diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index bc4a432834e1e270a9ad5bffdd5b4ba053e7f2b1..4a8e771e090ac3beca48b655c6432c13c01bb539 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -527,9 +527,9 @@ properties = TypeDict({
'Display.brightness' : 'Brightness',
'Display.contrast' : 'Contrast',
- 'ImageOpts.resolution' : 'Resolution',
- 'ImageOpts.transform' : 'Image transform',
- 'ImageOpts.volume' : 'Volume',
+ 'Nifti1Opts.resolution' : 'Resolution',
+ 'Nifti1Opts.transform' : 'Image transform',
+ 'Nifti1Opts.volume' : 'Volume',
'VolumeOpts.displayRange' : 'Display range',
'VolumeOpts.clippingRange' : 'Clipping range',
@@ -616,12 +616,12 @@ choices = TypeDict({
'ModelOpts.refImage.none' : 'No reference image',
- 'ImageOpts.transform' : {'affine' : 'Use qform/sform transformation '
- 'matrix',
- 'pixdim' : 'Use pixdims only',
- 'id' : 'Do not use qform/sform or pixdims',
- 'custom' : 'Apply a custom transformation '
- 'matrix'},
+ 'Nifti1Opts.transform' : {'affine' : 'Use qform/sform transformation '
+ 'matrix',
+ 'pixdim' : 'Use pixdims only',
+ 'id' : 'Do not use qform/sform or pixdims',
+ 'custom' : 'Apply a custom transformation '
+ 'matrix'},
'VolumeOpts.interpolation' : {'none' : 'No interpolation',
'linear' : 'Linear interpolation',
diff --git a/fsl/fsleyes/controls/locationpanel.py b/fsl/fsleyes/controls/locationpanel.py
index 568d653fb3393b65786a05b3dfa6794aaf58cd28..ead2b822edd92d8636f1b0bb4940cacc2b2bee3a 100644
--- a/fsl/fsleyes/controls/locationpanel.py
+++ b/fsl/fsleyes/controls/locationpanel.py
@@ -113,7 +113,7 @@ class LocationPanel(fslpanel.FSLEyesPanel):
# this attribute will refer to the
# corresponding DisplayOpts instance, which
# has a volume property that controls the
- # volume - see e.g. the ImageOpts class. This
+ # volume - see e.g. the Nifti1Opts class. This
# attribute is set in _selectedOverlayChanged.
self.__volumeTarget = None
@@ -425,7 +425,7 @@ class LocationPanel(fslpanel.FSLEyesPanel):
# Enable/disable the volume widget if the
# overlay is a 4D image, and bind/unbind
# the widget to the volume property of
- # the associated ImageOpts instance
+ # the associated Nifti1Opts instance
if haveRef and refImage.is4DImage():
opts = self._displayCtx.getOpts(refImage)
self.__volumeTarget = opts
diff --git a/fsl/fsleyes/controls/melodicclassificationgrid.py b/fsl/fsleyes/controls/melodicclassificationgrid.py
index a242bd69eb0c61c93e5df19bc1fa021da36deb1f..aa19e52336d61736a398631e79145289d223168f 100644
--- a/fsl/fsleyes/controls/melodicclassificationgrid.py
+++ b/fsl/fsleyes/controls/melodicclassificationgrid.py
@@ -335,7 +335,7 @@ class ComponentGrid(fslpanel.FSLEyesPanel):
def __volumeChanged(self, *a):
- """Called when the :attr:`.ImageOpts.volume` property changes. Selects
+ """Called when the :attr:`.Nifti1Opts.volume` property changes. Selects
the corresponding row in the :class:`.WidgetGrid`.
"""
@@ -613,7 +613,7 @@ class LabelGrid(fslpanel.FSLEyesPanel):
def __onTagSelect(self, ev):
"""Called when a tag from a :class:`.TextTagPanel` is selected.
- Changes the current :attr:`.ImageOpts.volume` to the component
+ Changes the current :attr:`.Nifti1Opts.volume` to the component
corresponding to the selected tag.
"""
diff --git a/fsl/fsleyes/displaycontext/__init__.py b/fsl/fsleyes/displaycontext/__init__.py
index 0ed0227690e75d27004ce9bf38b8f60c31e78f4a..6158b792dd610d006fb49b8435143257710a9840 100644
--- a/fsl/fsleyes/displaycontext/__init__.py
+++ b/fsl/fsleyes/displaycontext/__init__.py
@@ -72,7 +72,7 @@ new one accordingly. The following ``DisplayOpts`` sub-classes exist:
.. autosummary::
:nosignatures:
- ~fsl.fsleyes.displaycontext.volumeopts.ImageOpts
+ ~fsl.fsleyes.displaycontext.volumeopts.Nifti1Opts
~fsl.fsleyes.displaycontext.volumeopts.VolumeOpts
~fsl.fsleyes.displaycontext.maskopts.MaskOpts
~fsl.fsleyes.displaycontext.vectoropts.VectorOpts
@@ -80,6 +80,7 @@ new one accordingly. The following ``DisplayOpts`` sub-classes exist:
~fsl.fsleyes.displaycontext.vectoropts.LineVectorOpts
~fsl.fsleyes.displaycontext.modelopts.ModelOpts
~fsl.fsleyes.displaycontext.labelopts.LabelOpts
+ ~fsl.fsleyes.displaycontext.tensoropts.TensorOpts
--------------
@@ -142,7 +143,7 @@ from group import OverlayGroup
from sceneopts import SceneOpts
from orthoopts import OrthoOpts
from lightboxopts import LightBoxOpts
-from volumeopts import ImageOpts
+from volumeopts import Nifti1Opts
from volumeopts import VolumeOpts
from maskopts import MaskOpts
from vectoropts import VectorOpts
@@ -150,6 +151,7 @@ from vectoropts import RGBVectorOpts
from vectoropts import LineVectorOpts
from modelopts import ModelOpts
from labelopts import LabelOpts
+from tensoropts import TensorOpts
from displaycontext import InvalidOverlayError
diff --git a/fsl/fsleyes/displaycontext/display.py b/fsl/fsleyes/displaycontext/display.py
index e7a0f9da1a5171b30d8cdb3af282cb03791c3522..e934a12c307b25d937484d090e41a52080f4b3aa 100644
--- a/fsl/fsleyes/displaycontext/display.py
+++ b/fsl/fsleyes/displaycontext/display.py
@@ -263,7 +263,7 @@ class Display(props.SyncableHasProperties):
Furthermore, in order for the property values of a common
``DisplayOpts`` base type to be shared across sub types (e.g. copying
- the :attr:`.ImageOpts.transform` property between :class:`.VolumeOpts`
+ the :attr:`.Nifti1Opts.transform` property between :class:`.VolumeOpts`
and :class:`.LabelOpts` instances), we need to store the name of the
common base type in the dictionary.
@@ -337,7 +337,7 @@ class DisplayOpts(props.SyncableHasProperties, actions.ActionProvider):
The ``DisplayOpts`` class is not meant to be created directly - it is a
- base class for type specific implementations (e.g. the :class:`.ImageOpts`
+ base class for type specific implementations (e.g. the :class:`.VolumeOpts`
class).
@@ -473,7 +473,7 @@ class DisplayOpts(props.SyncableHasProperties, actions.ActionProvider):
the display space representation may change - for example, the
:class:`.Image` overlays can be transformed into the display
coordinate system in different ways, as defined by the
- :attr:`.ImageOpts.transform` property.
+ :attr:`.Nifti1Opts.transform` property.
"""
return coords
diff --git a/fsl/fsleyes/displaycontext/displaycontext.py b/fsl/fsleyes/displaycontext/displaycontext.py
index a877173e60f913146af868a90d43233628bba5e3..941bd7ba6df49ac791944ba48b3b28362faccba9 100644
--- a/fsl/fsleyes/displaycontext/displaycontext.py
+++ b/fsl/fsleyes/displaycontext/displaycontext.py
@@ -119,36 +119,36 @@ 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`
+ controls the :attr:`.Nifti1Opts.transform` property of all :class:`.Nifti1`
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
+ All :class:`.Nifti1` overlays are displayed with scaled voxels - the
+ :attr:`.Nifti1Opts.transform` property for every ``Nifti1`` 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``.
+ All :class:`.Nifti1` overlays are displayed in the space defined by
+ their affine transformation matrix - the :attr:`.Nifti1Opts.transform`
+ property for every ``Nifti1`` 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
+ A single :class:`.Nifti1` overlay is selected as a *reference* image,
+ and is displayed in scaled voxel space (:attr:`.Nifti1Opts.transform` is
+ set to ``pixdim``). All other ``Nifti1`` overlays are transformed into
+ this reference space - their :attr:`.Nifti1Opts.transform` property is
+ set to ``custom``, and their :attr:`.Nifti1Opts.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`
+ .. note:: The :attr:`.Nifti1Opts.transform` property of any :class:`.Nifti1`
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.
+ whenever *this* property changes, it will change the ``transform``
+ property for every ``Nifti1``, in the manner described above.
"""
@@ -564,8 +564,8 @@ class DisplayContext(props.SyncableHasProperties):
def __setTransform(self, image):
- """Sets the :attr:`.ImageOpts.transform` property associated with
- the given :class:`.Image` overlay to a sensible value, given the
+ """Sets the :attr:`.Nifti1Opts.transform` property associated with
+ the given :class:`.Nifti1` overlay to a sensible value, given the
current value of the :attr:`.displaySpace` property.
Called by the :meth:`__displaySpaceChanged` method, and by
@@ -593,7 +593,7 @@ class DisplayContext(props.SyncableHasProperties):
def __displaySpaceChanged(self, *a):
"""Called when the :attr:`displaySpace` property changes. Updates the
- :attr:`.ImageOpts.transform` property for all :class:`.Image` overlays
+ :attr:`.Nifti1Opts.transform` property for all :class:`.Nifti1` overlays
in the :class:`.OverlayList`.
"""
diff --git a/fsl/fsleyes/displaycontext/group.py b/fsl/fsleyes/displaycontext/group.py
index a95965433d6af791c0405dd02b450693cc72ce73..4d9885fe297899d97b1eb949cfd7e29393e050f8 100644
--- a/fsl/fsleyes/displaycontext/group.py
+++ b/fsl/fsleyes/displaycontext/group.py
@@ -63,7 +63,7 @@ class OverlayGroup(props.HasProperties):
_groupBindings = td.TypeDict({
'Display' : ['enabled'],
- 'ImageOpts' : ['volume'],
+ 'Nifti1Opts' : ['volume'],
'VolumeOpts' : ['interpolation'],
'LabelOpts' : ['outline',
'outlineWidth'],
@@ -79,6 +79,9 @@ class OverlayGroup(props.HasProperties):
'LineVectorOpts' : ['lineWidth',
'directed'],
'RGBVectorOpts' : ['interpolation'],
+ 'TensorOpts' : ['outline',
+ 'lighting',
+ 'tensorResolution'],
})
"""This dictionary defines the properties which are bound across
:class:`.Display` instances :class:`.DisplayOpts` sub-class instances, for
@@ -107,14 +110,15 @@ class OverlayGroup(props.HasProperties):
# classes into the local namespace
from fsl.fsleyes.displaycontext import \
Display, \
- ImageOpts, \
+ Nifti1Opts, \
VolumeOpts, \
MaskOpts, \
VectorOpts, \
RGBVectorOpts, \
LineVectorOpts, \
ModelOpts, \
- LabelOpts
+ LabelOpts, \
+ TensorOpts
# Add all of the properties listed
# in the _groupBindings dict as
@@ -130,9 +134,9 @@ class OverlayGroup(props.HasProperties):
self.__hasBeenSet[clsName, propName] = False
- # Special case - make sure that the ImageOpts
+ # Special case - make sure that the Nifti1Opts
# volume property is not constrained
- self.setConstraint('ImageOpts_volume', 'maxval', sys.maxint)
+ self.setConstraint('Nifti1Opts_volume', 'maxval', sys.maxint)
def __copy__(self):
diff --git a/fsl/fsleyes/displaycontext/labelopts.py b/fsl/fsleyes/displaycontext/labelopts.py
index 1665e762d893f5fac04c01b6862de48a571abc27..eca1efa7577cd957af9039cb84666e9c90a6fae4 100644
--- a/fsl/fsleyes/displaycontext/labelopts.py
+++ b/fsl/fsleyes/displaycontext/labelopts.py
@@ -16,7 +16,7 @@ import volumeopts
import fsl.fsleyes.colourmaps as fslcm
-class LabelOpts(volumeopts.ImageOpts):
+class LabelOpts(volumeopts.Nifti1Opts):
"""The ``LabelOpts`` class defines settings for displaying
:class:`.Image` overlays as label images., such as anatomical atlas
images, tissue segmentation images, and so on.
@@ -47,10 +47,10 @@ class LabelOpts(volumeopts.ImageOpts):
def __init__(self, overlay, *args, **kwargs):
"""Create a ``LabelOpts`` instance for the specified ``overlay``.
- All arguments are passed through to the :class:`.ImageOpts`
+ All arguments are passed through to the :class:`.Nifti1Opts`
constructor.
"""
- volumeopts.ImageOpts.__init__(self, overlay, *args, **kwargs)
+ volumeopts.Nifti1Opts.__init__(self, overlay, *args, **kwargs)
luts = fslcm.getLookupTables()
alts = [[l.name, l.key] for l in luts]
diff --git a/fsl/fsleyes/displaycontext/maskopts.py b/fsl/fsleyes/displaycontext/maskopts.py
index 972f1eb18ca0a7e919c1e096cfdc21fc2c2481ef..24c7cd4370af1fd12515ce4a8764b11a2a33987a 100644
--- a/fsl/fsleyes/displaycontext/maskopts.py
+++ b/fsl/fsleyes/displaycontext/maskopts.py
@@ -17,7 +17,7 @@ import fsl.data.strings as strings
import volumeopts
-class MaskOpts(volumeopts.ImageOpts):
+class MaskOpts(volumeopts.Nifti1Opts):
"""The ``MaskOpts`` class defines settings for displaying an
:class:`.Image` overlay as a binary mask.
"""
@@ -42,7 +42,7 @@ class MaskOpts(volumeopts.ImageOpts):
def __init__(self, overlay, *args, **kwargs):
"""Create a ``MaskOpts`` instance for the given overlay. All arguments
- are passed through to the :class:`.ImageOpts` constructor.
+ are passed through to the :class:`.Nifti1Opts` constructor.
"""
if np.prod(overlay.shape) > 2 ** 30:
@@ -80,4 +80,4 @@ class MaskOpts(volumeopts.ImageOpts):
self.threshold.xhi = self.dataMax + dMinDistance
self.setConstraint('threshold', 'minDistance', dMinDistance)
- volumeopts.ImageOpts.__init__(self, overlay, *args, **kwargs)
+ volumeopts.Nifti1Opts.__init__(self, overlay, *args, **kwargs)
diff --git a/fsl/fsleyes/displaycontext/modelopts.py b/fsl/fsleyes/displaycontext/modelopts.py
index d9b8dfc05fbeb20bb58698179cc186f70ecb7cf8..184bc6ad9b1e6e46c2c104b907fdeae60631646c 100644
--- a/fsl/fsleyes/displaycontext/modelopts.py
+++ b/fsl/fsleyes/displaycontext/modelopts.py
@@ -62,7 +62,7 @@ class ModelOpts(fsldisplay.DisplayOpts):
"""
- coordSpace = copy.copy(volumeopts.ImageOpts.transform)
+ coordSpace = copy.copy(volumeopts.Nifti1Opts.transform)
"""If :attr:`refImage` is not ``None``, this property defines the
reference image coordinate space in whihc the model coordinates are
defined (i.e. voxels, scaled voxels, or world coordinates).
@@ -193,8 +193,8 @@ class ModelOpts(fsldisplay.DisplayOpts):
This method is called whenever the :attr:`refImage` or
:attr:`coordSpace` properties change and, if a ``refImage`` is
- specified, whenever the :attr:`.ImageOpts.transform` or
- :attr:`.ImageOpts.customXform` properties change.
+ specified, whenever the :attr:`.Nifti1Opts.transform` or
+ :attr:`.Nifti1Opts.customXform` properties change.
:arg refImage: Reference image to use to calculate the coordinates.
If ``-1`` the :attr:`refImage` is used (``-1`` is
@@ -205,13 +205,13 @@ class ModelOpts(fsldisplay.DisplayOpts):
:attr:`coordSpace` is used.
:arg transform: Transform to use - if ``None``, and a ``refImage`` is
- defined, the :attr:`.ImageOpts.transform` value is
+ defined, the :attr:`.Nifti1Opts.transform` value is
used.
:arg customXform: Custom transform to use (if
``transform=custom``). If ``None``, and a
``refImage`` is defined, the
- :attr:`.ImageOpts.customXform` value is used.
+ :attr:`.Nifti1Opts.customXform` value is used.
"""
if refImage is -1: refImage = self.refImage
@@ -237,8 +237,8 @@ class ModelOpts(fsldisplay.DisplayOpts):
def __transformChanged(self, value, valid, ctx, name):
- """Called when the :attr:`.ImageOpts.transfrom` or
- :attr:`.ImageOpts.customXform` properties of the current
+ """Called when the :attr:`.Nifti1Opts.transfrom` or
+ :attr:`.Nifti1Opts.customXform` properties of the current
:attr:`refImage` change. Calls :meth:`__updateBounds`.
"""
@@ -274,7 +274,7 @@ class ModelOpts(fsldisplay.DisplayOpts):
If a new reference image has been specified, removes listeners from
the old one (if necessary), and adds listeners to the
- :attr:`.ImageOptstransform` and :attr:`.ImageOpts.customXform`
+ :attr:`.Nifti1Opts.transform` and :attr:`.Nifti1Opts.customXform`
properties associated with the new image. Calls
:meth:`__updateBounds`.
"""
diff --git a/fsl/fsleyes/displaycontext/vectoropts.py b/fsl/fsleyes/displaycontext/vectoropts.py
index 2f318375e645982859fba89553bbbf2646923ebe..6311eeca81918f0bd6a199b8f7609fd7a8b5464e 100644
--- a/fsl/fsleyes/displaycontext/vectoropts.py
+++ b/fsl/fsleyes/displaycontext/vectoropts.py
@@ -18,7 +18,7 @@ import fsl.data.image as fslimage
import volumeopts
-class VectorOpts(volumeopts.ImageOpts):
+class VectorOpts(volumeopts.Nifti1Opts):
"""The ``VectorOpts`` class is the base class for :class:`LineVectorOpts`,
:class:`RGBVectorOpts`, and :class:`.TensorOpts`. It contains display
settings which are common to each of them.
@@ -67,11 +67,11 @@ class VectorOpts(volumeopts.ImageOpts):
def __init__(self, *args, **kwargs):
"""Create a ``VectorOpts`` instance for the given image. All
- arguments are passed through to the :class:`.ImageOpts`
+ arguments are passed through to the :class:`.Nifti1Opts`
constructor.
"""
- volumeopts.ImageOpts.__init__(self, *args, **kwargs)
+ volumeopts.Nifti1Opts.__init__(self, *args, **kwargs)
self.overlayList.addListener('overlays',
self.name,
@@ -82,7 +82,7 @@ class VectorOpts(volumeopts.ImageOpts):
def destroy(self):
"""Removes some property listeners, and calls the
- :meth:`.ImageOpts.destroy` method.
+ :meth:`.Nifti1Opts.destroy` method.
"""
self.overlayList.removeListener('overlays', self.name)
@@ -90,7 +90,7 @@ class VectorOpts(volumeopts.ImageOpts):
display = self.displayCtx.getDisplay(overlay)
display.removeListener('name', self.name)
- volumeopts.ImageOpts.destroy(self)
+ volumeopts.Nifti1Opts.destroy(self)
def __overlayListChanged(self, *a):
diff --git a/fsl/fsleyes/displaycontext/volumeopts.py b/fsl/fsleyes/displaycontext/volumeopts.py
index 599bce8b9bc4ab89c32a9bc660eb2441e6dbc6a4..b164f7b4316e6f58116c8df1cdc08e913de351a1 100644
--- a/fsl/fsleyes/displaycontext/volumeopts.py
+++ b/fsl/fsleyes/displaycontext/volumeopts.py
@@ -4,7 +4,7 @@
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-"""This module defines the :class:`ImageOpts` and :class:`VolumeOpts` classes.
+"""This module defines the :class:`Nifti1Opts` and :class:`VolumeOpts` classes.
.. _volumeopts-coordinate-systems:
@@ -15,7 +15,7 @@ An important note on coordinate systems
*FSLeyes* displays all overlays in a single coordinate system, referred
-throughout as the *display coordinate system*. However, :class:`.Image`
+throughout as the *display coordinate system*. However, :class:`.Nifti1`
overlays can potentially be displayed in one of three coordinate systems:
@@ -33,14 +33,14 @@ overlays can potentially be displayed in one of three coordinate systems:
====================== ====================================================
-The :attr:`ImageOpts.transform` property controls how the image data is
+The :attr:`Nifti1Opts.transform` property controls how the image data is
transformed into the display coordinate system. It allows any of the above
spaces to be specified (as ``id``, ``pixdim`` or ``affine``` respectively),
and also allows a ``custom`` transformation to be specified (see the
:attr:`customXform` property).
-Regardless of the space in which the ``Image`` is displayed , the
+Regardless of the space in which the ``Nifti1`` is displayed , the
voxel-to-display space transformation assumes that integer voxel coordinates
correspond to the centre of the voxel in the display coordinate system. In
other words, a voxel at location::
@@ -54,7 +54,7 @@ the space::
[x-0.5 - x+0.5, y-0.5 - y+0.5, z-0.5 - z+0.5]
-For example, if the :attr:`ImageOpts.transform` property is set to ``id``, the
+For example, if the :attr:`Nifti1Opts.transform` property is set to ``id``, the
voxel::
[2, 3, 4]
@@ -85,12 +85,12 @@ import display as fsldisplay
log = logging.getLogger(__name__)
-class ImageOpts(fsldisplay.DisplayOpts):
- """The ``ImageOpts`` class describes how an :class:`.Image` overlay
+class Nifti1Opts(fsldisplay.DisplayOpts):
+ """The ``Nifti1Opts`` class describes how a :class:`.Nifti1` overlay
should be displayed.
- ``ImageOpts`` is the base class for a number of :class:`.DisplayOpts`
+ ``Nifti1Opts`` is the base class for a number of :class:`.DisplayOpts`
sub-classes - it contains display options which are common to all overlay
types that represent a NIFTI1 image.
"""
@@ -127,7 +127,7 @@ class ImageOpts(fsldisplay.DisplayOpts):
def __init__(self, *args, **kwargs):
- """Create an ``ImageOpts`` instance.
+ """Create a ``Nifti1Opts`` instance.
All arguments are passed through to the :class:`.DisplayOpts`
constructor.
@@ -391,8 +391,8 @@ class ImageOpts(fsldisplay.DisplayOpts):
def getVoxel(self):
"""Calculates and returns the voxel coordinates corresponding to the
- current :attr:`.DisplayContext.location` for the :class:`.Image`
- associated with this ``ImageOpts`` instance.
+ current :attr:`.DisplayContext.location` for the :class:`.Nifti1`
+ associated with this ``Nifti1Opts`` instance.
Returns ``None`` if the current location is outside of the image
bounds.
@@ -418,8 +418,8 @@ class ImageOpts(fsldisplay.DisplayOpts):
def displayToStandardCoordinates(self, coords):
"""Overrides :meth:`.DisplayOpts.displayToStandardCoordinates`.
Transforms the given display system coordinates into the world
- coordinates of the :class:`.Image` associated with this
- ``ImageOpts`` instance.
+ coordinates of the :class:`.Nifti1` associated with this
+ ``Nifti1Opts`` instance.
"""
return self.transformCoords(coords, 'display', 'world')
@@ -427,13 +427,13 @@ class ImageOpts(fsldisplay.DisplayOpts):
def standardToDisplayCoordinates(self, coords):
"""Overrides :meth:`.DisplayOpts.standardToDisplayCoordinates`.
Transforms the given coordinates (assumed to be in the world
- coordinate system of the ``Image`` associated with this ``ImageOpts``
+ coordinate system of the ``Nifti1`` associated with this ``Nifti1Opts``
instance) into the display coordinate system.
"""
return self.transformCoords(coords, 'world', 'display')
-class VolumeOpts(ImageOpts):
+class VolumeOpts(Nifti1Opts):
"""The ``VolumeOpts`` class defines options for displaying :class:`.Image`
instances as regular 3D volumes.
@@ -590,12 +590,12 @@ class VolumeOpts(ImageOpts):
self.setConstraint('displayRange', 'minDistance', dMinDistance)
self.setConstraint('clippingRange', 'minDistance', dMinDistance)
- ImageOpts.__init__(self,
- overlay,
- display,
- overlayList,
- displayCtx,
- **kwargs)
+ Nifti1Opts.__init__(self,
+ overlay,
+ display,
+ overlayList,
+ displayCtx,
+ **kwargs)
# The displayRange property of every child VolumeOpts
# instance is linked to the corresponding
@@ -646,7 +646,7 @@ class VolumeOpts(ImageOpts):
def destroy(self):
- """Removes property listeners, and calls the :meth:`ImageOpts.destroy`
+ """Removes property listeners, and calls the :meth:`Nifti1Opts.destroy`
method.
"""
@@ -662,7 +662,7 @@ class VolumeOpts(ImageOpts):
display,
display.getSyncPropertyName('contrast'))
- ImageOpts.destroy(self)
+ Nifti1Opts.destroy(self)
def __toggleListeners(self, enable=True):
diff --git a/fsl/fsleyes/fsleyes_parseargs.py b/fsl/fsleyes/fsleyes_parseargs.py
index 35f0f6fbe998f45b706e1ea016d1a1aca173ac0e..a4d98a98b58a69a91e9305b0b150f23fbfbfcf19 100644
--- a/fsl/fsleyes/fsleyes_parseargs.py
+++ b/fsl/fsleyes/fsleyes_parseargs.py
@@ -187,7 +187,7 @@ OPTIONS = td.TypeDict({
'alpha',
'brightness',
'contrast'],
- 'ImageOpts' : ['transform',
+ 'Nifti1Opts' : ['transform',
'resolution',
'volume'],
'VolumeOpts' : ['cmap',
@@ -236,7 +236,7 @@ GROUPNAMES = td.TypeDict({
'LightBoxOpts' : 'LightBox display options',
'Display' : 'Overlay display options',
- 'ImageOpts' : 'Options for NIFTI images',
+ 'Nifti1Opts' : 'Options for NIFTI images',
'VolumeOpts' : 'Volume options',
'MaskOpts' : 'Mask options',
'VectorOpts' : 'Vector options',
@@ -323,9 +323,9 @@ ARGUMENTS = td.TypeDict({
'Display.brightness' : ('b', 'brightness'),
'Display.contrast' : ('c', 'contrast'),
- 'ImageOpts.resolution' : ('r', 'resolution'),
- 'ImageOpts.transform' : ('tf', 'transform'),
- 'ImageOpts.volume' : ('vl', 'volume'),
+ 'Nifti1Opts.resolution' : ('r', 'resolution'),
+ 'Nifti1Opts.transform' : ('tf', 'transform'),
+ 'Nifti1Opts.volume' : ('vl', 'volume'),
'VolumeOpts.displayRange' : ('dr', 'displayRange'),
'VolumeOpts.interpolation' : ('in', 'interp'),
@@ -428,9 +428,9 @@ HELP = td.TypeDict({
'Display.brightness' : 'Brightness',
'Display.contrast' : 'Contrast',
- 'ImageOpts.resolution' : 'Resolution',
- 'ImageOpts.transform' : 'Transformation',
- 'ImageOpts.volume' : 'Volume',
+ 'Nifti1Opts.resolution' : 'Resolution',
+ 'Nifti1Opts.transform' : 'Transformation',
+ 'Nifti1Opts.volume' : 'Volume',
'VolumeOpts.displayRange' : 'Display range',
'VolumeOpts.clippingRange' : 'Clipping range',
@@ -687,7 +687,7 @@ def _configOverlayParser(ovlParser):
"""
Display = fsldisplay.Display
- ImageOpts = fsldisplay.ImageOpts
+ Nifti1Opts = fsldisplay.Nifti1Opts
VolumeOpts = fsldisplay.VolumeOpts
VectorOpts = fsldisplay.VectorOpts
RGBVectorOpts = fsldisplay.RGBVectorOpts
@@ -698,7 +698,7 @@ def _configOverlayParser(ovlParser):
dispParser = ovlParser.add_argument_group(GROUPNAMES[ Display],
GROUPDESCS.get(Display))
- imgParser = ovlParser.add_argument_group(GROUPNAMES[ImageOpts])
+ imgParser = ovlParser.add_argument_group(GROUPNAMES[Nifti1Opts])
volParser = ovlParser.add_argument_group(GROUPNAMES[VolumeOpts])
vecParser = ovlParser.add_argument_group(GROUPNAMES[VectorOpts])
lvParser = ovlParser.add_argument_group(GROUPNAMES[LineVectorOpts])
@@ -708,7 +708,7 @@ def _configOverlayParser(ovlParser):
labelParser = ovlParser.add_argument_group(GROUPNAMES[LabelOpts])
targets = [(Display, dispParser),
- (ImageOpts, imgParser),
+ (Nifti1Opts, imgParser),
(VolumeOpts, volParser),
(VectorOpts, vecParser),
(LineVectorOpts, lvParser),
diff --git a/fsl/fsleyes/gl/gllinevector.py b/fsl/fsleyes/gl/gllinevector.py
index d9c834a0e144956f3cb103c354acfd7ac77bd53c..ef416c710c427210a153cd8ad565361875f90fa2 100644
--- a/fsl/fsleyes/gl/gllinevector.py
+++ b/fsl/fsleyes/gl/gllinevector.py
@@ -251,7 +251,7 @@ class GLLineVertices(object):
.. note:: The vertex/texture coordinate generation takes into
account the current value of the
- :attr:`.ImageOpts.resolution` property of the
+ :attr:`.Nifti1Opts.resolution` property of the
:class:`.LineVectorOpts` instance; if this is set to
something other than the image resolution, the
sub-sampled starting indices and steps are stored
diff --git a/fsl/fsleyes/gl/globject.py b/fsl/fsleyes/gl/globject.py
index 4eb8aacb38c0315371e8c5fd8ad5caebff928f05..6bbf1c059d69fa5448bf460a883116fc8b0e51de 100644
--- a/fsl/fsleyes/gl/globject.py
+++ b/fsl/fsleyes/gl/globject.py
@@ -329,7 +329,7 @@ class GLImageObject(GLObject):
associated with the ``image``.
``displayOpts`` A reference to the :class:`.DisplayOpts` instance,
containing overlay type-specific display options. This
- is assumed to be a sub-class of :class:`.ImageOpts`.
+ is assumed to be a sub-class of :class:`.Nifti1Opts`.
=============== =======================================================
:arg image: The :class:`.Nifti1` instance
diff --git a/fsl/fsleyes/gl/glvector.py b/fsl/fsleyes/gl/glvector.py
index 7a905fa1bd65537c9a57a4061318c20a183bf8d7..6f6cdd0de8487d798b56d0ba107a69ea9f30a009 100644
--- a/fsl/fsleyes/gl/glvector.py
+++ b/fsl/fsleyes/gl/glvector.py
@@ -99,6 +99,7 @@ class GLVector(globject.GLImageObject):
self.yColourTexture = textures.ColourMapTexture('{}_y'.format(name))
self.zColourTexture = textures.ColourMapTexture('{}_z'.format(name))
self.modImage = None
+ self.modOpts = None
self.modTexture = None
self.imageTexture = None
self.prefilter = prefilter
@@ -128,6 +129,7 @@ class GLVector(globject.GLImageObject):
self.imageTexture = None
self.modTexture = None
self.modImage = None
+ self.modOpts = None
globject.GLImageObject.destroy(self)
@@ -286,12 +288,14 @@ class GLVector(globject.GLImageObject):
def registerModulateImage(self):
"""Called when the :attr:`.VectorOpts.modulate` property changes.
- Registers a listener with the :attr:`.ImageOpts.volume` property
+ Registers a listener with the :attr:`.Nifti1Opts.volume` property
of the modulate image, so the modulate texture can be updated when
the image volume changes.
"""
modImage = self.displayOpts.modulate
+
+ self.modOpts = None
if modImage is None or modImage == 'none': self.modImage = None
else: self.modImage = modImage
@@ -299,31 +303,30 @@ class GLVector(globject.GLImageObject):
if self.modImage is None:
return
- modOpts = self.displayOpts.displayCtx.getOpts(modImage)
+ self.modOpts = self.displayOpts.displayCtx.getOpts(modImage)
def volumeChange(*a):
- self.modTexture.set(volume=modOpts.volume)
+ self.modTexture.set(volume=self.modOpts.volume)
self.refreshModulateTexture()
self.onUpdate()
- modOpts.addListener('volume', self.name, volumeChange, weak=False)
+ self.modOpts.addListener('volume', self.name, volumeChange, weak=False)
def deregisterModulateImage(self):
"""Called when the :attr:`.VectorOpts.modulate` property changes.
- Deregisters the :attr:`.ImageOpts.volume` listener that was
+ Deregisters the :attr:`.Nifti1Opts.volume` listener that was
registered in :meth:`registerModulateImage`.
"""
if self.modImage is None:
return
- modOpts = self.displayOpts.displayCtx.getOpts(self.modImage)
-
- modOpts.removeListener('volume', self.name)
+ self.modOpts.removeListener('volume', self.name)
self.modImage = None
+ self.modOpts = None
def refreshModulateTexture(self):
@@ -338,18 +341,17 @@ class GLVector(globject.GLImageObject):
if self.modTexture is not None:
glresources.delete(self.modTexture.getTextureName())
- modImage = self.displayOpts.modulate
+ modImage = self.modImage
+ modOpts = self.modOpts
if modImage is None or modImage == 'none':
textureData = np.zeros((5, 5, 5), dtype=np.uint8)
textureData[:] = 255
modImage = fslimage.Image(textureData)
- modOpts = None
norm = False
else:
- modOpts = self.displayOpts.displayCtx.getOpts(modImage)
- norm = True
+ norm = True
texName = '{}_{}_{}_modulate'.format(
type(self).__name__, id(self.image), id(modImage))
diff --git a/fsl/fsleyes/gl/slicecanvas.py b/fsl/fsleyes/gl/slicecanvas.py
index fb3ef0f12e48d336c35527e265f5649b91f9b0db..05541fd8635f1676bb1eeabde110d1bc57dc64dc 100644
--- a/fsl/fsleyes/gl/slicecanvas.py
+++ b/fsl/fsleyes/gl/slicecanvas.py
@@ -82,7 +82,7 @@ class SliceCanvas(props.HasProperties):
The :attr:`resolutionLimit` property controls the highest resolution at
which :class:`.Image` overlays are displayed on the ``SliceCanvas``. A
higher value will result in faster rendering performance. When this
- property is changed, the :attr:`.ImageOpts.resolution` property for every
+ property is changed, the :attr:`.Nifti1Opts.resolution` property for every
:class:`.Image` overlay is updated.
@@ -580,7 +580,7 @@ class SliceCanvas(props.HasProperties):
def __resolutionLimitChange(self, *a):
"""Called when the :attr:`resolutionLimit` property changes.
- Updates the :attr:`.ImageOpts.resolution` of all :class:`.Image`
+ Updates the :attr:`.Nifti1Opts.resolution` of all :class:`.Nifti1`
overlays in the overlay list. Whenever the resolution of an
overlay is changed, its old value is saved, so it can be restored
later on when possible.
@@ -594,7 +594,7 @@ class SliceCanvas(props.HasProperties):
# No support for non-volumetric overlay
# types yet (or maybe ever?)
- if not isinstance(opts, fsldisplay.ImageOpts):
+ if not isinstance(opts, fsldisplay.Nifti1Opts):
continue
currRes = opts.resolution
@@ -648,7 +648,7 @@ class SliceCanvas(props.HasProperties):
def __overlayResolutionChanged(self, value, valid, opts, name):
- """Called when the :attr:`.ImageOpts.resolution` property for any
+ """Called when the :attr:`.Nifti1Opts.resolution` property for any
:class:`.Image` overlay changes. Clears the saved resolution for
the overlay if necessary (see :meth:`__resolutionLimitChange`).
"""
diff --git a/fsl/fsleyes/plotting/powerspectrumseries.py b/fsl/fsleyes/plotting/powerspectrumseries.py
index 8fcbe2fd08c96f9ac5e211c84dcb75dcae415cdb..fa8aefdbe795fe142214e66506d2ba9dfb77845f 100644
--- a/fsl/fsleyes/plotting/powerspectrumseries.py
+++ b/fsl/fsleyes/plotting/powerspectrumseries.py
@@ -149,7 +149,7 @@ class VoxelPowerSpectrumSeries(PowerSpectrumSeries):
class MelodicPowerSpectrumSeries(PowerSpectrumSeries):
"""The ``MelodicPowerSpectrumSeries`` class encapsulates the power spectrum
of the time course for a single component of a :class:`.MelodicImage`. The
- component is dictated by the :attr:`.ImageOpts.volume` property.
+ component is dictated by the :attr:`.Nifti1Opts.volume` property.
"""
@@ -179,7 +179,7 @@ class MelodicPowerSpectrumSeries(PowerSpectrumSeries):
def getData(self):
"""Returns the power spectrum for the current component of the
- :class:`.MelodicImage`, as defined by the :attr:`.ImageOpts.volume`
+ :class:`.MelodicImage`, as defined by the :attr:`.Nifti1Opts.volume`
property.
"""
diff --git a/fsl/fsleyes/plotting/timeseries.py b/fsl/fsleyes/plotting/timeseries.py
index e39b5d27009171d7c8846f80f78e91c27711e03e..f06ed3633fed735c18578d73c764e338b4f9aa74 100644
--- a/fsl/fsleyes/plotting/timeseries.py
+++ b/fsl/fsleyes/plotting/timeseries.py
@@ -729,7 +729,7 @@ class MelodicTimeSeries(TimeSeries):
"""A :class:`.TimeSeries` class which encapsulates the time course for
one component of a :class:`.MelodicImage`. The :meth:`getData` method
returns the time course of the component specified by the current
- :class:`.ImageOpts.volume`.
+ :class:`.Nifti1Opts.volume`.
"""
def __init__(self, tsPanel, overlay, displayCtx):
@@ -746,7 +746,7 @@ class MelodicTimeSeries(TimeSeries):
def getComponent(self):
"""Returns the index (starting from 0) of the current Melodic
- component, as dictated by the :class:`.ImageOpts.volume` property.
+ component, as dictated by the :class:`.Nifti1Opts.volume` property.
"""
opts = self.displayCtx.getOpts(self.overlay)
return opts.volume
diff --git a/fsl/fsleyes/profiles/orthoviewprofile.py b/fsl/fsleyes/profiles/orthoviewprofile.py
index 6c4b8849b41c5686a5364b406d1f305a9c4229c6..55a13ba6166bab8ddc26b677a3c96d85a0c60886 100644
--- a/fsl/fsleyes/profiles/orthoviewprofile.py
+++ b/fsl/fsleyes/profiles/orthoviewprofile.py
@@ -152,9 +152,9 @@ class OrthoViewProfile(profiles.Profile):
values, one per display space axis, which specify the distance that
a navigation operation should move the display.
- If the currently selected overlay is an :class:`.Image` instance, the
+ If the currently selected overlay is an :class:`.Nifti1` instance, the
distance that a navigation operation should shift the display will
- differ depending on the value of the :attr:`.ImageOpts.transform`
+ differ depending on the value of the :attr:`.Nifti1Opts.transform`
property. For example, if ``transform`` is ``id``, the display should
be moved by one unit (which corresponds to one voxel). But if the
``transform`` is ``pixdim``, the display should be moved by one pixdim
diff --git a/fsl/fsleyes/tooltips.py b/fsl/fsleyes/tooltips.py
index 674becd8e8ee22494da8b8d7529b0b6cdb317ca8..de98df739e96cf8f8e4bc5c5fa8d76409435dbd1 100644
--- a/fsl/fsleyes/tooltips.py
+++ b/fsl/fsleyes/tooltips.py
@@ -56,16 +56,16 @@ properties = TypeDict({
# Overlay DisplayOpts
- 'ImageOpts.volume' : 'The volume number (for 4D images).',
- 'ImageOpts.resolution' : 'Spatial display resolution, in mm.',
- 'ImageOpts.transform' : 'The affine transformation matrix to apply '
- 'to this image. You can choose to display '
- 'the image without any transformation (as if '
- 'the image voxels are 1mm isotropic); or you '
- 'can choose to scale the voxels by the pixdim '
- 'values in the NIFTI header; or you can choose '
- 'to apply the affine transformation as defined '
- 'in the NIFTI header.',
+ 'Nifti1Opts.volume' : 'The volume number (for 4D images).',
+ 'Nifti1Opts.resolution' : 'Spatial display resolution, in mm.',
+ 'Nifti1Opts.transform' : 'The affine transformation matrix to apply '
+ 'to this image. You can choose to display '
+ 'the image without any transformation (as if '
+ 'the image voxels are 1mm isotropic); or you '
+ 'can choose to scale the voxels by the pixdim '
+ 'values in the NIFTI header; or you can choose '
+ 'to apply the affine transformation as defined '
+ 'in the NIFTI header.',
'VolumeOpts.displayRange' : 'Data display range - the low value '
'corresponds to the low colour, and the '
diff --git a/fsl/fsleyes/views/canvaspanel.py b/fsl/fsleyes/views/canvaspanel.py
index 10823a2a0d50d2dc1aea0a1a52465a4959dbcc93..313779332d9de0fdd9578fc452bfe39a75a08007 100644
--- a/fsl/fsleyes/views/canvaspanel.py
+++ b/fsl/fsleyes/views/canvaspanel.py
@@ -571,7 +571,7 @@ class CanvasPanel(viewpanel.ViewPanel):
If the currently selected overlay (see
:attr:`.DisplayContext.selectedOverlay`) is a 4D :class:`.Image`
being displayed as a ``volume`` (see the :class:`.VolumeOpts` class),
- the :attr:`.ImageOpts.volume` property is incremented.
+ the :attr:`.Nifti1Opts.volume` property is incremented.
"""
overlay = self._displayCtx.getSelectedOverlay()
diff --git a/fsl/fsleyes/views/lightboxpanel.py b/fsl/fsleyes/views/lightboxpanel.py
index 9ab54b1b6c75ecb5cc487ddf120574728d8870aa..543f5de7172b155a57da3bcb197caa1d66e09d19 100644
--- a/fsl/fsleyes/views/lightboxpanel.py
+++ b/fsl/fsleyes/views/lightboxpanel.py
@@ -233,10 +233,10 @@ class LightBoxPanel(canvaspanel.CanvasPanel):
def __selectedOverlayChanged(self, *a):
"""Called when the :attr:`.DisplayContext.selectedOverlay` changes.
- If the currently selected overlay is an :class:`.Image` instance, or
+ If the currently selected overlay is a :class:`.Nifti1` instance, or
has an associated reference image (see
:meth:`.DisplayOpts.getReferenceImage`), a listener is registered on
- the reference image :attr:`.ImageOpts.transform` property, so that the
+ the reference image :attr:`.Nifti1Opts.transform` property, so that the
:meth:`__transformChanged` method will be called when it changes.
"""
@@ -265,7 +265,7 @@ class LightBoxPanel(canvaspanel.CanvasPanel):
def __transformChanged(self, *a):
- """Called when the :attr:`.ImageOpts.transform` property for the
+ """Called when the :attr:`.Nifti1Opts.transform` property for the
reference image of the currently selected overlay changes.
Updates the :attr:`.LightBoxOpts.sliceSpacing` and
diff --git a/fsl/fsleyes/views/timeseriespanel.py b/fsl/fsleyes/views/timeseriespanel.py
index 4bcf9475886fb3c41f079bb5911cf6eb1dcc74a3..dde4ece00d06acd3781cdc225d853b026c900286 100644
--- a/fsl/fsleyes/views/timeseriespanel.py
+++ b/fsl/fsleyes/views/timeseriespanel.py
@@ -95,7 +95,7 @@ class TimeSeriesPanel(plotpanel.OverlayPlotPanel):
The ``TimeSeriesPanel`` also has some functionality for
:class:`.MelodicImage` overlays - a :class:`.MelodicTimeSeries` instance
is used to plot the component time courses for the current component (as
- defined by the :attr:`.ImageOpts.volume` property).
+ defined by the :attr:`.Nifti1Opts.volume` property).
"""