From ee993e1daa4920cca79eafdbe8b6314df7b9351d Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Fri, 26 Jun 2015 17:07:43 +0100
Subject: [PATCH] Improved log scale plotting, and added neato option to apply
smoothing to time courses. Improved time series control panel layout too.
---
fsl/data/strings.py | 8 ++-
.../controls/timeseriescontrolpanel.py | 30 +++++++---
fsl/fslview/controls/timeserieslistpanel.py | 2 +-
fsl/fslview/views/timeseriespanel.py | 60 ++++++++++++-------
4 files changed, 66 insertions(+), 34 deletions(-)
diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index 02057b5b3..c220f46f3 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -203,8 +203,9 @@ labels = TypeDict({
'TimeSeriesControlPanel.xlim' : 'X limits',
'TimeSeriesControlPanel.ylim' : 'Y limits',
- 'TimeSeriesControlPanel.xlabel' : 'X label',
- 'TimeSeriesControlPanel.ylabel' : 'Y label',
+ 'TimeSeriesControlPanel.labels' : 'Labels',
+ 'TimeSeriesControlPanel.xlabel' : 'X',
+ 'TimeSeriesControlPanel.ylabel' : 'Y',
})
@@ -247,6 +248,7 @@ properties = TypeDict({
'TimeSeriesPanel.legend' : 'Show legend',
'TimeSeriesPanel.ticks' : 'Show ticks',
'TimeSeriesPanel.grid' : 'Show grid',
+ 'TimeSeriesPanel.smooth' : 'Smooth data',
'TimeSeriesPanel.autoScale' : 'Auto-scale',
'TimeSeriesPanel.xLogScale' : 'Log scale (x axis)',
'TimeSeriesPanel.yLogScale' : 'Log scale (y axis)',
@@ -355,7 +357,7 @@ choices = TypeDict({
'ColourBarCanvas.orientation.horizontal' : 'Horizontal',
'ColourBarCanvas.orientation.vertical' : 'Vertical',
- 'ColourBarCanvas.labelSide.top-left' : 'Top / Left',
+ 'ColourBarCanvas.labelSide.top-left' : 'Top / Left',
'ColourBarCanvas.labelSide.bottom-right' : 'Bottom / Right',
'VolumeOpts.displayRange.min' : 'Min.',
diff --git a/fsl/fslview/controls/timeseriescontrolpanel.py b/fsl/fslview/controls/timeseriescontrolpanel.py
index 7b4bc5b59..7a853d7fa 100644
--- a/fsl/fslview/controls/timeseriescontrolpanel.py
+++ b/fsl/fslview/controls/timeseriescontrolpanel.py
@@ -25,6 +25,7 @@ class TimeSeriesControlPanel(fslpanel.FSLViewPanel):
self.__usePixdim = props.makeWidget(self, tsPanel, 'usePixdim')
self.__logx = props.makeWidget(self, tsPanel, 'xLogScale')
self.__logy = props.makeWidget(self, tsPanel, 'yLogScale')
+ self.__smooth = props.makeWidget(self, tsPanel, 'smooth')
self.__legend = props.makeWidget(self, tsPanel, 'legend')
self.__ticks = props.makeWidget(self, tsPanel, 'ticks')
self.__grid = props.makeWidget(self, tsPanel, 'grid')
@@ -38,6 +39,7 @@ class TimeSeriesControlPanel(fslpanel.FSLViewPanel):
self.__ymin = props.makeWidget(self, tsPanel, 'ymin')
self.__ymax = props.makeWidget(self, tsPanel, 'ymax')
+ self.__lblLabel = wx.StaticText(self)
self.__xlblLabel = wx.StaticText(self)
self.__ylblLabel = wx.StaticText(self)
self.__xlimLabel = wx.StaticText(self)
@@ -47,42 +49,56 @@ class TimeSeriesControlPanel(fslpanel.FSLViewPanel):
self.__usePixdim.SetLabel(strings.properties[tsPanel, 'usePixdim'])
self.__logx .SetLabel(strings.properties[tsPanel, 'xLogScale'])
self.__logy .SetLabel(strings.properties[tsPanel, 'yLogScale'])
+ self.__smooth .SetLabel(strings.properties[tsPanel, 'smooth'])
self.__legend .SetLabel(strings.properties[tsPanel, 'legend'])
self.__ticks .SetLabel(strings.properties[tsPanel, 'ticks'])
self.__grid .SetLabel(strings.properties[tsPanel, 'grid'])
self.__autoScale.SetLabel(strings.properties[tsPanel, 'autoScale'])
self.__xlimLabel.SetLabel(strings.labels[ self, 'xlim'])
self.__ylimLabel.SetLabel(strings.labels[ self, 'ylim'])
+ self.__lblLabel .SetLabel(strings.labels[ self, 'labels'])
self.__xlblLabel.SetLabel(strings.labels[ self, 'xlabel'])
self.__ylblLabel.SetLabel(strings.labels[ self, 'ylabel'])
- self.__sizer = wx.GridSizer(10, 2)
+ self.__sizer = wx.GridSizer(6, 3)
self.SetSizer(self.__sizer)
+ self.__xlblSizer = wx.BoxSizer(wx.HORIZONTAL)
+ self.__xlblSizer.Add(self.__xlblLabel)
+ self.__xlblSizer.Add(self.__xlabel, flag=wx.EXPAND, proportion=1)
+
+ self.__ylblSizer = wx.BoxSizer(wx.HORIZONTAL)
+ self.__ylblSizer.Add(self.__ylblLabel)
+ self.__ylblSizer.Add(self.__ylabel, flag=wx.EXPAND, proportion=1)
+
self.__sizer.Add(self.__demean, flag=wx.EXPAND)
self.__sizer.Add(self.__usePixdim, flag=wx.EXPAND)
+ self.__sizer.Add(self.__smooth, flag=wx.EXPAND)
+
self.__sizer.Add(self.__logx, flag=wx.EXPAND)
self.__sizer.Add(self.__logy, flag=wx.EXPAND)
self.__sizer.Add(self.__legend, flag=wx.EXPAND)
+
self.__sizer.Add(self.__ticks, flag=wx.EXPAND)
self.__sizer.Add(self.__grid, flag=wx.EXPAND)
self.__sizer.Add(self.__autoScale, flag=wx.EXPAND)
- self.__sizer.Add(self.__xlblLabel, flag=wx.EXPAND)
- self.__sizer.Add(self.__ylblLabel, flag=wx.EXPAND)
- self.__sizer.Add(self.__xlabel, flag=wx.EXPAND)
- self.__sizer.Add(self.__ylabel, flag=wx.EXPAND)
+
+ self.__sizer.Add(self.__lblLabel, flag=wx.EXPAND)
+ self.__sizer.Add(self.__xlblSizer, flag=wx.EXPAND)
+ self.__sizer.Add(self.__ylblSizer, flag=wx.EXPAND)
+
self.__sizer.Add(self.__xlimLabel, flag=wx.EXPAND)
- self.__sizer.Add((-1, -1), flag=wx.EXPAND)
self.__sizer.Add(self.__xmin, flag=wx.EXPAND)
self.__sizer.Add(self.__xmax, flag=wx.EXPAND)
+
self.__sizer.Add(self.__ylimLabel, flag=wx.EXPAND)
- self.__sizer.Add((-1, -1), flag=wx.EXPAND)
self.__sizer.Add(self.__ymin, flag=wx.EXPAND)
self.__sizer.Add(self.__ymax, flag=wx.EXPAND)
self.Layout()
self.SetMinSize(self.__sizer.GetMinSize())
+ self.SetMaxSize(self.__sizer.GetMinSize())
tsPanel.addListener('autoScale', self._name, self.__autoScaleChanged)
diff --git a/fsl/fslview/controls/timeserieslistpanel.py b/fsl/fslview/controls/timeserieslistpanel.py
index cea9384e4..21e6670dc 100644
--- a/fsl/fslview/controls/timeserieslistpanel.py
+++ b/fsl/fslview/controls/timeserieslistpanel.py
@@ -133,7 +133,7 @@ class TimeSeriesListPanel(fslpanel.FSLViewPanel):
return
ts.alpha = 1
- ts.lineWidth = 1
+ ts.lineWidth = 2
ts.lineStyle = '-'
ts.colour = fslcm.randomColour()
ts.label = self.__makeLabel(ts)
diff --git a/fsl/fslview/views/timeseriespanel.py b/fsl/fslview/views/timeseriespanel.py
index 4765436ca..0c7a313c5 100644
--- a/fsl/fslview/views/timeseriespanel.py
+++ b/fsl/fslview/views/timeseriespanel.py
@@ -15,6 +15,7 @@ of overlay objects stored in an :class:`.OverlayList`.
import logging
import wx
+import scipy.interpolate as interp
import numpy as np
import props
@@ -66,6 +67,7 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
yLogScale = props.Boolean(default=False)
ticks = props.Boolean(default=True)
grid = props.Boolean(default=True)
+ smooth = props.Boolean(default=False)
xlabel = props.String()
ylabel = props.String()
xmin = props.Real()
@@ -239,21 +241,9 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
xlims.append(xlim)
ylims.append(ylim)
- if self.xLogScale: axis.set_xscale('log')
- else: axis.set_xscale('linear')
- if self.yLogScale: axis.set_yscale('log')
- else: axis.set_yscale('linear')
-
- xlim, ylim = self.__calcLimits(xlims, ylims)
-
- bPad = (ylim[1] - ylim[0]) * (50.0 / height)
- tPad = (ylim[1] - ylim[0]) * (20.0 / height)
- lPad = (xlim[1] - xlim[0]) * (50.0 / width)
- rPad = (xlim[1] - xlim[0]) * (20.0 / width)
-
- axis.set_xlim((xlim[0] - lPad, xlim[1] + rPad))
- axis.set_ylim((ylim[0] - bPad, ylim[1] + tPad))
+ (xmin, xmax), (ymin, ymax) = self.__calcLimits(xlims, ylims)
+ # x/y axis labels
xlabel = self.xlabel
ylabel = self.ylabel
@@ -271,9 +261,10 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
axis.set_ylabel(self.ylabel, va='top')
axis.yaxis.set_label_coords(10.0 / width, 0.5)
+ # Ticks
if self.ticks:
- xticks = np.linspace(xlim[0], xlim[1], 4)
- yticks = np.linspace(ylim[0], ylim[1], 4)
+ xticks = np.linspace(xmin, xmax, 4)
+ yticks = np.linspace(ymin, ymax, 4)
axis.tick_params(direction='in', pad=-5)
@@ -289,6 +280,15 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
axis.set_xticks([])
axis.set_yticks([])
+ # Limits
+ bPad = (ymax - ymin) * (50.0 / height)
+ tPad = (ymax - ymin) * (20.0 / height)
+ lPad = (xmax - xmin) * (50.0 / width)
+ rPad = (xmax - xmin) * (20.0 / width)
+
+ axis.set_xlim((xmin - lPad, xmax + rPad))
+ axis.set_ylim((ymin - bPad, ymax + tPad))
+
# legend - don't show if we're only
# plotting the current location
if len(self.timeSeries) > 0 and self.legend:
@@ -300,7 +300,6 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
fancybox=True)
legend.get_frame().set_alpha(0.3)
-
if self.grid:
axis.grid()
@@ -312,14 +311,29 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
if ts.alpha == 0:
return (0, 0), (0, 0)
-
- ydata = ts.data
+ ydata = np.array(ts.data, dtype=np.float32)
+ npoints = len(ydata)
+
if self.demean:
ydata = ydata - ydata.mean()
- if self.usePixdim: xdata = np.arange(len(ydata)) * ts.overlay.pixdim[3]
- else: xdata = np.arange(len(ydata))
+ if self.smooth:
+ tck = interp.splrep(np.arange(npoints), ydata)
+ ydata = interp.splev(np.linspace(0, npoints - 1, 5 * npoints), tck)
+
+ xdata = np.linspace(0, npoints - 1, len(ydata), dtype=np.float32)
+
+ if self.usePixdim:
+ xdata *= ts.overlay.pixdim[3]
+
+ if self.xLogScale: xdata = np.log10(xdata)
+ if self.yLogScale: ydata = np.log10(ydata)
+
+ nans = ~(np.isfinite(xdata) & np.isfinite(ydata))
+
+ xdata[nans] = np.nan
+ ydata[nans] = np.nan
kwargs = {}
kwargs['lw'] = ts.lineWidth
@@ -330,5 +344,5 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
self.getAxis().plot(xdata, ydata, **kwargs)
- return ((xdata.min(), xdata.max()),
- (ydata.min(), ydata.max()))
+ return ((np.nanmin(xdata), np.nanmax(xdata)),
+ (np.nanmin(ydata), np.nanmax(ydata)))
--
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