostics.timediff
• algorithms.diagnostics.tsdiffplot
  • Module: algorithms.diagnostics.tsdiffplot
  • Functions
• algorithms.fwhm
  • Module: algorithms.fwhm
  • Classes
    • ReselImage
    • Resels
• algorithms.interpolation
  • Module: algorithms.interpolation
  • ImageInterpolator
• algorithms.kernel_smooth
  • Module: algorithms.kernel_smooth
  • Class
  • LinearFilter
  • Functions
• algorithms.resample
  • Module: algorithms.resample
  • Functions
• algorithms.statistics.classification
  • Module: algorithms.statistics.classification
  • Classifier
• algorithms.statistics.nlsmodel
  • Module: algorithms.statistics.nlsmodel
  • NLSModel
• algorithms.statistics.onesample
  • Module: algorithms.statistics.onesample
  • Functions
• algorithms.statistics.regression
  • Module: algorithms.statistics.regression
  • Classes
    • AREstimator
    • ArrayOutput
    • RegressionOutput
    • RegressionOutputList
    • TOutput
  • Functions
• algorithms.statistics.rft
  • Module: algorithms.statistics.rft
  • Classes
    • ChiBarSquared
    • ChiSquared
    • ECcone
    • ECquasi
    • FStat
    • Hotelling
    • IntrinsicVolumes
    • MultilinearForm
    • OneSidedF
    • Roy
    • TStat
    • fnsum
  • Functions
• algorithms.statistics.utils
  • Module: algorithms.statistics.utils
  • Functions
• core.image.affine_image
  • Module: core.image.affine_image
  • AffineImage
• core.image.generators
  • Module: core.image.generators
  • Functions
• core.image.image
  • Module: core.image.image
  • Classes
    • Image
    • SliceMaker
  • Functions
• core.image.image_list
  • Module: core.image.image_list
  • ImageList
• core.image.roi
  • Module: core.image.roi
  • Classes
    • ContinuousROI
    • CoordinateMapROI
    • DiscreteROI
    • ROI
    • ROISequence
    • ROIall
  • Functions
• core.image.xyz_image
  • Module: core.image.xyz_image
  • Classes
    • XYZImage
    • XYZTransform
  • Function
• core.reference.array_coords
  • Module: core.reference.array_coords
  • Classes
    • ArrayCoordMap
    • Grid
• core.reference.coordinate_map
  • Module: core.reference.coordinate_map
    • Common API
    • Operations on mappings (module level functions)
  • Classes
    • AffineTransform
    • CoordinateMap
  • Functions
• core.reference.coordinate_system
  • Module: core.reference.coordinate_system
  • Class
  • CoordinateSystem
  • Functions
• core.reference.slices
  • Module: core.reference.slices
  • Functions
• core.transforms.affines
  • Module: core.transforms.affines
  • Functions
• interfaces.matlab
  • Module: interfaces.matlab
  • Functions
• interfaces.spm
  • Module: interfaces.spm
  • Class
  • SpmInfo
  • Functions
• io.files
  • Module: io.files
    • Examples
  • Functions
• io.imageformats.analyze
  • Module: io.imageformats.analyze
    • Header checking
  • Classes
    • AnalyzeHeader
    • AnalyzeImage
• io.imageformats.batteryrunners
  • Module: io.imageformats.batteryrunners
  • Classes
    • BatteryRunner
    • Report
• io.imageformats.binaryheaders
  • Module: io.imageformats.binaryheaders
  • BinaryHeader
• io.imageformats.compat
  • Module: io.imageformats.compat
  • NiftiImage
• io.imageformats.eulerangles
  • Module: io.imageformats.eulerangles
  • Functions
• io.imageformats.filename_parser
  • Module: io.imageformats.filename_parser
  • Class
  • TypesFilenamesError
  • Functions
• io.imageformats.filetuples
  • Module: io.imageformats.filetuples
  • Classes
    • FileTuples
    • FileTuplesError
• io.imageformats.funcs
  • Module: io.imageformats.funcs
  • Functions
• io.imageformats.header_ufuncs
  • Module: io.imageformats.header_ufuncs
  • Functions
• io.imageformats.headers
  • Module: io.imageformats.headers
  • Header
• io.imageformats.loadsave
  • Module: io.imageformats.loadsave
  • Functions
• io.imageformats.minc
  • Module: io.imageformats.minc
  • Classes
    • MincError
    • MincHeader
    • MincImage
    • netcdf_fileobj
• io.imageformats.nifti1
  • Module: io.imageformats.nifti1
  • Classes
    • Nifti1Extension
    • Nifti1Extensions
    • Nifti1Header
    • Nifti1Image
• io.imageformats.orientations
  • Module: io.imageformats.orientations
  • Class
  • OrientationError
  • Functions
• io.imageformats.quaternions
  • Module: io.imageformats.quaternions
  • Functions
• io.imageformats.spatialimages
  • Module: io.imageformats.spatialimages
    • There are several ways of writing data.
  • SpatialImage
• io.imageformats.spm2analyze
  • Module: io.imageformats.spm2analyze
  • Classes
    • Spm2AnalyzeHeader
    • Spm2AnalyzeImage
• io.imageformats.spm99analyze
  • Module: io.imageformats.spm99analyze
  • Classes
    • Spm99AnalyzeHeader
    • Spm99AnalyzeImage
    • SpmAnalyzeHeader
• io.imageformats.testing.lightunit
  • Module: io.imageformats.testing.lightunit
    • Authors
• io.imageformats.testing.nosepatch
  • Module: io.imageformats.testing.nosepatch
• io.imageformats.volumeutils
  • Module: io.imageformats.volumeutils
  • Classes
    • HeaderDataError
    • HeaderTypeError
    • Recoder
    • UnsupportedDataType
  • Functions
• io.nifti_ref
  • Module: io.nifti_ref
    • Axes:
  • Functions
• modalities.fmri.design
  • Module: modalities.fmri.design
  • Functions
• modalities.fmri.fmri
  • Module: modalities.fmri.fmri
  • FmriImageList
• modalities.fmri.fmristat.delay
  • Module: modalities.fmri.fmristat.delay
  • Contrast
• modalities.fmri.fmristat.hrf
  • Module: modalities.fmri.fmristat.hrf
    • References
  • Functions
• modalities.fmri.fmristat.invert
  • Module: modalities.fmri.fmristat.invert
• modalities.fmri.fmristat.model
  • Module: modalities.fmri.fmristat.model
  • Classes
    • AR1
    • ModelOutputImage
    • OLS
  • Functions
• modalities.fmri.fmristat.utils
  • Module: modalities.fmri.fmristat.utils
  • WholeBrainNormalize
• modalities.fmri.formula
  • Module: modalities.fmri.formula
    • Formula objects
  • Classes
    • Beta
    • Factor
    • FactorTerm
    • Formula
    • RandomEffects
    • Term
  • Functions
• modalities.fmri.hrf
  • Module: modalities.fmri.hrf
  • Functions
• modalities.fmri.pca
  • Module: modalities.fmri.pca
  • Functions
• modalities.fmri.spm.correlation
  • Module: modalities.fmri.spm.correlation
  • Functions
• modalities.fmri.spm.model
  • Module: modalities.fmri.spm.model
  • Class
  • SecondStage
  • Functions
• modalities.fmri.spm.reml
  • Module: modalities.fmri.spm.reml
  • Functions
• modalities.fmri.spm.trace
  • Module: modalities.fmri.spm.trace
• modalities.fmri.utils
  • Module: modalities.fmri.utils
  • Functions
• neurospin.clustering.bgmm
  • Module: neurospin.clustering.bgmm
  • Classes
    • BGMM
    • VBGMM
  • Functions
• neurospin.clustering.bootstrap_hc
  • Module: neurospin.clustering.bootstrap_hc
  • Functions
• neurospin.clustering.clustering
  • Module: neurospin.clustering.clustering
  • Functions
• neurospin.clustering.ggmixture
  • Module: neurospin.clustering.ggmixture
  • Classes
    • GGGM
    • GGM
    • Gamma
• neurospin.clustering.gmm
  • Module: neurospin.clustering.gmm
  • Classes
    • GMM
    • grid_descriptor
  • Functions
• neurospin.clustering.hierarchical_clustering
  • Module: neurospin.clustering.hierarchical_clustering
  • Class
  • WeightedForest
  • Functions
• neurospin.datasets.converters
  • Module: neurospin.datasets.converters
  • Functions
• neurospin.datasets.transforms.affine_transform
  • Module: neurospin.datasets.transforms.affine_transform
  • AffineTransform
• neurospin.datasets.transforms.affine_utils
  • Module: neurospin.datasets.transforms.affine_utils
  • Functions
• neurospin.datasets.transforms.transform
  • Module: neurospin.datasets.transforms.transform
  • Classes
    • CompositionError
    • Transform
• neurospin.datasets.volumes.volume_data
  • Module: neurospin.datasets.volumes.volume_data
  • VolumeData
• neurospin.datasets.volumes.volume_field
  • Module: neurospin.datasets.volumes.volume_field
  • VolumeField
• neurospin.datasets.volumes.volume_grid
  • Module: neurospin.datasets.volumes.volume_grid
  • VolumeGrid
• neurospin.datasets.volumes.volume_img
  • Module: neurospin.datasets.volumes.volume_img
  • VolumeImg
• neurospin.eda.dimension_reduction
  • Module: neurospin.eda.dimension_reduction
  • Classes
    • MDS
    • NLDR
    • PCA
    • eps_Isomap
    • knn_Isomap
    • knn_LE
    • knn_LPP
  • Functions
• neurospin.glm.glm
  • Module: neurospin.glm.glm
  • Classes
    • contrast
    • glm
  • Functions
• neurospin.graph.BPmatch
  • Module: neurospin.graph.BPmatch
  • Functions
• neurospin.graph.field
  • Module: neurospin.graph.field
  • Field
• neurospin.graph.forest
  • Module: neurospin.graph.forest
  • Forest
• neurospin.graph.graph
  • Module: neurospin.graph.graph
  • Classes
    • BipartiteGraph
    • Graph
    • WeightedGraph
  • Function
• neurospin.group.displacement_field
  • Module: neurospin.group.displacement_field
  • Classes
    • displacement_field
    • gaussian_random_field
  • Functions
• neurospin.group.permutation_test
  • Module: neurospin.group.permutation_test
  • Classes
    • permutation_test
    • permutation_test_onesample
    • permutation_test_onesample_graph
    • permutation_test_twosample
  • Functions
• neurospin.group.spatial_relaxation_onesample
  • Module: neurospin.group.spatial_relaxation_onesample
  • Class
  • multivariate_stat
  • Functions
• neurospin.image.image
  • Module: neurospin.image.image
  • Classes
    • Image
    • MaskedImage
  • Functions
• neurospin.registration.affine
  • Module: neurospin.registration.affine
  • Classes
    • Affine
    • Rigid
    • Similarity
  • Functions
• neurospin.registration.grid_transform
  • Module: neurospin.registration.grid_transform
  • Classes
    • GridTransform
    • SplineTransform
• neurospin.registration.iconic_registration
  • Module: neurospin.registration.iconic_registration
  • Class
  • IconicRegistration
  • Functions
• neurospin.registration.registration
  • Module: neurospin.registration.registration
  • Class
  • FmriRealign4d
  • Functions
• neurospin.registration.spacetime_registration
  • Module: neurospin.registration.spacetime_registration
  • Classes
    • Image4d
    • Realign4d
  • Functions
• neurospin.segmentation.vem
  • Module: neurospin.segmentation.vem
  • Class
  • VemTissueClassification
  • Functions
• neurospin.spatial_models.bayesian_structural_analysis
  • Module: neurospin.spatial_models.bayesian_structural_analysis
  • Functions
• neurospin.spatial_models.bsa_io
  • Module: neurospin.spatial_models.bsa_io
• neurospin.spatial_models.hierarchical_parcellation
  • Module: neurospin.spatial_models.hierarchical_parcellation
  • Functions
• neurospin.spatial_models.hroi
  • Module: neurospin.spatial_models.hroi
  • Class
  • NROI
  • Functions
• neurospin.spatial_models.parcel_io
  • Module: neurospin.spatial_models.parcel_io
  • Functions
• neurospin.spatial_models.parcellation
  • Module: neurospin.spatial_models.parcellation
  • Parcellation
• neurospin.spatial_models.roi
  • Module: neurospin.spatial_models.roi
  • Classes
    • DiscreteROI
    • MultiROI
    • MultipleROI
    • ROI
• neurospin.spatial_models.structural_bfls
  • Module: neurospin.spatial_models.structural_bfls
  • Class
  • landmark_regions
  • Functions
• neurospin.statistical_mapping
  • Module: neurospin.statistical_mapping
  • Class
  • LinearModel
  • Functions
• neurospin.utils.design_matrix
  • Module: neurospin.utils.design_matrix
  • Classes
    • BlockParadigm
    • DesignMatrix
    • EventRelatedParadigm
    • Paradigm
  • Functions
• neurospin.utils.emp_null
  • Module: neurospin.utils.emp_null
  • Classes
    • ENN
    • FDR
  • Functions
• neurospin.utils.ffx
  • Module: neurospin.utils.ffx
  • Functions
• neurospin.utils.mask
  • Module: neurospin.utils.mask
  • Functions
• neurospin.utils.optimize
  • Module: neurospin.utils.optimize
• neurospin.utils.random_threshold
  • Module: neurospin.utils.random_threshold
  • Functions
• neurospin.utils.reproducibility_measures
  • Module: neurospin.utils.reproducibility_measures
  • Functions
• neurospin.utils.simul_multisubject_fmri_dataset
  • Module: neurospin.utils.simul_multisubject_fmri_dataset
  • Functions
• neurospin.utils.smoothing
  • Module: neurospin.utils.smoothing
• neurospin.utils.two_binomial_mixture
  • Module: neurospin.utils.two_binomial_mixture
  • TwoBinomialMixture
• neurospin.utils.zscore
  • Module: neurospin.utils.zscore
• neurospin.viz_tools.activation_maps
  • Module: neurospin.viz_tools.activation_maps
  • Functions
• neurospin.viz_tools.anat_cache
  • Module: neurospin.viz_tools.anat_cache
• neurospin.viz_tools.cm
  • Module: neurospin.viz_tools.cm
  • Functions
• neurospin.viz_tools.coord_tools
  • Module: neurospin.viz_tools.coord_tools
  • Functions
• neurospin.viz_tools.maps_3d
  • Module: neurospin.viz_tools.maps_3d
  • Functions
• neurospin.viz_tools.ortho_slicer
  • Module: neurospin.viz_tools.ortho_slicer
  • OrthoSlicer
• testing.decorators
  • Module: testing.decorators
  • Functions
• testing.lightunit
  • Module: testing.lightunit
    • Authors
• testing.nitest
  • Module: testing.nitest
• testing.nosepatch
  • Module: testing.nosepatch
• utils.data
  • Module: utils.data
  • Classes
    • Bomber
    • DataError
    • Datasource
    • VersionedDatasource
  • Functions
• utils.environment
  • Module: utils.environment
  • Functions
• utils.onetime
  • Module: utils.onetime
    • References
  • OneTimeProperty
• utils.perlpie
  • Module: utils.perlpie
    • Parameters
    • Requires
    • Examples
  • Functions
• utils.tmpdirs
  • Module: utils.tmpdirs
  • Classes
    • InTemporaryDirectory
    • TemporaryDirectory