From 118dbbc8e2ae1f415172fc79620f1d8269e277aa Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Wed, 8 Jul 2015 16:53:06 +0100
Subject: [PATCH] Ability to plot 'reduced' data (with respect to a specific
PE/COPE), and residuals.
---
fsl/data/featimage.py | 33 +++++--
fsl/data/strings.py | 2 +
.../controls/timeseriescontrolpanel.py | 13 +++
fsl/fslview/views/timeseriespanel.py | 89 +++++++++++++++++--
4 files changed, 124 insertions(+), 13 deletions(-)
diff --git a/fsl/data/featimage.py b/fsl/data/featimage.py
index 384dfd0a5..b5eb96ea8 100644
--- a/fsl/data/featimage.py
+++ b/fsl/data/featimage.py
@@ -154,6 +154,7 @@ class FEATImage(fslimage.Image):
self.__contrasts = cons
self.__settings = settings
+ self.__residuals = None
self.__pes = [None] * self.numEVs()
self.__copes = [None] * self.numContrasts()
@@ -183,24 +184,37 @@ class FEATImage(fslimage.Image):
return [list(c) for c in self.__contrasts]
- def __getPEFile(self, prefix, ev):
- prefix = op.join(self.__featDir, 'stats', '{}{}'.format(
- prefix, ev + 1))
+ def __getStatsFile(self, prefix, ev=None):
+
+ if ev is not None: prefix = '{}{}'.format(prefix, ev + 1)
+
+ prefix = op.join(self.__featDir, 'stats', prefix)
+
return glob.glob('{}.*'.format(prefix))[0]
def getPE(self, ev):
if self.__pes[ev] is None:
- pefile = self.__getPEFile('pe', ev)
+ pefile = self.__getStatsFile('pe', ev)
self.__pes[ev] = nib.load(pefile).get_data()
return self.__pes[ev]
+
+ def getResiduals(self):
+
+ if self.__residuals is None:
+ resfile = self.__getStatsFile('res4d')
+ self.__residuals = nib.load(resfile).get_data()
+
+ return self.__residuals
+
def getCOPE(self, num):
+
if self.__copes[num] is None:
- copefile = self.__getPEFile('cope', num)
+ copefile = self.__getStatsFile('cope', num)
self.__copes[num] = nib.load(copefile).get_data()
return self.__copes[num]
@@ -229,6 +243,15 @@ class FEATImage(fslimage.Image):
return modelfit + data.mean()
+
+ def reducedData(self, xyz, contrast, fullmodel=False):
+
+ x, y, z = xyz
+ residuals = self.getResiduals()[x, y, z, :]
+ modelfit = self.fit(contrast, xyz, fullmodel)
+
+ return residuals + modelfit
+
# def getThresholdedZStats(self):
# pass
diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index 01a649224..d3f168057 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -290,6 +290,8 @@ 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',
'OrthoEditProfile.selectionSize' : 'Selection size',
'OrthoEditProfile.selectionIs3D' : '3D selection',
diff --git a/fsl/fslview/controls/timeseriescontrolpanel.py b/fsl/fslview/controls/timeseriescontrolpanel.py
index bdec0f8e0..f3302a830 100644
--- a/fsl/fslview/controls/timeseriescontrolpanel.py
+++ b/fsl/fslview/controls/timeseriescontrolpanel.py
@@ -198,12 +198,25 @@ class TimeSeriesControlPanel(fslpanel.FSLViewPanel):
display.name))
full = props.makeWidget( self.__widgets, ts, 'plotFullModelFit')
+ 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')
+
self.__widgets.AddWidget(
full,
displayName=strings.properties[ts, 'plotFullModelFit'],
groupName='currentFEATSettings')
+
+ self.__widgets.AddWidget(
+ res,
+ displayName=strings.properties[ts, 'plotResiduals'],
+ groupName='currentFEATSettings')
+
+ self.__widgets.AddWidget(
+ reduce,
+ displayName=strings.properties[ts, 'reduceAgainst'],
+ groupName='currentFEATSettings')
for i, pe in enumerate(pes):
self.__widgets.AddWidget(
diff --git a/fsl/fslview/views/timeseriespanel.py b/fsl/fslview/views/timeseriespanel.py
index e5c26f64c..4ddb0a88a 100644
--- a/fsl/fslview/views/timeseriespanel.py
+++ b/fsl/fslview/views/timeseriespanel.py
@@ -56,9 +56,16 @@ class TimeSeries(plotpanel.DataSeries):
return True
- def getData(self):
- ydata = np.array( self.data, dtype=np.float32)
- xdata = np.arange(len(ydata), dtype=np.float32)
+ def getData(self, xdata=None, ydata=None):
+ """
+
+ :arg xdata:
+ :arg ydata: Used by subclasses in case they have already done some
+ processing on the data.
+ """
+
+ if xdata is None: xdata = np.arange(len(self.data), dtype=np.float32)
+ if ydata is None: ydata = np.array( self.data, dtype=np.float32)
if self.tsPanel.usePixdim:
xdata *= self.overlay.pixdim[3]
@@ -77,19 +84,28 @@ class FEATTimeSeries(TimeSeries):
plotFullModelFit = props.Boolean(default=False)
+ plotResiduals = props.Boolean(default=False)
plotPEFits = props.List(props.Boolean(default=False))
plotCOPEFits = props.List(props.Boolean(default=False))
-
- # TODO 'None', or any PE/COPE
- reduceDataAgainst = props.Choice()
+ reduceAgainst = props.Choice()
def __init__(self, *args, **kwargs):
TimeSeries.__init__(self, *args, **kwargs)
self.name = '{}_{}'.format(type(self).__name__, id(self))
- numEVs = self.overlay.numEVs()
- numCOPEs = self.overlay.numContrasts()
+ numEVs = self.overlay.numEVs()
+ numCOPEs = self.overlay.numContrasts()
+ copeNames = self.overlay.contrastNames()
+
+ reduceOpts = ['none'] + \
+ ['PE{}'.format(i + 1) for i in range(numEVs)]
+
+ for i in range(numCOPEs):
+ name = 'COPE{} ({})'.format(i + 1, copeNames[i])
+ reduceOpts.append(name)
+
+ self.getProp('reduceAgainst').setChoices(reduceOpts, instance=self)
for i in range(numEVs):
self.plotPEFits.append(False)
@@ -98,12 +114,17 @@ class FEATTimeSeries(TimeSeries):
self.plotCOPEFits.append(False)
self.__fullModelTs = None
+ self.__resTs = None
self.__peTs = [None] * numEVs
self.__copeTs = [None] * numCOPEs
self.addListener('plotFullModelFit',
self.name,
self.__plotFullModelFitChanged)
+
+ self.addListener('plotResiduals',
+ self.name,
+ self.__plotResidualsChanged)
for i, plotPEFit in enumerate(
self.plotPEFits.getPropertyValueList()):
@@ -121,6 +142,28 @@ 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)
@@ -148,6 +191,9 @@ class FEATTimeSeries(TimeSeries):
if self.plotFullModelFit:
modelts.append(self.__fullModelTs)
+ if self.plotResiduals:
+ modelts.append(self.__resTs)
+
for i in range(self.overlay.numEVs()):
if self.plotPEFits[i]:
modelts.append(self.__peTs[i])
@@ -158,6 +204,25 @@ class FEATTimeSeries(TimeSeries):
return modelts
+
+ def __plotResidualsChanged(self, *a):
+ if not self.plotResiduals:
+ self.__resTs = None
+ return
+
+ rts = FEATResidualTimeSeries(
+ self.tsPanel,
+ self.overlay,
+ self.coords)
+
+ rts.colour = (0.8, 0.4, 0)
+ rts.alpha = self.alpha
+ rts.label = self.label
+ rts.lineWidth = self.lineWidth
+ rts.lineStyle = self.lineStyle
+
+ self.__resTs = rts
+
def __plotCOPEFitChanged(self, copenum):
if not self.plotCOPEFits[copenum]:
@@ -237,6 +302,14 @@ class FEATTimeSeries(TimeSeries):
return True
+class FEATResidualTimeSeries(TimeSeries):
+ def getData(self):
+ x, y, z = self.coords
+ data = self.overlay.getResiduals()[x, y, z, :]
+
+ return TimeSeries.getData(self, ydata=data)
+
+
class FEATModelFitTimeSeries(TimeSeries):
--
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