diff --git a/fsl/fsleyes/controls/clusterpanel.py b/fsl/fsleyes/controls/clusterpanel.py
index 45fc578b41f70dcda1fb112e24af880495696fcb..01cc671e8d4053c376f5329f6e1755912daef6aa 100644
--- a/fsl/fsleyes/controls/clusterpanel.py
+++ b/fsl/fsleyes/controls/clusterpanel.py
@@ -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()