Bug fix to contrast vector normalisation - sum of squares, not squared

sum. 'Current time course' settings only shown if current time course is
being shown. Other little changes.

fsl/data/featimage.py

@@ -210,7 +210,7 @@ class FEATImage(fslimage.Image):
 
         if not fullmodel:
             contrast  = np.array(contrast)
-            contrast /= np.sqrt(contrast.sum() ** 2)
+            contrast /= np.sqrt((contrast ** 2).sum())
 
         x, y, z = xyz
         numEVs  = self.numEVs()

fsl/fslview/controls/timeseriescontrolpanel.py

@@ -30,11 +30,6 @@ class TimeSeriesControlPanel(fslpanel.FSLViewPanel):
         tsProps   = ['demean',
                      'usePixdim',
                      'showCurrent']
-        curProps  = ['currentColour',
-                     'currentAlpha',
-                     'currentLineWidth',
-                     'currentLineStyle']
-                     
         plotProps = ['xLogScale',
                      'yLogScale',
                      'smooth',
@@ -48,22 +43,6 @@ 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'])
@@ -115,6 +94,12 @@ class TimeSeriesControlPanel(fslpanel.FSLViewPanel):
                                 self._name,
                                 self.__selectedOverlayChanged)
 
+        tsPanel.addListener('showCurrent',
+                            self._name,
+                            self.__showCurrentChanged)
+
+        self.__showCurrentChanged()
+
         # This attribute keeps track of the currently
         # selected overlay, but only if said overlay
         # is a FEATImage.
@@ -131,6 +116,44 @@ class TimeSeriesControlPanel(fslpanel.FSLViewPanel):
             display.removeListener('name', self._name)
 
 
+    def __showCurrentChanged(self, *a):
+        widgets     = self.__widgets
+        tsPanel     = self.__tsPanel
+        showCurrent = tsPanel.showCurrent
+        areShown    = widgets.HasGroup('currentSettings')
+
+        if (not showCurrent) and areShown:
+            widgets.RemoveGroup('currentSettings')
+
+        elif showCurrent and (not areShown):
+
+            self.__widgets.AddGroup('currentSettings',
+                                    strings.labels[self, 'currentSettings'])
+
+            colour    = props.makeWidget(widgets, tsPanel, 'currentColour')
+            alpha     = props.makeWidget(widgets, tsPanel, 'currentAlpha',
+                                         showLimits=False, spin=False)
+            lineWidth = props.makeWidget(widgets, tsPanel, 'currentLineWidth')
+            lineStyle = props.makeWidget(widgets, tsPanel, 'currentLineStyle')
+
+            self.__widgets.AddWidget(
+                colour,
+                displayName=strings.properties[tsPanel, 'currentColour'],
+                groupName='currentSettings')
+            self.__widgets.AddWidget(
+                alpha,
+                displayName=strings.properties[tsPanel, 'currentAlpha'],
+                groupName='currentSettings')
+            self.__widgets.AddWidget(
+                lineWidth,
+                displayName=strings.properties[tsPanel, 'currentLineWidth'],
+                groupName='currentSettings') 
+            self.__widgets.AddWidget(
+                lineStyle,
+                displayName=strings.properties[tsPanel, 'currentLineStyle'],
+                groupName='currentSettings')
+            
+
     def __selectedOverlayNameChanged(self, *a):
         display = self._displayCtx.getDisplay(self.__selectedOverlay)
         self.__widgets.RenameGroup(

fsl/fslview/views/timeseriespanel.py

@@ -29,6 +29,7 @@ import fsl.utils.transform        as transform
 
 log = logging.getLogger(__name__)
 
+
 class TimeSeries(plotpanel.DataSeries):
 
     
@@ -198,7 +199,7 @@ class FEATTimeSeries(TimeSeries):
             self.overlay,
             self.coords)
         
-        pets.colour    = (1, 0, 0)
+        pets.colour    = (0.7, 0, 0)
         pets.alpha     = self.alpha
         pets.label     = self.label
         pets.lineWidth = self.lineWidth
@@ -322,7 +323,6 @@ 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)
@@ -344,7 +344,12 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
             tss.extend(self.__currentTs.getModelTimeSeries())
 
             for ts in tss:
-                ts.colour    = self.currentColour
+
+                # Don't change the colour for associated
+                # time courses (e.g. model fits)
+                if ts is self.__currentTs:
+                    ts.colour = self.currentColour
+                    
                 ts.alpha     = self.currentAlpha
                 ts.lineWidth = self.currentLineWidth
                 ts.lineStyle = self.currentLineStyle