diff --git a/fsl/fsleyes/controls/timeserieslistpanel.py b/fsl/fsleyes/controls/timeserieslistpanel.py
index 86f406b419d320a57fe7a77d97492b1e7f9520ac..c3d500fb48be3bc98aa70c8d1b0947d43b7ea45d 100644
--- a/fsl/fsleyes/controls/timeserieslistpanel.py
+++ b/fsl/fsleyes/controls/timeserieslistpanel.py
@@ -13,12 +13,12 @@
import wx
import numpy as np
-import props
-import pwidgets.elistbox as elistbox
-import fsl.fsleyes.panel as fslpanel
-import fsl.fsleyes.tooltips as fsltooltips
-import fsl.fsleyes.plotting as plotting
-import fsl.data.strings as strings
+import props
+import pwidgets.elistbox as elistbox
+import fsl.fsleyes.panel as fslpanel
+import fsl.fsleyes.tooltips as fsltooltips
+import fsl.fsleyes.plotting.timeseries as timeseries
+import fsl.data.strings as strings
class TimeSeriesListPanel(fslpanel.FSLEyesPanel):
@@ -161,7 +161,7 @@ class TimeSeriesListPanel(fslpanel.FSLEyesPanel):
if ts is None:
return
- if isinstance(ts, plotting.FEATTimeSeries):
+ if isinstance(ts, timeseries.FEATTimeSeries):
toAdd = list(ts.getModelTimeSeries())
else:
toAdd = [ts]
@@ -170,7 +170,9 @@ class TimeSeriesListPanel(fslpanel.FSLEyesPanel):
for ts in toAdd:
- copy = plotting.DataSeries(ts.overlay)
+ copy = timeseries.TimeSeries(self.__tsPanel,
+ overlay,
+ self._displayCtx)
copy.alpha = ts.alpha
copy.lineWidth = ts.lineWidth
@@ -182,7 +184,7 @@ class TimeSeriesListPanel(fslpanel.FSLEyesPanel):
# This is hacky, and is here in order to
# make the __onLIstSelect method work.
- if isinstance(ts, plotting.MelodicTimeSeries):
+ if isinstance(ts, timeseries.MelodicTimeSeries):
copy.tsLoc = 'volume'
copy.coord = ts.getComponent()
else:
diff --git a/fsl/fsleyes/plotting/__init__.py b/fsl/fsleyes/plotting/__init__.py
index 202ec69c2b4bc5ce95c0253311cf5535e021cc00..b991030c900898e40c24d874fd37db05ad17de0a 100644
--- a/fsl/fsleyes/plotting/__init__.py
+++ b/fsl/fsleyes/plotting/__init__.py
@@ -9,7 +9,8 @@ import dataseries
import timeseries
DataSeries = dataseries.DataSeries
-TimeSeries = timeseries.TimeSeries
+TimeSeries = timeseries.TimeSeries
+VoxelTimeSeries = timeseries.VoxelTimeSeries
FEATTimeSeries = timeseries.FEATTimeSeries
FEATPartialFitTimeSeries = timeseries.FEATPartialFitTimeSeries
FEATEVTimeSeries = timeseries.FEATEVTimeSeries
diff --git a/fsl/fsleyes/plotting/timeseries.py b/fsl/fsleyes/plotting/timeseries.py
index c60cfdb9911bd6cd744309971937c5ede849ecb6..8d484aa16aed370f6a7cdb12149774f16aeff847 100644
--- a/fsl/fsleyes/plotting/timeseries.py
+++ b/fsl/fsleyes/plotting/timeseries.py
@@ -11,6 +11,7 @@ are use by the :class:`.TimeSeriesPanel`. The following classes are provided:
:nosignatures:
TimeSeries
+ VoxelTimeSeries
FEATTimeSeries
FEATModelTimeSeries
FEATPartialFitTimeSeries
@@ -20,7 +21,6 @@ are use by the :class:`.TimeSeriesPanel`. The following classes are provided:
MelodicTimeSeries
"""
-import logging
import numpy as np
@@ -30,26 +30,19 @@ import dataseries
import fsl.data.strings as strings
-log = logging.getLogger(__name__)
-
-
class TimeSeries(dataseries.DataSeries):
- """Encapsulates time series data from a specific voxel in an
- :class:`.Image` overlay. The voxel data may be accessed through
- the :meth:`getData` method, where the voxel is defined by the
- :attr:`.DisplayContext.location` property (transformed into the
- image voxel coordinate system).
-
- The ``TimeSeries`` class is the base-class for all other classes
- in this module.
-
- A ``TimeSeries`` instance provides the following methods:
+ """Encapsulates time series data from an overlay. :class:`.Image`
+ overlay. The ``TimeSeries`` class is the base-class for all other classes
+ in this module - its :meth:`getData` method implements some pre-processing
+ routines which are required by the :class:`.TimeSeriesPanel`.
+ The following methods are intended to be overridden and/or called by
+ sub-class implementations:
+
.. autosummary::
:nosignatures:
makeLabel
- getVoxel
getData
"""
@@ -69,9 +62,78 @@ class TimeSeries(dataseries.DataSeries):
self.tsPanel = tsPanel
self.displayCtx = displayCtx
+
+ def makeLabel(self):
+ """Return a label for this ``TimeSeries``. """
+ display = self.displayCtx.getDisplay(self.overlay)
+ return display.name
+
+
+ def getData(self, xdata=None, ydata=None):
+ """Overrides :meth:`.DataSeries.getData`. Returns the data associated
+ with this ``TimeSeries`` instance, pre-processed according to the
+ current :class:`.TimeSeriesPanel` settings.
+
+ 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 :meth:`.DataSeries.setData`.
+ """
+
+ dsXData, dsYData = dataseries.DataSeries.getData(self)
+
+ if xdata is None: xdata = dsXData
+ if ydata is None: ydata = dsYData
+ if xdata is None or len(xdata) == 0: xdata = np.arange(len(ydata))
+
+ xdata = np.array(xdata, dtype=np.float32)
+ ydata = np.array(ydata, dtype=np.float32)
+
+ if self.tsPanel.usePixdim:
+ xdata *= self.overlay.pixdim[3]
+
+ if self.tsPanel.plotMode == 'demean':
+ ydata = ydata - ydata.mean()
+
+ elif self.tsPanel.plotMode == 'normalise':
+ ymin = ydata.min()
+ ymax = ydata.max()
+ ydata = 2 * (ydata - ymin) / (ymax - ymin) - 1
+
+ elif self.tsPanel.plotMode == 'percentChange':
+ mean = ydata.mean()
+ ydata = 100 * (ydata / mean) - 100
+
+ return xdata, ydata
+
+
+class VoxelTimeSeries(TimeSeries):
+ """A :class:`TimeSeries` sub-class which encapsulates data from a
+ specific voxel of a :class:`.Image` overlay.
+ The voxel data may be accessed through the :meth:`getData` method, where
+ the voxel is defined by current value of the
+ :attr:`.DisplayContext.location` property (transformed into the image
+ voxel coordinate system).
+ """
+
+ def __init__(self, tsPanel, overlay, displayCtx):
+ """Create a ``VoxelTimeSeries`` instance.
+
+ :arg tsPanel: The :class:`TimeSeriesPanel` which owns this
+ ``VoxelTimeSeries``.
+
+ :arg overlay: The :class:`.Image` instance to extract the data from.
+
+ :arg displayCtx: The :class:`.DisplayContext`.
+ """
+ TimeSeries.__init__(self, tsPanel, overlay, displayCtx)
+
+
def makeLabel(self):
- """Returns a string representation of this ``TimeSeries`` instance. """
+ """Returns a string representation of this ``VoxelTimeSeries``
+ instance.
+ """
display = self.displayCtx.getDisplay(self.overlay)
coords = self.getVoxel()
@@ -88,7 +150,7 @@ class TimeSeries(dataseries.DataSeries):
def getVoxel(self):
"""Calculates and returns the voxel coordinates corresponding to the
current :attr:`.DisplayContext.location` for the overlay associated
- with this ``TimeSeries``.
+ with this ``VoxelTimeSeries``.
Returns ``None`` if the current location is outside of the image
bounds.
@@ -111,14 +173,11 @@ class TimeSeries(dataseries.DataSeries):
return vox
-
- def getData(self, xdata=None, ydata=None):
- """Overrides :meth:`.DataSeries.getData`. Returns the data associated
- with this ``TimeSeries`` instance.
- The ``xdata`` and ``ydata`` arguments may be used by subclasses to
- override the x/y data in the event that they have already performed
- some processing on the data.
+ def getData(self, xdata=None, ydata=None):
+ """Returns the data at the current voxel location. The ``xdata`` and
+ ``ydata`` parameters may be used by sub-classes to override this
+ default behaviour.
"""
if ydata is None:
@@ -128,32 +187,18 @@ class TimeSeries(dataseries.DataSeries):
return [], []
x, y, z = xyz
- ydata = np.array(self.overlay.data[x, y, z, :], dtype=np.float32)
- if xdata is None:
- xdata = np.arange(len(ydata), dtype=np.float32)
+ ydata = self.overlay.data[x, y, z, :]
- if self.tsPanel.usePixdim:
- xdata *= self.overlay.pixdim[3]
+ if xdata is None:
+ xdata = np.arange(len(ydata))
- if self.tsPanel.plotMode == 'demean':
- ydata = ydata - ydata.mean()
-
- elif self.tsPanel.plotMode == 'normalise':
- ymin = ydata.min()
- ymax = ydata.max()
- ydata = 2 * (ydata - ymin) / (ymax - ymin) - 1
-
- elif self.tsPanel.plotMode == 'percentChange':
- mean = ydata.mean()
- ydata = 100 * (ydata / mean) - 100
-
- return xdata, ydata
+ return TimeSeries.getData(self, xdata=xdata, ydata=ydata)
-class FEATTimeSeries(TimeSeries):
- """A :class:`TimeSeries` class for use with :class:`FEATImage` instances,
- containing some extra FEAT specific options.
+class FEATTimeSeries(VoxelTimeSeries):
+ """A :class:`VoxelTimeSeries` class for use with :class:`FEATImage`
+ instances, containing some extra FEAT specific options.
The ``FEATTimeSeries`` class acts as a container for several
@@ -237,11 +282,11 @@ class FEATTimeSeries(TimeSeries):
def __init__(self, *args, **kwargs):
"""Create a ``FEATTimeSeries``.
- All arguments are passed through to the :class:`TimeSeries`
+ All arguments are passed through to the :class:`VoxelTimeSeries`
constructor.
"""
- TimeSeries.__init__(self, *args, **kwargs)
+ VoxelTimeSeries.__init__(self, *args, **kwargs)
self.name = '{}_{}'.format(type(self).__name__, id(self))
numEVs = self.overlay.numEVs()
@@ -489,10 +534,10 @@ class FEATTimeSeries(TimeSeries):
FEATModelFitTimeSeries, self.__getContrast('full', -1), 'full', -1)
-class FEATPartialFitTimeSeries(TimeSeries):
- """A :class:`TimeSeries` class which represents the partial model fit
- of an EV or contrast from a FEAT analysis. Instances of this class
- are created by the :class:`FEATTimeSeries` class.
+class FEATPartialFitTimeSeries(VoxelTimeSeries):
+ """A :class:`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 :class:`FEATTimeSeries` class.
"""
def __init__(self,
tsPanel,
@@ -523,7 +568,7 @@ class FEATPartialFitTimeSeries(TimeSeries):
:arg idx: If the model fit type is ``'pe'`` or ``'cope'``,
the EV/contrast index.
"""
- TimeSeries.__init__(self, tsPanel, overlay, displayCtx)
+ VoxelTimeSeries.__init__(self, tsPanel, overlay, displayCtx)
self.parentTs = parentTs
self.contrast = contrast
@@ -543,7 +588,7 @@ class FEATPartialFitTimeSeries(TimeSeries):
return [], []
data = self.overlay.partialFit(self.contrast, coords, False)
- return TimeSeries.getData(self, ydata=data)
+ return VoxelTimeSeries.getData(self, ydata=data)
class FEATEVTimeSeries(TimeSeries):
@@ -577,23 +622,25 @@ class FEATEVTimeSeries(TimeSeries):
"""Returns a string representation of this ``FEATEVTimeSeries``
instance.
"""
+
+ display = self.displayCtx.getDisplay(self.overlay)
- return '{} (EV{} - {})'.format(
- self.parentTs.makeLabel(),
+ return '{} EV{} ({})'.format(
+ display.name,
self.idx + 1,
self.overlay.evNames()[self.idx])
def getData(self):
"""Returns the time course of the EV specified in the constructor. """
- data = np.array(self.overlay.getDesign()[:, self.idx])
+ data = self.overlay.getDesign()[:, self.idx]
return TimeSeries.getData(self, ydata=data)
-class FEATResidualTimeSeries(TimeSeries):
- """A :class:`TimeSeries` class which represents the time course of the
- residuals from a FEAT analysis. Instances of this class are created by
- the :class:`FEATTimeSeries` class.
+class FEATResidualTimeSeries(VoxelTimeSeries):
+ """A :class:`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 :class:`FEATTimeSeries` class.
"""
def __init__(self, tsPanel, overlay, displayCtx, parentTs):
@@ -609,7 +656,7 @@ class FEATResidualTimeSeries(TimeSeries):
:arg parentTs: The :class:`.FEATTimeSeries` instance that has
created this ``FEATResidualTimeSeries``.
"""
- TimeSeries.__init__(self, tsPanel, overlay, displayCtx)
+ VoxelTimeSeries.__init__(self, tsPanel, overlay, displayCtx)
self.parentTs = parentTs
@@ -629,15 +676,15 @@ class FEATResidualTimeSeries(TimeSeries):
return [], []
x, y, z = voxel
- data = np.array(self.overlay.getResiduals().data[x, y, z, :])
+ data = self.overlay.getResiduals().data[x, y, z, :]
- return TimeSeries.getData(self, ydata=data)
+ return VoxelTimeSeries.getData(self, ydata=data)
-class FEATModelFitTimeSeries(TimeSeries):
+class FEATModelFitTimeSeries(VoxelTimeSeries):
"""A :class:`TimeSeries` class which represents the time course for
- a model fit from a FEAT analysis. Instances of this class are created by
- the :class:`FEATTimeSeries` class.
+ a model fit from a FEAT analysis at a specific voxel. Instances of this
+ class are created by the :class:`FEATTimeSeries` class.
"""
def __init__(self,
@@ -673,7 +720,7 @@ class FEATModelFitTimeSeries(TimeSeries):
if fitType not in ('full', 'cope', 'pe'):
raise ValueError('Unknown model fit type {}'.format(fitType))
- TimeSeries.__init__(self, tsPanel, overlay, displayCtx)
+ VoxelTimeSeries.__init__(self, tsPanel, overlay, displayCtx)
self.parentTs = parentTs
self.fitType = fitType
self.idx = idx
@@ -712,16 +759,13 @@ class FEATModelFitTimeSeries(TimeSeries):
data = self.overlay.fit(contrast, voxel, fitType == 'full')
- return TimeSeries.getData(self, ydata=data)
-
+ return VoxelTimeSeries.getData(self, ydata=data)
class MelodicTimeSeries(TimeSeries):
"""A :class:`.TimeSeries` class which encapsulates the time course for
- one component of a :class:`.MelodicImage`. Where the :class:`.TimeSeries`
- class returns the time course of the voxel at the current
- :class:`.DisplayContext.location`, the :class:`.MelodicTimeSeries` returns
- the time course of the component specified by the current
+ one component of a :class:`.MelodicImage`. The :meth:`getData` method
+ returns the time course of the component specified by the current
:class:`.ImageOpts.volume`.
"""
@@ -747,6 +791,7 @@ class MelodicTimeSeries(TimeSeries):
def makeLabel(self):
"""Returns a string representation of this ``MelodicTimeSeries``. """
+
display = self.displayCtx.getDisplay(self.overlay)
return '{} [component {}]'.format(display.name, self.getComponent())
@@ -755,5 +800,5 @@ class MelodicTimeSeries(TimeSeries):
"""Returns the time course of the current Melodic component. """
component = self.getComponent()
- ydata = np.array(self.overlay.getComponentTimeSeries(component))
+ ydata = self.overlay.getComponentTimeSeries(component)
return TimeSeries.getData(self, ydata=ydata)
diff --git a/fsl/fsleyes/views/timeseriespanel.py b/fsl/fsleyes/views/timeseriespanel.py
index 02d2c6dceddad0f3388f3c80e0edcf7aac1bb879..5a879e526528b542ece4f59efe961faa81221d1b 100644
--- a/fsl/fsleyes/views/timeseriespanel.py
+++ b/fsl/fsleyes/views/timeseriespanel.py
@@ -413,7 +413,7 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
propNames = ['volume']
else:
- ts = timeseries.TimeSeries(self, overlay, self._displayCtx)
+ ts = timeseries.VoxelTimeSeries(self, overlay, self._displayCtx)
targets = [self._displayCtx]
propNames = ['location']