From 234aa550e92b73a08a8e3fcd0ce62d7ade593e88 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Thu, 9 Jul 2015 11:30:25 +0100
Subject: [PATCH] Removed 'demean' option - replaced with 'plotMode' option
which allows demeaning, or scaling to percent-changed. Added ability to plot
data reduced against a PE/COPE, and the ability to hide the raw data plot for
a currently-selected FEAT time series (as the plot can get pretty messy).
---
fsl/data/featimage.py | 27 ++-
fsl/data/strings.py | 24 ++-
.../controls/timeseriescontrolpanel.py | 17 +-
fsl/fslview/controls/timeserieslistpanel.py | 17 +-
fsl/fslview/views/histogrampanel.py | 5 +-
fsl/fslview/views/timeseriespanel.py | 184 ++++++++++++------
6 files changed, 180 insertions(+), 94 deletions(-)
diff --git a/fsl/data/featimage.py b/fsl/data/featimage.py
index b5eb96ea8..4346d51c8 100644
--- a/fsl/data/featimage.py
+++ b/fsl/data/featimage.py
@@ -221,6 +221,13 @@ class FEATImage(fslimage.Image):
def fit(self, contrast, xyz, fullmodel=False):
+ """
+
+ Passing in a contrast of all 1s, and ``fullmodel=True`` will
+ get you the full model fit. Pass in ``fullmodel=False`` for
+ all other contrasts, otherwise the model fit values will not
+ be scaled correctly.
+ """
if not fullmodel:
contrast = np.array(contrast)
@@ -245,24 +252,14 @@ class FEATImage(fslimage.Image):
def reducedData(self, xyz, contrast, fullmodel=False):
+ """
+
+ Passing in a contrast of all 1s, and ``fullmodel=True`` will
+ get you the model fit residuals.
+ """
x, y, z = xyz
residuals = self.getResiduals()[x, y, z, :]
modelfit = self.fit(contrast, xyz, fullmodel)
return residuals + modelfit
-
-
- # def getThresholdedZStats(self):
- # pass
-
-
- # def getSomethingForClusters(self):
- # pass
-
-
- # # Return a copy of this image, transformed
- # # to the specified spaced (e.g. MNI152,
- # # structural, functional, etc)
- # def getInSpace(self, space):
- # pass
diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index d3f168057..3ef12575f 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -218,10 +218,16 @@ labels = TypeDict({
'TimeSeriesControlPanel.currentFEATSettings' : 'FEAT settings for '
'selected overlay ({})',
+ 'TimeSeriesListPanel.featReduced' : 'Reduced against {}',
+
'FEATModelFitTimeSeries.full' : 'Full model fit',
'FEATModelFitTimeSeries.cope' : 'COPE{} fit: {}',
'FEATModelFitTimeSeries.pe' : 'PE{} fit',
-
+
+ 'FEATReducedTimeSeries.cope' : 'Reduced against COPE{}: {}',
+ 'FEATReducedTimeSeries.pe' : 'Reduced against PE{}',
+
+ 'FEATResidualTimeSeries' : 'Residuals',
})
@@ -265,7 +271,7 @@ properties = TypeDict({
'PlotPanel.xlabel' : 'X label',
'PlotPanel.ylabel' : 'Y label',
- 'TimeSeriesPanel.demean' : 'Demean',
+ 'TimeSeriesPanel.plotMode' : 'Plotting mode',
'TimeSeriesPanel.usePixdim' : 'Use pixdims',
'TimeSeriesPanel.showCurrent' : 'Plot time series for current voxel',
'TimeSeriesPanel.currentColour' : 'Colour for current time course',
@@ -290,8 +296,9 @@ properties = TypeDict({
'FEATTimeSeries.plotFullModelFit' : 'Plot full model fit',
'FEATTimeSeries.plotPEFits' : 'Plot PE{} fit',
'FEATTimeSeries.plotCOPEFits' : 'Plot COPE{} fit ({})',
- 'FEATTimeSeries.plotResiduals' : 'Show residuals',
- 'FEATTimeSeries.reduceAgainst' : 'Reduce data against',
+ 'FEATTimeSeries.plotResiduals' : 'Plot residuals',
+ 'FEATTimeSeries.plotReduced' : 'Plot data reduced against',
+ 'FEATTimeSeries.plotData' : 'Plot data',
'OrthoEditProfile.selectionSize' : 'Selection size',
'OrthoEditProfile.selectionIs3D' : '3D selection',
@@ -420,7 +427,14 @@ choices = TypeDict({
'Display.overlayType.label' : 'Label image',
'Display.overlayType.rgbvector' : '3-direction vector image (RGB)',
'Display.overlayType.linevector' : '3-direction vector image (Line)',
- 'Display.overlayType.model' : '3D model'
+ 'Display.overlayType.model' : '3D model',
+
+ 'HistogramPanel.histType.probability' : 'Probability',
+ 'HistogramPanel.histType.count' : 'Count',
+
+ 'TimeSeriesPanel.plotMode.normal' : 'Normal',
+ 'TimeSeriesPanel.plotMode.demean' : 'Demeaned',
+ 'TimeSeriesPanel.plotMode.percentChange' : 'Percent changed',
})
diff --git a/fsl/fslview/controls/timeseriescontrolpanel.py b/fsl/fslview/controls/timeseriescontrolpanel.py
index f3302a830..bf4a6082c 100644
--- a/fsl/fslview/controls/timeseriescontrolpanel.py
+++ b/fsl/fslview/controls/timeseriescontrolpanel.py
@@ -27,7 +27,7 @@ class TimeSeriesControlPanel(fslpanel.FSLViewPanel):
self.SetSizer(self.__sizer)
self.__sizer.Add(self.__widgets, flag=wx.EXPAND, proportion=1)
- tsProps = ['demean',
+ tsProps = ['plotMode',
'usePixdim',
'showCurrent']
plotProps = ['xLogScale',
@@ -201,8 +201,13 @@ class TimeSeriesControlPanel(fslpanel.FSLViewPanel):
res = props.makeWidget( self.__widgets, ts, 'plotResiduals')
pes = props.makeListWidgets(self.__widgets, ts, 'plotPEFits')
copes = props.makeListWidgets(self.__widgets, ts, 'plotCOPEFits')
- reduce = props.makeWidget( self.__widgets, ts, 'reduceAgainst')
-
+ reduced = props.makeWidget( self.__widgets, ts, 'plotReduced')
+ data = props.makeWidget( self.__widgets, ts, 'plotData')
+
+ self.__widgets.AddWidget(
+ data,
+ displayName=strings.properties[ts, 'plotData'],
+ groupName='currentFEATSettings')
self.__widgets.AddWidget(
full,
displayName=strings.properties[ts, 'plotFullModelFit'],
@@ -214,9 +219,9 @@ class TimeSeriesControlPanel(fslpanel.FSLViewPanel):
groupName='currentFEATSettings')
self.__widgets.AddWidget(
- reduce,
- displayName=strings.properties[ts, 'reduceAgainst'],
- groupName='currentFEATSettings')
+ reduced,
+ displayName=strings.properties[ts, 'plotReduced'],
+ groupName='currentFEATSettings')
for i, pe in enumerate(pes):
self.__widgets.AddWidget(
diff --git a/fsl/fslview/controls/timeserieslistpanel.py b/fsl/fslview/controls/timeserieslistpanel.py
index df7b1ea55..7fbefc46d 100644
--- a/fsl/fslview/controls/timeserieslistpanel.py
+++ b/fsl/fslview/controls/timeserieslistpanel.py
@@ -102,13 +102,21 @@ class TimeSeriesListPanel(fslpanel.FSLViewPanel):
def __makeLabel(self, ts):
+
return '{} [{} {} {}]'.format(ts.overlay.name,
ts.coords[0],
ts.coords[1],
ts.coords[2])
- def __makeFEATModelFitLabel(self, parentTs, modelTs):
+ def __makeFEATModelTSLabel(self, parentTs, modelTs):
+
+ import fsl.fslview.views.timeseriespanel as tsp
+
+ if isinstance(modelTs, tsp.FEATResidualTimeSeries):
+ return '{} ({})'.format(
+ parentTs.label,
+ strings.labels[modelTs])
label = '{} ({})'.format(
parentTs.label,
@@ -156,7 +164,7 @@ class TimeSeriesListPanel(fslpanel.FSLViewPanel):
if ts is None:
return
- ts = copy.copy(ts)
+ ts = copy.copy(ts)
ts.alpha = 1
ts.lineWidth = 2
@@ -167,13 +175,16 @@ class TimeSeriesListPanel(fslpanel.FSLViewPanel):
self.__tsPanel.dataSeries.append(ts)
if isinstance(ts, tsp.FEATTimeSeries):
+
modelTs = ts.getModelTimeSeries()
+ modelTs.remove(ts)
for mts in modelTs:
+
mts.alpha = 1
mts.lineWidth = 2
mts.lineStyle = '-'
- mts.label = self.__makeFEATModelFitLabel(ts, mts)
+ mts.label = self.__makeFEATModelTSLabel(ts, mts)
self.__tsPanel.dataSeries.extend(modelTs)
diff --git a/fsl/fslview/views/histogrampanel.py b/fsl/fslview/views/histogrampanel.py
index 865b4960d..cfcf7c998 100644
--- a/fsl/fslview/views/histogrampanel.py
+++ b/fsl/fslview/views/histogrampanel.py
@@ -341,7 +341,10 @@ class HistogramPanel(plotpanel.PlotPanel):
autoBin = props.Boolean(default=True)
showCurrent = props.Boolean(default=True)
- histType = props.Choice(('probability', 'count'))
+ histType = props.Choice(
+ ('probability', 'count'),
+ labels=[strings.choices['HistogramPanel.histType.probability'],
+ strings.choices['HistogramPanel.histType.count']])
selectedSeries = props.Int(minval=0, clamped=True)
diff --git a/fsl/fslview/views/timeseriespanel.py b/fsl/fslview/views/timeseriespanel.py
index 4ddb0a88a..aad982f89 100644
--- a/fsl/fslview/views/timeseriespanel.py
+++ b/fsl/fslview/views/timeseriespanel.py
@@ -22,6 +22,7 @@ import props
import plotpanel
import fsl.data.featimage as fslfeatimage
import fsl.data.image as fslimage
+import fsl.data.strings as strings
import fsl.fslview.displaycontext as fsldisplay
import fsl.fslview.controls as fslcontrols
import fsl.utils.transform as transform
@@ -70,9 +71,13 @@ class TimeSeries(plotpanel.DataSeries):
if self.tsPanel.usePixdim:
xdata *= self.overlay.pixdim[3]
- if self.tsPanel.demean:
+ if self.tsPanel.plotMode == 'demean':
ydata = ydata - ydata.mean()
+ elif self.tsPanel.plotMode == 'percentChange':
+ mean = ydata.mean()
+ ydata = 100 * (ydata / mean) - 100
+
return xdata, ydata
@@ -82,13 +87,14 @@ class FEATTimeSeries(TimeSeries):
containing some extra FEAT specific options.
"""
-
+
+ plotData = props.Boolean(default=True)
plotFullModelFit = props.Boolean(default=False)
plotResiduals = props.Boolean(default=False)
plotPEFits = props.List(props.Boolean(default=False))
plotCOPEFits = props.List(props.Boolean(default=False))
- reduceAgainst = props.Choice()
-
+ plotReduced = props.Choice()
+
def __init__(self, *args, **kwargs):
TimeSeries.__init__(self, *args, **kwargs)
@@ -105,7 +111,7 @@ class FEATTimeSeries(TimeSeries):
name = 'COPE{} ({})'.format(i + 1, copeNames[i])
reduceOpts.append(name)
- self.getProp('reduceAgainst').setChoices(reduceOpts, instance=self)
+ self.getProp('plotReduced').setChoices(reduceOpts, instance=self)
for i in range(numEVs):
self.plotPEFits.append(False)
@@ -114,6 +120,7 @@ class FEATTimeSeries(TimeSeries):
self.plotCOPEFits.append(False)
self.__fullModelTs = None
+ self.__reducedTs = None
self.__resTs = None
self.__peTs = [None] * numEVs
self.__copeTs = [None] * numCOPEs
@@ -121,10 +128,12 @@ class FEATTimeSeries(TimeSeries):
self.addListener('plotFullModelFit',
self.name,
self.__plotFullModelFitChanged)
-
self.addListener('plotResiduals',
self.name,
self.__plotResidualsChanged)
+ self.addListener('plotReduced',
+ self.name,
+ self.__plotReducedChanged)
for i, plotPEFit in enumerate(
self.plotPEFits.getPropertyValueList()):
@@ -142,30 +151,9 @@ class FEATTimeSeries(TimeSeries):
plotCOPEFit.addListener(self.name, onChange)
-
- def getData(self):
-
- reduce = self.reduceAgainst
-
- if reduce == 'none':
- data = None
-
- else:
- idx = int(reduce.split()[0][-1]) - 1
- numEVs = self.overlay.numEVs()
-
- if reduce.startswith('PE'):
- contrast = [0] * numEVs
- contrast[idx] = 1
- else:
- contrast = self.overlay.contrasts()[idx]
-
- data = self.overlay.reducedData(self.coords, contrast, False)
-
- return TimeSeries.getData(self, ydata=data)
-
def __copy__(self):
+
copy = type(self)(self.tsPanel, self.overlay, self.coords)
copy.colour = self.colour
@@ -181,31 +169,77 @@ class FEATTimeSeries(TimeSeries):
copy.plotFullModelFit = self.plotFullModelFit
copy.plotPEFits[ :] = self.plotPEFits[ :]
copy.plotCOPEFits[:] = self.plotCOPEFits[:]
+ copy.plotReduced = self.plotReduced
+ copy.plotResiduals = self.plotResiduals
return copy
def getModelTimeSeries(self):
+
modelts = []
- if self.plotFullModelFit:
- modelts.append(self.__fullModelTs)
-
- if self.plotResiduals:
- modelts.append(self.__resTs)
-
+ if self.plotData: modelts.append(self)
+ if self.plotFullModelFit: modelts.append(self.__fullModelTs)
+ if self.plotResiduals: modelts.append(self.__resTs)
+ if self.plotReduced != 'none': modelts.append(self.__reducedTs)
+
for i in range(self.overlay.numEVs()):
if self.plotPEFits[i]:
modelts.append(self.__peTs[i])
for i in range(self.overlay.numContrasts()):
if self.plotCOPEFits[i]:
- modelts.append(self.__copeTs[i])
-
+ modelts.append(self.__copeTs[i])
+
return modelts
+ def __getContrast(self, fitType, idx):
+
+ if fitType == 'full':
+ return [1] * self.overlay.numEVs()
+ elif fitType == 'pe':
+ con = [0] * self.overlay.numEVs()
+ con[idx] = 1
+ return con
+ elif fitType == 'cope':
+ return self.overlay.getContrasts()[idx]
+
+
+ def __plotReducedChanged(self, *a):
+
+ reduced = self.plotReduced
+
+ if reduced == 'none' and self.__reducedTs is not None:
+ self.__reducedTs = None
+ return
+
+ reduced = reduced.split()[0]
+
+ # fitType is either 'cope' or 'pe'
+ fitType = reduced[:-1].lower()
+ idx = int(reduced[-1]) - 1
+
+ rts = FEATReducedTimeSeries(
+ self.__getContrast(fitType, idx),
+ fitType,
+ idx,
+ self.tsPanel,
+ self.overlay,
+ self.coords)
+
+ rts.colour = (0, 0.6, 0.6)
+ rts.alpha = self.alpha
+ rts.label = self.label
+ rts.lineWidth = self.lineWidth
+ rts.lineStyle = self.lineStyle
+
+ self.__reducedTs = rts
+
+
def __plotResidualsChanged(self, *a):
+
if not self.plotResiduals:
self.__resTs = None
return
@@ -225,14 +259,13 @@ class FEATTimeSeries(TimeSeries):
def __plotCOPEFitChanged(self, copenum):
+
if not self.plotCOPEFits[copenum]:
self.__copeTs[copenum] = None
return
- con = self.overlay.contrasts()[copenum]
-
copets = FEATModelFitTimeSeries(
- con,
+ self.__getContrast('cope', copenum),
'cope',
copenum,
self.tsPanel,
@@ -249,21 +282,19 @@ class FEATTimeSeries(TimeSeries):
def __plotPEFitChanged(self, evnum):
+
if not self.plotPEFits[evnum]:
self.__peTs[evnum] = None
return
- con = [0] * self.overlay.numEVs()
- con[evnum] = 1
-
pets = FEATModelFitTimeSeries(
- con,
+ self.__getContrast('pe', evnum),
'pe',
evnum,
self.tsPanel,
self.overlay,
self.coords)
-
+
pets.colour = (0.7, 0, 0)
pets.alpha = self.alpha
pets.label = self.label
@@ -274,34 +305,55 @@ class FEATTimeSeries(TimeSeries):
def __plotFullModelFitChanged(self, *a):
+
if not self.plotFullModelFit:
self.__fullModelTs = None
return
- self.__fullModelTs = FEATModelFitTimeSeries(
- [1] * self.overlay.numEVs(),
+ fts = FEATModelFitTimeSeries(
+ self.__getContrast('full', -1),
'full',
-1,
self.tsPanel,
self.overlay,
self.coords)
- self.__fullModelTs.colour = (0, 0, 1)
- self.__fullModelTs.alpha = self.alpha
- self.__fullModelTs.label = self.label
- self.__fullModelTs.lineWidth = self.lineWidth
- self.__fullModelTs.lineStyle = self.lineStyle
+
+ fts.colour = (0, 0, 1)
+ fts.alpha = self.alpha
+ fts.label = self.label
+ fts.lineWidth = self.lineWidth
+ fts.lineStyle = self.lineStyle
+
+ self.__fullModelTs = fts
def update(self, coords):
+
if not TimeSeries.update(self, coords):
return False
for modelTs in self.getModelTimeSeries():
+ if modelTs is self:
+ continue
modelTs.update(coords)
return True
+class FEATReducedTimeSeries(TimeSeries):
+ def __init__(self, contrast, fitType, idx, *args, **kwargs):
+ TimeSeries.__init__(self, *args, **kwargs)
+
+ self.contrast = contrast
+ self.fitType = fitType
+ self.idx = idx
+
+ def getData(self):
+
+ data = self.overlay.reducedData(self.coords, self.contrast, False)
+ return TimeSeries.getData(self, ydata=data)
+
+
class FEATResidualTimeSeries(TimeSeries):
def getData(self):
x, y, z = self.coords
@@ -311,7 +363,6 @@ class FEATResidualTimeSeries(TimeSeries):
class FEATModelFitTimeSeries(TimeSeries):
-
def __init__(self, contrast, fitType, idx, *args, **kwargs):
@@ -348,12 +399,13 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
"""
- demean = props.Boolean(default=True)
usePixdim = props.Boolean(default=False)
showCurrent = props.Boolean(default=True)
-
- # TODO
- percentChange = props.Boolean(default=False)
+ plotMode = props.Choice(
+ ('normal', 'demean', 'percentChange'),
+ labels=[strings.choices['TimeSeriesPanel.plotMode.normal'],
+ strings.choices['TimeSeriesPanel.plotMode.demean'],
+ strings.choices['TimeSeriesPanel.plotMode.percentChange']])
currentColour = copy.copy(TimeSeries.colour)
currentAlpha = copy.copy(TimeSeries.alpha)
@@ -392,7 +444,7 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
displayCtx .addListener('selectedOverlay', self._name, self.draw)
displayCtx .addListener('location', self._name, self.draw)
- self.addListener('demean', self._name, self.draw)
+ self.addListener('plotMode', self._name, self.draw)
self.addListener('usePixdim', self._name, self.draw)
self.addListener('showCurrent', self._name, self.draw)
@@ -413,11 +465,15 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
return
tss = [self.__currentTs]
+
if isinstance(self.__currentTs, FEATTimeSeries):
- tss.extend(self.__currentTs.getModelTimeSeries())
+ tss = self.__currentTs.getModelTimeSeries()
for ts in tss:
+ if ts is self.__currentTs:
+ continue
+
# Don't change the colour for associated
# time courses (e.g. model fits)
if ts is self.__currentTs:
@@ -431,7 +487,7 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
def destroy(self):
plotpanel.PlotPanel.destroy(self)
- self.removeListener('demean', self._name)
+ self.removeListener('plotMode', self._name)
self.removeListener('usePixdim', self._name)
self.removeListener('showCurrent', self._name)
@@ -524,12 +580,12 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
if self.showCurrent and \
current is not None:
-
- extras = [current]
-
+
if isinstance(current, FEATTimeSeries):
- extras += current.getModelTimeSeries()
-
+ extras = current.getModelTimeSeries()
+ else:
+ extras = [current]
+
self.drawDataSeries(extras)
else:
self.drawDataSeries()
--
GitLab