#
# plotpanel.py - The PlotPanel class.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""This module provides the :class:`PlotPanel` and :class:`.OverlayPlotPanel`
classes. The ``PlotPanel`` class is the base class for all *FSLeyes views*
which display some sort of data plot. The ``OverlayPlotPanel`` is a
``PlotPanel`` which contains some extra logic for displaying plots related to
the currently selected overlay.
"""
import logging
import collections
import wx
import numpy as np
import scipy.interpolate as interp
import matplotlib.pyplot as plt
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas
import fsl.utils.idle as idle
import fsleyes_props as props
import fsleyes_widgets as fwidgets
import fsleyes_widgets.elistbox as elistbox
import fsleyes.strings as strings
import fsleyes.actions as actions
import fsleyes.overlay as fsloverlay
import fsleyes.colourmaps as fslcm
import fsleyes.plotting as plotting
import fsleyes.controls.overlaylistpanel as overlaylistpanel
import fsleyes.controls.plotlistpanel as plotlistpanel
from . import viewpanel
log = logging.getLogger(__name__)
[docs]class PlotPanel(viewpanel.ViewPanel):
"""The ``PlotPanel`` class is the base class for all *FSLeyes views*
which display some sort of 2D data plot, such as the
:class:`.TimeSeriesPanel`, and the :class:`.HistogramPanel`.
See also the :class:`OverlayPlotPanel`, which contains extra logic for
displaying plots related to the currently selected overlay.
``PlotPanel`` uses :mod:`matplotlib` for its plotting. The ``matplotlib``
``Figure``, ``Axis``, and ``Canvas`` instances can be accessed via the
:meth:`getFigure`, :meth:`getAxis`, and :meth:`getCanvas` methods, if they
are needed. Various display settings can be configured through
``PlotPanel`` properties, including :attr:`legend`, :attr:`smooth`, etc.
**Sub-class requirements**
Sub-class implementations of ``PlotPanel`` must do the following:
1. Call the ``PlotPanel`` constructor.
2. Define a :class:`.DataSeries` sub-class.
3. Override the :meth:`draw` method, so it calls the
:meth:`drawDataSeries` method.
4. If necessary, override the :meth:`prepareDataSeries` method to
perform any preprocessing on ``extraSeries`` passed to the
:meth:`drawDataSeries` method (but not applied to
:class:`.DataSeries` that have been added to the :attr:`dataSeries`
list).
5. If necessary, override the :meth:`destroy` method, but make
sure that the base-class implementation is called.
**Data series**
A ``PlotPanel`` instance plots data contained in one or more
:class:`.DataSeries` instances; all ``DataSeries`` classes are defined in
the :mod:`.plotting` sub-package. Therefore, ``PlotPanel`` sub-classes
also need to define a sub-class of the :class:`.DataSeries` base class.
``DataSeries`` objects can be plotted by passing them to the
:meth:`drawDataSeries` method.
Or, if you want one or more ``DataSeries`` to be *held*, i.e. plotted
every time, you can add them to the :attr:`dataSeries` list. The
``DataSeries`` in the :attr:`dataSeries` list will be plotted on every
call to :meth:`drawDataSeries` (in addition to any ``DataSeries`` passed
directly to :meth:`drawDataSeries`) until they are removed from the
:attr:`dataSeries` list.
**The draw queue**
The ``PlotPanel`` uses a :class:`.async.TaskThread` to asynchronously
extract and prepare data for plotting, This is because data preparation
may take a long time for large :class:`.Image` overlays, and the main
application thread should not be blocked while this is occurring. The
``TaskThread`` instance is accessible through the :meth:`getDrawQueue`
method, in case anything needs to be scheduled on it.
**Plot panel actions**
A number of :mod:`actions` are also provided by the ``PlotPanel`` class:
.. autosummary::
:nosignatures:
screenshot
importDataSeries
exportDataSeries
"""
dataSeries = props.List()
"""This list contains :class:`.DataSeries` instances which are plotted
on every call to :meth:`drawDataSeries`. ``DataSeries`` instances can
be added/removed directly to/from this list.
"""
artists = props.List()
"""This list contains any ``matplotlib.Artist`` instances which are
plotted every call to :meth:`drawArtists`.
"""
legend = props.Boolean(default=True)
"""If ``True``, a legend is added to the plot, with an entry for every
``DataSeries`` instance in the :attr:`dataSeries` list.
"""
xAutoScale = props.Boolean(default=True)
"""If ``True``, the plot :attr:`limits` for the X axis are automatically
updated to fit all plotted data.
"""
yAutoScale = props.Boolean(default=True)
"""If ``True``, the plot :attr:`limits` for the Y axis are automatically
updated to fit all plotted data.
"""
xLogScale = props.Boolean(default=False)
"""Toggle a :math:`log_{10}` x axis scale. """
yLogScale = props.Boolean(default=False)
"""Toggle a :math:`log_{10}` y axis scale. """
invertX = props.Boolean(default=False)
"""Invert the plot along the X axis. """
invertY = props.Boolean(default=False)
"""Invert the plot along the Y axis. """
xScale = props.Real(default=1)
"""Scale to apply to the X axis data. """
yScale = props.Real(default=1)
"""Scale to apply to the Y axis data. """
xOffset = props.Real(default=0)
"""Offset to apply to the X axis data. """
yOffset = props.Real(default=0)
"""Offset to apply to the Y axis data. """
ticks = props.Boolean(default=True)
"""Toggle axis ticks and tick labels on/off."""
grid = props.Boolean(default=True)
"""Toggle an axis grid on/off."""
gridColour = props.Colour(default=(1, 1, 1))
"""Grid colour (if :attr:`grid` is ``True``)."""
bgColour = props.Colour(default=(0.8, 0.8, 0.8))
"""Plot background colour."""
smooth = props.Boolean(default=False)
"""If ``True`` all plotted data is up-sampled, and smoothed using
spline interpolation.
"""
xlabel = props.String()
"""A label to show on the x axis. """
ylabel = props.String()
"""A label to show on the y axis. """
limits = props.Bounds(ndims=2)
"""The x/y axis limits. If :attr:`xAutoScale` and :attr:`yAutoScale` are
``True``, these limit values are automatically updated on every call to
:meth:`drawDataSeries`.
"""
[docs] def __init__(self, parent, overlayList, displayCtx, frame):
"""Create a ``PlotPanel``.
:arg parent: The :mod:`wx` parent object.
:arg overlayList: An :class:`.OverlayList` instance.
:arg displayCtx: A :class:`.DisplayContext` instance.
:arg frame: The :class:`.FSLeyesFrame` instance.
"""
viewpanel.ViewPanel.__init__(
self, parent, overlayList, displayCtx, frame)
figure = plt.Figure()
axis = figure.add_subplot(111)
canvas = Canvas(self, -1, figure)
figure.subplots_adjust(top=1.0, bottom=0.0, left=0.0, right=1.0)
figure.patch.set_visible(False)
self.centrePanel = canvas
self.__figure = figure
self.__axis = axis
self.__canvas = canvas
self.__name = 'PlotPanel_{}'.format(self.name)
# Accessing data from large compressed
# files may take time, so we maintain
# a queue of plotting requests. The
# functions executed on this task
# thread are used to prepare data for
# plotting - the plotting occurs on
# the main WX event loop.
#
# The drawDataSeries method sets up the
# asynchronous data preparation, and the
# __drawDataSeries method does the actual
# plotting.
self.__drawQueue = idle.TaskThread()
self.__drawQueue.daemon = True
self.__drawQueue.start()
# Whenever a new request comes in to
# draw the plot, we can't cancel any
# pending requests, as they are running
# on separate threads and out of our
# control (and could be blocking on I/O).
#
# Instead, we keep track of the total
# number of pending requests. The
# __drawDataSeries method (which does the
# actual plotting) will only draw the
# plot if there are no pending requests
# (because otherwise it would be drawing
# out-of-date data).
self.__drawRequests = 0
# The getDrawnDataSeries method returns
# data as it is shown on the plot - some
# pre/post-processing may be applied to
# the data as retrieved by DataSeries
# instances, so this dictionary is used
# to keep copies of the mpl Artist object
# which contains the data with all
# processing applied, that is currrently
# on the plot (and accessible via
# getDrawnDataSeries).
self.__drawnDataSeries = collections.OrderedDict()
# Redraw whenever any property changes,
for propName in ['legend',
'xAutoScale',
'yAutoScale',
'xLogScale',
'yLogScale',
'invertX',
'invertY',
'xScale',
'yScale',
'xOffset',
'yOffset',
'ticks',
'grid',
'gridColour',
'bgColour',
'smooth',
'xlabel',
'ylabel']:
self.addListener(propName, self.__name, self.asyncDraw)
# custom listeners for a couple of properties
self.addListener('dataSeries',
self.__name,
self.__dataSeriesChanged)
self.addListener('artists',
self.__name,
self.__artistsChanged)
self.addListener('limits',
self.__name,
self.__limitsChanged)
[docs] def getAxis(self):
"""Returns the ``matplotlib`` ``Axis`` instance."""
return self.__axis
[docs] def getCanvas(self):
"""Returns the ``matplotlib`` ``Canvas`` instance."""
return self.__canvas
[docs] def getDrawQueue(self):
"""Returns the :class`.idle.TaskThread` instance used for data
preparation.
"""
return self.__drawQueue
[docs] def draw(self, *a):
"""This method must be overridden by ``PlotPanel`` sub-classes.
It is called whenever a :class:`.DataSeries` is added to the
:attr:`dataSeries` list, or when any plot display properties change.
Sub-class implementations should call the :meth:`drawDataSeries`
and meth:`drawArtists` methods.
"""
raise NotImplementedError('The draw method must be '
'implemented by PlotPanel subclasses')
[docs] def asyncDraw(self, *a):
"""Schedules :meth:`draw` to be run asynchronously. This method
should be used in preference to calling :meth:`draw` directly
in most cases, particularly where the call occurs within a
property callback function.
"""
idleName = '{}.draw'.format(id(self))
if not self.destroyed and not idle.idleLoop.inIdle(idleName):
idle.idle(self.draw, name=idleName)
[docs] def destroy(self):
"""Removes some property listeners, and then calls
:meth:`.ViewPanel.destroy`.
"""
self.removeListener('dataSeries', self.__name)
self.removeListener('artists', self.__name)
self.removeListener('limits', self.__name)
for propName in ['legend',
'xAutoScale',
'yAutoScale',
'xLogScale',
'yLogScale',
'invertX',
'invertY',
'xScale',
'yScale',
'xOffset',
'yOffset',
'ticks',
'grid',
'gridColour',
'bgColour',
'smooth',
'xlabel',
'ylabel']:
self.removeListener(propName, self.__name)
for ds in self.dataSeries:
for propName in ds.redrawProperties():
ds.removeListener(propName, self.__name)
ds.destroy()
self.__drawQueue.stop()
self.__drawQueue = None
self.__drawnDataSeries = None
self.dataSeries = []
self.artists = []
self.__figure = None
self.__axis = None
self.__canvas = None
viewpanel.ViewPanel.destroy(self)
[docs] @actions.action
def screenshot(self, *a):
"""Prompts the user to select a file name, then saves a screenshot
of the current plot.
See the :class:`.ScreenshotAction`.
"""
from fsleyes.actions.screenshot import ScreenshotAction
ScreenshotAction(self.overlayList,
self.displayCtx,
self)()
[docs] @actions.action
def importDataSeries(self, *a):
"""Imports data series from a text file.
See the :class:`.ImportDataSeriesAction`.
"""
from fsleyes.actions.importdataseries import ImportDataSeriesAction
ImportDataSeriesAction(self.overlayList,
self.displayCtx,
self)()
[docs] @actions.action
def exportDataSeries(self, *args, **kwargs):
"""Exports displayed data series to a text file.
See the :class:`.ExportDataSeriesAction`.
"""
from fsleyes.actions.exportdataseries import ExportDataSeriesAction
ExportDataSeriesAction(self.overlayList,
self.displayCtx,
self)()
[docs] def message(self, msg, clear=True, border=False):
"""Displays the given message in the centre of the figure.
This is a convenience method provided for use by subclasses.
"""
axis = self.getAxis()
if clear:
self.__drawnDataSeries.clear()
axis.clear()
axis.set_xlim((0.0, 1.0))
axis.set_ylim((0.0, 1.0))
if border:
bbox = {'facecolor' : '#ffffff',
'edgecolor' : '#cdcdff',
'boxstyle' : 'round,pad=1'}
else:
bbox = None
axis.text(0.5, 0.5,
msg,
ha='center', va='center',
transform=axis.transAxes,
bbox=bbox)
self.getCanvas().draw()
self.Refresh()
[docs] def getArtist(self, ds):
"""Returns the ``matplotlib.Artist`` (typically a ``Line2D`` instance)
associated with the given :class:`.DataSeries` instance. A
``KeyError`` is raised if there is no such artist.
"""
return self.__drawnDataSeries[ds]
[docs] def getDrawnDataSeries(self):
"""Returns a list of tuples, each tuple containing the
``(DataSeries, x, y)`` data for one ``DataSeries`` instance
as it is shown on the plot.
"""
return [(ds, np.array(l.get_xdata()), np.array(l.get_ydata()))
for ds, l in self.__drawnDataSeries.items()]
[docs] def prepareDataSeries(self, ds):
"""Prepares the data from the given :class:`.DataSeries` so it is
ready to be plotted. Called by the :meth:`__drawOneDataSeries` method
for any ``extraSeries`` passed to the :meth:`drawDataSeries` method
(but not applied to :class:`.DataSeries` that have been added to the
:attr:`dataSeries` list).
This implementation just returns :class:`.DataSeries.getData` -
override it to perform any custom preprocessing.
"""
return ds.getData()
[docs] def drawArtists(self, refresh=True, immediate=False):
"""Draw all ``matplotlib.Artist`` instances in the :attr:`artists`
list, then refresh the canvas.
:arg refresh: If ``True`` (default), the canvas is refreshed.
"""
axis = self.getAxis()
canvas = self.getCanvas()
def realDraw():
# Just in case this PlotPanel is destroyed
# before this task gets executed
if not fwidgets.isalive(self):
return
for artist in self.artists:
if artist not in axis.findobj(type(artist)):
axis.add_artist(artist)
if immediate: realDraw()
else:
self.__drawQueue.enqueue(idle.idle, realDraw)
def refreshCanvas():
if not self.destroyed:
canvas.draw()
if refresh:
if immediate: refreshCanvas()
else: self.__drawQueue.enqueue(idle.idle, refreshCanvas)
[docs] def drawDataSeries(self, extraSeries=None, refresh=False, **plotArgs):
"""Queues a request to plot all of the :class:`.DataSeries` instances
in the :attr:`dataSeries` list.
This method does not do the actual plotting - it is performed
asynchronously, to avoid locking up the GUI:
1. The data for each ``DataSeries`` instance is prepared on
separate threads (using :func:`.idle.run`).
2. A call to :func:`.idle.wait` is enqueued on a
:class:`.TaskThread`.
3. This ``wait`` function waits until all of the data preparation
threads have completed, and then passes all of the data to
the :meth:`__drawDataSeries` method.
:arg extraSeries: A sequence of additional ``DataSeries`` to be
plotted. These series are passed through the
:meth:`prepareDataSeries` method before being
plotted.
:arg refresh: If ``True``, the canvas is refreshed. Otherwise,
you must call ``getCanvas().draw()`` manually.
Defaults to ``False`` - the :meth:`drawArtists`
method will refresh the canvas, so if you call
:meth:`drawArtists` immediately after calling
this method (which you should), then you don't
need to manually refresh the canvas.
:arg plotArgs: Passed through to the :meth:`__drawDataSeries`
method.
.. note:: This method must only be called from the main application
thread (the ``wx`` event loop).
"""
if extraSeries is None:
extraSeries = []
canvas = self.getCanvas()
axis = self.getAxis()
toPlot = self.dataSeries[:]
toPlot = [ds for ds in toPlot if ds.enabled]
extraSeries = [ds for ds in extraSeries if ds.enabled]
toPlot = extraSeries + toPlot
preprocs = [True] * len(extraSeries) + [False] * len(toPlot)
if len(toPlot) == 0:
self.__drawnDataSeries.clear()
axis.clear()
canvas.draw()
self.Refresh()
return
# Before clearing/redrawing, save
# a copy of the x/y axis limits -
# the user may have changed them
# via panning/zooming and, if
# autoLimit is off, we will want
# to preserve the limits that the
# user set. These are passed to
# the __drawDataSeries method.
#
# Make sure the limits are ordered
# as (min, max), as they won't be
# if invertX/invertY are active.
axxlim = list(sorted(axis.get_xlim()))
axylim = list(sorted(axis.get_ylim()))
# Here we are preparing the data for
# each data series on separate threads,
# as data preparation can be time
# consuming for large images. We
# display a message on the canvas
# during preparation.
tasks = []
allXdata = [None] * len(toPlot)
allYdata = [None] * len(toPlot)
# Create a separate function
# for each data series
for idx, (ds, preproc) in enumerate(zip(toPlot, preprocs)):
def getData(d=ds, p=preproc, i=idx):
if not d.enabled:
return
if p: xdata, ydata = self.prepareDataSeries(d)
else: xdata, ydata = d.getData()
allXdata[i] = xdata
allYdata[i] = ydata
tasks.append(getData)
# Run the data preparation tasks,
# a separate thread for each.
tasks = [idle.run(t) for t in tasks]
# Show a message while we're
# preparing the data.
self.message(strings.messages[self, 'preparingData'],
clear=False,
border=True)
# Wait until data preparation is
# done, then call __drawDataSeries.
self.__drawRequests += 1
self.__drawQueue.enqueue(idle.wait,
tasks,
self.__drawDataSeries,
toPlot,
allXdata,
allYdata,
axxlim,
axylim,
refresh,
taskName='{}.wait'.format(id(self)),
wait_direct=True,
**plotArgs)
def __drawDataSeries(
self,
dataSeries,
allXdata,
allYdata,
oldxlim,
oldylim,
refresh,
xlabel=None,
ylabel=None,
**plotArgs):
"""Called by :meth:`__drawDataSeries`. Plots all of the data
associated with the given ``dataSeries``.
:arg dataSeries: The list of :class:`.DataSeries` instances to plot.
:arg allXdata: A list of arrays containing X axis data, one for each
``DataSeries``.
:arg allYdata: A list of arrays containing Y axis data, one for each
``DataSeries``.
:arg oldxlim: X plot limits from the previous draw. If
``xAutoScale`` is disabled, this limit is preserved.
:arg oldylim: Y plot limits from the previous draw. If
``yAutoScale`` is disabled, this limit is preserved.
:arg refresh: Refresh the canvas - see :meth:`drawDataSeries`.
:arg xlabel: If provided, overrides the value of the :attr:`xlabel`
property.
:arg ylabel: If provided, overrides the value of the :attr:`ylabel`
property.
:arg plotArgs: Remaining arguments passed to the
:meth:`__drawOneDataSeries` method.
"""
# Avoid spursious post-destruction
# notifications (occur sporadically
# during testing)
if self.destroyed:
return
# Only draw the plot if there are no
# pending draw requests. Otherwise
# we would be drawing out-of-date data.
self.__drawRequests -= 1
if self.__drawRequests != 0:
return
axis = self.getAxis()
canvas = self.getCanvas()
width, height = canvas.get_width_height()
self.__drawnDataSeries.clear()
axis.clear()
xlims = []
ylims = []
for ds, xdata, ydata in zip(dataSeries, allXdata, allYdata):
if any((ds is None, xdata is None, ydata is None)):
continue
if not ds.enabled:
continue
xdata = self.xOffset + self.xScale * xdata
ydata = self.yOffset + self.yScale * ydata
xlim, ylim = self.__drawOneDataSeries(ds,
xdata,
ydata,
**plotArgs)
if np.any(np.isclose([xlim[0], ylim[0]], [xlim[1], ylim[1]])):
continue
xlims.append(xlim)
ylims.append(ylim)
if len(xlims) == 0:
xmin, xmax = 0.0, 0.0
ymin, ymax = 0.0, 0.0
else:
(xmin, xmax), (ymin, ymax) = self.__calcLimits(
xlims, ylims, oldxlim, oldylim, width, height)
# x/y axis labels
if xlabel is None: xlabel = self.xlabel
if ylabel is None: ylabel = self.ylabel
if xlabel is None: xlabel = ''
if ylabel is None: ylabel = ''
xlabel = xlabel.strip()
ylabel = ylabel.strip()
if xlabel != '':
axis.set_xlabel(xlabel, va='bottom')
axis.xaxis.set_label_coords(0.5, 10.0 / height)
if ylabel != '':
axis.set_ylabel(ylabel, va='top')
axis.yaxis.set_label_coords(10.0 / width, 0.5)
# Ticks
if self.ticks:
axis.tick_params(direction='in', pad=-5)
axis.tick_params(axis='both', which='both', length=3)
for ytl in axis.yaxis.get_ticklabels():
ytl.set_horizontalalignment('left')
for xtl in axis.xaxis.get_ticklabels():
xtl.set_verticalalignment('bottom')
else:
# we clear the labels, but
# leave the ticks, so the
# axis grid gets drawn
xlabels = ['' for i in range(len(axis.xaxis.get_ticklabels()))]
ylabels = ['' for i in range(len(axis.yaxis.get_ticklabels()))]
axis.set_xticklabels(xlabels)
axis.set_yticklabels(ylabels)
axis.tick_params(axis='both', which='both', length=0)
# Limits
if xmin != xmax:
if self.invertX: axis.set_xlim((xmax, xmin))
else: axis.set_xlim((xmin, xmax))
if self.invertY: axis.set_ylim((ymax, ymin))
else: axis.set_ylim((ymin, ymax))
# legend
labels = [ds.label for ds in dataSeries if ds.label is not None]
if len(labels) > 0 and self.legend:
handles, labels = axis.get_legend_handles_labels()
legend = axis.legend(
handles,
labels,
loc='upper right',
fontsize=10,
handlelength=3,
fancybox=True)
legend.get_frame().set_alpha(0.6)
if self.grid:
axis.grid(linestyle='-',
color=self.gridColour,
linewidth=0.5,
zorder=0)
else:
axis.grid(False)
axis.spines['right'] .set_visible(False)
axis.spines['left'] .set_visible(False)
axis.spines['top'] .set_visible(False)
axis.spines['bottom'].set_visible(False)
axis.set_axisbelow(True)
axis.patch.set_facecolor(self.bgColour)
self.getFigure().patch.set_alpha(0)
if refresh:
canvas.draw()
def __drawOneDataSeries(self, ds, xdata, ydata, **plotArgs):
"""Plots a single :class:`.DataSeries` instance. This method is called
by the :meth:`drawDataSeries` method.
:arg ds: The ``DataSeries`` instance.
:arg xdata: X axis data.
:arg ydata: Y axis data.
:arg plotArgs: May be used to customise the plot - these
arguments are all passed through to the
``Axis.plot`` function.
"""
if ds.alpha == 0:
return (0, 0), (0, 0)
if len(xdata) != len(ydata) or len(xdata) == 0:
log.debug('{}: data series length mismatch, or '
'no data points (x: {}, y: {})'.format(
ds.overlay.name, len(xdata), len(ydata)))
return (0, 0), (0, 0)
xdata = np.asarray(xdata, dtype=np.float)
ydata = np.asarray(ydata, dtype=np.float)
log.debug('Drawing {} for {}'.format(type(ds).__name__, ds.overlay))
# Note to self: If the smoothed data is
# filled with NaNs, it is possibly due
# to duplicate values in the x data, which
# are not handled very well by splrep.
if self.smooth:
tck = interp.splrep(xdata, ydata)
xdata = np.linspace(xdata[0],
xdata[-1],
len(xdata) * 5,
dtype=np.float32)
ydata = interp.splev(xdata, tck)
nans = ~(np.isfinite(xdata) & np.isfinite(ydata))
xdata[nans] = np.nan
ydata[nans] = np.nan
if self.xLogScale: xdata[xdata <= 0] = np.nan
if self.yLogScale: ydata[ydata <= 0] = np.nan
if np.all(np.isnan(xdata) | np.isnan(ydata)):
return (0, 0), (0, 0)
kwargs = plotArgs
kwargs['lw'] = kwargs.get('lw', ds.lineWidth)
kwargs['alpha'] = kwargs.get('alpha', ds.alpha)
kwargs['color'] = kwargs.get('color', ds.colour)
kwargs['label'] = kwargs.get('label', ds.label)
kwargs['ls'] = kwargs.get('ls', ds.lineStyle)
axis = self.getAxis()
line = axis.plot(xdata, ydata, **kwargs)[0]
self.__drawnDataSeries[ds] = line
if self.xLogScale:
axis.set_xscale('log')
posx = xdata[xdata > 0]
xlimits = np.nanmin(posx), np.nanmax(posx)
else:
xlimits = np.nanmin(xdata), np.nanmax(xdata)
if self.yLogScale:
axis.set_yscale('log')
posy = ydata[ydata > 0]
ylimits = np.nanmin(posy), np.nanmax(posy)
else:
ylimits = np.nanmin(ydata), np.nanmax(ydata)
return xlimits, ylimits
def __dataSeriesChanged(self, *a):
"""Called when the :attr:`dataSeries` list changes. Adds listeners
to any new :class:`.DataSeries` instances, and then calls
:meth:`asyncDraw`.
"""
for ds in self.dataSeries:
for propName in ds.redrawProperties():
ds.addListener(propName,
self.__name,
self.asyncDraw,
overwrite=True)
self.asyncDraw()
def __artistsChanged(self, *a):
"""Called when the :attr:`artists` list changes. Calls
:meth:`asyncDraw`.
"""
self.asyncDraw()
def __limitsChanged(self, *a):
"""Called when the :attr:`limits` change. Updates the axis limits
accordingly.
"""
axis = self.getAxis()
axis.set_xlim(self.limits.x)
axis.set_ylim(self.limits.y)
self.asyncDraw()
def __calcLimits(self,
dataxlims,
dataylims,
axisxlims,
axisylims,
axWidth,
axHeight):
"""Calculates and returns suitable axis limits for the current plot.
Also updates the :attr:`limits` property. This method is called by
the :meth:`drawDataSeries` method.
If :attr:`xAutoScale` or :attr:`yAutoScale` are enabled, the limits are
calculated from the data range, using the canvas width and height to
maintain consistent padding around the plotted data, irrespective of
the canvas size.
. Otherwise, the existing axis limits are retained.
:arg dataxlims: A tuple containing the (min, max) x data range.
:arg dataylims: A tuple containing the (min, max) y data range.
:arg axisxlims: A tuple containing the current (min, max) x axis
limits.
:arg axisylims: A tuple containing the current (min, max) y axis
limits.
:arg axWidth: Canvas width in pixels
:arg axHeight: Canvas height in pixels
"""
if self.xAutoScale:
xmin = min([lim[0] for lim in dataxlims])
xmax = max([lim[1] for lim in dataxlims])
lPad = (xmax - xmin) * (50.0 / axWidth)
rPad = (xmax - xmin) * (50.0 / axWidth)
xmin = xmin - lPad
xmax = xmax + rPad
else:
xmin = axisxlims[0]
xmax = axisxlims[1]
if self.yAutoScale:
ymin = min([lim[0] for lim in dataylims])
ymax = max([lim[1] for lim in dataylims])
bPad = (ymax - ymin) * (50.0 / axHeight)
tPad = (ymax - ymin) * (50.0 / axHeight)
ymin = ymin - bPad
ymax = ymax + tPad
else:
ymin = axisylims[0]
ymax = axisylims[1]
self.disableListener('limits', self.__name)
self.limits[:] = [xmin, xmax, ymin, ymax]
self.enableListener('limits', self.__name)
return (xmin, xmax), (ymin, ymax)
[docs]class OverlayPlotPanel(PlotPanel):
"""The ``OverlayPlotPanel`` is a :class:`.PlotPanel` which contains
some extra logic for creating, storing, and drawing :class:`.DataSeries`
instances for each overlay in the :class:`.OverlayList`.
**Subclass requirements**
Sub-classes must:
1. Implement the :meth:`createDataSeries` method, so it creates a
:class:`.DataSeries` instance for a specified overlay.
2. Implement the :meth:`PlotPanel.draw` method so it calls the
:meth:`.PlotPanel.drawDataSeries`, passing :class:`.DataSeries`
instances for all overlays where :attr:`.Display.enabled` is
``True``.
3. Optionally implement the :meth:`prepareDataSeries` method to
perform any custom preprocessing.
**The internal data series store**
The ``OverlayPlotPanel`` maintains a store of :class:`.DataSeries`
instances, one for each compatible overlay in the
:class:`.OverlayList`. The ``OverlayPlotPanel`` manages the property
listeners that must be registered with each of these ``DataSeries`` to
refresh the plot. These instances are created by the
:meth:`createDataSeries` method, which is implemented by sub-classes. The
following methods are available to sub-classes, for managing the internal
store of :class:`.DataSeries` instances:
.. autosummary::
:nosignatures:
getDataSeries
getDataSeriesToPlot
clearDataSeries
updateDataSeries
addDataSeries
removeDataSeries
**Proxy images**
The ``OverlayPlotPanel`` will replace all :class:`.ProxyImage` instances
with their base images. This functionality was originally added to support
the :attr:`.HistogramSeries.showOverlay` functionality - it adds a mask
image to the :class:`.OverlayList` to display the histogram range.
Sub-classes may wish to adhere to the same logic (replacing ``ProxyImage``
instances with their bases)
**Control panels**
The :class:`.PlotControlPanel`, :class:`.PlotListPanel`, and
:class:`.OverlayListPanel` are *FSLeyes control* panels which work with
the :class:`.OverlayPlotPanel`. The ``PlotControlPanel`` is not intended
to be used directly - plot-specific sub-classes are used instead. The
following actions can be used to toggle control panels on an
``OverlayPlotPanel``:
.. autosummary::
:nosignatures:
toggleOverlayList
togglePlotList
**Sub-classes**
The ``OverlayPlotPanel`` is the base class for:
.. autosummary::
:nosignatures:
~fsleyes.views.timeseriespanel.TimeSeriesPanel
~fsleyes.views.histogrampanel.HistogramPanel
~fsleyes.views.powerspectrumpanel.PowerSpectrumPanel
"""
plotColours = {}
"""This dictionary is used to store a collection of ``{overlay : colour}``
mappings. It is shared across all ``OverlayPlotPanel`` instances, so that
the same (initial) colour is used for the same overlay, across multiple
plots.
See also :attr:`plotStyles`.
Sub-classes should use the :meth:`getOverlayPlotColour` and
:meth:`getOverlayPlotStyle`methods to retrieve the initial colour and
linestyle to use for a given overlay.
"""
plotStyles = {}
"""This dictionary is used to store a collection of ``{overlay : colour}``
mappings - it is used in conjunction with :attr:`plotColours`.
"""
[docs] def __init__(self, *args, **kwargs):
"""Create an ``OverlayPlotPanel``.
:arg initialState: Must be passed as a keyword argument. Allows you to
specify the initial enabled/disabled state for each
overlay. See :meth:`updateDataSeries`. If not
provided, only the data series for the currently
selected overlay is shown (if possible).
All other argumenst are passed through to :meth:`PlotPanel.__init__`.
"""
initialState = kwargs.pop('initialState', None)
PlotPanel.__init__(self, *args, **kwargs)
self.__name = 'OverlayPlotPanel_{}'.format(self.name)
# The dataSeries attribute is a dictionary of
#
# {overlay : DataSeries}
#
# mappings, containing a DataSeries instance for
# each compatible overlay in the overlay list.
#
# refreshProps is a dict of
#
# {overlay : ([targets], [propNames]}
#
# mappings, containing the target instances and
# properties which, when those properties change,
# need to trigger a refresh of the plot.
#
# refreshCounts is a dict of:
#
# {target, propName : dscount}
# mappings, containing all targets and
# associated property names on which a listener
# is currently registered, and the count of
# DataSeries instances which are interested
# in them.
self.__dataSeries = {}
self.__refreshProps = {}
self.__refreshCounts = {}
# Pre-generated default colours and line
# styles to use - see plotColours, plotStyles,
# getOverlayPlotColour, and getOverlayPlotStyle
lut = fslcm.getLookupTable('paul_tol_accessible')
styles = plotting.DataSeries.lineStyle.getChoices()
limit = min(len(lut), len(styles))
self.__defaultColours = [l.colour for l in lut[ :limit]]
self.__defaultStyles = [s for s in styles[:limit]]
self .addListener('dataSeries',
self.__name,
self.__dataSeriesChanged)
self.overlayList.addListener('overlays',
self.__name,
self.__overlayListChanged)
self.__overlayListChanged(initialState=initialState)
self.__dataSeriesChanged()
[docs] def destroy(self):
"""Must be called when this ``OverlayPlotPanel`` is no longer needed.
Removes some property listeners, and calls :meth:`PlotPanel.destroy`.
"""
self.overlayList.removeListener('overlays', self.__name)
self .removeListener('dataSeries', self.__name)
for overlay in list(self.__dataSeries.keys()):
self.clearDataSeries(overlay)
self.__dataSeries = None
self.__refreshProps = None
self.__refreshCounts = None
PlotPanel.destroy(self)
[docs] def getDataSeriesToPlot(self):
"""Convenience method which returns a list of overlays which have
:class:`.DataSeries` that should be plotted.
"""
overlays = self.overlayList[:]
# Display.enabled
overlays = [o for o in overlays
if self.displayCtx.getDisplay(o).enabled]
# Replace proxy images
overlays = [o.getBase() if isinstance(o, fsloverlay.ProxyImage)
else o for o in overlays]
# Have data series
dss = [self.getDataSeries(o) for o in overlays]
dss = [ds for ds in dss if ds is not None]
# Gather any extra time series
# associated with the base time
# series objects.
for i, ds in enumerate(list(reversed(dss))):
extras = ds.extraSeries()
dss = dss[:i + 1] + extras + dss[i + 1:]
# If a base time series is disabled,
# its additional ones should also
# be disabled
for eds in extras:
eds.enabled = ds.enabled
# Remove duplicates
unique = []
for ds in dss:
if ds not in unique:
unique.append(ds)
return unique
[docs] def getDataSeries(self, overlay):
"""Returns the :class:`.DataSeries` instance associated with the
specified overlay, or ``None`` if there is no ``DataSeries`` instance.
"""
if isinstance(overlay, fsloverlay.ProxyImage):
overlay = overlay.getBase()
return self.__dataSeries.get(overlay)
[docs] def getOverlayPlotColour(self, overlay):
"""Returns an initial colour to use for plots associated with the
given overlay. If a colour is present in the :attr:`plotColours`
dictionary, it is returned. Otherwise a random colour is generated,
added to ``plotColours``, and returned.
"""
if isinstance(overlay, fsloverlay.ProxyImage):
overlay = overlay.getBase()
colour = self.plotColours.get(overlay)
if colour is None:
idx = len(self.plotColours) % len(self.__defaultColours)
colour = self.__defaultColours[idx]
self.plotColours[overlay] = colour
return colour
[docs] def getOverlayPlotStyle(self, overlay):
"""Returns an initial line style to use for plots associated with the
given overlay. If a colour is present in the :attr:`plotStyles`
dictionary, it is returned. Otherwise a line style is generated,
added to ``plotStyles``, and returned.
The format of the returned line style is suitable for use with the
``linestyle`` argument of the ``matplotlib`` ``plot``functions.
"""
if isinstance(overlay, fsloverlay.ProxyImage):
overlay = overlay.getBase()
style = self.plotStyles.get(overlay)
if style is None:
idx = len(self.plotStyles) % len(self.__defaultStyles)
style = self.__defaultStyles[idx]
self.plotStyles[overlay] = style
return style
[docs] @actions.action
def addDataSeries(self):
"""Every :class:`.DataSeries` which is currently plotted, and has not
been added to the :attr:`PlotPanel.dataSeries` list, is added to said
list.
"""
# Get all the DataSeries objects which
# have been drawn, and are not in the
# dataSeries list.
toAdd = self.getDrawnDataSeries()
toAdd = [d[0] for d in toAdd if d[0] not in self.dataSeries]
if len(toAdd) == 0:
return
# Replace each DataSeries instance with a copy.
# This is necessary because some DataSeries
# sub-classes have complicated behaviour (e.g.
# changing their data when some properties
# change). But we just want to 'freeze' the
# data as it is currently shown. So we create
# a dumb copy.
for i, ds in enumerate(toAdd):
copy = plotting.DataSeries(ds.overlay,
self.overlayList,
self.displayCtx,
self)
toAdd[i] = copy
copy.alpha = ds.alpha
copy.lineWidth = ds.lineWidth
copy.lineStyle = ds.lineStyle
copy.label = ds.label
copy.colour = ds.colour
# We have to re-generate the data,
# because the x/y data returned by
# the getDrawnDataSeries method
# above may have had post-processing
# applied to it (e.g. smoothing)
xdata, ydata = self.prepareDataSeries(ds)
copy.setData(xdata, ydata)
# This is disgraceful. It wasn't too bad
# when this function was defined in the
# PlotListPanel class, but is a horrendous
# hack now that it is defined here in the
# PlotPanel class.
#
# At some stage I will remove this offensive
# code, and figure out a more robust system
# for appending this metadata to DataSeries
# instances.
#
# When the user selects a data series in
# the list, we want to change the selected
# overlay/location/volume/etc to the
# properties associated with the data series.
# So here we're adding some attributes to
# each data series instance so that the
# PlotListPanel.__onListSelect method can
# update the display properties.
opts = self.displayCtx.getOpts(ds.overlay)
if isinstance(ds, (plotting.MelodicTimeSeries,
plotting.MelodicPowerSpectrumSeries)):
copy._volume = opts.volume
elif isinstance(ds, plotting.VoxelDataSeries):
copy._location = opts.getVoxel()
self.dataSeries.extend(toAdd)
[docs] @actions.action
def removeDataSeries(self, *a):
"""Removes the most recently added :class:`.DataSeries` from this
``OverlayPlotPanel``.
"""
if len(self.dataSeries) > 0:
self.dataSeries.pop()
[docs] def createDataSeries(self, overlay):
"""This method must be implemented by sub-classes. It must create and
return a :class:`.DataSeries` instance for the specified overlay.
.. note:: Sub-class implementations should set the
:attr:`.DataSeries.colour` property to that returned by
the :meth:`getOverlayPlotColour` method, and the
:attr:`.DataSeries.lineStyle` property to that returned by
the :meth:`getOverlayPlotStyle` method
Different ``DataSeries`` types need to be re-drawn when different
properties change. For example, a :class:`.VoxelTimeSeries`` instance
needs to be redrawn when the :attr:`.DisplayContext.location` property
changes, whereas a :class:`.MelodicTimeSeries` instance needs to be
redrawn when the :attr:`.VolumeOpts.volume` property changes.
Therefore, in addition to creating and returning a ``DataSeries``
instance for the given overlay, sub-class implementations must also
specify the properties which affect the state of the ``DataSeries``
instance. These must be specified as two lists:
- the *targets* list, a list of objects which own the dependant
properties (e.g. the :class:`.DisplayContext` or
:class:`.VolumeOpts` instance).
- The *properties* list, a list of names, each specifying the
property on the corresponding target.
This method must therefore return a tuple containing:
- A :class:`.DataSeries` instance, or ``None`` if the overlay
is incompatible.
- A list of *target* instances.
- A list of *property names*.
The target and property name lists must have the same length.
"""
raise NotImplementedError('createDataSeries must be '
'implemented by sub-classes')
[docs] def clearDataSeries(self, overlay):
"""Destroys the internally cached :class:`.DataSeries` for the given
overlay.
"""
if isinstance(overlay, fsloverlay.ProxyImage):
overlay = overlay.getBase()
ds = self.__dataSeries .pop(overlay, None)
targets, propNames = self.__refreshProps.pop(overlay, ([], []))
if ds is not None:
log.debug('Destroying {} for {}'.format(
type(ds).__name__, overlay))
for propName in ds.redrawProperties():
ds.removeListener(propName, self.__name)
ds.destroy()
for t, p in zip(targets, propNames):
count = self.__refreshCounts[t, p]
if count - 1 == 0:
self.__refreshCounts.pop((t, p))
t.removeListener(p, self.__name)
else:
self.__refreshCounts[t, p] = count - 1
[docs] def updateDataSeries(self, initialState=None):
"""Makes sure that a :class:`.DataSeries` instance has been created
for every compatible overlay, and that property listeners are
correctly registered, so the plot can be refreshed when needed.
:arg initialState: If provided, must be a ``dict`` of ``{ overlay :
bool }`` mappings, specifying the initial value
of the :attr:`.DataSeries.enabled` property for
newly created instances. If not provided, only
the data series for the currently selected
overlay (if it has been newly added) is initially
enabled.
"""
# Default to showing the
# currently selected overlay
if initialState is None:
if len(self.overlayList) > 0:
initialState = {self.displayCtx.getSelectedOverlay() : True}
else:
initialState = {}
# Make sure that a DataSeries
# exists for every compatible overlay
newOverlays = []
for ovl in self.overlayList:
if ovl in self.__dataSeries:
continue
if isinstance(ovl, fsloverlay.ProxyImage):
continue
ds, refreshTargets, refreshProps = self.createDataSeries(ovl)
display = self.displayCtx.getDisplay(ovl)
if ds is None:
# "Disable" overlays which don't have any data
# to plot. We do this mostly so the overlay
# appears greyed out in the OverlayListPanel.
display.enabled = False
continue
# Display.enabled == DataSeries.enabled
ds.bindProps('enabled', display)
ds.enabled = initialState.get(ovl, False)
log.debug('Created {} for overlay {} (enabled: {})'.format(
type(ds).__name__, ovl, ds.enabled))
newOverlays.append(ovl)
self.__dataSeries[ ovl] = ds
self.__refreshProps[ovl] = (refreshTargets, refreshProps)
# Make sure that property listeners are
# registered all of these overlays
for overlay in newOverlays:
targets, propNames = self.__refreshProps.get(overlay, (None, None))
if targets is None:
continue
ds = self.__dataSeries[overlay]
for propName in ds.redrawProperties():
ds.addListener(propName,
self.__name,
self.asyncDraw,
overwrite=True)
for target, propName in zip(targets, propNames):
count = self.__refreshCounts.get((target, propName), 0)
self.__refreshCounts[target, propName] = count + 1
if count == 0:
log.debug('Adding listener on {}.{} for {} data '
'series'.format(type(target).__name__,
propName,
overlay))
target.addListener(propName,
self.__name,
self.asyncDraw,
overwrite=True)
[docs] @actions.toggleControlAction(overlaylistpanel.OverlayListPanel)
def toggleOverlayList(self):
"""Shows/hides an :class:`.OverlayListPanel`. See
:meth:`.ViewPanel.togglePanel`.
"""
# Tell the overlay list panel to disable
# all overlays that aren't being plotted.
#
# This OverlayPlotPanel will always be
# notified about a new overlay before
# this OverlayListPanel, so a DataSeries
# instance will always have been created
# by the time the list panel calls this
# filter function.
def listFilter(overlay):
return self.getDataSeries(overlay) is not None
self.togglePanel(overlaylistpanel.OverlayListPanel,
showVis=True,
showSave=False,
showGroup=False,
propagateSelect=True,
elistboxStyle=(elistbox.ELB_REVERSE |
elistbox.ELB_TOOLTIP_DOWN |
elistbox.ELB_NO_ADD |
elistbox.ELB_NO_REMOVE |
elistbox.ELB_NO_MOVE),
location=wx.LEFT,
filterFunc=listFilter)
[docs] @actions.toggleControlAction(plotlistpanel.PlotListPanel)
def togglePlotList(self, floatPane=False):
"""Shows/hides a :class:`.PlotListPanel`. See
:meth:`.ViewPanel.togglePanel`.
"""
self.togglePanel(plotlistpanel.PlotListPanel,
self,
location=wx.LEFT,
floatPane=floatPane)
def __dataSeriesChanged(self, *a):
"""Called when the :attr:`dataSeries` list changes. Enables/disables
the :meth:`removeDataSeries` action accordingly.
"""
self.removeDataSeries.enabled = len(self.dataSeries) > 0
def __overlayListChanged(self, *a, **kwa):
"""Called when the :class:`.OverlayList` changes. Makes sure that
there are no :class:`.DataSeries` instances in the
:attr:`.PlotPanel.dataSeries` list, or in the internal cache, which
refer to overlays that no longer exist.
:arg initialState: Must be passed as a keyword argument. If provided,
passed through to the :meth:`updateDataSeries`
method.
"""
initialState = kwa.get('initialState', None)
for ds in list(self.dataSeries):
if ds.overlay is not None and ds.overlay not in self.overlayList:
self.dataSeries.remove(ds)
ds.destroy()
for overlay in list(self.__dataSeries.keys()):
if overlay not in self.overlayList:
self.clearDataSeries(overlay)
for overlay in self.overlayList:
display = self.displayCtx.getDisplay(overlay)
# PlotPanels use the Display.enabled property
# to toggle on/off overlay plots. We don't want
# this to interfere with CanvasPanels, which
# use Display.enabled to toggle on/off overlays.
display.detachFromParent('enabled')
self.updateDataSeries(initialState=initialState)
self.asyncDraw()