diff --git a/fsl/data/image.py b/fsl/data/image.py
index e6a0513142d5180d22d09e123f57776a4cac673e..725951a5207002e8254da4aef58dfd32b1c76177 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -26,22 +26,23 @@ import fsl.data.imagefile as imagefile
log = logging.getLogger(__name__)
-L2R = 0
-R2L = 1
-P2A = 2
-A2P = 3
-I2S = 4
-S2I = 5
-
-orientationLabels = {
- L2R : ('L', 'R'),
- R2L : ('R', 'L'),
- P2A : ('P', 'A'),
- A2P : ('A', 'P'),
- S2I : ('S', 'I'),
- I2S : ('I', 'S')
-}
-
+# Constants which represent the orientation of an axis,
+# in either voxel or world space.
+ORIENT_UNKNOWN = -1
+ORIENT_L2R = 0
+ORIENT_R2L = 1
+ORIENT_P2A = 2
+ORIENT_A2P = 3
+ORIENT_I2S = 4
+ORIENT_S2I = 5
+
+# Constants from the NIFTI1 specification that define
+# the 'space' in which an image is assumed to be.
+NIFTI_XFORM_UNKNOWN = 0
+NIFTI_XFORM_SCANNER_ANAT = 1
+NIFTI_XFORM_ALIGNED_ANAT = 2
+NIFTI_XFORM_TALAIRACH = 3
+NIFTI_XFORM_MNI_152 = 4
def _loadImageFile(filename):
"""Given the name of an image file, loads it using nibabel.
@@ -384,15 +385,78 @@ class Image(props.HasProperties):
else: return worldp
- def getOrientation(self, axis):
+ def getXFormCode(self):
+ """This method returns the code contained in the NIFTI1 header,
+ indicating the space to which the (transformed) image is oriented.
+
+ """
+ sform_code = self.nibImage.get_header()['sform_code']
+ qform_code = self.nibImage.get_header()['qform_code']
+
+ # if the qform and sform codes don't
+ # match, I don't know what to do
+ if sform_code != qform_code: return NIFTI_XFORM_UNKNOWN
+
+ # Invalid values
+ elif sform_code > 4: return NIFTI_XFORM_UNKNOWN
+ elif sform_code < 0: return NIFTI_XFORM_UNKNOWN
+
+ # All is well
+ else: return sform_code
+
+
+ def getWorldOrientation(self, axis):
+ """Returns a code representing the orientation of the specified axis
+ in world space.
+
+ This method returns one of the following values, indicating the
+ direction in which coordinates along the specified axis increase:
+ - :attr:`~fsl.data.image.ORIENT_L2R`: Left to right
+ - :attr:`~fsl.data.image.ORIENT_R2L`: Right to left
+ - :attr:`~fsl.data.image.ORIENT_A2P`: Anterior to posterior
+ - :attr:`~fsl.data.image.ORIENT_P2A`: Posterior to anterior
+ - :attr:`~fsl.data.image.ORIENT_I2S`: Inferior to superior
+ - :attr:`~fsl.data.image.ORIENT_S2I`: Superior to inferior
+ - :attr:`~fsl.data.image.ORIENT_UNKNOWN`: Orientation is unknown
+
+ The returned value is dictated by the XForm code contained in the
+ image file header (see the :meth:`getXFormCode` method). Basically,
+ if the XForm code is 'unknown', this method will return -1 for all
+ axes. Otherwise, it is assumed that the image is in RAS orientation
+ (i.e. the X axis increases from left to right, the Y axis increases
+ from posterior to anterior, and the Z axis increases from inferior
+ to superior).
+ """
+
+ if self.getXFormCode() == NIFTI_XFORM_UNKNOWN:
+ return -1
+
+ if axis == 0: return ORIENT_L2R
+ elif axis == 1: return ORIENT_P2A
+ elif axis == 2: return ORIENT_I2S
+
+ else: return -1
+
+
+ def getVoxelOrientation(self, axis):
+ """Returns a code representing the (estimated) orientation of the
+ specified voxelwise axis.
+
+ See the :meth:`getWorldOrientation` method for a description
+ of the return value.
+ """
+
+ if self.getXFormCode() == NIFTI_XFORM_UNKNOWN:
+ return -1
+
# the aff2axcodes returns one code for each
# axis in the image array (i.e. in voxel space),
# which denotes the real world direction
code = nib.orientations.aff2axcodes(self.nibImage.get_affine(),
- ((R2L, L2R),
- (A2P, P2A),
- (S2I, I2S)))[axis]
- return orientationLabels[code]
+ ((ORIENT_R2L, ORIENT_L2R),
+ (ORIENT_A2P, ORIENT_P2A),
+ (ORIENT_S2I, ORIENT_I2S)))[axis]
+ return code
def _transform(self, p, a, axes):
diff --git a/fsl/fslview/strings.py b/fsl/fslview/strings.py
index bad57e3546e2bde8effdc724423bb14ce5a59a0e..cb0c7cbfbb1fda0bc279c1bc797bc74a8c34803e 100644
--- a/fsl/fslview/strings.py
+++ b/fsl/fslview/strings.py
@@ -5,6 +5,8 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
+import fsl.data.image as fslimage
+
from views .orthopanel import OrthoPanel
from views .lightboxpanel import LightBoxPanel
from views .timeseriespanel import TimeSeriesPanel
@@ -49,3 +51,48 @@ orthoConfigMenu = '{} display'
lightBoxConfigMenu = '{} display'
locationPanelOutOfBounds = 'Out of bounds'
+
+
+
+imageAxisLowLongLabels = {
+ fslimage.ORIENT_A2P : 'Anterior',
+ fslimage.ORIENT_P2A : 'Posterior',
+ fslimage.ORIENT_L2R : 'Left',
+ fslimage.ORIENT_R2L : 'Right',
+ fslimage.ORIENT_I2S : 'Inferior',
+ fslimage.ORIENT_S2I : 'Superior',
+ fslimage.ORIENT_UNKNOWN : 'Unknown'}
+
+imageAxisHighLongLabels = {
+ fslimage.ORIENT_A2P : 'Posterior',
+ fslimage.ORIENT_P2A : 'Anterior',
+ fslimage.ORIENT_L2R : 'Right',
+ fslimage.ORIENT_R2L : 'Left',
+ fslimage.ORIENT_I2S : 'Superior',
+ fslimage.ORIENT_S2I : 'Inferior',
+ fslimage.ORIENT_UNKNOWN : 'Unknown'}
+
+imageAxisLowShortLabels = {
+ fslimage.ORIENT_A2P : 'A',
+ fslimage.ORIENT_P2A : 'P',
+ fslimage.ORIENT_L2R : 'L',
+ fslimage.ORIENT_R2L : 'R',
+ fslimage.ORIENT_I2S : 'I',
+ fslimage.ORIENT_S2I : 'S',
+ fslimage.ORIENT_UNKNOWN : '?'}
+
+imageAxisHighShortLabels = {
+ fslimage.ORIENT_A2P : 'P',
+ fslimage.ORIENT_P2A : 'A',
+ fslimage.ORIENT_L2R : 'R',
+ fslimage.ORIENT_R2L : 'L',
+ fslimage.ORIENT_I2S : 'S',
+ fslimage.ORIENT_S2I : 'I',
+ fslimage.ORIENT_UNKNOWN : '?'}
+
+imageSpaceLabels = {
+ fslimage.NIFTI_XFORM_UNKNOWN : 'Unknown',
+ fslimage.NIFTI_XFORM_SCANNER_ANAT : 'Scanner anatomical',
+ fslimage.NIFTI_XFORM_ALIGNED_ANAT : 'Aligned anatomical',
+ fslimage.NIFTI_XFORM_TALAIRACH : 'Talairach',
+ fslimage.NIFTI_XFORM_MNI_152 : 'MNI152'}
diff --git a/fsl/fslview/views/orthopanel.py b/fsl/fslview/views/orthopanel.py
index 4b5d924f5fd07db297efed906253ab03750bdb3d..cd343f5c70bd7ae467e9471adf42ca71ba84ab8d 100644
--- a/fsl/fslview/views/orthopanel.py
+++ b/fsl/fslview/views/orthopanel.py
@@ -19,6 +19,8 @@ log = logging.getLogger(__name__)
import wx
import props
+import fsl.data.image as fslimage
+
import fsl.fslview.gl as fslgl
import fsl.fslview.gl.wxglslicecanvas as slicecanvas
import canvaspanel
@@ -221,16 +223,25 @@ class OrthoPanel(canvaspanel.CanvasPanel):
self.bindProps('invertZ_X', self._zcanvas, 'invertX')
self.bindProps('invertZ_Y', self._zcanvas, 'invertY')
- llName = '{}_layout'.format(self._name)
-
- self.addListener('layout', llName, self._layoutChanged)
- self.addListener('showColourBar', llName, self._layoutChanged)
- self.addListener('colourBarLocation', llName, self._layoutChanged)
- self.addListener('showLabels', llName, self._toggleLabels)
-
+ # Callbacks for ortho panel layout options
+ self.addListener('layout', self._name, self._layoutChanged)
+ self.addListener('showColourBar', self._name, self._layoutChanged)
+ self.addListener('colourBarLocation', self._name, self._layoutChanged)
+ self.addListener('showLabels', self._name, self._toggleLabels)
+
+ # Callbacks for image list/selected image changes
+ self._imageList.addListener( 'images',
+ self._name,
+ self._imageListChanged)
+ self._displayCtx.addListener('selectedImage',
+ self._name,
+ self._imageListChanged)
+
+ self._imageListChanged()
self._layoutChanged()
self._toggleLabels()
+ # Callbacks for mouse events on the three xcanvases
self._xcanvas.Bind(wx.EVT_LEFT_DOWN, self._onMouseEvent)
self._ycanvas.Bind(wx.EVT_LEFT_DOWN, self._onMouseEvent)
self._zcanvas.Bind(wx.EVT_LEFT_DOWN, self._onMouseEvent)
@@ -238,20 +249,16 @@ class OrthoPanel(canvaspanel.CanvasPanel):
self._ycanvas.Bind(wx.EVT_MOTION, self._onMouseEvent)
self._zcanvas.Bind(wx.EVT_MOTION, self._onMouseEvent)
+ # Callback for the display context location - when it
+ # changes, update the displayed canvas locations
def move(*a):
if self.posSync:
self.setPosition(*self._displayCtx.location)
self.setPosition(*self._displayCtx.location)
self._displayCtx.addListener('location', self._name, move)
-
- def onDestroy(ev):
- self._displayCtx.removeListener('location', self._name)
- ev.Skip()
-
- self.Bind(wx.EVT_WINDOW_DESTROY, onDestroy)
- self.Bind(wx.EVT_SIZE, self._resize)
+ # Callbacks for toggling x/y/z canvas display
def toggle(canvas, toggle):
self._canvasSizer.Show(canvas, toggle)
if self.layout.lower() == 'grid':
@@ -268,6 +275,55 @@ class OrthoPanel(canvaspanel.CanvasPanel):
lambda *a: toggle(self._zCanvasPanel,
self.showZCanvas))
+ # Do some cleaning up if/when this panel is destroyed
+ self.Bind(wx.EVT_WINDOW_DESTROY, self._onDestroy)
+
+ # And finally, call the _resize method to
+ # re-layout things when this panel is resized
+ self.Bind(wx.EVT_SIZE, self._resize)
+
+
+ def _imageListChanged(self, *a):
+ """Called when the image list or selected image is changed.
+
+ Adds a listener to the currently selected image, to listen
+ for changes on its affine transformation matrix.
+ """
+ if len(self._imageList) == 0: return
+
+ for i, img in enumerate(self._imageList):
+
+ # Update anatomy labels when the image
+ # transformation matrix changes
+ if i == self._displayCtx.selectedImage:
+ img.addListener('transform', self._name, self._toggleLabels)
+ else:
+ img.removeListener('transform', self._name)
+
+
+ def _onDestroy(self, ev):
+ """Called when this panel is destroyed.
+
+ The display context and image list will probably live longer than
+ this OrthoPanel. So when this panel is destroyed, all those
+ registered listeners are removed.
+ """
+ ev.Skip()
+
+ # Do nothing if the destroyed window is not
+ # this panel (i.e. it is a child of this panel)
+ if ev.GetEventObject() != self: return
+
+ self._displayCtx.removeListener('location', self._name)
+ self._displayCtx.removeListener('selectedImage', self._name)
+ self._imageList .removeListener('images', self._name)
+
+ # The _imageListChanged method adds
+ # listeners to individual images,
+ # so we have to remove them too
+ for img in self._imageList:
+ img.removeListener('transform', self._name)
+
def _resize(self, ev):
"""
@@ -284,34 +340,79 @@ class OrthoPanel(canvaspanel.CanvasPanel):
def _toggleLabels(self, *a):
"""Shows/hides labels depicting anatomical orientation on each canvas.
"""
+
+ allLabels = [self._xLeftLabel, self._xRightLabel,
+ self._xTopLabel, self._xBottomLabel,
+ self._yLeftLabel, self._yRightLabel,
+ self._yTopLabel, self._yBottomLabel,
+ self._zLeftLabel, self._zRightLabel,
+ self._zTopLabel, self._zBottomLabel]
+
+
+ # Are we showing or hiding the labels?
if self.showLabels: show = True
else: show = False
- self._xLeftLabel .Show(show)
- self._xRightLabel .Show(show)
- self._xTopLabel .Show(show)
- self._xBottomLabel.Show(show)
- self._yLeftLabel .Show(show)
- self._yRightLabel .Show(show)
- self._yTopLabel .Show(show)
- self._yBottomLabel.Show(show)
- self._zLeftLabel .Show(show)
- self._zRightLabel .Show(show)
- self._zTopLabel .Show(show)
- self._zBottomLabel.Show(show)
-
- self._xLeftLabel .SetLabel('?')
- self._xRightLabel .SetLabel('?')
- self._xTopLabel .SetLabel('?')
- self._xBottomLabel.SetLabel('?')
- self._yLeftLabel .SetLabel('?')
- self._yRightLabel .SetLabel('?')
- self._yTopLabel .SetLabel('?')
- self._yBottomLabel.SetLabel('?')
- self._zLeftLabel .SetLabel('?')
- self._zRightLabel .SetLabel('?')
- self._zTopLabel .SetLabel('?')
- self._zBottomLabel.SetLabel('?')
+ for lbl in allLabels:
+ lbl.Show(show)
+
+ # If we're hiding the labels, do no more
+ if not show:
+ return
+
+ # Default colour is white - if the orientation labels
+ # cannot be determined, the background colour will be
+ # changed to red
+ colour = 'white'
+
+ if len(self._imageList) > 0:
+ image = self._imageList[self._displayCtx.selectedImage]
+
+ # The image is being displayed as it is stored on
+ # disk - the image.getOrientation method calculates
+ # and returns labels for each voxelwise axis.
+ if image.transform in ('pixdim', 'id'):
+ xorient = image.getVoxelOrientation(0)
+ yorient = image.getVoxelOrientation(1)
+ zorient = image.getVoxelOrientation(2)
+
+ # The image is being displayed in 'real world' space -
+ # the definition of this space may be present in the
+ # image meta data
+ else:
+ xorient = image.getWorldOrientation(0)
+ yorient = image.getWorldOrientation(1)
+ zorient = image.getWorldOrientation(2)
+
+
+ if fslimage.ORIENT_UNKNOWN in (xorient, yorient, zorient):
+ colour = 'red'
+
+ # Imported here to avoid circular import issues
+ import fsl.fslview.strings as strings
+
+ xlo = strings.imageAxisLowShortLabels[ xorient]
+ ylo = strings.imageAxisLowShortLabels[ yorient]
+ zlo = strings.imageAxisLowShortLabels[ zorient]
+ xhi = strings.imageAxisHighShortLabels[xorient]
+ yhi = strings.imageAxisHighShortLabels[yorient]
+ zhi = strings.imageAxisHighShortLabels[zorient]
+
+ for lbl in allLabels:
+ lbl.SetForegroundColour(colour)
+
+ self._xLeftLabel .SetLabel(ylo)
+ self._xRightLabel .SetLabel(yhi)
+ self._xBottomLabel.SetLabel(zlo)
+ self._xTopLabel .SetLabel(zhi)
+ self._yLeftLabel .SetLabel(xlo)
+ self._yRightLabel .SetLabel(xhi)
+ self._yBottomLabel.SetLabel(zlo)
+ self._yTopLabel .SetLabel(zhi)
+ self._zLeftLabel .SetLabel(xlo)
+ self._zRightLabel .SetLabel(xhi)
+ self._zBottomLabel.SetLabel(ylo)
+ self._zTopLabel .SetLabel(yhi)
self._xCanvasPanel.Layout()
self._yCanvasPanel.Layout()