diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index f346ff53c1709ecea41edd649f2cf17298ef6b70..84de9338088142ba4eb673ff3ecf305713673f27 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -334,7 +334,9 @@ labels = TypeDict({
properties = TypeDict({
- 'Profile.mode' : 'Profile',
+ 'Profile.mode' : 'Profile',
+
+ 'DisplayContext.displaySpace' : 'Display space',
'CanvasPanel.syncLocation' : 'Sync location',
'CanvasPanel.syncOverlayOrder' : 'Sync overlay order',
@@ -470,6 +472,9 @@ properties = TypeDict({
choices = TypeDict({
+ 'DisplayContext.displaySpace' : {'world' : 'World coordinates',
+ 'pixdim' : 'Scaled voxels'},
+
'SceneOpts.colourBarLocation' : {'top' : 'Top',
'bottom' : 'Bottom',
'left' : 'Left',
diff --git a/fsl/fsleyes/controls/canvassettingspanel.py b/fsl/fsleyes/controls/canvassettingspanel.py
index a4ac500b6f21971990cbcadc40829025687f472b..95a0877d4dbe927ab4b23286b9307725d260ad52 100644
--- a/fsl/fsleyes/controls/canvassettingspanel.py
+++ b/fsl/fsleyes/controls/canvassettingspanel.py
@@ -16,6 +16,7 @@ import props
import pwidgets.widgetlist as widgetlist
import fsl.data.strings as strings
+import fsl.data.image as fslimage
import fsl.fsleyes.panel as fslpanel
import fsl.fsleyes.tooltips as fsltooltips
@@ -51,6 +52,7 @@ class CanvasSettingsPanel(fslpanel.FSLEyesPanel):
_CANVASPANEL_PROPS
_SCENEOPTS_PROPS
+ _DISPLAYCTX_PROPS
_ORTHOOPTS_PROPS
_LIGHTBOXOPTS_PROPS
"""
@@ -114,7 +116,19 @@ class CanvasSettingsPanel(fslpanel.FSLEyesPanel):
widget,
displayName=strings.properties[opts, dispProp.key],
tooltip=fsltooltips.properties[opts, dispProp.key],
- groupName='scene')
+ groupName='scene')
+
+ for dispProp in _DISPLAYCTX_PROPS:
+ widget = props.buildGUI(self.__widgets,
+ displayCtx,
+ dispProp,
+ showUnlink=False)
+
+ self.__widgets.AddWidget(
+ widget,
+ displayName=strings.properties[displayCtx, dispProp.key],
+ tooltip=fsltooltips.properties[displayCtx, dispProp.key],
+ groupName='scene')
for dispProp in panelProps:
@@ -168,6 +182,22 @@ display for :class:`.SceneOpts` properties.
"""
+def _displaySpaceOptionName(opt):
+
+ if isinstance(opt, fslimage.Image):
+ return opt.name
+ else:
+ return strings.choices['DisplayContext.displaySpace'][opt]
+
+
+_DISPLAYCTX_PROPS = [
+ props.Widget('displaySpace', labels=_displaySpaceOptionName)
+]
+"""A list of :class:`props.Widget` items defining controls to
+display for :class:`.DisplayContext` properties.
+"""
+
+
_ORTHOOPTS_PROPS = [
props.Widget('layout', labels=strings.choices['OrthoOpts.layout']),
props.Widget('zoom', spin=False, showLimits=False),
diff --git a/fsl/fsleyes/controls/lightboxtoolbar.py b/fsl/fsleyes/controls/lightboxtoolbar.py
index 0e4289f6e27637e6327d2765a01c8484a5c5b573..fc1d5e3b44d1f08b9ea0fcbfd36f46523e8336a2 100644
--- a/fsl/fsleyes/controls/lightboxtoolbar.py
+++ b/fsl/fsleyes/controls/lightboxtoolbar.py
@@ -18,6 +18,7 @@ import fsl.fsleyes.actions as actions
import fsl.fsleyes.icons as fslicons
import fsl.fsleyes.tooltips as fsltooltips
import fsl.data.strings as strings
+import fsl.data.image as fslimage
class LightBoxToolBar(fsltoolbar.FSLEyesToolBar):
@@ -75,7 +76,16 @@ class LightBoxToolBar(fsltoolbar.FSLEyesToolBar):
'sliceSpacing' : fsltooltips.properties[lbOpts, 'sliceSpacing'],
'zrange' : fsltooltips.properties[lbOpts, 'zrange'],
'zoom' : fsltooltips.properties[lbOpts, 'zoom'],
+ 'displaySpace' : fsltooltips.properties[displayCtx,
+ 'displaySpace']
}
+
+ def displaySpaceOptionName(opt):
+
+ if isinstance(opt, fslimage.Image):
+ return opt.name
+ else:
+ return strings.choices['DisplayContext.displaySpace'][opt]
specs = {
@@ -117,6 +127,11 @@ class LightBoxToolBar(fsltoolbar.FSLEyesToolBar):
spin=False,
showLimits=False,
tooltip=tooltips['zoom']),
+
+ 'displaySpace' : props.Widget(
+ 'displaySpace',
+ labels=displaySpaceOptionName,
+ tooltip=tooltips['displaySpace'])
}
# Slice spacing and zoom go on a single panel
@@ -124,25 +139,30 @@ class LightBoxToolBar(fsltoolbar.FSLEyesToolBar):
sizer = wx.FlexGridSizer(2, 2)
panel.SetSizer(sizer)
- more = props.buildGUI(self, self, specs['more'])
- screenshot = props.buildGUI(self, lb, specs['screenshot'])
- movieMode = props.buildGUI(self, lb, specs['movieMode'])
- zax = props.buildGUI(self, lbOpts, specs['zax'])
- zrange = props.buildGUI(self, lbOpts, specs['zrange'])
- zoom = props.buildGUI(panel, lbOpts, specs['zoom'])
- spacing = props.buildGUI(panel, lbOpts, specs['sliceSpacing'])
+ more = props.buildGUI(self, self, specs['more'])
+ screenshot = props.buildGUI(self, lb, specs['screenshot'])
+ movieMode = props.buildGUI(self, lb, specs['movieMode'])
+ zax = props.buildGUI(self, lbOpts, specs['zax'])
+ zrange = props.buildGUI(self, lbOpts, specs['zrange'])
+ zoom = props.buildGUI(panel, lbOpts, specs['zoom'])
+ spacing = props.buildGUI(panel, lbOpts, specs['sliceSpacing'])
+ displaySpace = props.buildGUI(panel, displayCtx, specs['displaySpace'])
zoomLabel = wx.StaticText(panel)
spacingLabel = wx.StaticText(panel)
zoomLabel .SetLabel(strings.properties[lbOpts, 'zoom'])
spacingLabel.SetLabel(strings.properties[lbOpts, 'sliceSpacing'])
+ displaySpace = self.MakeLabelledTool(
+ displaySpace,
+ strings.properties[displayCtx, 'displaySpace'])
+
sizer.Add(zoomLabel)
sizer.Add(zoom, flag=wx.EXPAND)
sizer.Add(spacingLabel)
sizer.Add(spacing, flag=wx.EXPAND)
- tools = [more, screenshot, zax, movieMode, zrange, panel]
+ tools = [more, screenshot, zax, movieMode, displaySpace, zrange, panel]
self.SetTools(tools)
diff --git a/fsl/fsleyes/controls/orthotoolbar.py b/fsl/fsleyes/controls/orthotoolbar.py
index 8ad584f39a032f7b5fd7c1b9913a0237314b95f3..62813a43ec5d7ede8d090cec9a474ed4fe840c73 100644
--- a/fsl/fsleyes/controls/orthotoolbar.py
+++ b/fsl/fsleyes/controls/orthotoolbar.py
@@ -11,6 +11,7 @@
import props
+import fsl.data.image as fslimage
import fsl.fsleyes.toolbar as fsltoolbar
import fsl.fsleyes.icons as fslicons
import fsl.fsleyes.tooltips as fsltooltips
@@ -78,7 +79,8 @@ class OrthoToolBar(fsltoolbar.FSLEyesToolBar):
Re-creates all tools shown on this ``OrthoToolBar``.
"""
-
+
+ dctx = self._displayCtx
ortho = self.orthoPanel
orthoOpts = ortho.getSceneOptions()
profile = ortho.getCurrentProfile()
@@ -109,9 +111,11 @@ class OrthoToolBar(fsltoolbar.FSLEyesToolBar):
'showXCanvas' : fsltooltips.properties[orthoOpts, 'showXCanvas'],
'showYCanvas' : fsltooltips.properties[orthoOpts, 'showYCanvas'],
'showZCanvas' : fsltooltips.properties[orthoOpts, 'showZCanvas'],
+ 'displaySpace' : fsltooltips.properties[dctx, 'displaySpace'],
'resetZoom' : fsltooltips.actions[ profile, 'resetZoom'],
'centreCursor' : fsltooltips.actions[ profile, 'centreCursor'],
'more' : fsltooltips.actions[ self, 'more'],
+
}
targets = {'screenshot' : ortho,
@@ -121,10 +125,18 @@ class OrthoToolBar(fsltoolbar.FSLEyesToolBar):
'showXCanvas' : orthoOpts,
'showYCanvas' : orthoOpts,
'showZCanvas' : orthoOpts,
+ 'displaySpace' : dctx,
'resetZoom' : profile,
'centreCursor' : profile,
'more' : self}
+ def displaySpaceOptionName(opt):
+
+ if isinstance(opt, fslimage.Image):
+ return opt.name
+ else:
+ return strings.choices['DisplayContext.displaySpace'][opt]
+
toolSpecs = [
@@ -155,7 +167,9 @@ class OrthoToolBar(fsltoolbar.FSLEyesToolBar):
actions.ActionButton('centreCursor',
icon=icons['centreCursor'],
tooltip=tooltips['centreCursor']),
-
+ props.Widget( 'displaySpace',
+ labels=displaySpaceOptionName,
+ tooltip=tooltips['displaySpace']),
props.Widget( 'zoom',
spin=False,
showLimits=False,
@@ -167,10 +181,10 @@ class OrthoToolBar(fsltoolbar.FSLEyesToolBar):
for spec in toolSpecs:
widget = props.buildGUI(self, targets[spec.key], spec)
- if spec.key == 'zoom':
+ if spec.key in ('zoom', 'displaySpace'):
widget = self.MakeLabelledTool(
widget,
- strings.properties[targets[spec.key], 'zoom'])
+ strings.properties[targets[spec.key], spec.key])
tools.append(widget)
diff --git a/fsl/fsleyes/displaycontext/displaycontext.py b/fsl/fsleyes/displaycontext/displaycontext.py
index 53d6217f905b7d2c89a6255aae855dc73ed6a83e..c547ded1fd749f7e952f8b83ae769623b38cecfc 100644
--- a/fsl/fsleyes/displaycontext/displaycontext.py
+++ b/fsl/fsleyes/displaycontext/displaycontext.py
@@ -14,7 +14,9 @@ import logging
import props
-import display as fsldisplay
+import display as fsldisplay
+import fsl.data.image as fslimage
+import fsl.utils.transform as transform
log = logging.getLogger(__name__)
@@ -35,11 +37,11 @@ class DisplayContext(props.SyncableHasProperties):
A ``DisplayContext`` instance is responsible for creating and destroying
- :class:`.Display` instances for every overlay in the ``OverlayList``. These
- ``Display`` instances, and the corresponding ``DisplayOpts`` instances
- (which, in turn, are created/destroyed by ``Display`` instances) can be
- accessed with the :meth:`getDisplay` and :meth:`getOpts` method
- respectively.
+ :class:`.Display` instances for every overlay in the
+ ``OverlayList``. These ``Display`` instances, and the corresponding
+ :class:`.DisplayOpts` instances (which, in turn, are created/destroyed by
+ ``Display`` instances) can be accessed with the :meth:`getDisplay` and
+ :meth:`getOpts` method respectively.
A number of other useful methods are provided by a ``DisplayContext``
@@ -79,7 +81,7 @@ class DisplayContext(props.SyncableHasProperties):
bounds = props.Bounds(ndims=3)
"""This property contains the min/max values of a bounding box (in display
coordinates) which is big enough to contain all of the overlays in the
- :attr:`overlays` list.
+ :class:`.OverlayList`.
.. warning:: This property shouid be treated as read-only.
"""
@@ -113,6 +115,41 @@ class DisplayContext(props.SyncableHasProperties):
"""
+ displaySpace = props.Choice(('pixdim', 'world'), default='pixdim')
+ """The *space* in which overlays are displayed. This property globally
+ controls the :attr:`.ImageOpts.transform` property of all :class:`.Image`
+ overlays. It has three settings, described below.
+
+
+ 1. **Scaled voxel** space (a.k.a. ``pixdim``)
+
+ All :class:`.Image` overlays are displayed with scaled voxels - the
+ :attr:`.ImageOpts.transform` property for every ``Image`` overlay is
+ set to ``pixdim``.
+
+ 2. **World** space (a.k.a. ``world``)
+
+ All :class:`.Image` overlays are displayed in the space defined by
+ their affine transformation matrix - the :attr:`.ImageOpts.transform`
+ property for every ``Image`` overlay is set to ``affine``.
+
+ 3. **Reference image** space
+
+ A single :class:`.Image` overlay is selected as a *reference* image,
+ and is displayed in scaled voxel space (:attr:`.ImageOpts.transform` is
+ set to ``pixdim``). All other ``Image`` overlays are transformed into
+ this reference space - their :attr:`.ImageOpts.transform` property is
+ set to ``custom``, and their :attr:`.ImageOpts.customXform` matrix is
+ set such that it transforms from the image voxel space to the scaled
+ voxel space of the reference image.
+
+ .. note:: The :attr:`.ImageOpts.transform` property of any :class:`.Image`
+ overlay can be set independently of this property. However,
+ whenever this property changes, it will change the ``transform``
+ property for every ``Image``, in the manner described above.
+ """
+
+
def __init__(self, overlayList, parent=None):
"""Create a ``DisplayContext``.
@@ -126,7 +163,7 @@ class DisplayContext(props.SyncableHasProperties):
props.SyncableHasProperties.__init__(
self,
parent=parent,
- nounbind=['overlayGroups'],
+ nounbind=['overlayGroups', 'displaySpace'],
nobind=[ 'syncOverlayDisplay'])
self.__overlayList = overlayList
@@ -154,12 +191,11 @@ class DisplayContext(props.SyncableHasProperties):
if parent is None: self.__prevOverlayListLen = 0
else: self.__prevOverlayListLen = len(overlayList)
-
- # Ensure that a Display object exists
- # for every overlay, and that the display
- # bounds property is initialised
+ # The overlayListChanged and displaySpaceChanged
+ # methods do important things - check them out
self.__displays = {}
self.__overlayListChanged()
+ self.__displaySpaceChanged()
overlayList.addListener('overlays',
self.__name,
@@ -168,6 +204,9 @@ class DisplayContext(props.SyncableHasProperties):
self.addListener('syncOverlayDisplay',
self.__name,
self.__syncOverlayDisplayChanged)
+ self.addListener('displaySpace',
+ self.__name,
+ self.__displaySpaceChanged)
log.memory('{}.init ({})'.format(type(self).__name__, id(self)))
@@ -374,17 +413,38 @@ class DisplayContext(props.SyncableHasProperties):
# property is valid
self.__syncOverlayOrder()
- # Ensure that the bounds property is accurate
+ # Ensure that the bounds
+ # property is accurate
self.__updateBounds()
- # If the overlay list was empty, and is
- # now non-empty, centre the currently
- # selected location (but see the comments
- # in __init__ about this).
+ # Ensure that the displaySpace
+ # property options are in sync
+ # with the overlay list
+ self.__updateDisplaySpaceOptions()
+
+ # Initliase the transform property
+ # of any Image overlays which have
+ # just been added to the list,
+ oldList = self.__overlayList.getLastValue('overlays')[:]
+ for overlay in self.__overlayList:
+ if isinstance(overlay, fslimage.Image) and \
+ (overlay not in oldList):
+ self.__setTransform(overlay)
+
+ # If the overlay list was empty,
+ # and is now non-empty ...
if (self.__prevOverlayListLen == 0) and (len(self.__overlayList) > 0):
+
+ # Set the displaySpace to
+ # the first new image
+ for overlay in self.__overlayList:
+ if isinstance(overlay, fslimage.Image):
+ self.displaySpace = overlay
+ break
- # initialise the location to be
- # the centre of the world
+ # Centre the currently selected
+ # location (but see the comments
+ # in __init__ about this).
b = self.bounds
self.location.xyz = [
b.xlo + b.xlen / 2.0,
@@ -403,6 +463,65 @@ class DisplayContext(props.SyncableHasProperties):
self.setConstraint('selectedOverlay', 'maxval', 0)
+ def __updateDisplaySpaceOptions(self):
+ """Updates the :attr:`displaySpace` property so it is synchronised with
+ the current contents of the :class:`.OverlayList`
+
+ This method is called by the :meth:`__overlayListChanged` method.
+ """
+
+ choiceProp = self.getProp('displaySpace')
+ choices = ['pixdim', 'world']
+
+ for overlay in self.__overlayList:
+ if isinstance(overlay, fslimage.Image):
+ choices.append(overlay)
+
+ choiceProp.setChoices(choices, instance=self)
+
+
+ def __setTransform(self, image):
+ """Sets the :attr:`.ImageOpts.transform` property associated with
+ the given :class:`.Image` overlay to a sensible value, given the
+ current value of the :attr:`.displaySpace` property.
+
+ Called by the :meth:`__displaySpaceChanged` method, and by
+ :meth:`__overlayListChanged` for any :class:`.Image` overlays which
+ have been newly added to the :class:`.OverlayList`.
+
+ :arg image: An :class:`.Image` overlay.
+ """
+
+ space = self.displaySpace
+ opts = self.getOpts(image)
+
+ if space == 'pixdim': opts.transform = 'pixdim'
+ elif space == 'world': opts.transform = 'affine'
+ elif image is space: opts.transform = 'pixdim'
+ else:
+ refOpts = self.getOpts(space)
+ xform = transform.concat(
+ opts .getTransform('voxel', 'world'),
+ refOpts.getTransform('world', 'pixdim'))
+
+ opts.customXform = xform
+ opts.transform = 'custom'
+
+
+ def __displaySpaceChanged(self, *a):
+ """Called when the :attr:`displaySpace` property changes. Updates the
+ :attr:`.ImageOpts.transform` property for all :class:`.Image` overlays
+ in the :class:`.OverlayList`.
+ """
+
+ for overlay in self.__overlayList:
+
+ if not isinstance(overlay, fslimage.Image):
+ continue
+
+ self.__setTransform(overlay)
+
+
def __syncOverlayOrder(self):
"""Ensures that the :attr:`overlayOrder` property is up to date
with respect to the :class:`.OverlayList`.
diff --git a/fsl/fsleyes/displaycontext/volumeopts.py b/fsl/fsleyes/displaycontext/volumeopts.py
index 61966f8f62c1af98fffccdef695028d4495676a5..8dbad52349ab14933cad5d33e9ff75d76d48904a 100644
--- a/fsl/fsleyes/displaycontext/volumeopts.py
+++ b/fsl/fsleyes/displaycontext/volumeopts.py
@@ -166,6 +166,8 @@ class ImageOpts(fsldisplay.DisplayOpts):
def destroy(self):
"""Calls the :meth:`.DisplayOpts.destroy` method. """
+ self.removeListener('transform', self.name)
+ self.removeListener('customXform', self.name)
fsldisplay.DisplayOpts.destroy(self)
diff --git a/fsl/fsleyes/tooltips.py b/fsl/fsleyes/tooltips.py
index 02d5542a5b71e3774714abb5efdd8c45554cc3f1..6878df2f53effa951a6f1912cfe5a7bfc99ff029 100644
--- a/fsl/fsleyes/tooltips.py
+++ b/fsl/fsleyes/tooltips.py
@@ -22,6 +22,11 @@ from fsl.utils.typedict import TypeDict
properties = TypeDict({
+ # DisplayContext
+
+ 'DisplayContext.displaySpace' : 'The space in which overlays are '
+ 'displayed.',
+
# Overlay Display
'Display.name' : 'The name of this overlay.',