`fsleyes.plotting.timeseries`¶

This module provides a number of DataSeries sub-classes which are use by the TimeSeriesPanel. The following classes are provided:

`TimeSeries`	Encapsulates time series data from an overlay.
`VoxelTimeSeries`	A `TimeSeries` sub-class which encapsulates data from a specific voxel of a `Image` overlay.
`FEATTimeSeries`	A `VoxelTimeSeries` class for use with `FEATImage` instances, containing some extra FEAT specific options.
`FEATPartialFitTimeSeries`	A `VoxelTimeSeries` class which represents the partial model fit of an EV or contrast from a FEAT analysis at a specific voxel.
`FEATEVTimeSeries`	A `TimeSeries` class which represents the time course of an EV from a FEAT analysis.
`FEATResidualTimeSeries`	A `VoxelTimeSeries` class which represents the time course of the residuals from a FEAT analysis at a specific voxel.
`FEATModelFitTimeSeries`	A `TimeSeries` class which represents the time course for a model fit from a FEAT analysis at a specific voxel.
`MelodicTimeSeries`	A `TimeSeries` class which encapsulates the time course for one component of a `MelodicImage`.
`MeshTimeSeries`	A `MeshTimeSeries` object encapsulates the time course for a `Mesh` overlay which has some time series vertex data associated with it.

class fsleyes.plotting.timeseries.TimeSeries(overlay, overlayList, displayCtx, plotPanel)¶

Bases: fsleyes.plotting.dataseries.DataSeries

Encapsulates time series data from an overlay. The TimeSeries class is the base-class for all other classes in this module - its getData() method implements some pre-processing routines which are required by the TimeSeriesPanel.

The following methods are intended to be overridden and/or called by sub-class implementations:

`makeLabel`	Return a label for this `TimeSeries`.
`getData`	Overrides `DataSeries.getData()`.

__init__(overlay, overlayList, displayCtx, plotPanel)¶

Create a TimeSeries instance.

Parameters:	overlay – The overlay to extract the data from. overlayList – The `OverlayList` instance. displayCtx – The `DisplayContext` instance. plotPanel – The `TimeSeriesPanel` which owns this `TimeSeries`.

makeLabel()¶: Return a label for this TimeSeries.

getData(xdata=None, ydata=None)¶

Overrides DataSeries.getData(). Returns the data associated with this TimeSeries instance.

The xdata and ydata arguments may be used by sub-classes to override the x/y data in the event that they have already performed some processing on the data. The default implementation returns whatever has been set through DataSeries.setData().

__module__ = 'fsleyes.plotting.timeseries'¶

class fsleyes.plotting.timeseries.VoxelTimeSeries(overlay, overlayList, displayCtx, plotPanel)¶

Bases: fsleyes.plotting.timeseries.TimeSeries

A TimeSeries sub-class which encapsulates data from a specific voxel of a Image overlay.

The voxel data may be accessed through the getData() method, where the voxel is defined by current value of the DisplayContext.location property (transformed into the image voxel coordinate system).

__init__(overlay, overlayList, displayCtx, plotPanel)¶

Create a VoxelTimeSeries instance.

Parameters:	overlay – The `Image` instance to extract the data from. overlayList – The `OverlayList` instance. displayCtx – The `DisplayContext` instance. plotPanel – The `TimeSeriesPanel` which owns this `VoxelTimeSeries`.

makeLabel()¶: Returns a string representation of this VoxelTimeSeries instance.

getData = <MagicMock name='mock.utils.idle.mutex()' id='139845839620640'>¶

__module__ = 'fsleyes.plotting.timeseries'¶

class fsleyes.plotting.timeseries.FEATTimeSeries(*args, **kwargs)¶

Bases: fsleyes.plotting.timeseries.VoxelTimeSeries

A VoxelTimeSeries class for use with FEATImage instances, containing some extra FEAT specific options.

The FEATTimeSeries class acts as a container for several TimeSeries instances, each of which represent some part of a FEAT analysis. Therefore, the data returned by a call to TimeSeries.getData() on a FEATTimeSeries instance should not be plotted.

Instead, the getModelTimeSeries() method should be used to retrieve a list of all the TimeSeries instances which are associated with the FEATTimeSeries instance - all of these TimeSeries instances should be plotted instead.

For example, if the plotData and plotFullModelFit settings are True, the getModelTimeSeries() method will return a list containing two TimeSeries instances - one which will return the FEAT analysis input data, and another which will return the full model fit, for the voxel in question.

Note

The getData method of a FEATTimeSeries instance will return the FEAT input data. Therefore, when plotData is True, the FEATTimeSeries instance will itself be included in the list returned by getModelTimeSeries().

The following classes are used to represent the various parts of a FEAT analysis:

`FEATEVTimeSeries`	A `TimeSeries` class which represents the time course of an EV from a FEAT analysis.
`FEATResidualTimeSeries`	A `VoxelTimeSeries` class which represents the time course of the residuals from a FEAT analysis at a specific voxel.
`FEATPartialFitTimeSeries`	A `VoxelTimeSeries` class which represents the partial model fit of an EV or contrast from a FEAT analysis at a specific voxel.
`FEATModelFitTimeSeries`	A `TimeSeries` class which represents the time course for a model fit from a FEAT analysis at a specific voxel.

plotData = <MagicMock name='mock.Boolean()' id='139845844115072'>¶: If True, the FEAT input data is plotted.

plotResiduals = <MagicMock name='mock.Boolean()' id='139845844115072'>¶: If True, the FEAT model residuals are plotted.

plotEVs = <MagicMock name='mock.List()' id='139845843011176'>¶: A list of Boolean properties, one for each EV in the FEAT analysis. For elements that are True, the corresponding FEAT EV time course is plotted.

plotPEFits = <MagicMock name='mock.List()' id='139845843011176'>¶: A list of Boolean properties, one for each EV in the FEAT analysis. For elements that are True, the model fit for the corresponding FEAT EV is plotted.

plotCOPEFits = <MagicMock name='mock.List()' id='139845843011176'>¶: A list of Boolean properties, one for each EV in the FEAT analysis. For elements that are True, the model fit for the corresponding FEAT contrast is plotted.

plotPartial = <MagicMock name='mock.Choice()' id='139845843612560'>¶: Plot the raw data, after regression against a chosen EV or contrast. The options are populated in the __init__() method.

__init__(*args, **kwargs)¶

Create a FEATTimeSeries.

All arguments are passed through to the VoxelTimeSeries constructor.

plotFullModelFit = <MagicMock name='mock.Boolean()' id='139845844115072'>¶: If True, the FEAT full model fit is plotted.

getModelTimeSeries()¶: Returns a list containing all of the TimeSeries instances which should be plotted in place of this FEATTimeSeries.

_FEATTimeSeries__createModelTs(tsType, *args, **kwargs)¶

Creates a TimeSeries instance of the given tsType, and sets its display settings according to those of this FEATTimeSeries.

Parameters:	tsType – The type to create, e.g. `FEATModelFitTimeSeries`, `FEATEVTimeSeries`, etc. args – Passed to the `tsType` constructor. kwargs – Passed to the `tsType` constructor.

_FEATTimeSeries__getContrast(fitType, idx)¶

Returns a contrast vector for the given model fit type, and index.

Parameters:	fitType – either `'full'`, `'pe'`, or `'cope'`. If `'full'`, the `idx` argument is ignored. idx – The EV or contrast index for `'pe'` or `'cope'` model fits.

_FEATTimeSeries__plotCOPEFitChanged(*a)¶

Called when the plotCOPEFits setting changes.

If necessary, creates and caches one or more FEATModelFitTimeSeries instances.

_FEATTimeSeries__plotEVChanged(*a)¶

Called when the plotEVs setting changes.

If necessary, creates and caches one or more FEATEVTimeSeries instances.

_FEATTimeSeries__plotFullModelFitChanged(*a)¶

Called when the plotFullModelFit setting changes.

If necessary, creates and caches a FEATModelFitTimeSeries instance.

_FEATTimeSeries__plotPEFitChanged(*a)¶

Called when the plotPEFits setting changes.

If necessary, creates and caches one or more FEATModelFitTimeSeries instances.

_FEATTimeSeries__plotPartialChanged(*a)¶

Called when the plotPartial setting changes.

If necessary, creates and caches a FEATPartialFitTimeSeries instance.

_FEATTimeSeries__plotResidualsChanged(*a)¶

Called when the plotResiduals setting changes.

If necessary, creates and caches a FEATResidualTimeSeries instance.

__module__ = 'fsleyes.plotting.timeseries'¶

class fsleyes.plotting.timeseries.FEATPartialFitTimeSeries(overlay, overlayList, displayCtx, plotPanel, parentTs, contrast, fitType, idx)¶

Bases: fsleyes.plotting.timeseries.VoxelTimeSeries

A VoxelTimeSeries class which represents the partial model fit of an EV or contrast from a FEAT analysis at a specific voxel. Instances of this class are created by the FEATTimeSeries class.

__init__(overlay, overlayList, displayCtx, plotPanel, parentTs, contrast, fitType, idx)¶

Create a FEATPartialFitTimeSeries.

Parameters:

overlay – The FEATImage instance to extract the data from.
overlayList – The OverlayList instance.
displayCtx – The DisplayContext instance.
plotPanel – The TimeSeriesPanel which owns this FEATPartialFitTimeSeries.
parentTs – The FEATTimeSeries instance that has created this FEATPartialFitTimeSeries.
contrast – The contrast vector to calculate the partial model fit for.
fitType – The model fit type, either 'full', 'pe' or 'cope'.
idx – If the model fit type is 'pe' or 'cope', the EV/contrast index.

getData()¶

Returns the partial model fit for the voxel and model fit type specified in the constructop.

See the FEATImage.partialFit() method.

__module__ = 'fsleyes.plotting.timeseries'¶

class fsleyes.plotting.timeseries.FEATEVTimeSeries(overlay, overlayList, displayCtx, plotPanel, parentTs, idx)¶

Bases: fsleyes.plotting.timeseries.TimeSeries

A TimeSeries class which represents the time course of an EV from a FEAT analysis. Instances of this class are created by the FEATTimeSeries class.

__init__(overlay, overlayList, displayCtx, plotPanel, parentTs, idx)¶

Create a FEATEVTimeSeries.

Parameters:	overlay – The `FEATImage` instance to extract the data from. overlayList – The `OverlayList` instance. displayCtx – The `DisplayContext` instance. plotPanel – The `TimeSeriesPanel` which owns this `FEATEVTimeSeries`. parentTs – The `FEATTimeSeries` instance that has created this `FEATEVTimeSeries`. idx – The EV index.

makeLabel()¶: Returns a string representation of this FEATEVTimeSeries instance.

getData()¶: Returns the time course of the EV specified in the constructor.

__module__ = 'fsleyes.plotting.timeseries'¶

class fsleyes.plotting.timeseries.FEATResidualTimeSeries(overlay, overlayList, displayCtx, plotPanel, parentTs)¶

Bases: fsleyes.plotting.timeseries.VoxelTimeSeries

A VoxelTimeSeries class which represents the time course of the residuals from a FEAT analysis at a specific voxel. Instances of this class are created by the FEATTimeSeries class.

__init__(overlay, overlayList, displayCtx, plotPanel, parentTs)¶

Create a FEATResidualTimeSeries.

Parameters:	overlay – The `FEATImage` instance to extract the data from. overlayList – The `OverlayList` instance. displayCtx – The `DisplayContext` instance. plotPanel – The `TimeSeriesPanel` which owns this `FEATResidualTimeSeries`. parentTs – The `FEATTimeSeries` instance that has created this `FEATResidualTimeSeries`.

makeLabel()¶: Returns a string representation of this FEATResidualTimeSeries instance.

getData()¶: Returns the residuals for the current voxel.

__module__ = 'fsleyes.plotting.timeseries'¶

class fsleyes.plotting.timeseries.FEATModelFitTimeSeries(overlay, overlayList, displayCtx, plotPanel, parentTs, contrast, fitType, idx)¶

Bases: fsleyes.plotting.timeseries.VoxelTimeSeries

A TimeSeries class which represents the time course for a model fit from a FEAT analysis at a specific voxel. Instances of this class are created by the FEATTimeSeries class.

__init__(overlay, overlayList, displayCtx, plotPanel, parentTs, contrast, fitType, idx)¶

Create a FEATModelFitTimeSeries.

Parameters:

overlay – The FEATImage instance to extract the data from.
overlayList – The OverlayList instance.
displayCtx – The DisplayContext instance.
plotPanel – The TimeSeriesPanel which owns this FEATModelFitTimeSeries.
parentTs – The FEATTimeSeries instance that has created this FEATModelFitTimeSeries.
contrast – The contrast vector to calculate the partial model fit for.
fitType – The model fit type, either 'full', 'pe' or 'cope'.
idx – If the model fit type is 'pe' or 'cope',

makeLabel()¶: Returns a string representation of this FEATModelFitTimeSeries instance.

getData()¶: Returns the FEAT model fit at the current voxel.

__module__ = 'fsleyes.plotting.timeseries'¶

class fsleyes.plotting.timeseries.MelodicTimeSeries(overlay, overlayList, displayCtx, plotPanel)¶

Bases: fsleyes.plotting.timeseries.TimeSeries

A TimeSeries class which encapsulates the time course for one component of a MelodicImage. The getData() method returns the time course of the component specified by the current NiftiOpts.volume.

__init__(overlay, overlayList, displayCtx, plotPanel)¶

Create a MelodicTimeSeries.

Parameters:	overlay – A `MelodicImage` overlay. overlayList – The `OverlayList` instance. displayCtx – The `DisplayContext` instance. plotPanel – The `TimeSeriesPanel` which owns this `MelodicTimeSeries`.

__module__ = 'fsleyes.plotting.timeseries'¶

getComponent()¶: Returns the index (starting from 0) of the current Melodic component, as dictated by the NiftiOpts.volume property.

makeLabel()¶: Returns a string representation of this MelodicTimeSeries.

getData()¶: Returns the time course of the current Melodic component.

class fsleyes.plotting.timeseries.MeshTimeSeries(overlay, overlayList, displayCtx, plotPanel)¶

Bases: fsleyes.plotting.timeseries.TimeSeries

A MeshTimeSeries object encapsulates the time course for a Mesh overlay which has some time series vertex data associated with it. See the MeshOpts.vertexData property.

_MeshTimeSeries__haveData()¶: Returns True if there is currently time series data to show for this MeshTimeSeries, False otherwise.

__module__ = 'fsleyes.plotting.timeseries'¶

__init__(overlay, overlayList, displayCtx, plotPanel)¶

Create a MeshTimeSeries instance.

Parameters:	overlay – The `Mesh` instance to extract the data from. overlayList – The `OverlayList` instance. displayCtx – The `DisplayContext` instance. plotPanel – The `TimeSeriesPanel` which owns this `TimeSeries`.

makeLabel()¶: Returns a label to use for this MeshTimeSeries on the legend.

getData(xdata=None, ydata=None)¶: Returns the data at the current location for the Mesh, or [], [] if there is no data.

fsleyes.plotting.timeseries¶

`fsleyes.plotting.timeseries`¶