diff --git a/TODO b/TODO
index c6ac63343c7527a145700fb25b6b9030008a0062..52fe8a59ac5e28312eae400e88a9d2baf2afd054 100644
--- a/TODO
+++ b/TODO
@@ -7,13 +7,17 @@ https://internal.fmrib.ox.ac.uk/i-wiki/Analysis/Todos/FSLView regularly, too.
* February 2015 internal release
-** Git release pipeline
** UI design
** Atlas tools
+** Histogram?
** SSH / VNC performance
** Fix all the bugs
*** Command line
*** Offscreen rendering
+** DONE Git release pipeline
+We now have an 'oxford' branch, which is linked to the jalapeno installation.
+When you want to 'release' something, merge from the master branch to the
+oxford branch, and push to jalapeno
* Things to do in props package
@@ -102,6 +106,7 @@ perhaps into a standalone module...
** DONE Graceful handling of bad input filenames
** DONE Aspect ratio on slicecanvas zoom, and panning is broken.
* Little things
+** Ability to display vector data as directional (i.e. starting from voxel centre)
** Ortho canvases not taking up all the available space
** 'Annotation' image type that allows the user to highlight regions in different colours.
** Support ANALYZE75
diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index 9a4287f80fb8838ca49fcfc5b78bf921da6c680f..9b536c9c496b4b7009e55080a5d0058a18a6bb48 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -49,6 +49,7 @@ import os
import xml.etree.ElementTree as et
import os.path as op
import glob
+import collections
import logging
import numpy as np
@@ -67,28 +68,74 @@ if os.environ.get('FSLDIR', None) is None:
else:
ATLAS_DIR = op.join(os.environ['FSLDIR'], 'data', 'atlases')
+
+ATLAS_DESCRIPTIONS = collections.OrderedDict()
+
-def listAtlases():
+def listAtlases(refresh=False):
"""Returns a dictionary containing :class:`AtlasDescription` objects for
all available atlases.
+
+ :arg refresh: If ``True``, or if the atlas desriptions have not
+ previously been loaded, atlas descriptions are
+ loaded from the atlas files. Otherwise, prefviously
+ loaded descriptions are returned (see
+ :attr:`ATLAS_DESCRIPTIONS`).
"""
+ if len(ATLAS_DESCRIPTIONS) == 0:
+ refresh = True
+
+ if not refresh:
+ return ATLAS_DESCRIPTIONS.values()
+
atlasFiles = glob.glob(op.join(ATLAS_DIR, '*.xml'))
atlasDescs = map(AtlasDescription, atlasFiles)
+ atlasDescs = sorted(atlasDescs, key=lambda d: d.name)
- return {d.atlasID: d for d in atlasDescs}
+ ATLAS_DESCRIPTIONS.clear()
+ for desc in atlasDescs:
+ ATLAS_DESCRIPTIONS[desc.atlasID] = desc
-def loadAtlas(atlasDesc, loadSummary=False):
+ return atlasDescs
- if loadSummary or atlasDesc.atlasType == 'label':
- return LabelAtlas(atlasDesc)
+
+def getAtlasDescription(atlasID):
+ """Returns an :class:`AtlasDescription` instance describing the
+ atlas with the given ``atlasID``.
+ """
- if atlasDesc.atlasType == 'probabilistic':
- return ProbabilisticAtlas(atlasDesc)
- else:
- raise ValueError('Unknown atlas type: {}'.format(atlasDesc.atlasType))
+ if len(ATLAS_DESCRIPTIONS) == 0:
+ listAtlases()
+
+ return ATLAS_DESCRIPTIONS[atlasID]
+
+
+def loadAtlas(atlasID, loadSummary=False):
+ """Loads and returns an :class:`Atlas` instance for the atlas
+ with the given ``atlasID``.
+
+ :arg loadSummary: If ``True``, a 3D :class:`LabelAtlas` image is
+ loaded. Otherwise, if the atlas is probabilistic,
+ a 4D :class:`ProbabilisticAtlas` image is loaded.
+ """
+
+ if len(ATLAS_DESCRIPTIONS) == 0:
+ listAtlases()
+
+ atlasDesc = ATLAS_DESCRIPTIONS[atlasID]
+
+ # label atlases are only
+ # available in 'summary' form
+ if atlasDesc.atlasType == 'label':
+ loadSummary = True
+
+ if loadSummary: atlas = LabelAtlas( atlasDesc)
+ else: atlas = ProbabilisticAtlas(atlasDesc)
+
+ return atlas
class AtlasDescription(object):
diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index f82b42375c7799a37f6c6701434a593d67159994..42cbe247dbdd795a2219ad4e14f8633306bb6536 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -48,6 +48,8 @@ titles = TypeDict({
'TimeSeriesPanel' : 'Time series',
'SpacePanel' : 'Space inspector',
+ 'AtlasInfoPanel' : 'Atlas information',
+ 'AtlasOverlayPanel' : 'Atlas overlays'
})
@@ -88,10 +90,6 @@ labels = TypeDict({
'LocationPanel.volumeLabel' : 'Volume',
'LocationPanel.spaceLabel' : 'Space',
'LocationPanel.outOfBounds' : 'Out of bounds',
-
- 'AtlasPanel.infoPanel' : 'Information',
- 'AtlasPanel.atlasListPanel' : 'Choose atlases',
- 'AtlasPanel.overlayPanel' : 'Choose overlays'
})
diff --git a/fsl/fslview/controls/atlasinfopanel.py b/fsl/fslview/controls/atlasinfopanel.py
new file mode 100644
index 0000000000000000000000000000000000000000..43156bb61f881ba9ade90c60d6c4fd6be8f28163
--- /dev/null
+++ b/fsl/fslview/controls/atlasinfopanel.py
@@ -0,0 +1,165 @@
+#!/usr/bin/env python
+#
+# atlasinfopanel.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import logging
+
+import wx
+import wx.html as wxhtml
+
+import pwidgets.elistbox as elistbox
+
+import fsl.fslview.panel as fslpanel
+import fsl.data.atlases as atlases
+
+
+log = logging.getLogger(__name__)
+
+
+
+class AtlasListWidget(wx.Panel):
+
+ def __init__(self, parent, atlasPanel, atlasID):
+
+ wx.Panel.__init__(self, parent)
+
+ self.atlasID = atlasID
+ self.atlasPanel = atlasPanel
+ self.enableBox = wx.CheckBox(self)
+
+ self.sizer = wx.BoxSizer(wx.HORIZONTAL)
+ self.sizer.Add(self.enableBox, flag=wx.EXPAND)
+
+ self.enableBox.Bind(wx.EVT_CHECKBOX, self.onEnable)
+
+
+ def onEnable(self, ev):
+
+ if self.enableBox.GetValue():
+ self.atlasPanel.enableAtlasInfo(self.atlasID)
+ else:
+ self.atlasPanel.disableAtlasInfo(self.atlasID)
+
+
+# TODO
+#
+# Actions to show/hide atlas overlays are managed by the AtlasPanel,
+# which provides methods to do so, and maintains the state required
+# to track whether an overlay is enabled/disabled. Thec
+# AtlasInfoPanel and AtlasOverlayPanel implement the GUI
+# functionality, and the event handling needed to allow the user
+# to toggle atlas information/overlays on/off, but management
+# of the in-memory atlas images is handled by the AtlasPanel.
+
+
+# Info panel, containing atlas-based regional
+# proportions/labels for the current location
+
+# Atlas list, containing a list of atlases
+# that the user can choose from
+class AtlasInfoPanel(fslpanel.FSLViewPanel):
+
+ def __init__(self, parent, imageList, displayCtx, atlasPanel):
+ fslpanel.FSLViewPanel.__init__(self, parent, imageList, displayCtx)
+
+
+ self.atlasPanel = atlasPanel
+ self.contentPanel = wx.SplitterWindow(self)
+ self.infoPanel = wxhtml.HtmlWindow(self.notebook)
+
+ self.atlasList = elistbox.EditableListBox(
+ self,
+ style=(elistbox.ELB_NO_ADD |
+ elistbox.ELB_NO_REMOVE |
+ elistbox.ELB_NO_MOVE))
+
+ for i, atlasDesc in enumerate(atlases.listAtlases()):
+
+ self.atlasList.Append(atlasDesc.name, atlasDesc.atlasID)
+ widget = AtlasListWidget(self.atlasList, atlasPanel, atlasDesc)
+ self.atlasList.SetItemWidget(i, widget)
+
+ # The info panel contains clickable links
+ # for the currently displayed regions -
+ # when a link is clicked, the location
+ # is centred at the corresponding region
+ self.infoPanel.Bind(wxhtml.EVT_HTML_LINK_CLICKED,
+ self._infoPanelLinkClicked)
+
+ displayCtx.addListener('location', self._name, self._locationChanged)
+
+
+ def _infoPanelLinkClicked(self, ev):
+
+ showType, atlasID, labelIndex = ev.GetLinkInfo().GetHref().split()
+ labelIndex = int(labelIndex)
+ atlas = self.enabledAtlases[atlasID]
+ label = atlas.desc.labels[labelIndex]
+
+ log.debug('{}/{} ({}) clicked'.format(atlasID, label.name, showType))
+
+ if showType == 'summary':
+ self.overlayPanel.toggleSummaryOverlay(atlas.desc)
+
+ elif showType == 'prob':
+ self.overlayPanel.toggleOverlay(atlas.desc, labelIndex, False)
+
+ elif showType == 'label':
+ self.overlayPanel.toggleOverlay(atlas.desc, labelIndex, True)
+
+
+ def _locationChanged(self, *a):
+
+ image = self._displayCtx.getSelectedImage()
+ display = self._displayCtx.getDisplayProperties(image)
+ loc = self._displayCtx.location
+ text = self.infoPanel
+ loc = transform.transform([loc], display.displayToWorldMat)[0]
+
+ if len(self.enabledAtlases) == 0:
+ text.SetPage(strings.messages['atlaspanel.chooseAnAtlas'])
+ return
+
+ if image.getXFormCode() != constants.NIFTI_XFORM_MNI_152:
+ text.SetPage(strings.messages['atlaspanel.notMNISpace'])
+ return
+
+ lines = []
+
+
+ titleTemplate = '<b>{}</b> (<a href="summary {} {}">Show/Hide</a>)'
+ labelTemplate = '{} (<a href="label {} {}">Show/Hide</a>)'
+ probTemplate = '{:0.2f}% {} (<a href="prob {} {}">Show/Hide</a>)'
+
+ for atlasID, atlas in self.enabledAtlases.items():
+
+ lines.append(titleTemplate.format(atlas.desc.name, atlasID, 0))
+
+ if isinstance(atlas, atlases.ProbabilisticAtlas):
+ proportions = atlas.proportions(loc)
+
+ for label, prop in zip(atlas.desc.labels, proportions):
+ if prop == 0.0:
+ continue
+ lines.append(probTemplate.format(prop,
+ label.name,
+ atlasID,
+ label.index,
+ atlasID,
+ label.index))
+
+ elif isinstance(atlas, atlases.LabelAtlas):
+
+ labelVal = atlas.label(loc)
+ label = atlas.desc.labels[int(labelVal)]
+ lines.append(labelTemplate.format(label.name,
+ atlasID,
+ label.index,
+ atlasID,
+ label.index))
+
+ text.SetPage('<br>'.join(lines))
+
diff --git a/fsl/fslview/controls/atlasoverlaypanel.py b/fsl/fslview/controls/atlasoverlaypanel.py
new file mode 100644
index 0000000000000000000000000000000000000000..6d149201a69b4a83d416ed81575ed48d2e211d78
--- /dev/null
+++ b/fsl/fslview/controls/atlasoverlaypanel.py
@@ -0,0 +1,246 @@
+#!/usr/bin/env python
+#
+# atlasoverlaypanel.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""
+"""
+
+import logging
+
+import wx
+import numpy as np
+
+import pwidgets.elistbox as elistbox
+
+import fsl.data.atlases as atlases
+import fsl.data.image as fslimage
+import fsl.data.constants as constants
+import fsl.fslview.panel as fslpanel
+
+
+log = logging.getLogger(__name__)
+
+
+
+
+class OverlayListWidget(wx.CheckBox):
+
+ def __init__(self, parent, atlasDesc, label=None):
+
+ wx.CheckBox.__init__(self, parent)
+
+ self.parent = parent
+ self.atlasDesc = atlasDesc
+ self.label = label
+
+
+ def _onCheck(self, ev):
+
+ pass
+
+
+class AtlasOverlayPanel(fslpanel.FSLViewPanel):
+
+ def __init__(self, parent, imageList, displayCtx, atlasPanel):
+
+ fslpanel.FSLViewPanel.__init__(self, parent, imageList, displayCtx)
+
+ self.atlasPanel = atlasPanel
+
+ self.enabledOverlays = {}
+ self.atlasList = elistbox.EditableListBox(
+ self,
+ style=(elistbox.ELB_NO_ADD |
+ elistbox.ELB_NO_REMOVE |
+
+ elistbox.ELB_NO_MOVE))
+
+ self.regionPanel = wx.Panel( self)
+ self.regionFilter = wx.TextCtrl(self.regionPanel)
+
+ self.regionLists = [None] * len(atlasDescs)
+
+ self.sizer = wx.BoxSizer(wx.HORIZONTAL)
+ self.regionSizer = wx.BoxSizer(wx.VERTICAL)
+
+ self.sizer .Add(self.atlasList, flag=wx.EXPAND, proportion=1)
+ self.regionSizer.Add(self.regionFilter, flag=wx.EXPAND)
+ self.regionSizer.AddStretchSpacer()
+ self.sizer .Add(self.regionPanel, flag=wx.EXPAND, proportion=1)
+
+ self.regionPanel.SetSizer(self.regionSizer)
+ self .SetSizer(self.sizer)
+
+ for i, atlasDesc in enumerate(atlasDescs):
+ self.atlasList.Append(atlasDesc.name, atlasDesc)
+ self._updateAtlasState(i)
+
+ self.regionFilter.Bind(wx.EVT_TEXT, self._onRegionFilter)
+ self.atlasList.Bind(elistbox.EVT_ELB_SELECT_EVENT, self._onAtlasSelect)
+
+ self.regionSizer.Layout()
+ self.sizer .Layout()
+
+
+ def _onRegionFilter(self, ev):
+
+ filterStr = self.regionFilter.GetValue().lower()
+
+ for i, listBox in enumerate(self.regionLists):
+
+ if listBox is None:
+ continue
+
+ listBox.ApplyFilter(filterStr, ignoreCase=True)
+ self._updateAtlasState(i)
+
+
+ def _updateAtlasState(self, atlasIdx):
+
+ listBox = self.regionLists[atlasIdx]
+
+ if listBox is None:
+ weight = wx.FONTWEIGHT_LIGHT
+ colour = '#a0a0a0'
+
+ elif listBox.VisibleItemCount() == 0:
+ weight = wx.FONTWEIGHT_LIGHT
+ colour = '#303030'
+ else:
+ weight = wx.FONTWEIGHT_BOLD
+ colour = '#000000'
+
+ font = self.atlasList.GetItemFont(atlasIdx)
+ font.SetWeight(weight)
+
+ self.atlasList.SetItemFont(atlasIdx, font)
+ self.atlasList.SetItemForegroundColour(atlasIdx, colour, colour)
+
+
+ def _onAtlasSelect(self, ev):
+
+ atlasDesc = ev.data
+ atlasIdx = ev.idx
+ regionList = self.regionLists[atlasIdx]
+
+ if regionList is None:
+
+ regionList = elistbox.EditableListBox(
+ self.regionPanel,
+ style=(elistbox.ELB_NO_ADD |
+ elistbox.ELB_NO_REMOVE |
+ elistbox.ELB_NO_MOVE))
+
+ print 'Creating region list for {} ({})'.format(
+ atlasDesc.atlasID, id(regionList))
+
+ self.regionLists[atlasIdx] = regionList
+
+ for label in atlasDesc.labels:
+ regionList.Append(label.name)
+
+ filterStr = self.regionFilter.GetValue().lower()
+ regionList.ApplyFilter(filterStr, ignoreCase=True)
+
+ self._updateAtlasState(atlasIdx)
+
+ print 'Showing region list for {} ({})'.format(
+ atlasDesc.atlasID, id(regionList))
+
+ old = self.regionSizer.GetItem(1).GetWindow()
+
+ if old is not None:
+ old.Show(False)
+
+ regionList.Show(True)
+ self.regionSizer.Remove(1)
+
+ self.regionSizer.Insert(1, regionList, flag=wx.EXPAND, proportion=1)
+ self.regionSizer.Layout()
+
+
+ def overlayIsEnabled(self, atlasDesc, label=None, summary=False):
+ pass
+
+
+ def toggleSummaryOverlay(self, atlasDesc):
+
+ atlasID = atlasDesc.atlasID
+ overlayName = '{}/all'.format(atlasID)
+ overlay = self._imageList.find(overlayName)
+
+ if overlay is not None:
+ self._imageList.remove(overlay)
+ log.debug('Removed summary overlay {}'.format(overlayName))
+
+ else:
+ overlay = self.enabledAtlases.get(atlasID, None)
+ if overlay is None or \
+ isinstance(overlay, atlases.ProbabilisticAtlas):
+ overlay = atlases.loadAtlas(atlasDesc, True)
+
+ overlay.name = overlayName
+
+ # Even though all the FSL atlases
+ # are in MNI152 space, not all of
+ # their sform_codes are correctly set
+ overlay.nibImage.get_header().set_sform(
+ None, code=constants.NIFTI_XFORM_MNI_152)
+
+ self._imageList.append(overlay)
+ log.debug('Added summary overlay {}'.format(overlayName))
+
+
+ def toggleOverlay(self, atlasDesc, labelIndex, label):
+ """
+ """
+
+ atlasID = atlasDesc.atlasID
+ overlayName = '{}/{}'.format(atlasID,
+ atlasDesc.labels[labelIndex].name)
+ overlay = self._imageList.find(overlayName)
+
+ if overlay is not None:
+ self._imageList.remove(overlay)
+ log.debug('Removed overlay {}'.format(overlayName))
+
+ else:
+ atlas = self.enabledAtlases.get(atlasID, None)
+ if atlas is None or \
+ (label and isinstance(overlay, atlases.LabelAtlas)):
+ atlas = atlases.loadAtlas(atlasDesc, True)
+
+ if label:
+ if atlasDesc.atlasType == 'probabilistic':
+ labelVal = labelIndex + 1
+ elif atlasDesc.atlasType == 'label':
+ labelVal = labelIndex
+
+ mask = np.zeros(atlas.shape, dtype=np.uint8)
+ mask[atlas.data == labelIndex] = labelVal
+ else:
+ mask = atlas.data[..., labelIndex]
+
+ overlay = fslimage.Image(
+ mask,
+ header=atlas.nibImage.get_header(),
+ name=overlayName)
+
+ # See comment in toggleSummaryOverlay
+ overlay.nibImage.get_header().set_sform(
+ None, code=constants.NIFTI_XFORM_MNI_152)
+
+ if label:
+ overlay.imageType = 'mask'
+
+ self._imageList.append(overlay)
+ log.debug('Added overlay {}'.format(overlayName))
+
+ display = self._displayCtx.getDisplayProperties(overlay)
+
+ if label:
+ display.getDisplayOpts().colour = np.random.random(3)
+ else:
+ display.getDisplayOpts().cmap = 'hot'
diff --git a/fsl/fslview/controls/atlaspanel.py b/fsl/fslview/controls/atlaspanel.py
index 036cb4915656d749e26428d391be59b601879e24..874a32adc66a9901c5c4eb8880460433b5abc8ba 100644
--- a/fsl/fslview/controls/atlaspanel.py
+++ b/fsl/fslview/controls/atlaspanel.py
@@ -7,47 +7,27 @@
import logging
-import wx
-import wx.html as wxhtml
-import numpy as np
+import wx
+import wx.html as wxhtml
+import wx.lib.newevent as wxevent
+import numpy as np
import pwidgets.elistbox as elistbox
import pwidgets.notebook as notebook
-import fsl.utils.transform as transform
-import fsl.data.image as fslimage
-import fsl.data.atlases as atlases
-import fsl.data.strings as strings
-import fsl.data.constants as constants
-import fsl.fslview.panel as fslpanel
+import fsl.utils.transform as transform
+import fsl.data.image as fslimage
+import fsl.data.atlases as atlases
+import fsl.data.strings as strings
+import fsl.data.constants as constants
+import fsl.fslview.panel as fslpanel
+import fsl.fslview.controls.atlasoverlaypanel as atlasoverlaypanel
+import fsl.fslview.controls.atlasinfopanel as atlasinfopanel
log = logging.getLogger(__name__)
-class AtlasListWidget(wx.Panel):
-
- def __init__(self, parent, atlasPanel, atlasDesc):
-
- wx.Panel.__init__(self, parent)
-
- self.atlasDesc = atlasDesc
- self.atlasPanel = atlasPanel
- self.enableBox = wx.CheckBox(self)
-
- self.sizer = wx.BoxSizer(wx.HORIZONTAL)
- self.sizer.Add(self.enableBox, flag=wx.EXPAND)
-
- self.enableBox.Bind(wx.EVT_CHECKBOX, self.onEnable)
-
- def onEnable(self, ev):
-
- if self.enableBox.GetValue():
- self.atlasPanel.enableAtlasInfo(self.atlasDesc.atlasID)
- else:
- self.atlasPanel.disableAtlasInfo(self.atlasDesc.atlasID)
-
-
class AtlasPanel(fslpanel.FSLViewPanel):
@@ -55,6 +35,10 @@ class AtlasPanel(fslpanel.FSLViewPanel):
fslpanel.FSLViewPanel.__init__(self, parent, imageList, displayCtx)
+ self.atlasDescs = sorted(atlases.listAtlases(),
+ key=lambda d: d.name)
+ self.enabledAtlases = {}
+
self.notebook = notebook.Notebook(self)
self.sizer = wx.BoxSizer(wx.HORIZONTAL)
@@ -62,237 +46,39 @@ class AtlasPanel(fslpanel.FSLViewPanel):
self.SetSizer(self.sizer)
- # Info panel, containing atlas-based regional
- # proportions/labels for the current location
- self.infoPanel = wxhtml.HtmlWindow(self.notebook)
- self.infoPanel.SetMinSize((-1, 100))
+ # Temporary
+ self.SetMaxSize((-1, 200))
- # Atlas list, containing a list of atlases
- # that the user can choose from
- self.atlasPanel = wx.Panel(self.notebook)
- self.atlasFilter = wx.TextCtrl(self.atlasPanel)
- self.atlasList = elistbox.EditableListBox(
- self.atlasPanel,
- style=(elistbox.ELB_NO_ADD |
- elistbox.ELB_NO_REMOVE |
- elistbox.ELB_NO_MOVE))
+ self.atlasInfoPanel = atlasinfopanel.AtlasInfoPanel(
+ self.notebook, imageList, displayCtx, self)
# Overlay panel, containing a list of regions,
# allowing the user to add/remove overlays
- self.overlayPanel = wx.Panel(self.notebook)
+ self.overlayPanel = atlasoverlaypanel.AtlasOverlayPanel(
+ self.notebook, imageList, displayCtx, self)
self.notebook.AddPage(self.infoPanel,
- strings.labels['AtlasPanel.infoPanel'])
- self.notebook.AddPage(self.atlasPanel,
- strings.labels['AtlasPanel.atlasListPanel'])
+ strings.labels[self.infoPanel])
self.notebook.AddPage(self.overlayPanel,
- strings.labels['AtlasPanel.overlayPanel'])
+ strings.labels[self.overlayPanel])
self.notebook.ShowPage(0)
- # The info panel contains clickable links
- # for the currently displayed regions -
- # when a link is clicked, the location
- # is centred at the corresponding region
- self.infoPanel.Bind(wxhtml.EVT_HTML_LINK_CLICKED,
- self._infoPanelLinkClicked)
- # Set up the atlas list, allowing the
- # user to choose which atlases information
- # (in the info panel) is shown for
- self.atlasSizer = wx.BoxSizer(wx.VERTICAL)
- self.atlasSizer.Add(self.atlasFilter, flag=wx.EXPAND)
- self.atlasSizer.Add(self.atlasList, flag=wx.EXPAND, proportion=1)
- self.atlasPanel.SetSizer(self.atlasSizer)
-
- self.atlasFilter.Bind(wx.EVT_TEXT, self._onAtlasFilter)
-
- self.atlasDescs = atlases.listAtlases()
- self.enabledAtlases = {}
-
- listItems = sorted(self.atlasDescs.items(), key=lambda (a, d): d.name)
-
- for i, (atlasID, desc) in enumerate(listItems):
-
- self.atlasList.Append(desc.name, atlasID)
- widget = AtlasListWidget(self.atlasList, self, desc)
- self.atlasList.SetItemWidget(i, widget)
-
- displayCtx.addListener('location', self._name, self._locationChanged)
self.Layout()
-
- def _infoPanelLinkClicked(self, ev):
-
- showType, atlasID, labelIndex = ev.GetLinkInfo().GetHref().split()
- labelIndex = int(labelIndex)
- atlas = self.enabledAtlases[atlasID]
- label = atlas.desc.labels[labelIndex]
-
- log.debug('{}/{} ({}) clicked'.format(atlasID, label.name, showType))
-
- if showType == 'summary':
- self.toggleSummaryOverlay(atlasID)
-
- elif showType == 'prob':
- self.toggleOverlay(atlasID, labelIndex, False)
-
- elif showType == 'label':
- self.toggleOverlay(atlasID, labelIndex, True)
-
-
- def _onAtlasFilter(self, ev):
- filterStr = self.atlasFilter.GetValue().lower()
- self.atlasList.ApplyFilter(filterStr, ignoreCase=True)
-
- def enableAtlasInfo(self, atlasID):
-
- desc = self.atlasDescs[atlasID]
- atlasImage = atlases.loadAtlas(desc)
+ def enableAtlasInfo(self, atlasDesc):
- self.enabledAtlases[atlasID] = atlasImage
+ atlasImage = atlases.loadAtlas(atlasDesc)
+ self.enabledAtlases[atlasDesc.atlasID] = atlasImage
self._locationChanged()
- def disableAtlasInfo(self, atlasID):
+ def disableAtlasInfo(self, atlasDesc):
- self.enabledAtlases.pop(atlasID, None)
+ self.enabledAtlases.pop(atlasDesc.atlasID, None)
self._locationChanged()
-
- def toggleSummaryOverlay(self, atlasID):
-
- overlayName = '{}/all'.format(atlasID)
- overlay = self._imageList.find(overlayName)
-
- if overlay is not None:
- self._imageList.remove(overlay)
- log.debug('Removed summary overlay {}'.format(overlayName))
-
- else:
- overlay = self.enabledAtlases.get(atlasID, None)
- if overlay is None or \
- isinstance(overlay, atlases.ProbabilisticAtlas):
- overlay = atlases.loadAtlas(self.atlasDescs[atlasID], True)
-
- overlay.name = overlayName
-
- # Even though all the FSL atlases
- # are in MNI152 space, not all of
- # their sform_codes are correctly set
- overlay.nibImage.get_header().set_sform(
- None, code=constants.NIFTI_XFORM_MNI_152)
-
- self._imageList.append(overlay)
- log.debug('Added summary overlay {}'.format(overlayName))
-
-
-
-
- def toggleOverlay(self, atlasID, labelIndex, label):
- """
- """
-
- desc = self.atlasDescs[atlasID]
- overlayName = '{}/{}'.format(atlasID, desc.labels[labelIndex].name)
- overlay = self._imageList.find(overlayName)
-
- if overlay is not None:
- self._imageList.remove(overlay)
- log.debug('Removed overlay {}'.format(overlayName))
-
- else:
- atlas = self.enabledAtlases.get(atlasID, None)
- if atlas is None or \
- (label and isinstance(overlay, atlases.LabelAtlas)):
- atlas = atlases.loadAtlas(self.atlasDescs[atlasID], True)
-
- if label:
- if desc.atlasType == 'probabilistic':
- labelVal = labelIndex + 1
- elif desc.atlasType == 'label':
- labelVal = labelIndex
-
- mask = np.zeros(atlas.shape, dtype=np.uint8)
- mask[atlas.data == labelIndex] = labelVal
- else:
- mask = atlas.data[..., labelIndex]
-
- overlay = fslimage.Image(
- mask,
- header=atlas.nibImage.get_header(),
- name=overlayName)
-
- # See comment in toggleSummaryOverlay
- overlay.nibImage.get_header().set_sform(
- None, code=constants.NIFTI_XFORM_MNI_152)
-
- if label:
- overlay.imageType = 'mask'
-
- self._imageList.append(overlay)
- log.debug('Added overlay {}'.format(overlayName))
-
- display = self._displayCtx.getDisplayProperties(overlay)
-
- if label:
- display.getDisplayOpts().colour = np.random.random(3)
- else:
- display.getDisplayOpts().cmap = 'hot'
-
-
-
- def _locationChanged(self, *a):
-
- image = self._displayCtx.getSelectedImage()
- display = self._displayCtx.getDisplayProperties(image)
- loc = self._displayCtx.location
- text = self.infoPanel
- loc = transform.transform([loc], display.displayToWorldMat)[0]
-
- if len(self.enabledAtlases) == 0:
- text.SetPage(strings.messages['atlaspanel.chooseAnAtlas'])
- return
-
- if image.getXFormCode() != constants.NIFTI_XFORM_MNI_152:
- text.SetPage(strings.messages['atlaspanel.notMNISpace'])
- return
-
- lines = []
-
-
- titleTemplate = '<b>{}</b> (<a href="summary {} {}">Show/Hide</a>)'
- labelTemplate = '{} (<a href="label {} {}">Show/Hide</a>)'
- probTemplate = '{:0.2f}% {} (<a href="prob {} {}">Show/Hide</a>)'
-
- for atlasID, atlas in self.enabledAtlases.items():
-
- lines.append(titleTemplate.format(atlas.desc.name, atlasID, 0))
-
- if isinstance(atlas, atlases.ProbabilisticAtlas):
- proportions = atlas.proportions(loc)
-
- for label, prop in zip(atlas.desc.labels, proportions):
- if prop == 0.0:
- continue
- lines.append(probTemplate.format(prop,
- label.name,
- atlasID,
- label.index,
- atlasID,
- label.index))
-
- elif isinstance(atlas, atlases.LabelAtlas):
-
- labelVal = atlas.label(loc)
- label = atlas.desc.labels[int(labelVal)]
- lines.append(labelTemplate.format(label.name,
- atlasID,
- label.index,
- atlasID,
- label.index))
-
- text.SetPage('<br>'.join(lines))