fsleyes.plotting.timeseries
¶
This module provides a number of DataSeries
sub-classes which
are use by the TimeSeriesPanel
. The following classes are provided:
Encapsulates time series data from an overlay. |
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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 - itsgetData()
method implements some pre-processing routines which are required by theTimeSeriesPanel
.The following methods are intended to be overridden and/or called by sub-class implementations:
Return a label for this
TimeSeries
.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 thisTimeSeries
.
-
makeLabel
()¶ Return a label for this
TimeSeries
.
-
getData
(xdata=None, ydata=None)¶ Overrides
DataSeries.getData()
. Returns the data associated with thisTimeSeries
instance.The
xdata
andydata
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 throughDataSeries.setData()
.
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__module__
= 'fsleyes.plotting.timeseries'¶
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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 aImage
overlay.The voxel data may be accessed through the
getData()
method, where the voxel is defined by current value of theDisplayContext.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 thisVoxelTimeSeries
.
-
makeLabel
()¶ Returns a string representation of this
VoxelTimeSeries
instance.
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getData
= <MagicMock name='mock.utils.idle.mutex()' id='140736143971344'>¶
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__module__
= 'fsleyes.plotting.timeseries'¶
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class
fsleyes.plotting.timeseries.
FEATTimeSeries
(*args, **kwargs)¶ Bases:
fsleyes.plotting.timeseries.VoxelTimeSeries
A
VoxelTimeSeries
class for use withFEATImage
instances, containing some extra FEAT specific options.The
FEATTimeSeries
class acts as a container for severalTimeSeries
instances, each of which represent some part of a FEAT analysis. Therefore, the data returned by a call toTimeSeries.getData()
on aFEATTimeSeries
instance should not be plotted.Instead, the
getModelTimeSeries()
method should be used to retrieve a list of all theTimeSeries
instances which are associated with theFEATTimeSeries
instance - all of theseTimeSeries
instances should be plotted instead.For example, if the
plotData
andplotFullModelFit
settings areTrue
, thegetModelTimeSeries()
method will return a list containing twoTimeSeries
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 aFEATTimeSeries
instance will return the FEAT input data. Therefore, whenplotData
isTrue
, theFEATTimeSeries
instance will itself be included in the list returned bygetModelTimeSeries()
.The following classes are used to represent the various parts of a FEAT analysis:
A
TimeSeries
class which represents the time course of an EV from a FEAT analysis.A
VoxelTimeSeries
class which represents the time course of the residuals from a FEAT analysis at a specific voxel.A
VoxelTimeSeries
class which represents the partial model fit of an EV or contrast from a FEAT analysis at a specific voxel.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='140736147064976'>¶ If
True
, the FEAT input data is plotted.
-
plotResiduals
= <MagicMock name='mock.Boolean()' id='140736147064976'>¶ If
True
, the FEAT model residuals are plotted.
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plotEVs
= <MagicMock name='mock.List()' id='140736143989392'>¶ A list of
Boolean
properties, one for each EV in the FEAT analysis. For elements that areTrue
, the corresponding FEAT EV time course is plotted.
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plotPEFits
= <MagicMock name='mock.List()' id='140736143989392'>¶ A list of
Boolean
properties, one for each EV in the FEAT analysis. For elements that areTrue
, the model fit for the corresponding FEAT EV is plotted.
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plotCOPEFits
= <MagicMock name='mock.List()' id='140736143989392'>¶ A list of
Boolean
properties, one for each EV in the FEAT analysis. For elements that areTrue
, the model fit for the corresponding FEAT contrast is plotted.
-
plotPartial
= <MagicMock name='mock.Choice()' id='140736145814032'>¶ 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='140736147064976'>¶ 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 thisFEATTimeSeries
.
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_FEATTimeSeries__createModelTs
(tsType, *args, **kwargs)¶ Creates a
TimeSeries
instance of the giventsType
, and sets its display settings according to those of thisFEATTimeSeries
.- 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'
, theidx
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.
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__module__
= 'fsleyes.plotting.timeseries'¶
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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 theFEATTimeSeries
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 thisFEATPartialFitTimeSeries
.parentTs – The
FEATTimeSeries
instance that has created thisFEATPartialFitTimeSeries
.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.
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__module__
= 'fsleyes.plotting.timeseries'¶
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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 theFEATTimeSeries
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 thisFEATEVTimeSeries
.parentTs – The
FEATTimeSeries
instance that has created thisFEATEVTimeSeries
.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.
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__module__
= 'fsleyes.plotting.timeseries'¶
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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 theFEATTimeSeries
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 thisFEATResidualTimeSeries
.parentTs – The
FEATTimeSeries
instance that has created thisFEATResidualTimeSeries
.
-
makeLabel
()¶ Returns a string representation of this
FEATResidualTimeSeries
instance.
-
getData
()¶ Returns the residuals for the current voxel.
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__module__
= 'fsleyes.plotting.timeseries'¶
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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 theFEATTimeSeries
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 thisFEATModelFitTimeSeries
.parentTs – The
FEATTimeSeries
instance that has created thisFEATModelFitTimeSeries
.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.
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getData
()¶ Returns the FEAT model fit at the current voxel.
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__module__
= 'fsleyes.plotting.timeseries'¶
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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 aMelodicImage
. ThegetData()
method returns the time course of the component specified by the currentNiftiOpts.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 thisMelodicTimeSeries
.
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__module__
= 'fsleyes.plotting.timeseries'¶
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getComponent
()¶ Returns the index (starting from 0) of the current Melodic component, as dictated by the
NiftiOpts.volume
property.
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makeLabel
()¶ Returns a string representation of this
MelodicTimeSeries
.
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getData
()¶ Returns the time course of the current Melodic component.
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class
fsleyes.plotting.timeseries.
MeshTimeSeries
(overlay, overlayList, displayCtx, plotPanel)¶ Bases:
fsleyes.plotting.timeseries.TimeSeries
A
MeshTimeSeries
object encapsulates the time course for aMesh
overlay which has some time series vertex data associated with it. See theMeshOpts.vertexData
property.-
_MeshTimeSeries__haveData
()¶ Returns
True
if there is currently time series data to show for thisMeshTimeSeries
,False
otherwise.
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__module__
= 'fsleyes.plotting.timeseries'¶
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__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 thisTimeSeries
.
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makeLabel
()¶ Returns a label to use for this
MeshTimeSeries
on the legend.
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getData
(xdata=None, ydata=None)¶ Returns the data at the current location for the
Mesh
, or[], []
if there is no data.
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