From b9715c92d065a7bdaa4bb5909e10558902c5546a Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Wed, 8 Jul 2015 14:49:57 +0100
Subject: [PATCH] 'Current' plot settings can be changed; Contrast vectors are
scaled correctly
---
fsl/data/featimage.py | 10 ++-
fsl/data/strings.py | 9 ++-
.../controls/timeseriescontrolpanel.py | 21 ++++++
fsl/fslview/views/timeseriespanel.py | 69 +++++++++++++++----
4 files changed, 93 insertions(+), 16 deletions(-)
diff --git a/fsl/data/featimage.py b/fsl/data/featimage.py
index 19d267a57..77eeb1ee6 100644
--- a/fsl/data/featimage.py
+++ b/fsl/data/featimage.py
@@ -206,14 +206,18 @@ class FEATImage(fslimage.Image):
return self.__copes[num]
- def fit(self, contrast, xyz):
+ def fit(self, contrast, xyz, fullmodel=False):
+
+ if not fullmodel:
+ contrast = np.array(contrast)
+ contrast /= np.sqrt(contrast.sum() ** 2)
x, y, z = xyz
numEVs = self.numEVs()
if len(contrast) != numEVs:
raise ValueError('Contrast is wrong length')
-
+
X = self.__design
data = self.data[x, y, z, :]
modelfit = np.zeros(len(data))
@@ -221,7 +225,7 @@ class FEATImage(fslimage.Image):
for i in range(numEVs):
pe = self.getPE(i)[x, y, z]
- modelfit += np.dot(X[:, i], pe) * contrast[i]
+ modelfit += X[:, i] * pe * contrast[i]
return modelfit + data.mean()
diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index f9daa0065..01a649224 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -213,11 +213,13 @@ labels = TypeDict({
'PlotPanel.xlabel' : 'X',
'PlotPanel.ylabel' : 'Y',
+ 'TimeSeriesControlPanel.currentSettings' : 'Settings for current '
+ 'voxel time course',
'TimeSeriesControlPanel.currentFEATSettings' : 'FEAT settings for '
'selected overlay ({})',
'FEATModelFitTimeSeries.full' : 'Full model fit',
- 'FEATModelFitTimeSeries.cope' : 'COPE{} fit ({})',
+ 'FEATModelFitTimeSeries.cope' : 'COPE{} fit: {}',
'FEATModelFitTimeSeries.pe' : 'PE{} fit',
})
@@ -266,6 +268,11 @@ properties = TypeDict({
'TimeSeriesPanel.demean' : 'Demean',
'TimeSeriesPanel.usePixdim' : 'Use pixdims',
'TimeSeriesPanel.showCurrent' : 'Plot time series for current voxel',
+ 'TimeSeriesPanel.currentColour' : 'Colour for current time course',
+ 'TimeSeriesPanel.currentAlpha' : 'Transparency for current '
+ 'time course',
+ 'TimeSeriesPanel.currentLineWidth' : 'Line width for current time course',
+ 'TimeSeriesPanel.currentLineStyle' : 'Line style for current time course',
'TimeSeriesPanel.plotFullModelFit' : 'Plot full model fit',
'TimeSeriesPanel.plotResiduals' : 'Plot residuals',
diff --git a/fsl/fslview/controls/timeseriescontrolpanel.py b/fsl/fslview/controls/timeseriescontrolpanel.py
index 1e6159e04..461eefc96 100644
--- a/fsl/fslview/controls/timeseriescontrolpanel.py
+++ b/fsl/fslview/controls/timeseriescontrolpanel.py
@@ -30,6 +30,11 @@ class TimeSeriesControlPanel(fslpanel.FSLViewPanel):
tsProps = ['demean',
'usePixdim',
'showCurrent']
+ curProps = ['currentColour',
+ 'currentAlpha',
+ 'currentLineWidth',
+ 'currentLineStyle']
+
plotProps = ['xLogScale',
'yLogScale',
'smooth',
@@ -43,6 +48,22 @@ class TimeSeriesControlPanel(fslpanel.FSLViewPanel):
props.makeWidget(self.__widgets, tsPanel, prop),
displayName=strings.properties[tsPanel, prop])
+ self.__widgets.AddGroup('currentSettings',
+ strings.labels[self, 'currentSettings'])
+
+ # TODO Hide these when tsPanel.showCurrent is false
+ for prop in curProps:
+ if prop == 'currentAlpha':
+ kwargs = {'showLimits' : False, 'spin' : False}
+ else:
+ kwargs = {}
+
+ self.__widgets.AddWidget(
+ props.makeWidget(self.__widgets, tsPanel, prop, **kwargs),
+ displayName=strings.properties[tsPanel, prop],
+ groupName='currentSettings')
+
+
self.__widgets.AddGroup(
'plotSettings',
strings.labels[tsPanel, 'plotSettings'])
diff --git a/fsl/fslview/views/timeseriespanel.py b/fsl/fslview/views/timeseriespanel.py
index 99dcc7267..0668476e1 100644
--- a/fsl/fslview/views/timeseriespanel.py
+++ b/fsl/fslview/views/timeseriespanel.py
@@ -12,6 +12,7 @@ of overlay objects stored in an :class:`.OverlayList`.
"""
+import copy
import logging
import numpy as np
@@ -78,6 +79,9 @@ class FEATTimeSeries(TimeSeries):
plotPEFits = props.List(props.Boolean(default=False))
plotCOPEFits = props.List(props.Boolean(default=False))
+ # TODO 'None', or any PE/COPE
+ reduceDataAgainst = props.Choice()
+
def __init__(self, *args, **kwargs):
TimeSeries.__init__(self, *args, **kwargs)
@@ -226,8 +230,8 @@ class FEATTimeSeries(TimeSeries):
if not TimeSeries.update(self, coords):
return False
- if self.__fullModelTs is not None:
- self.__fullModelTs.update(coords)
+ for modelTs in self.getModelTimeSeries():
+ modelTs.update(coords)
return True
@@ -254,10 +258,11 @@ class FEATModelFitTimeSeries(TimeSeries):
def updateModelFit(self):
- x, y, z = self.coords
- self.data = self.overlay.fit(self.contrast, (x, y, z))
-
+ fitType = self.fitType
+ contrast = self.contrast
+ xyz = self.coords
+ self.data = self.overlay.fit(contrast, xyz, fitType == 'full')
class TimeSeriesPanel(plotpanel.PlotPanel):
@@ -269,13 +274,26 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
"""
- demean = props.Boolean(default=True)
- usePixdim = props.Boolean(default=False)
- showCurrent = props.Boolean(default=True)
+ demean = props.Boolean(default=True)
+ usePixdim = props.Boolean(default=False)
+ showCurrent = props.Boolean(default=True)
+
+ # TODO
+ percentChange = props.Boolean(default=False)
+
+ currentColour = copy.copy(TimeSeries.colour)
+ currentAlpha = copy.copy(TimeSeries.alpha)
+ currentLineWidth = copy.copy(TimeSeries.lineWidth)
+ currentLineStyle = copy.copy(TimeSeries.lineStyle)
def __init__(self, parent, overlayList, displayCtx):
+ self.currentColour = (0, 0, 0)
+ self.currentAlpha = 1
+ self.currentLineWidth = 1
+ self.currentLineStyle = ':'
+
actionz = {
'toggleTimeSeriesList' : lambda *a: self.togglePanel(
fslcontrols.TimeSeriesListPanel, False, self),
@@ -304,11 +322,33 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
self.addListener('usePixdim', self._name, self.draw)
self.addListener('showCurrent', self._name, self.draw)
+
+ csc = self.__currentSettingsChanged
+ self.addListener('currentColour', self._name, csc)
+ self.addListener('currentAlpha', self._name, csc)
+ self.addListener('currentLineWidth', self._name, csc)
+ self.addListener('currentLineStyle', self._name, csc)
+
self.__currentOverlay = None
self.__currentTs = None
self.Layout()
self.draw()
+
+ def __currentSettingsChanged(self, *a):
+ if self.__currentTs is None:
+ return
+
+ tss = [self.__currentTs]
+ if isinstance(self.__currentTs, FEATTimeSeries):
+ tss.extend(self.__currentTs.getModelTimeSeries())
+
+ for ts in tss:
+ ts.colour = self.currentColour
+ ts.alpha = self.currentAlpha
+ ts.lineWidth = self.currentLineWidth
+ ts.lineStyle = self.currentLineStyle
+
def destroy(self):
plotpanel.PlotPanel.destroy(self)
@@ -378,12 +418,17 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
else:
ts = TimeSeries(self, overlay, vox)
- ts.colour = [0, 0, 0]
- ts.alpha = 1
- ts.lineWidth = 2
- ts.lineStyle = ':'
+ ts.colour = self.currentColour
+ ts.alpha = self.currentAlpha
+ ts.lineWidth = self.currentLineWidth
+ ts.lineStyle = self.currentLineStyle
ts.label = None
+ ts.bindProps('colour' , self, 'currentColour')
+ ts.bindProps('alpha' , self, 'currentAlpha')
+ ts.bindProps('lineWidth', self, 'currentLineWidth')
+ ts.bindProps('lineStyle', self, 'currentLineStyle')
+
self.__currentTs = ts
self.__currentOverlay = overlay
--
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