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Commit e106f941 authored by Paul McCarthy's avatar Paul McCarthy
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Half documented HistogramPanel. More work to be done.

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fsl/fsleyes/views/histogrampanel.py
+ 340
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#!/usr/bin/env python
#
# histogrampanel.py - A panel which plots a histogram for the data from the
# currently selected overlay.
# histogrampanel.py - The HistogramPanel class.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""This module provides the :class:`HistogramPanel`, which is a *FSLeyes view*
that plots the histogram of data from :class:`.Image` overlays. A
``HistogramPanel`` looks something like this:
.. image:: images/histogrampanel.png
:scale: 50%
:align: center
``HistogramPanel`` instances use the :class:`HistogramSeries` class (a
:class:`.DataSeries` sub-class) to encapsulate histogram data.
"""
import logging
......@@ -23,32 +35,312 @@ import plotpanel
log = logging.getLogger(__name__)
def autoBin(data, dataRange):
# Automatic histogram bin calculation
# as implemented in the original FSLView
class HistogramPanel(plotpanel.PlotPanel):
"""A :class:`.PlotPanel` which plots histograms from :class:`.Image`
overlay data.
A ``HistogramPanel`` plots one or more :class:`HistogramSeries` instances,
each of which encapsulate histogram data from an :class:`.Image` overlay.
By default, a ``HistogramPanel`` plots a histogram from the currently
selected overlay (dictated by the :attr:`.DisplayContext.selectedOverlay`
property), if it is an :class:`.Image` instance. In a similar manner to
the :class:`.TimeSeriesPanel`, this histogram is referred to as the
*current* histogram, and it can be enabled/disabled with the
:attr:`showCurrent` setting.
dMin, dMax = dataRange
dRange = dMax - dMin
binSize = np.power(10, np.ceil(np.log10(dRange) - 1) - 1)
A couple of control panels may be shown on a ``HistogramPanel``::
.. autosummary::
:nosignatures:
~fsl.fsleyes.controls.histogramlistpanel.HistogramListPanel
~fsl.fsleyes.controls.histogramcontrolpanel.HistogramControlPanel
The following actions are provided, in addition to those already provided
by the :class:`.PlotPanel:
========================== ===========================================
``toggleHistogramList`` Show/hide a :cass:`.HistogramListPanel`.
``toggleHistogramControl`` Show/hide a :cass:`.HistogramControlPanel`.
========================== ===========================================
"""
autoBin = props.Boolean(default=True)
"""If ``True``, the number of bins used for each :class:`HistogramSeries`
is calculated automatically. Otherwise, :attr:`HistogramSeries.nbins` bins
are used.
"""
nbins = dRange / binSize
while nbins < 100:
binSize /= 2
nbins = dRange / binSize
showCurrent = props.Boolean(default=True)
"""If ``True``, a histogram for the currently selected overlay (if it is
an :class:`.Image` instance) is always plotted.
"""
histType = props.Choice(('probability', 'count'))
"""The histogram type:
=============== ==========================================================
``count`` The y axis represents the absolute number of values within
each bin
``probability`` The y axis represents the nuymber of values within each
bin, divided by the total number of values.
=============== ==========================================================
"""
selectedSeries = props.Int(minval=0, clamped=True)
"""The currently selected :class:`HistogramSeries` - an index into the
:attr:`.PlotPanel.dataSeries` list.
This property is used by the :class:`.HistogramListPanel` and the
:class:`.HistogramControlPanel`, to allow the user to change the settings
of individual :class:`HistogramSeries` instances.
"""
def __init__(self, parent, overlayList, displayCtx):
"""Create a ``HistogramPanel``.
:arg parent: The :mod:`wx` parent.
:arg overlayList: The :class:`.OverlayList` instance.
:arg displayCtx: The :class:`.DisplayContext` instance.
"""
actionz = {
'toggleHistogramList' : self.toggleHistogramList,
'toggleHistogramControl' : lambda *a: self.togglePanel(
fslcontrols.HistogramControlPanel, self, location=wx.TOP)
}
plotpanel.PlotPanel.__init__(
self, parent, overlayList, displayCtx, actionz)
figure = self.getFigure()
figure.subplots_adjust(
top=1.0, bottom=0.0, left=0.0, right=1.0)
figure.patch.set_visible(False)
self._overlayList.addListener('overlays',
self._name,
self.__overlaysChanged)
self._displayCtx .addListener('selectedOverlay',
self._name,
self.__selectedOverlayChanged)
self.addListener('showCurrent', self._name, self.draw)
self.addListener('histType', self._name, self.draw)
self.addListener('autoBin', self._name, self.__autoBinChanged)
self.addListener('dataSeries', self._name, self.__dataSeriesChanged)
# Creating a HistogramSeries is a bit expensive
# as it needs to, well, create a histogram. So
# we only create one HistogramSeries per overlay,
# and we cache them here so that the user only
# has to wait the first time they select an
# overlay for its histogram to be calculated.
#
# When a HistogramSeries is added to the dataSeries
# list, it is copied from the cached one so, again,
# the histogram calculation doesn't need to be done.
self.__histCache = {}
self.__current = None
self.__updateCurrent()
self.Layout()
def destroy(self):
"""Removes some property listeners, destroys all existing
:class:`HistogramSeries` instances, and calls
:meth:`.PlotPanel.destroy`.
"""
self.removeListener('showCurrent', self._name)
self.removeListener('histType', self._name)
self.removeListener('autoBin', self._name)
self.removeListener('dataSeries', self._name)
self._overlayList.removeListener('overlays', self._name)
self._displayCtx .removeListener('selectedOverlay', self._name)
for hs in set(self.dataSeries[:] + self.__histCache.values()):
hs.destroy()
plotpanel.PlotPanel.destroy(self)
def getCurrent(self):
"""Return the :class:`HistogramSeries` instance for the currently
selected overlay. Returns ``None`` if :attr:``showCurrent` is
``False``, or the current overlay is not an :class:`.Image`.
"""
if self.__current is None:
self.__updateCurrent()
if self.__current is None:
return None
return HistogramSeries(self.__current.overlay,
self,
self._displayCtx,
self._overlayList,
baseHs=self.__current)
def draw(self, *a):
"""Draws the current :class:`HistogramSeries` if there is one,, and
any ``HistogramSeries`` that are in the :attr:`.PlotPanel.dataSeries`
list, via a call to :meth:`.PlotPanel.drawDataSeries`.
"""
extra = None
if self.showCurrent:
if self.__current is not None:
extra = [self.__current]
if self.smooth: self.drawDataSeries(extra)
else: self.drawDataSeries(extra, drawstyle='steps-pre')
def toggleHistogramList(self, *a):
"""Shows/hides a :class:`.HistogramListPanel`. See the
:meth:`.ViewPanel.togglePanel` method.
"""
self.togglePanel(fslcontrols.HistogramListPanel, self, location=wx.TOP)
def __dataSeriesChanged(self, *a):
"""Called when the :attr:`.PlotPanel.dataSeries` property changes.
"""
self.setConstraint('selectedSeries',
'maxval',
len(self.dataSeries) - 1)
listPanel = self.getPanel(fslcontrols.HistogramListPanel)
if listPanel is None:
self.selectedSeries = 0
else:
self.selectedSeries = listPanel.getListBox().GetSelection()
def __overlaysChanged(self, *a):
self.disableListener('dataSeries', self._name)
for ds in self.dataSeries:
if ds.overlay not in self._overlayList:
self.dataSeries.remove(ds)
self.enableListener('dataSeries', self._name)
# Remove any dead overlays
# from the histogram cache
for overlay in list(self.__histCache.keys()):
if overlay not in self._overlayList:
log.debug('Removing cached histogram series '
'for overlay {}'.format(overlay.name))
hs = self.__histCache.pop(overlay)
hs.destroy()
self.__selectedOverlayChanged()
if issubclass(data.dtype.type, np.integer):
binSize = max(1, np.ceil(binSize))
def __selectedOverlayChanged(self, *a):
adjMin = np.floor(dMin / binSize) * binSize
adjMax = np.ceil( dMax / binSize) * binSize
self.__updateCurrent()
self.draw()
def __autoBinChanged(self, *a):
"""Called when the :attr:`autoBin` property changes. Makes sure that
all existing :class:`HistogramSeries` instances are updated before
the plot is refreshed.
"""
nbins = int((adjMax - adjMin) / binSize) + 1
for ds in self.dataSeries:
ds.histPropsChanged()
if self.__current is not None:
self.__current.histPropsChanged()
self.draw()
def __updateCurrent(self):
# Make sure that the previous HistogramSeries
# cleans up after itself, unless it has been
# cached
if self.__current is not None and \
self.__current not in self.__histCache.values():
self.__current.destroy()
self.__current = None
overlay = self._displayCtx.getSelectedOverlay()
if len(self._overlayList) == 0 or \
not isinstance(overlay, fslimage.Image):
return
# See if there is already a HistogramSeries based on the
# current overlay - if there is, use it as the 'base' HS
# for the new one, as it will save us some processing time
if overlay in self.__histCache:
log.debug('Creating new histogram series for overlay {} '
'from cached copy'.format(overlay.name))
baseHs = self.__histCache[overlay]
else:
baseHs = None
def loadHs():
return HistogramSeries(overlay,
self,
self._displayCtx,
self._overlayList,
baseHs=baseHs)
# We are creating a new HS instance, so it
# needs to do some initla data range/histogram
# calculations. Show a message while this is
# happening.
if baseHs is None:
hs = fsldlg.ProcessingDialog(
None,
strings.messages[self, 'calcHist'].format(overlay.name),
loadHs).Run()
# Put the initial HS instance for this
# overlay in the cache so we don't have
# to re-calculate it later
log.debug('Caching histogram series for '
'overlay {}'.format(overlay.name))
self.__histCache[overlay] = hs
# The new HS instance is being based on the
# current instance, so it can just copy the
# histogram data over - no message dialog
# is needed
else:
hs = loadHs()
hs.colour = [0, 0, 0]
hs.alpha = 1
hs.lineWidth = 1
hs.lineStyle = '-'
hs.label = None
return nbins
self.__current = hs
class HistogramSeries(plotpanel.DataSeries):
......@@ -139,7 +431,7 @@ class HistogramSeries(plotpanel.DataSeries):
self.dataRange.xlo = nzmin
self.dataRange.xhi = nzmax + dist
self.nbins = autoBin(nzData, self.dataRange.x)
self.nbins = self.autoBin(nzData, self.dataRange.x)
if not self.overlay.is4DImage():
self.finiteData = finData
......@@ -228,7 +520,7 @@ class HistogramSeries(plotpanel.DataSeries):
else: data = self.clippedFiniteData
if self.hsPanel.autoBin:
nbins = autoBin(data, self.dataRange.x)
nbins = self.autoBin(data, self.dataRange.x)
self.disableListener('nbins', self.name)
self.nbins = nbins
......@@ -304,6 +596,33 @@ class HistogramSeries(plotpanel.DataSeries):
self.showOverlayChanged()
self.enableListener('showOverlay', self.name)
def autoBin(self, data, dataRange):
# Automatic histogram bin calculation
# as implemented in the original FSLView
dMin, dMax = dataRange
dRange = dMax - dMin
binSize = np.power(10, np.ceil(np.log10(dRange) - 1) - 1)
nbins = dRange / binSize
while nbins < 100:
binSize /= 2
nbins = dRange / binSize
if issubclass(data.dtype.type, np.integer):
binSize = max(1, np.ceil(binSize))
adjMin = np.floor(dMin / binSize) * binSize
adjMax = np.ceil( dMax / binSize) * binSize
nbins = int((adjMax - adjMin) / binSize) + 1
return nbins
def getData(self):
......@@ -337,229 +656,3 @@ class HistogramSeries(plotpanel.DataSeries):
if histType == 'count': return xdata, ydata
elif histType == 'probability': return xdata, ydata / nvals
class HistogramPanel(plotpanel.PlotPanel):
autoBin = props.Boolean(default=True)
showCurrent = props.Boolean(default=True)
histType = props.Choice(('probability', 'count'))
selectedSeries = props.Int(minval=0, clamped=True)
def __init__(self, parent, overlayList, displayCtx):
actionz = {
'toggleHistogramList' : self.toggleHistogramList,
'toggleHistogramControl' : lambda *a: self.togglePanel(
fslcontrols.HistogramControlPanel, self, location=wx.TOP)
}
plotpanel.PlotPanel.__init__(
self, parent, overlayList, displayCtx, actionz)
figure = self.getFigure()
figure.subplots_adjust(
top=1.0, bottom=0.0, left=0.0, right=1.0)
figure.patch.set_visible(False)
self._overlayList.addListener('overlays',
self._name,
self.__overlaysChanged)
self._displayCtx .addListener('selectedOverlay',
self._name,
self.__selectedOverlayChanged)
self.addListener('showCurrent', self._name, self.draw)
self.addListener('histType', self._name, self.draw)
self.addListener('autoBin', self._name, self.__autoBinChanged)
self.addListener('dataSeries', self._name, self.__dataSeriesChanged)
self.__histCache = {}
self.__current = None
self.__updateCurrent()
self.Layout()
def toggleHistogramList(self, *a):
self.togglePanel(fslcontrols.HistogramListPanel, self, location=wx.TOP)
panel = self.getPanel(fslcontrols.HistogramListPanel)
if panel is None:
return
def listSelect(ev):
ev.Skip()
self.selectedSeries = panel.GetSelection()
def destroy(self):
"""De-registers property listeners. """
self.removeListener('showCurrent', self._name)
self.removeListener('histType', self._name)
self.removeListener('autoBin', self._name)
self.removeListener('dataSeries', self._name)
self._overlayList.removeListener('overlays', self._name)
self._displayCtx .removeListener('selectedOverlay', self._name)
for hs in set(self.dataSeries[:] + self.__histCache.values()):
hs.destroy()
plotpanel.PlotPanel.destroy(self)
def __dataSeriesChanged(self, *a):
self.setConstraint('selectedSeries',
'maxval',
len(self.dataSeries) - 1)
listPanel = self.getPanel(fslcontrols.HistogramListPanel)
if listPanel is None:
self.selectedSeries = 0
else:
self.selectedSeries = listPanel.getListBox().GetSelection()
def __overlaysChanged(self, *a):
self.disableListener('dataSeries', self._name)
for ds in self.dataSeries:
if ds.overlay not in self._overlayList:
self.dataSeries.remove(ds)
self.enableListener('dataSeries', self._name)
# Remove any dead overlays
# from the histogram cache
for overlay in list(self.__histCache.keys()):
if overlay not in self._overlayList:
log.debug('Removing cached histogram series '
'for overlay {}'.format(overlay.name))
hs = self.__histCache.pop(overlay)
hs.destroy()
self.__selectedOverlayChanged()
def __selectedOverlayChanged(self, *a):
self.__updateCurrent()
self.draw()
def __autoBinChanged(self, *a):
"""Called when the :attr:`autoBin` property changes. Makes sure that
all existing :class:`HistogramSeries` instances are updated before
the plot is refreshed.
"""
for ds in self.dataSeries:
ds.histPropsChanged()
if self.__current is not None:
self.__current.histPropsChanged()
self.draw()
def __updateCurrent(self):
# Make sure that the previous HistogramSeries
# cleans up after itself, unless it has been
# cached
if self.__current is not None and \
self.__current not in self.__histCache.values():
self.__current.destroy()
self.__current = None
overlay = self._displayCtx.getSelectedOverlay()
if len(self._overlayList) == 0 or \
not isinstance(overlay, fslimage.Image):
return
# See if there is already a HistogramSeries based on the
# current overlay - if there is, use it as the 'base' HS
# for the new one, as it will save us some processing time
if overlay in self.__histCache:
log.debug('Creating new histogram series for overlay {} '
'from cached copy'.format(overlay.name))
baseHs = self.__histCache[overlay]
else:
baseHs = None
def loadHs():
return HistogramSeries(overlay,
self,
self._displayCtx,
self._overlayList,
baseHs=baseHs)
# We are creating a new HS instance, so it
# needs to do some initla data range/histogram
# calculations. Show a message while this is
# happening.
if baseHs is None:
hs = fsldlg.ProcessingDialog(
None,
strings.messages[self, 'calcHist'].format(overlay.name),
loadHs).Run()
# Put the initial HS instance for this
# overlay in the cache so we don't have
# to re-calculate it later
log.debug('Caching histogram series for '
'overlay {}'.format(overlay.name))
self.__histCache[overlay] = hs
# The new HS instance is being based on the
# current instance, so it can just copy the
# histogram data over - no message dialog
# is needed
else:
hs = loadHs()
hs.colour = [0, 0, 0]
hs.alpha = 1
hs.lineWidth = 1
hs.lineStyle = '-'
hs.label = None
self.__current = hs
def getCurrent(self):
if self.__current is None:
self.__updateCurrent()
if self.__current is None:
return None
return HistogramSeries(self.__current.overlay,
self,
self._displayCtx,
self._overlayList,
baseHs=self.__current)
def draw(self, *a):
extra = None
if self.showCurrent:
if self.__current is not None:
extra = [self.__current]
if self.smooth: self.drawDataSeries(extra)
else: self.drawDataSeries(extra, drawstyle='steps-pre')
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