From c84d4d520fd94e94a4e1df42c75fd2e051ecf139 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Thu, 21 May 2015 10:48:12 +0100
Subject: [PATCH] Various bugfixes to AtlasPanel - it now supports reference
images.
---
fsl/data/atlases.py | 2 +-
fsl/data/strings.py | 5 +-
fsl/fslview/controls/atlasinfopanel.py | 67 +++++++++++++++++++-------
fsl/fslview/controls/atlaspanel.py | 25 ++++++----
4 files changed, 68 insertions(+), 31 deletions(-)
diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index 32e633f7e..b9ddf49d5 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -297,6 +297,6 @@ class ProbabilisticAtlas(Atlas):
voxelLoc[0] >= self.shape[0] or \
voxelLoc[1] >= self.shape[1] or \
voxelLoc[2] >= self.shape[2]:
- return np.nan
+ return []
return self.data[voxelLoc[0], voxelLoc[1], voxelLoc[2], :]
diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index 87552843d..ee69c6d36 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -38,10 +38,9 @@ messages = TypeDict({
'installing the colour map',
'AtlasInfoPanel.notMNISpace' : 'Atlas lookup can only be performed on '
- 'images registered to MNI152 space',
+ 'images oriented to MNI152 space',
- 'AtlasInfoPanel.nonVolumetric' : 'Atlas lookup can only be performed on '
- 'volumetric images',
+ 'AtlasInfoPanel.noReference' : 'No reference image available',
'AtlasInfoPanel.chooseAnAtlas' : 'Choose an atlas!',
'AtlasInfoPanel.atlasDisabled' : 'Atlases are not available',
diff --git a/fsl/fslview/controls/atlasinfopanel.py b/fsl/fslview/controls/atlasinfopanel.py
index 8619812b2..749da973c 100644
--- a/fsl/fslview/controls/atlasinfopanel.py
+++ b/fsl/fslview/controls/atlasinfopanel.py
@@ -14,7 +14,6 @@ import pwidgets.elistbox as elistbox
import fsl.fslview.panel as fslpanel
import fsl.data.atlases as atlases
-import fsl.data.image as fslimage
import fsl.data.strings as strings
import fsl.data.constants as constants
import fsl.utils.transform as transform
@@ -88,14 +87,20 @@ class AtlasInfoPanel(fslpanel.FSLViewPanel):
self.__infoPanel.Bind(wxhtml.EVT_HTML_LINK_CLICKED,
self.__infoPanelLinkClicked)
- displayCtx.addListener('location',
- self._name,
- self.__locationChanged)
- displayCtx.addListener('selectedOverlay',
- self._name,
- self.__locationChanged)
-
- self.__locationChanged()
+ overlayList.addListener('overlays',
+ self._name,
+ self.__selectedOverlayChanged)
+ displayCtx .addListener('selectedOverlay',
+ self._name,
+ self.__selectedOverlayChanged)
+ displayCtx .addListener('overlayOrder',
+ self._name,
+ self.__selectedOverlayChanged)
+ displayCtx .addListener('location',
+ self._name,
+ self.__locationChanged)
+
+ self.__selectedOverlayChanged()
self.Layout()
self.SetMinSize(self.__sizer.GetMinSize())
@@ -107,8 +112,10 @@ class AtlasInfoPanel(fslpanel.FSLViewPanel):
"""
fslpanel.FSLViewPanel.destroy(self)
- self._displayCtx.removeListener('location', self._name)
- self._displayCtx.removeListener('selectedOverlay', self._name)
+ self._overlayList.removeListener('overlays', self._name)
+ self._displayCtx .removeListener('location', self._name)
+ self._displayCtx .removeListener('selectedOverlay', self._name)
+ self._displayCtx .removeListener('overlayOrder', self._name)
def enableAtlasInfo(self, atlasID):
@@ -139,17 +146,43 @@ class AtlasInfoPanel(fslpanel.FSLViewPanel):
self.__atlasPanel.toggleOverlay(atlasID, labelIndex, summary)
+ def __selectedOverlayChanged(self, *a):
+ """
+ """
+
+ if len(self._overlayList) == 0:
+ self.__locationChanged()
+ return
+
+ selOverlay = self._displayCtx.getSelectedOverlay()
+
+ for ovl in self._overlayList:
+
+ opts = self._displayCtx.getDisplay(ovl).getDisplayOpts()
+
+ if ovl == selOverlay:
+ opts.addGlobalListener( self._name,
+ self.__locationChanged,
+ overwrite=True)
+ else:
+ opts.removeGlobalListener(self._name)
+
+ self.__locationChanged()
+
+
def __locationChanged(self, *a):
overlay = self._displayCtx.getSelectedOverlay()
+ opts = self._displayCtx.getDisplay(overlay).getDisplayOpts()
+ overlay = opts.getReferenceImage()
text = self.__infoPanel
if len(atlases.listAtlases()) == 0:
text.SetPage(strings.messages['AtlasInfoPanel.atlasDisabled'])
return
- if not isinstance(overlay, fslimage.Image):
- text.SetPage(strings.messages['AtlasInfoPanel.nonVolumetric'])
+ if overlay is None:
+ text.SetPage(strings.messages['AtlasInfoPanel.noReference'])
return
if overlay.getXFormCode() != constants.NIFTI_XFORM_MNI_152:
@@ -159,11 +192,11 @@ class AtlasInfoPanel(fslpanel.FSLViewPanel):
if len(self.__enabledAtlases) == 0:
text.SetPage(strings.messages['AtlasInfoPanel.chooseAnAtlas'])
return
-
- display = self._displayCtx.getDisplay(overlay)
+
+ opts = self._displayCtx.getDisplay(overlay).getDisplayOpts()
loc = self._displayCtx.location
loc = transform.transform(
- [loc], display.getTransform('display', 'world'))[0]
+ [loc], opts.getTransform('display', 'world'))[0]
lines = []
titleTemplate = '<b>{}</b> (<a href="summary {} {}">Show/Hide</a>)'
@@ -172,7 +205,7 @@ class AtlasInfoPanel(fslpanel.FSLViewPanel):
for atlasID in self.__enabledAtlases:
- atlas = self.enabledAtlases[atlasID]
+ atlas = self.__enabledAtlases[atlasID]
lines.append(titleTemplate.format(atlas.desc.name, atlasID, None))
diff --git a/fsl/fslview/controls/atlaspanel.py b/fsl/fslview/controls/atlaspanel.py
index 5a8be8989..ad6a6e56c 100644
--- a/fsl/fslview/controls/atlaspanel.py
+++ b/fsl/fslview/controls/atlaspanel.py
@@ -151,7 +151,7 @@ class AtlasPanel(fslpanel.FSLViewPanel):
if overlay is not None:
self.clearAtlas(atlasID, summary)
self._overlayList.remove(overlay)
- self.overlayPanel.setOverlayState(
+ self.__overlayPanel.setOverlayState(
atlasID, labelIdx, summary, False)
log.debug('Removed overlay {}'.format(overlayName))
return
@@ -201,9 +201,12 @@ class AtlasPanel(fslpanel.FSLViewPanel):
else: display.getDisplayOpts().cmap = 'hot'
else:
# The Harvard-Oxford atlases have special colour maps
- if atlasID == 'HarvardOxford-Cortical': cmap = 'cortical'
- elif atlasID == 'HarvardOxford-Subcortical': cmap = 'subcortical'
- else: cmap = 'random'
+ if atlasID == 'HarvardOxford-Cortical':
+ cmap = 'MGH Cortical'
+ elif atlasID == 'HarvardOxford-Subcortical':
+ cmap = 'MGH Sub-cortical'
+ else:
+ cmap = 'Random'
display.getDisplayOpts().cmap = cmap
@@ -212,15 +215,17 @@ class AtlasPanel(fslpanel.FSLViewPanel):
atlasDesc = atlases.getAtlasDescription(atlasID)
label = atlasDesc.labels[labelIdx]
+ overlay = self._displayCtx.getSelectedOverlay()
+ opts = self._displayCtx.getDisplay(overlay).getDisplayOpts()
+ overlay = opts.getReferenceImage()
- overlay = self._displayCtx.getSelectedOverlay()
- display = self._displayCtx.getDisplay(overlay)
-
- if not isinstance(overlay, fslimage.Image):
- raise RuntimeError('Non-volumetric types not supported yet')
+ if overlay is None:
+ log.warn('No reference image available - cannot locate region')
+
+ opts = self._displayCtx.getDisplay(overlay).getDisplayOpts()
worldLoc = (label.x, label.y, label.z)
dispLoc = transform.transform(
- [worldLoc], display.getTransform('world', 'display'))[0]
+ [worldLoc], opts.getTransform('world', 'display'))[0]
self._displayCtx.location.xyz = dispLoc
--
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