From 9477aecab088932eab0fe6443552da3d1914b31e Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Thu, 29 Oct 2015 15:39:54 +0000
Subject: [PATCH] Simplified ortho orientation labelling, and made it less
inaccurate.
---
fsl/data/image.py | 46 ++++-------------
fsl/data/strings.py | 9 ++--
fsl/fsleyes/controls/overlayinfopanel.py | 27 +++++-----
fsl/fsleyes/profiles/orthoviewprofile.py | 2 +-
fsl/fsleyes/views/orthopanel.py | 65 ++++++++++--------------
fsl/tools/render.py | 20 ++------
6 files changed, 59 insertions(+), 110 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 31988dc6e..3dda62827 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -333,9 +333,14 @@ class Image(props.HasProperties):
return int(code)
- def getWorldOrientation(self, axis, code=None):
- """Returns a code representing the orientation of the specified axis
- in world space.
+ def getOrientation(self, axis, xform):
+ """Returns a code representing the orientation of the specified data
+ axis in the coordinate system defined by the given transformation
+ matrix.
+
+ :arg xform: A transformation matrix which is assumed to transform
+ coordinates from the image world coordinate system to
+ some other coordinate system.
This method returns one of the following values, indicating the
direction in which coordinates along the specified axis increase:
@@ -357,45 +362,16 @@ class Image(props.HasProperties):
increases from inferior to superior).
"""
- if self.getXFormCode(code) == constants.NIFTI_XFORM_UNKNOWN:
- return constants.ORIENT_UNKNOWN
-
- if axis == 0: return constants.ORIENT_L2R
- elif axis == 1: return constants.ORIENT_P2A
- elif axis == 2: return constants.ORIENT_I2S
-
- else: return constants.ORIENT_UNKNOWN
-
-
- def getVoxelOrientation(self, axis, code=None):
- """Returns a code representing the (estimated) orientation of the
- specified data axis.
-
- :arg code: May be either ``qform`` or ``sform``, specifying which
- transformation to use.
-
- See the :meth:`getWorldOrientation` method for a description
- of the return value.
- """
-
- if self.getXFormCode(code) == constants.NIFTI_XFORM_UNKNOWN:
- return constants.ORIENT_UNKNOWN
-
- if code is None: xform = self.nibImage.get_affine()
- elif code == 'sform': xform = self.nibImage.get_sform()
- elif code == 'qform': xform = self.nibImage.get_qform()
- else: raise ValueError('code must be None, qform, or sform')
+ if self.getXFormCode() == constants.NIFTI_XFORM_UNKNOWN:
+ return constants.ORIENT_UNKNOWN
- # the aff2axcodes returns one code for each
- # axis in the image array (i.e. in voxel space),
- # which denotes the real world direction
import nibabel as nib
code = nib.orientations.aff2axcodes(
xform,
((constants.ORIENT_R2L, constants.ORIENT_L2R),
(constants.ORIENT_A2P, constants.ORIENT_P2A),
(constants.ORIENT_S2I, constants.ORIENT_I2S)))[axis]
-
+
return code
diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index ba3d48926..a3846b2c8 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -616,12 +616,9 @@ nifti = TypeDict({
'voxOrient.0' : 'X voxel orientation',
'voxOrient.1' : 'Y voxel orientation',
'voxOrient.2' : 'Z voxel orientation',
- 'sformOrient.0' : 'X sform orientation',
- 'sformOrient.1' : 'Y sform orientation',
- 'sformOrient.2' : 'Z sform orientation',
- 'qformOrient.0' : 'X qform orientation',
- 'qformOrient.1' : 'Y qform orientation',
- 'qformOrient.2' : 'Z qform orientation',
+ 'worldOrient.0' : 'X world orientation',
+ 'worldOrient.1' : 'Y world orientation',
+ 'worldOrient.2' : 'Z world orientation',
'qform' : 'QForm matrix',
'sform' : 'SForm matrix',
diff --git a/fsl/fsleyes/controls/overlayinfopanel.py b/fsl/fsleyes/controls/overlayinfopanel.py
index f44baf590..7d340e171 100644
--- a/fsl/fsleyes/controls/overlayinfopanel.py
+++ b/fsl/fsleyes/controls/overlayinfopanel.py
@@ -14,9 +14,11 @@ import collections
import wx
import wx.html as wxhtml
-import fsl.data.strings as strings
-import fsl.data.constants as constants
-import fsl.fsleyes.panel as fslpanel
+import numpy as np
+
+import fsl.data.strings as strings
+import fsl.data.constants as constants
+import fsl.fsleyes.panel as fslpanel
class OverlayInfoPanel(fslpanel.FSLEyesPanel):
@@ -178,8 +180,10 @@ class OverlayInfoPanel(fslpanel.FSLEyesPanel):
info = OverlayInfo('{} - {}'.format(
display.name, strings.labels[self, overlay]))
+
img = overlay.nibImage
hdr = img.get_header()
+ opts = display.getDisplayOpts()
voxUnits, timeUnits = hdr.get_xyzt_units()
qformCode = int(hdr['qform_code'])
@@ -240,7 +244,8 @@ class OverlayInfoPanel(fslpanel.FSLEyesPanel):
section=xformSect)
for i in range(3):
- orient = overlay.getVoxelOrientation(i)
+ xform = opts.getTransform('world', 'id')
+ orient = overlay.getOrientation(i, xform)
orient = '{} - {}'.format(
strings.anatomy['Image', 'lowlong', orient],
strings.anatomy['Image', 'highlong', orient])
@@ -249,23 +254,15 @@ class OverlayInfoPanel(fslpanel.FSLEyesPanel):
section=orientSect)
for i in range(3):
- orient = overlay.getWorldOrientation(i, code='sform')
+ xform = np.eye(4)
+ orient = overlay.getOrientation(i, xform)
orient = '{} - {}'.format(
strings.anatomy['Image', 'lowlong', orient],
strings.anatomy['Image', 'highlong', orient])
- info.addInfo(strings.nifti['sformOrient.{}'.format(i)],
+ info.addInfo(strings.nifti['worldOrient.{}'.format(i)],
orient,
section=orientSect)
- for i in range(3):
- orient = overlay.getWorldOrientation(i, code='qform')
- orient = '{} - {}'.format(
- strings.anatomy['Image', 'lowlong', orient],
- strings.anatomy['Image', 'highlong', orient])
- info.addInfo(strings.nifti['qformOrient.{}'.format(i)],
- orient,
- section=orientSect)
-
return info
diff --git a/fsl/fsleyes/profiles/orthoviewprofile.py b/fsl/fsleyes/profiles/orthoviewprofile.py
index aa90f2099..dc5f3559c 100644
--- a/fsl/fsleyes/profiles/orthoviewprofile.py
+++ b/fsl/fsleyes/profiles/orthoviewprofile.py
@@ -309,7 +309,7 @@ class OrthoViewProfile(profiles.Profile):
if zoom == 0:
return
- self._zoomModeMouseWheel(canvas, zoom)
+ self._zoomModeMouseWheel(None, canvas, zoom)
def _zoomModeLeftMouseDrag(self, ev, canvas, mousePos, canvasPos):
diff --git a/fsl/fsleyes/views/orthopanel.py b/fsl/fsleyes/views/orthopanel.py
index 96e2f20ce..25ca142f5 100644
--- a/fsl/fsleyes/views/orthopanel.py
+++ b/fsl/fsleyes/views/orthopanel.py
@@ -359,16 +359,12 @@ class OrthoPanel(canvaspanel.CanvasPanel):
self.__zLabels.values()
if overlay is not None:
- opts = self._displayCtx.getOpts(overlay)
+ opts = self._displayCtx.getOpts(overlay)
+ xform = opts.getTransform('world', 'display')
- if opts.transform in ('pixdim', 'id'):
- xorient = overlay.getVoxelOrientation(0)
- yorient = overlay.getVoxelOrientation(1)
- zorient = overlay.getVoxelOrientation(2)
- else:
- xorient = overlay.getWorldOrientation(0)
- yorient = overlay.getWorldOrientation(1)
- zorient = overlay.getWorldOrientation(2)
+ xorient = overlay.getOrientation(0, xform)
+ yorient = overlay.getOrientation(1, xform)
+ zorient = overlay.getOrientation(2, xform)
if constants.ORIENT_UNKNOWN in (xorient, yorient, zorient):
@@ -429,13 +425,10 @@ class OrthoPanel(canvaspanel.CanvasPanel):
# Update anatomy labels when
# overlay bounds change
- if i == self._displayCtx.selectedOverlay:
- opts.addListener('bounds',
- self._name,
- self.__refreshLabels,
- overwrite=True)
- else:
- opts.removeListener('bounds', self._name)
+ opts.addListener('bounds',
+ self._name,
+ self.__refreshLabels,
+ overwrite=True)
# anatomical orientation may have changed with an image change
self.__refreshLabels()
@@ -480,23 +473,17 @@ class OrthoPanel(canvaspanel.CanvasPanel):
self.PostSizeEvent()
return
- opts = self._displayCtx.getOpts(overlay)
- # The image is being displayed as it is stored on
- # disk - the image.getOrientation method calculates
- # and returns labels for each voxelwise axis.
- if opts.transform in ('pixdim', 'id'):
- xorient = overlay.getVoxelOrientation(0)
- yorient = overlay.getVoxelOrientation(1)
- zorient = overlay.getVoxelOrientation(2)
+ log.debug('Refreshing orientation labels '
+ 'according to {}'.format(overlay.name))
- # The overlay is being displayed in 'real world' space -
- # the definition of this space may be present in the
- # overlay meta data
- else:
- xorient = overlay.getWorldOrientation(0)
- yorient = overlay.getWorldOrientation(1)
- zorient = overlay.getWorldOrientation(2)
+ # Figure out the orientation of the
+ # image in the display coordinate system
+ opts = self._displayCtx.getOpts(overlay)
+ xform = opts.getTransform('world', 'display')
+ xorient = overlay.getOrientation(0, xform)
+ yorient = overlay.getOrientation(1, xform)
+ zorient = overlay.getOrientation(2, xform)
xlo = strings.anatomy['Image', 'lowshort', xorient]
ylo = strings.anatomy['Image', 'lowshort', yorient]
@@ -505,6 +492,10 @@ class OrthoPanel(canvaspanel.CanvasPanel):
yhi = strings.anatomy['Image', 'highshort', yorient]
zhi = strings.anatomy['Image', 'highshort', zorient]
+ log.debug('X orientation: {} - {}'.format(xlo, xhi))
+ log.debug('Y orientation: {} - {}'.format(ylo, yhi))
+ log.debug('Z orientation: {} - {}'.format(zlo, zhi))
+
bg = sceneOpts.bgColour
fg = colourmaps.complementaryColour(bg)
bg = [int(round(c * 255)) for c in bg]
@@ -514,16 +505,16 @@ class OrthoPanel(canvaspanel.CanvasPanel):
self.__xLabels['left'] .SetLabel(ylo)
self.__xLabels['right'] .SetLabel(yhi)
- self.__xLabels['top'] .SetLabel(zlo)
- self.__xLabels['bottom'].SetLabel(zhi)
+ self.__xLabels['bottom'].SetLabel(zlo)
+ self.__xLabels['top'] .SetLabel(zhi)
self.__yLabels['left'] .SetLabel(xlo)
self.__yLabels['right'] .SetLabel(xhi)
- self.__yLabels['top'] .SetLabel(zlo)
- self.__yLabels['bottom'].SetLabel(zhi)
+ self.__yLabels['bottom'].SetLabel(zlo)
+ self.__yLabels['top'] .SetLabel(zhi)
self.__zLabels['left'] .SetLabel(xlo)
self.__zLabels['right'] .SetLabel(xhi)
- self.__zLabels['top'] .SetLabel(ylo)
- self.__zLabels['bottom'].SetLabel(yhi)
+ self.__zLabels['bottom'].SetLabel(ylo)
+ self.__zLabels['top'] .SetLabel(yhi)
self.PostSizeEvent()
diff --git a/fsl/tools/render.py b/fsl/tools/render.py
index e346114e1..f586153e2 100644
--- a/fsl/tools/render.py
+++ b/fsl/tools/render.py
@@ -77,22 +77,10 @@ def buildLabelBitmaps(overlayList,
display = displayCtx.getDisplay(overlay)
opts = display.getDisplayOpts()
-
- # The overlay is being displayed as it is stored on
- # disk - the image.getOrientation method calculates
- # and returns labels for each voxelwise axis.
- if opts.transform in ('pixdim', 'id'):
- xorient = overlay.getVoxelOrientation(0)
- yorient = overlay.getVoxelOrientation(1)
- zorient = overlay.getVoxelOrientation(2)
-
- # The overlay is being displayed in 'real world' space -
- # the definition of this space may be present in the
- # overlay meta data
- else:
- xorient = overlay.getWorldOrientation(0)
- yorient = overlay.getWorldOrientation(1)
- zorient = overlay.getWorldOrientation(2)
+ xform = opts.getTransform('world', 'display')
+ xorient = overlay.getOrientation(0, xform)
+ yorient = overlay.getOrientation(1, xform)
+ zorient = overlay.getOrientation(2, xform)
if constants.ORIENT_UNKNOWN in [xorient, yorient, zorient]:
fgColour = 'red'
--
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