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Commit ed2ee684 authored by Paul McCarthy's avatar Paul McCarthy
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ClusterPanel now works with any image in a FEAT analysis, instead of 

just with FEATImage overlays.
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fsl/fsleyes/controls/clusterpanel.py
+ 145
− 57
View file @ ed2ee684
......@@ -8,15 +8,17 @@
panel for viewing cluster results from a FEAT analysis.
"""
import logging
import wx
import logging
import wx
import pwidgets.widgetgrid as widgetgrid
import pwidgets.widgetgrid as widgetgrid
import fsl.fsleyes.panel as fslpanel
import fsl.utils.dialog as fsldlg
import fsl.data.strings as strings
import fsl.data.featimage as featimage
import fsl.fsleyes.panel as fslpanel
import fsl.utils.dialog as fsldlg
import fsl.data.strings as strings
import fsl.data.image as fslimage
import fsl.data.featimage as featimage
import fsl.data.featresults as featresults
log = logging.getLogger(__name__)
......@@ -64,18 +66,29 @@ class ClusterPanel(fslpanel.FSLEyesPanel):
self.__addClustMask = wx.Button( self)
self.__statSelect = wx.Choice( self)
# The featImages dictionary is a mapping
# of { overlay : FEATImage } pairs. The
# ClusterPanel will work with any overlay,
# if that overlay is contained within a
# feat analysis. The selectedOverlayChanged
# method identifies the FEAT analysis
# associated with the newly selected overlay,
# and stores the mapping here. Note that the
# FEATImage associated with an overlay might
# not be in the overlay list.
self.__featImages = {}
# A WidgetGrid is created for each
# contrast of a FEAT image, and cached
# in this dictionary. This is because
# it is quite expensive to create the
# grid widgets. This dictionary contains
# {overlay : [WidgetGrid]} mappings.
# {FEATImage : [WidgetGrid]} mappings.
self.__clusterGrids = {}
self.__addZStats .SetLabel(strings.labels[self, 'addZStats'])
self.__addClustMask.SetLabel(strings.labels[self, 'addClustMask'])
self.__sizer = wx.BoxSizer(wx.VERTICAL)
self.SetSizer(self.__sizer)
......@@ -125,6 +138,7 @@ class ClusterPanel(fslpanel.FSLEyesPanel):
grid.Destroy()
self.__clusterGrids = None
self.__featImages = None
self._overlayList.removeListener('overlays', self._name)
self._displayCtx .removeListener('selectedOverlay', self._name)
......@@ -173,13 +187,14 @@ class ClusterPanel(fslpanel.FSLEyesPanel):
self.__sizer.Show(self.__disabledText, False)
self.__sizer.Show(self.__mainSizer, True)
overlay = self.__selectedOverlay
contrast = self.__statSelect.GetSelection()
overlay = self.__selectedOverlay
featImage = self.__featImages[overlay]
contrast = self.__statSelect.GetSelection()
for ovl, grids in self.__clusterGrids.items():
for fimg, grids in self.__clusterGrids.items():
for i, grid in enumerate(grids):
if grid is not None:
show = ovl is overlay and i == contrast
show = fimg is featImage and i == contrast
self.__mainSizer.Show(grid, show)
self.Layout()
......@@ -190,21 +205,22 @@ class ClusterPanel(fslpanel.FSLEyesPanel):
displays clusters for the newly selected COPE (see the
:meth:`__displayClusterData` method)
"""
overlay = self.__selectedOverlay
idx = self.__statSelect.GetSelection()
data = self.__statSelect.GetClientData(idx)
overlay = self.__selectedOverlay
featImage = self.__featImages[overlay]
idx = self.__statSelect.GetSelection()
data = self.__statSelect.GetClientData(idx)
self.Refresh()
self.Update()
if overlay not in self.__clusterGrids:
self.__clusterGrids[overlay] = [None] * overlay.numContrasts()
if featImage not in self.__clusterGrids:
self.__clusterGrids[featImage] = [None] * featImage.numContrasts()
grid = self.__clusterGrids[overlay][idx]
grid = self.__clusterGrids[featImage][idx]
if grid is None:
grid = self.__genClusterGrid(overlay, idx, data)
self.__clusterGrids[overlay][idx] = grid
grid = self.__genClusterGrid(overlay, featImage, idx, data)
self.__clusterGrids[featImage][idx] = grid
self.__mainSizer.Add(grid, flag=wx.EXPAND, proportion=1)
self.__enable()
......@@ -218,9 +234,10 @@ class ClusterPanel(fslpanel.FSLEyesPanel):
to the :class:`.OverlayList`.
"""
overlay = self.__selectedOverlay
contrast = self.__statSelect.GetSelection()
zstats = overlay.getZStats(contrast)
overlay = self.__selectedOverlay
featImage = self.__featImages[overlay]
contrast = self.__statSelect.GetSelection()
zstats = featImage.getZStats(contrast)
for ol in self._overlayList:
......@@ -232,7 +249,7 @@ class ClusterPanel(fslpanel.FSLEyesPanel):
self._overlayList.append(zstats)
opts = self._displayCtx.getOpts(zstats)
zthres = float(overlay.thresholds()['z'])
zthres = float(featImage.thresholds()['z'])
# Set some display parameters if
# we have a z value threshold
......@@ -241,7 +258,8 @@ class ClusterPanel(fslpanel.FSLEyesPanel):
absmax = max(map(abs, (opts.dataMin, opts.dataMax)))
opts.cmap = 'Render3'
opts.invertClipping = True
opts.invertClipping = True
opts.centreRanges = True
opts.displayRange.x = -absmax, absmax
opts.clippingRange.x = -zthres, zthres
......@@ -252,10 +270,11 @@ class ClusterPanel(fslpanel.FSLEyesPanel):
:meth:`.FEATImage.getClusterMask` method)
"""
overlay = self.__selectedOverlay
contrast = self.__statSelect.GetSelection()
mask = overlay.getClusterMask(contrast)
overlay = self.__selectedOverlay
featImage = self.__featImages[overlay]
contrast = self.__statSelect.GetSelection()
mask = featImage.getClusterMask(contrast)
for ol in self._overlayList:
# Already in overlay list
......@@ -267,15 +286,28 @@ class ClusterPanel(fslpanel.FSLEyesPanel):
self._displayCtx.getDisplay(mask).overlayType = 'label'
def __genClusterGrid(self, overlay, contrast, clusters):
def __genClusterGrid(self, overlay, featImage, contrast, clusters):
"""Creates and returns a :class:`.WidgetGrid` which contains the given
list of clusters, which are related to the given contrast.
:arg contrast: The (0-indexed) number of the contrast to which the
clusters are related.
:arg clusters: A sequence of objects, each representing one cluster.
See the :meth:`.FEATImage.clusterResults` method.
.. note:: This method assumes that the given ``overlay`` is an
:class:`.Image` which has the same voxel dimensions as,
and shares the the same world coordinate system as the
``featImage``.
:arg overlay: The overlay for which clusters are currently being
displayed.
:arg featImage: The :class:`.FEATImage` to which the clusters are
related.
:arg contrast: The (0-indexed) number of the contrast to which the
clusters are related.
:arg clusters: A sequence of objects, each representing one cluster.
See the :meth:`.FEATImage.clusterResults` method.
"""
cols = {'index' : 0,
......@@ -290,7 +322,7 @@ class ClusterPanel(fslpanel.FSLEyesPanel):
'copemean' : 9}
grid = widgetgrid.WidgetGrid(self)
conName = overlay.contrastNames()[contrast]
conName = featImage.contrastNames()[contrast]
opts = self._displayCtx.getOpts(overlay)
grid.SetGridSize(len(clusters), 10)
......@@ -365,9 +397,12 @@ class ClusterPanel(fslpanel.FSLEyesPanel):
# WidgetGrid panels for overlays
# that have been removed from the
# list.
for overlay in self.__clusterGrids.keys():
for overlay in self.__featImages.keys():
if overlay not in self._overlayList:
grids = self.__clusterGrids.pop(overlay)
featImage = self.__featImages .pop(overlay)
grids = self.__clusterGrids.pop(featImage)
for grid in grids:
self.__mainSizer.Detach(grid)
grid.Destroy()
......@@ -385,11 +420,12 @@ class ClusterPanel(fslpanel.FSLEyesPanel):
if self.__selectedOverlay is None:
return
overlay = self.__selectedOverlay
contrast = self.__statSelect.GetSelection()
overlay = self.__selectedOverlay
featImage = self.__featImages[overlay]
contrast = self.__statSelect.GetSelection()
zstat = overlay.getZStats( contrast)
clustMask = overlay.getClusterMask(contrast)
zstat = featImage.getZStats( contrast)
clustMask = featImage.getClusterMask(contrast)
dss = [ovl.dataSource for ovl in self._overlayList]
......@@ -415,42 +451,92 @@ class ClusterPanel(fslpanel.FSLEyesPanel):
return
overlay = self._displayCtx.getSelectedOverlay()
# Not a FEAT image, can't
# do anything with that
if not isinstance(overlay, featimage.FEATImage):
featDir = featresults.getAnalysisDir(overlay.dataSource)
# Not a FEAT analysis image,
# can't do anything with that
if featDir is None or not isinstance(overlay, fslimage.Image):
log.debug('Overlay {} is not part of a feat '
'analysis, or is not an Image'.format(overlay))
self.__disable(strings.messages[self, 'notFEAT'])
return
# Selected overlay is either the
# same one (maybe the overlay list,
# rather than the selected overlay,
# changed) or the newly selected
# overlay is from the same FEAT
# analysis. No need to do anything.
if prevOverlay is not None and \
(prevOverlay is overlay or
prevOverlay.getFEATDir() == overlay.getFEATDir()):
self.__selectedOverlay = overlay
return
if prevOverlay is not None:
self.__statSelect.Clear()
prevFeatImage = self.__featImages.get(prevOverlay)
if prevOverlay is overlay or \
(prevFeatImage is not None and
featDir == prevFeatImage.getFEATDir()):
log.debug('Overlay {} is already selected.'.format(overlay))
# Make sure the overlay -> FEATImage
# mapping is present, and (re-)cache
# a reference to the selected overlay.
self.__featImages[overlay] = prevFeatImage
self.__selectedOverlay = overlay
return
# We're in business. The newly selected
# overlay is a part of a FEAT analysis
# which is not currently being displayed.
self.__selectedOverlay = overlay
# Clear the stat selection combo box.
self.__statSelect.Clear()
# Get the FEATImage associated with
# this overlay, so we can get
# information about the FEAT analysis
featImage = self.__featImages.get(overlay)
if featImage is None:
# If the overlay itself is a FEATImage,
# then we have nothing to do.
if isinstance(overlay, featimage.FEATImage):
featImage = overlay
else:
# The FEATImage might already
# be in the overlay list -
# let's search for it.
for ovl in self._overlayList:
if isinstance(ovl, featimage.FEATImage) and \
ovl.getFEATDir() == featDir:
featImage = ovl
# As a last resort, if the FEATImage is not
# in the overlay list, we'll create one.
if featImage is None:
featImage = featimage.FEATImage(featDir, loadData=False)
self.__featImages[overlay] = featImage
log.debug('FEAT analysis associated with overlay {}: {}'.format(
overlay,
featImage.getFEATDir()))
display = self._displayCtx.getDisplay(overlay)
numCons = overlay.numContrasts()
conNames = overlay.contrastNames()
numCons = featImage.numContrasts()
conNames = featImage.contrastNames()
try:
# clusts is a list of (contrast, clusterList) tuples
clusts = [(c, overlay.clusterResults(c)) for c in range(numCons)]
clusts = [(c, featImage.clusterResults(c)) for c in range(numCons)]
clusts = filter(lambda (con, clust): clust is not None, clusts)
# Error parsing the cluster data
except Exception as e:
log.warning('Error parsing cluster data for '
'{}: {}'.format(overlay.name, str(e)), exc_info=True)
'{}: {}'.format(featImage.name, str(e)), exc_info=True)
self.__disable(strings.messages[self, 'badData'])
return
......@@ -460,6 +546,7 @@ class ClusterPanel(fslpanel.FSLEyesPanel):
self.__disable(strings.messages[self, 'noClusters'])
return
# Populate the stat selection combo box
for contrast, clusterList in clusts:
name = conNames[contrast]
name = strings.labels[self, 'clustName'].format(contrast + 1, name)
......@@ -468,6 +555,7 @@ class ClusterPanel(fslpanel.FSLEyesPanel):
self.__overlayName.SetLabel(display.name)
# Refresh the widget grid
self.__statSelect.SetSelection(0)
self.__statSelected()
......
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