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Commit c1db01a5 authored by Paul McCarthy's avatar Paul McCarthy
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In process of improving time series functionality.

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fsl/data/strings.py
+ 5
− 2
View file @ c1db01a5
......@@ -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',
......
fsl/fslview/controls/__init__.py
+ 1
− 0
View file @ c1db01a5
......@@ -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
......
fsl/fslview/controls/timeserieslistpanel.py 0 → 100644
+ 59
− 0
View file @ c1db01a5
#!/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)
fsl/fslview/views/timeseriespanel.py
+ 91
− 117
View file @ c1db01a5
......@@ -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())
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