From e106f94166c90583d61855b3513a239b28f2b131 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Wed, 9 Sep 2015 17:28:48 +0100
Subject: [PATCH] Half documented HistogramPanel. More work to be done.
---
fsl/fsleyes/views/histogrampanel.py | 587 ++++++++++++++++------------
1 file changed, 340 insertions(+), 247 deletions(-)
diff --git a/fsl/fsleyes/views/histogrampanel.py b/fsl/fsleyes/views/histogrampanel.py
index 29436a43c..4e41a4b96 100644
--- a/fsl/fsleyes/views/histogrampanel.py
+++ b/fsl/fsleyes/views/histogrampanel.py
@@ -1,10 +1,22 @@
#!/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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