From c1db01a517da761479304f3426e97fdcd0eb17b4 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Thu, 25 Jun 2015 17:22:50 +0100
Subject: [PATCH] In process of improving time series functionality.
---
fsl/data/strings.py | 7 +-
fsl/fslview/controls/__init__.py | 1 +
fsl/fslview/controls/timeserieslistpanel.py | 59 ++++++
fsl/fslview/views/timeseriespanel.py | 208 +++++++++-----------
4 files changed, 156 insertions(+), 119 deletions(-)
create mode 100644 fsl/fslview/controls/timeserieslistpanel.py
diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index fab0d8759..ada85f980 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -116,6 +116,7 @@ titles = TypeDict({
'LookupTablePanel' : 'Lookup tables',
'LutLabelDialog' : 'New LUT label',
'NewLutDialog' : 'New LUT',
+ 'TimeSeriesListPanel' : 'Time series list',
'LookupTablePanel.loadLut' : 'Select a lookup table file',
'LookupTablePanel.labelExists' : 'Label already exists',
@@ -148,9 +149,11 @@ actions = TypeDict({
'LightBoxPanel.toggleLightBoxToolBar' : 'View properties',
- 'PlotPanel.screenshot' : 'Take screenshot',
+ 'PlotPanel.screenshot' : 'Take screenshot',
- 'HistogramPanel.toggleToolbar' : 'Histogram controls',
+ 'TimeSeriesPanel.toggleTimeSeriesList' : 'Time series list',
+ 'HistogramPanel.toggleToolbar' : 'Histogram controls',
+
'OrthoViewProfile.centreCursor' : 'Centre cursor',
diff --git a/fsl/fslview/controls/__init__.py b/fsl/fslview/controls/__init__.py
index 9ee27b304..fbfd7642b 100644
--- a/fsl/fslview/controls/__init__.py
+++ b/fsl/fslview/controls/__init__.py
@@ -13,6 +13,7 @@ from lightboxsettingspanel import LightBoxSettingsPanel
from locationpanel import LocationPanel
from orthosettingspanel import OrthoSettingsPanel
from lookuptablepanel import LookupTablePanel
+from timeserieslistpanel import TimeSeriesListPanel
from orthotoolbar import OrthoToolBar
from orthoprofiletoolbar import OrthoProfileToolBar
diff --git a/fsl/fslview/controls/timeserieslistpanel.py b/fsl/fslview/controls/timeserieslistpanel.py
new file mode 100644
index 000000000..346be2209
--- /dev/null
+++ b/fsl/fslview/controls/timeserieslistpanel.py
@@ -0,0 +1,59 @@
+#!/usr/bin/env python
+#
+# timeserieslistpanel.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import wx
+
+import pwidgets.elistbox as elistbox
+import fsl.fslview.panel as fslpanel
+import fsl.fslview.colourmaps as fslcm
+
+
+class TimeSeriesListPanel(fslpanel.FSLViewPanel):
+
+ def __init__(self, parent, overlayList, displayCtx, timeSeriesPanel):
+
+ fslpanel.FSLViewPanel.__init__(self, parent, overlayList, displayCtx)
+
+ self.__tsPanel = timeSeriesPanel
+ self.__currentLabel = wx.StaticText( self)
+ self.__tsList = elistbox.EditableListBox(self)
+
+ self.__sizer = wx.BoxSizer(wx.VERTICAL)
+ self.SetSizer(self.__sizer)
+
+ self.__sizer.Add(self.__currentLabel, flag=wx.EXPAND)
+ self.__sizer.Add(self.__tsList, flag=wx.EXPAND, proportion=1)
+
+
+ displayCtx .addListener('selectedOverlay',
+ self._name,
+ self.__locationChanged)
+ overlayList.addListener('overlays',
+ self._name,
+ self.__locationChanged)
+
+ self.Layout()
+
+
+ def destroy(self):
+ fslpanel.FSLViewPanel.destroy(self)
+ self._displayCtx .removeListener('selectedOverlay', self._name)
+ self._overlayList.removeListener('overlays', self._name)
+
+
+ def __locationChanged(self, *a):
+ pass
+
+
+ def __onListAdd(self, ev):
+
+ ts = self.__tsPanel.getCurrent()
+
+ ts.colour = fslcm.randomColour()
+
+ self.__tsPanel.timeSeries.append(ts)
+
diff --git a/fsl/fslview/views/timeseriespanel.py b/fsl/fslview/views/timeseriespanel.py
index bb61bfbca..310734d23 100644
--- a/fsl/fslview/views/timeseriespanel.py
+++ b/fsl/fslview/views/timeseriespanel.py
@@ -16,10 +16,14 @@ import logging
import numpy as np
+import props
+
import plotpanel
import fsl.data.image as fslimage
import fsl.data.strings as strings
import fsl.fslview.displaycontext as fsldisplay
+import fsl.fslview.colourmaps as fslcm
+import fsl.fslview.controls as fslcontrols
import fsl.utils.transform as transform
@@ -36,6 +40,16 @@ log = logging.getLogger(__name__)
# of each persistent time course
+class TimeSeries(object):
+
+ def __init__(self, overlay, coords, data, colour, label):
+ self.overlay = overlay
+ self.coords = coords
+ self.data = data
+ self.colour = colour
+ self.label = label
+
+
class TimeSeriesPanel(plotpanel.PlotPanel):
"""A panel with a :mod:`matplotlib` canvas embedded within.
@@ -44,38 +58,37 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
plotted on the canvas.
"""
+
+ timeSeries = props.List()
+
+
def __init__(self, parent, overlayList, displayCtx):
- plotpanel.PlotPanel.__init__(self, parent, overlayList, displayCtx)
+ actionz = {
+ 'toggleTimeSeriesList' : lambda *a: self.togglePanel(
+ fslcontrols.TimeSeriesListPanel, False, self)
+ }
+
+ plotpanel.PlotPanel.__init__(
+ self, parent, overlayList, displayCtx, actionz=actionz)
figure = self.getFigure()
- canvas = self.getCanvas()
figure.subplots_adjust(
top=1.0, bottom=0.0, left=0.0, right=1.0)
figure.patch.set_visible(False)
- self._mouseDown = False
- canvas.mpl_connect('button_press_event', self._onPlotMouseDown)
- canvas.mpl_connect('button_release_event', self._onPlotMouseUp)
- canvas.mpl_connect('motion_notify_event', self._onPlotMouseMove)
-
- self._overlayList.addListener(
- 'overlays',
- self._name,
- self._selectedOverlayChanged)
- self._displayCtx.addListener(
- 'selectedOverlay',
- self._name,
- self._selectedOverlayChanged)
- self._displayCtx.addListener(
- 'location',
- self._name,
- self._locationChanged)
+ name = self._name
+ draw = self._draw
+
+ self._overlayList.addListener('overlays', name, draw)
+ self._displayCtx .addListener('selectedOverlay', name, draw)
+ self._displayCtx .addListener('location', name, draw)
+ self .addListener('timeSeries', name, draw)
self.Layout()
- self._selectedOverlayChanged()
+ self._draw()
def destroy(self):
@@ -85,126 +98,87 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
self._displayCtx .removeListener('selectedOverlay', self._name)
self._displayCtx .removeListener('location', self._name)
- for ovl in self._overlayList:
- opts = self._displayCtx.getOpts(ovl)
-
- if isinstance(opts, fsldisplay.ImageOpts):
- opts.removeListener('volume', self._name)
-
-
- def _selectedOverlayChanged(self, *a):
-
- overlay = self._displayCtx.getSelectedOverlay()
-
- for ovl in self._overlayList:
-
- if not isinstance(ovl, fslimage.Image):
- continue
-
- opts = self._displayCtx.getOpts(ovl)
-
- if ovl is overlay:
- opts.addListener('volume',
- self._name,
- self._locationChanged,
- overwrite=True)
- else:
- opts.removeListener('volume', self._name)
-
- self._locationChanged()
-
-
- def _locationChanged(self, *a):
-
- self.getAxis().clear()
- if len(self._overlayList) == 0:
- self.getCanvas().draw()
- self.Refresh()
- else:
- self._drawPlot()
-
+ def getCurrent(self):
- def _drawPlot(self):
-
- axis = self.getAxis()
- canvas = self.getCanvas()
x, y, z = self._displayCtx.location.xyz
overlay = self._displayCtx.getSelectedOverlay()
+ opts = self._displayCtx.getOpts(overlay)
- if not isinstance(overlay, fslimage.Image):
- self.message(strings.messages[self, 'noData'])
-
- elif not overlay.is4DImage():
- self.message(strings.messages[self, 'not4D'])
+ if not isinstance(overlay, fslimage.Image) or \
+ not isinstance(opts, fsldisplay.VolumeOpts) or \
+ not overlay.is4DImage():
+ return None
+
+ xform = opts.getTransform('display', 'voxel')
+ vox = transform.transform([[x, y, z]], xform)[0]
+ vox = np.floor(vox + 0.5)
- else:
- opts = self._displayCtx.getOpts(overlay)
- xform = opts.getTransform('display', 'voxel')
+ if vox[0] < 0 or \
+ vox[1] < 0 or \
+ vox[2] < 0 or \
+ vox[0] >= overlay.shape[0] or \
+ vox[1] >= overlay.shape[1] or \
+ vox[2] >= overlay.shape[2]:
+ return None
- vox = transform.transform([[x, y, z]], xform)[0]
- vox = np.floor(vox + 0.5)
+ return TimeSeries(
+ overlay,
+ vox,
+ overlay.data[vox[0], vox[1], vox[2], :],
+ [0.5, 0.5, 0.5],
+ '{} [{} {} {}]'.format(overlay.name, vox[0], vox[1], vox[2]))
- if vox[0] < 0 or \
- vox[1] < 0 or \
- vox[2] < 0 or \
- vox[0] >= overlay.shape[0] or \
- vox[1] >= overlay.shape[1] or \
- vox[2] >= overlay.shape[2]:
-
- self.message(strings.messages[self, 'outOfBounds'])
- else:
- self._drawPlotOneOverlay(overlay, *vox)
- axis.axvline(opts.volume, c='#000080', lw=2, alpha=0.4)
+ def _draw(self, *a):
- canvas.draw()
- self.Refresh()
+ axis = self.getAxis()
+ canvas = self.getCanvas()
+ axis.clear()
- def _drawPlotOneOverlay(self, overlay, x, y, z):
+ toPlot = self.timeSeries[:]
+ currentTs = self.getCurrent()
- display = self._displayCtx.getDisplay(overlay)
+ if currentTs is not None:
+ toPlot = [currentTs] + toPlot
- if not overlay.is4DImage(): return None
- if not display.enabled: return None
+ if len(toPlot) == 0:
+ canvas.draw()
+ self.Refresh()
+ return
- for vox, shape in zip((x, y, z), overlay.shape):
- if vox >= shape or vox < 0:
- return None
+ xlims = []
+ ylims = []
- data = overlay.data[x, y, z, :]
- self.getAxis().plot(data, lw=2)
+ for ts in toPlot:
+ xlim, ylim = self._drawTimeSeries(ts)
+ xlims.append(xlim)
+ ylims.append(ylim)
- return data.min(), data.max(), len(data)
+ # Set x/ylim
+ xmin = min([lim[0] for lim in xlims])
+ xmax = max([lim[1] for lim in xlims])
+ ymin = min([lim[0] for lim in ylims])
+ ymax = max([lim[1] for lim in ylims])
+ axis.set_xlim((xmin, xmax))
+ axis.set_ylim((ymin, ymax))
- def _onPlotMouseDown(self, ev):
- if ev.inaxes != self.getAxis(): return
+ canvas.draw()
+ self.Refresh()
- overlay = self._displayCtx.getSelectedOverlay()
- if not isinstance(overlay, fslimage.Image) or not overlay.is4DImage():
- return
- self._mouseDown = True
+ def _drawTimeSeries(self, ts):
- opts = self._displayCtx.getOpts(overlay)
- opts.volume = np.floor(ev.xdata)
-
+ display = self._displayCtx.getDisplay(ts.overlay)
- def _onPlotMouseUp(self, ev):
- self._mouseDown = False
+ if not display.enabled:
+ return None
+ data = ts.data
- def _onPlotMouseMove(self, ev):
- if not self._mouseDown: return
- if ev.inaxes != self.getAxis(): return
-
- overlay = self._displayCtx.getSelectedOverlay()
+ self.getAxis().plot(data, lw=2, c=ts.colour, label=ts.label)
- if not isinstance(overlay, fslimage.Image) or not overlay.is4DImage():
- return
-
- opts = self._displayCtx.getOpts(overlay)
-
- opts.volume = np.floor(ev.xdata)
+ # TODO take into account TR
+ return (0, len(data)), (data.min(), data.max())
--
GitLab