From 8e11cc847bd9296f9a9722d00c5ca679005eebf0 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Mon, 7 Jul 2014 17:11:01 +0100
Subject: [PATCH] First go at time series panel, using matplotlib. It's slow.
---
fsl/data/fslimage.py | 17 ++++-
fsl/fslview/fslviewframe.py | 82 +++++++++++++--------
fsl/fslview/strings.py | 5 +-
fsl/fslview/views/__init__.py | 6 +-
fsl/fslview/views/timeseriespanel.py | 105 +++++++++++++++++++++++++++
5 files changed, 178 insertions(+), 37 deletions(-)
create mode 100644 fsl/fslview/views/timeseriespanel.py
diff --git a/fsl/data/fslimage.py b/fsl/data/fslimage.py
index f07748dfd..1766fa3ee 100644
--- a/fsl/data/fslimage.py
+++ b/fsl/data/fslimage.py
@@ -229,6 +229,12 @@ class Image(props.HasProperties):
return self.__str__()
+ def is4DImage(self):
+ """Returns ``True`` if this image is 4D, ``False`` otherwise.
+ """
+ return len(self.shape) > 3 and self.shape[3] > 1
+
+
def _transformChanged(self, *a):
"""This method is called when the :attr:`transform` property value
changes. It updates the :attr:`voxToWorldMat`, :attr:`worldToVoxMat`,
@@ -434,35 +440,44 @@ class ImageDisplay(props.HasProperties):
the associated :class:`ImageDisplay` object.
"""
+
enabled = props.Boolean(default=True)
"""Should this image be displayed at all?"""
+
alpha = props.Real(minval=0.0, maxval=1.0, default=1.0)
"""Transparency - 1.0 is fully opaque, and 0.0 is fully transparent."""
+
displayRange = props.Bounds(ndims=1, editLimits=True,
labels=['Min.', 'Max.'])
"""Image values which map to the minimum and maximum colour map colours."""
+
samplingRate = props.Int(minval=1, maxval=16, default=1, clamped=True)
"""Only display every Nth voxel (a performance tweak)."""
+
rangeClip = props.Boolean(default=False)
"""If ``True``, don't display voxel values which are beyond the
:attr:`displayRange`.
"""
+
cmap = props.ColourMap(default=mplcm.Greys_r)
"""The colour map, a :class:`matplotlib.colors.Colourmap` instance."""
+
volume = props.Int(minval=0, maxval=0, default=0, clamped=True)
"""If a 4D image, the current volume to display."""
+
def is4DImage(self):
"""Returns ``True`` if this image is 4D, ``False`` otherwise.
"""
- return len(self.image.shape) > 3 and self.image.shape[3] > 1
+ return self.image.is4DImage()
+
_view = props.VGroup(('enabled',
props.Widget('volume', enabledWhen=is4DImage),
'displayRange',
diff --git a/fsl/fslview/fslviewframe.py b/fsl/fslview/fslviewframe.py
index bb7ab3f30..780f351a8 100644
--- a/fsl/fslview/fslviewframe.py
+++ b/fsl/fslview/fslviewframe.py
@@ -81,61 +81,74 @@ class FSLViewFrame(wx.Frame):
self.Bind(wx.EVT_CLOSE, self._onClose)
- def _addViewPanel(self, panelCls):
+ def _addViewPanel(self, panel, title, configMenuText=None):
"""Adds a view panel to the centre of the frame, and a menu item
allowing the user to configure the view.
"""
- panel = panelCls(self._centrePane,
- self._imageList,
- glContext=self._glContext)
-
- if panelCls == views.OrthoPanel:
- title = strings.orthoTitle
- menuText = strings.configOrtho
-
- if self._glContext is None:
- self._glContext = panel.xcanvas.glContext
-
- elif panelCls == views.LightBoxPanel:
- title = strings.lightBoxTitle
- menuText = strings.configLightBox
-
- if self._glContext is None:
- self._glContext = panel.canvas.glContext
-
+
self._viewPanelCount = self._viewPanelCount + 1
title = '{} {}'.format(title, self._viewPanelCount)
- menuText = menuText.format(title)
+
self._viewPanelTitles[id(panel)] = title
self._centrePane.AddPage(panel, title)
self._centrePane.SetSelection(self._centrePane.GetPageIndex(panel))
- configAction = self._viewMenu.Append(wx.ID_ANY, menuText)
+ if configMenuText is not None:
+ configMenuText = configMenuText.format(title)
+ configAction = self._viewMenu.Append(wx.ID_ANY, configMenuText)
- def onConfig(ev):
- self._addViewConfigPanel(panel, title)
-
- def onDestroy(ev):
- ev.Skip()
- try: self._viewMenu.RemoveItem(configAction)
- except wx._core.PyDeadObjectError: pass
+ def onConfig(ev):
+ self._addViewConfigPanel(panel, title)
- self .Bind(wx.EVT_MENU, onConfig, configAction)
- panel.Bind(wx.EVT_WINDOW_DESTROY, onDestroy)
+ def onDestroy(ev):
+ ev.Skip()
+ try: self._viewMenu.RemoveItem(configAction)
+ except wx._core.PyDeadObjectError: pass
+
+ self .Bind(wx.EVT_MENU, onConfig, configAction)
+ panel.Bind(wx.EVT_WINDOW_DESTROY, onDestroy)
def addOrthoPanel(self):
"""Adds an :class:`~fsl.fslview.views.orthopanel.OrthoPanel` display
to the central :class:`~wx.aui.AuiNotebook` widget.
"""
- self._addViewPanel(views.OrthoPanel)
+
+ panel = views.OrthoPanel(self._centrePane,
+ self._imageList,
+ glContext=self._glContext)
+
+ if self._glContext is None:
+ self._glContext = panel.xcanvas.glContext
+
+ self._addViewPanel(panel,
+ strings.orthoTitle,
+ strings.orthoConfigMenu)
def addLightBoxPanel(self):
"""Adds a :class:`~fsl.fslview.views.lightboxpanel.LightBoxPanel`
display to the central :class:`~wx.aui.AuiNotebook` widget.
"""
- self._addViewPanel(views.LightBoxPanel)
+ panel = views.LightBoxPanel(self._centrePane,
+ self._imageList,
+ glContext=self._glContext)
+
+ if self._glContext is None:
+ self._glContext = panel.canvas.glContext
+
+ self._addViewPanel(panel,
+ strings.lightBoxTitle,
+ strings.lightBoxConfigMenu)
+
+
+ def addTimeSeriesPanel(self):
+ """Adds a :class:`~fsl.fslview.views.lightboxpanel.LightBoxPanel`
+ display to the central :class:`~wx.aui.AuiNotebook` widget.
+ """
+
+ panel = views.TimeSeriesPanel(self._centrePane, self._imageList)
+ self._addViewPanel(panel, strings.timeSeriesTitle)
def _addViewConfigPanel(self, viewPanel, title):
@@ -389,6 +402,8 @@ class FSLViewFrame(wx.Frame):
orthoAction = viewMenu.Append(wx.ID_ANY, strings.orthoTitle)
lightboxAction = viewMenu.Append(wx.ID_ANY, strings.lightBoxTitle)
+ timeSeriesAction = viewMenu.Append(wx.ID_ANY,
+ strings.timeSeriesTitle)
imageDisplayAction = viewMenu.Append(wx.ID_ANY,
strings.imageDisplayTitle)
imageListAction = viewMenu.Append(wx.ID_ANY, strings.imageListTitle)
@@ -402,6 +417,9 @@ class FSLViewFrame(wx.Frame):
self.Bind(wx.EVT_MENU,
lambda ev: self.addLightBoxPanel(),
lightboxAction)
+ self.Bind(wx.EVT_MENU,
+ lambda ev: self.addTimeSeriesPanel(),
+ timeSeriesAction)
self.Bind(wx.EVT_MENU,
lambda ev: self.addImageDisplayPanel(),
imageDisplayAction)
diff --git a/fsl/fslview/strings.py b/fsl/fslview/strings.py
index ca139615b..b8dea45cc 100644
--- a/fsl/fslview/strings.py
+++ b/fsl/fslview/strings.py
@@ -7,6 +7,7 @@
orthoTitle = 'Ortho view'
lightBoxTitle = 'Lightbox view'
+timeSeriesTitle = 'Time series'
imageDisplayTitle = 'Image display properties'
imageListTitle = 'Image list'
locationTitle = 'Cursor location'
@@ -14,5 +15,5 @@ locationTitle = 'Cursor location'
openFile = 'Add image file'
openStd = 'Add standard'
-configOrtho = '{} display'
-configLightBox = '{} display'
+orthoConfigMenu = '{} display'
+lightBoxConfigMenu = '{} display'
diff --git a/fsl/fslview/views/__init__.py b/fsl/fslview/views/__init__.py
index 86062b802..43ad54a2a 100644
--- a/fsl/fslview/views/__init__.py
+++ b/fsl/fslview/views/__init__.py
@@ -12,6 +12,8 @@ which provide a view of an image collection (see
import orthopanel
import lightboxpanel
+import timeseriespanel
-OrthoPanel = orthopanel .OrthoPanel
-LightBoxPanel = lightboxpanel.LightBoxPanel
+OrthoPanel = orthopanel .OrthoPanel
+LightBoxPanel = lightboxpanel .LightBoxPanel
+TimeSeriesPanel = timeseriespanel.TimeSeriesPanel
diff --git a/fsl/fslview/views/timeseriespanel.py b/fsl/fslview/views/timeseriespanel.py
new file mode 100644
index 000000000..83c61c491
--- /dev/null
+++ b/fsl/fslview/views/timeseriespanel.py
@@ -0,0 +1,105 @@
+#!/usr/bin/env python
+#
+# timeseriespanel.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import logging
+log = logging.getLogger(__name__)
+
+import wx
+
+import props
+
+import matplotlib as mpl
+
+mpl.use('WXAgg')
+
+import matplotlib.pyplot as plt
+from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas
+
+class TimeSeriesPanel(wx.Panel, props.HasProperties):
+
+
+ def __init__(self, parent, imageList):
+
+ wx.Panel.__init__(self, parent)
+ props.HasProperties.__init__(self)
+
+ self._imageList = imageList
+ self._name = '{}_{}'.format(self.__class__.__name__, id(self))
+
+ self._figure = plt.Figure()
+ self._axis = self._figure.add_subplot(1, 1, 1)
+ self._canvas = Canvas(self, -1, self._figure)
+
+ self._sizer = wx.BoxSizer(wx.VERTICAL)
+ self.SetSizer(self._sizer)
+ self._sizer.Add(self._canvas, flag=wx.EXPAND, proportion=1)
+
+ self._imageList.addListener(
+ 'selectedImage',
+ self._name,
+ self._selectedImageChanged)
+
+ self._imageList.addListener(
+ 'location',
+ self._name,
+ self._locationChanged)
+
+ def onDestroy(ev):
+ ev.Skip()
+ self._imageList.removeListener('selectedImage', self._name)
+ self._imageList.removeListener('location', self._name)
+
+ self.Bind(wx.EVT_WINDOW_DESTROY, onDestroy)
+
+ self._selectedImageChanged()
+
+
+ self.Layout()
+
+
+ def _selectedImageChanged(self, *a):
+
+ self._axis.clear()
+
+ if len(self._imageList) == 0:
+ return
+
+ image = self._imageList[self._imageList.selectedImage]
+
+ if not image.is4DImage():
+ return
+
+ self._voxPlot(image, *self._imageList.location.xyz)
+
+
+ def _locationChanged(self, *a):
+
+ self._axis.clear()
+
+ if len(self._imageList) == 0:
+ return
+
+ image = self._imageList[self._imageList.selectedImage]
+
+ if not image.is4DImage():
+ return
+
+ self._voxPlot(image, *self._imageList.location.xyz)
+
+
+ def _voxPlot(self, image, x, y, z):
+
+ x, y, z = image.worldToVox([[x, y, z]])[0]
+
+ data = image.data[x, y, z, :]
+
+ print
+ print 'Plot ({}, {}, {}): {}'.format(x, y, z, data)
+ print
+
+ self._axis.plot(data, 'r-', lw=2)
+ self._canvas.draw()
--
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