diff --git a/fsl/data/tensorimage.py b/fsl/data/tensorimage.py
index 02e5fc4e4189fb29316543a414f205b252f51cc7..5bfeb009e9bef893d86593b2529921510e861de9 100644
--- a/fsl/data/tensorimage.py
+++ b/fsl/data/tensorimage.py
@@ -61,13 +61,13 @@ def isPathToTensorData(path):
return getTensorDataPrefix(path) is not None
-class TensorImage(fslimage.Image):
+class TensorImage(fslimage.Nifti1):
"""The ``TensorImage`` class is able to load and encapsulate the diffusion
tensor data generated by the FSL ``dtifit`` tool.
"""
- def __init__(self, path, *args, **kwargs):
+ def __init__(self, path):
"""Create a ``TensorImage``.
:arg path: A path to a ``dtifit`` directory. Alternately, the ``path``
@@ -75,8 +75,6 @@ class TensorImage(fslimage.Image):
``{'v1', 'v2', 'v3', 'l1', 'l2', 'l3'}``, which specify
paths to images containing the tensor eigenvectors and
eigenvalues.
-
- All other arguments are passed through to :meth:`.Image.__init__`.
"""
dtifitDir = isinstance(path, basestring)
@@ -95,20 +93,15 @@ class TensorImage(fslimage.Image):
l2 = op.join(path, '{}_L2'.format(prefix))
l3 = op.join(path, '{}_L3'.format(prefix))
- paths = {
- 'v1' : v1,
- 'v2' : v2,
- 'v3' : v3,
- 'l1' : l1,
- 'l2' : l2,
- 'l3' : l3
- }
+ paths = {'v1' : v1, 'v2' : v2, 'v3' : v3,
+ 'l1' : l1, 'l2' : l2, 'l3' : l3}
+
else:
paths = path
- fslimage.Image.__init__(self, paths['v1'], *args, **kwargs)
+ fslimage.Nifti1.__init__(self, paths['v1'], loadData=False)
- self.__v1 = self
+ self.__v1 = fslimage.Image(paths['v1'])
self.__v2 = fslimage.Image(paths['v2'])
self.__v3 = fslimage.Image(paths['v3'])
self.__l1 = fslimage.Image(paths['l1'])
diff --git a/fsl/fsleyes/displaycontext/display.py b/fsl/fsleyes/displaycontext/display.py
index 627f6b6266240b3b9fe96624c0d0244f72a0da96..890e74769ef320deae290ec0f8ab51eafc827df1 100644
--- a/fsl/fsleyes/displaycontext/display.py
+++ b/fsl/fsleyes/displaycontext/display.py
@@ -497,7 +497,7 @@ OVERLAY_TYPES = td.TypeDict({
'Image' : ['volume', 'mask', 'rgbvector', 'linevector', 'label'],
'Model' : ['model'],
- 'TensorImage' : ['tensor', 'volume', 'rgbvector', 'linevector'],
+ 'TensorImage' : ['tensor', 'rgbvector', 'linevector'],
})
"""This dictionary provides a mapping between all overlay classes,
and the possible values that the :attr:`Display.overlayType` property
diff --git a/fsl/fsleyes/gl/gl14/gllinevector_funcs.py b/fsl/fsleyes/gl/gl14/gllinevector_funcs.py
index 1bb585acdc335ee0100263a0476aee5ccb5ed0be..0afb7fde1914ea2c8f4e10dfac0e4e11e0936f81 100644
--- a/fsl/fsleyes/gl/gl14/gllinevector_funcs.py
+++ b/fsl/fsleyes/gl/gl14/gllinevector_funcs.py
@@ -47,7 +47,7 @@ def init(self):
self.lineVertices = None
self._vertexResourceName = '{}_{}_vertices'.format(
- type(self).__name__, id(self.image))
+ type(self).__name__, id(self.vectorImage))
compileShaders( self)
updateShaderState(self)
@@ -114,15 +114,15 @@ def updateVertices(self):
:meth:`.GLLineVertices.calculateHash` method), this function does nothing.
"""
- image = self.image
-
if self.lineVertices is None:
self.lineVertices = glresources.get(
self._vertexResourceName, gllinevector.GLLineVertices, self)
if hash(self.lineVertices) != self.lineVertices.calculateHash(self):
- log.debug('Re-generating line vertices for {}'.format(image))
+ log.debug('Re-generating line vertices '
+ 'for {}'.format(self.vectorImage))
+
self.lineVertices.refresh(self)
glresources.set(self._vertexResourceName,
self.lineVertices,
@@ -131,8 +131,9 @@ def updateVertices(self):
def updateShaderState(self):
"""Updates all fragment/vertex shader program variables. """
-
- opts = self.displayOpts
+
+ image = self.vectorImage
+ opts = self.displayOpts
gl.glEnable(arbvp.GL_VERTEX_PROGRAM_ARB)
gl.glEnable(arbfp.GL_FRAGMENT_PROGRAM_ARB)
@@ -144,7 +145,7 @@ def updateShaderState(self):
voxValXform = self.imageTexture.voxValXform
cmapXform = self.xColourTexture.getCoordinateTransform()
- shape = np.array(list(self.image.shape[:3]) + [0], dtype=np.float32)
+ shape = np.array(list(image.shape[:3]) + [0], dtype=np.float32)
invShape = 1.0 / shape
modThreshold = [opts.modThreshold / 100.0, 0.0, 0.0, 0.0]
offset = [0.5, 0.5, 0.5, 0.0]
diff --git a/fsl/fsleyes/gl/gl14/glrgbvector_funcs.py b/fsl/fsleyes/gl/gl14/glrgbvector_funcs.py
index b420a1c31e6caca39dca56e07ea425d0f0fad26b..7d912e69b27890795a7232b85e2aeb2ee175f19f 100644
--- a/fsl/fsleyes/gl/gl14/glrgbvector_funcs.py
+++ b/fsl/fsleyes/gl/gl14/glrgbvector_funcs.py
@@ -80,7 +80,7 @@ def updateShaderState(self):
voxValXform = self.imageTexture.voxValXform
cmapXform = self.xColourTexture.getCoordinateTransform()
- shape = list(self.image.shape[:3]) + [0]
+ shape = list(self.vectorImage.shape[:3]) + [0]
modThreshold = [opts.modThreshold / 100.0, 0.0, 0.0, 0.0]
shaders.setFragmentProgramMatrix(0, voxValXform)
diff --git a/fsl/fsleyes/gl/gl21/gllinevector_funcs.py b/fsl/fsleyes/gl/gl21/gllinevector_funcs.py
index 8617f60fe715dec76d99fa222eea16c113481e34..c82a87d158987715ecbd04350ca7a2174caaad3f 100644
--- a/fsl/fsleyes/gl/gl21/gllinevector_funcs.py
+++ b/fsl/fsleyes/gl/gl21/gllinevector_funcs.py
@@ -48,9 +48,6 @@ def init(self):
self.texCoordBuffer = gl.glGenBuffers(1)
self.vertexIDBuffer = gl.glGenBuffers(1)
- self._vertexResourceName = '{}_{}_vertices'.format(
- type(self).__name__, id(self.image))
-
opts = self.displayOpts
def vertexUpdate(*a):
@@ -137,8 +134,9 @@ def compileShaders(self):
def updateShaderState(self):
"""Updates all variables used by the vertex/fragment shaders. """
-
- opts = self.displayOpts
+
+ image = self.vectorImage
+ opts = self.displayOpts
# The coordinate transformation matrices for
# each of the three colour textures are identical,
@@ -146,7 +144,7 @@ def updateShaderState(self):
cmapXform = self.xColourTexture.getCoordinateTransform()
voxValXform = self.imageTexture.voxValXform
useSpline = False
- imageShape = np.array(self.image.shape[:3], dtype=np.float32)
+ imageShape = np.array(image.shape[:3], dtype=np.float32)
voxValXform = np.array(voxValXform, dtype=np.float32).ravel('C')
cmapXform = np.array(cmapXform, dtype=np.float32).ravel('C')
@@ -168,7 +166,7 @@ def updateShaderState(self):
gl.glUniform1i(self.zColourTexturePos, 4)
directed = opts.directed
- imageDims = self.image.pixdim[:3]
+ imageDims = image.pixdim[:3]
d2vMat = opts.getTransform('display', 'voxel')
v2dMat = opts.getTransform('voxel', 'display')
@@ -207,7 +205,7 @@ def draw(self, zpos, xform=None):
"""
- image = self.image
+ image = self.vectorImage
opts = self.displayOpts
v2dMat = opts.getTransform('voxel', 'display')
resolution = np.array([opts.resolution] * 3)
diff --git a/fsl/fsleyes/gl/gl21/glrgbvector_funcs.py b/fsl/fsleyes/gl/gl21/glrgbvector_funcs.py
index de9009af559d77fcd6934293de8c4d39516e13e9..ab0c9b7b7f9c12c07dc0d6e45c3269baa8090d05 100644
--- a/fsl/fsleyes/gl/gl21/glrgbvector_funcs.py
+++ b/fsl/fsleyes/gl/gl21/glrgbvector_funcs.py
@@ -98,7 +98,7 @@ def updateShaderState(self):
voxValXform = self.imageTexture.voxValXform
cmapXform = self.xColourTexture.getCoordinateTransform()
useSpline = opts.interpolation == 'spline'
- imageShape = np.array(self.image.shape, dtype=np.float32)
+ imageShape = np.array(self.vectorImage.shape, dtype=np.float32)
gl.glUseProgram(self.shaders)
diff --git a/fsl/fsleyes/gl/gllabel.py b/fsl/fsleyes/gl/gllabel.py
index ae358a136aef4dd2ec4407b061741dff6f52d5ea..f9b4d38d69b602487cdc712ffad6403441910714 100644
--- a/fsl/fsleyes/gl/gllabel.py
+++ b/fsl/fsleyes/gl/gllabel.py
@@ -82,6 +82,7 @@ class GLLabel(globject.GLImageObject):
representation can be updated when they change.
"""
+ image = self.image
display = self.display
opts = self.displayOpts
name = self.name
@@ -137,6 +138,7 @@ class GLLabel(globject.GLImageObject):
opts .addListener('volume', name, imageUpdate, weak=False)
opts .addListener('resolution', name, imageUpdate, weak=False)
opts .addListener('transform', name, update, weak=False)
+ image .addListener('data', name, update, weak=False)
opts.lut.addListener('labels', name, lutUpdate, weak=False)
# See comment in GLVolume.addDisplayListeners about this
@@ -153,6 +155,8 @@ class GLLabel(globject.GLImageObject):
"""Called by :meth:`destroy`. Removes all of the listeners that were
added by :meth:`addListeners`.
"""
+
+ image = self.image
display = self.display
opts = self.displayOpts
name = self.name
@@ -166,6 +170,7 @@ class GLLabel(globject.GLImageObject):
opts .removeListener( 'volume', name)
opts .removeListener( 'resolution', name)
opts .removeListener( 'transform', name)
+ image .removeListener( 'data', name)
opts.lut.removeListener( 'labels', name)
if self.__syncListenersRegistered:
diff --git a/fsl/fsleyes/gl/gllinevector.py b/fsl/fsleyes/gl/gllinevector.py
index f26812089c2bc87197b9595dec15cbd46a12da86..d9c834a0e144956f3cb103c354acfd7ac77bd53c 100644
--- a/fsl/fsleyes/gl/gllinevector.py
+++ b/fsl/fsleyes/gl/gllinevector.py
@@ -19,6 +19,7 @@ import logging
import numpy as np
import fsl.utils.transform as transform
+import fsl.data.tensorimage as tensorimage
import fsl.fsleyes.gl as fslgl
import fsl.fsleyes.gl.glvector as glvector
import fsl.fsleyes.gl.routines as glroutines
@@ -55,20 +56,32 @@ class GLLineVector(glvector.GLVector):
def __init__(self, image, display):
"""Create a ``GLLineVector`` instance.
- :arg image: The :class:`.Image` instance.
+ :arg image: An :class:`.Image` or :class:`.TensorImage` instance.
:arg display: The associated :class:`.Display` instance.
"""
- glvector.GLVector.__init__(self, image, display)
+ # If the overlay is a TensorImage, use the
+ # V1 image is the vector data. Otherwise,
+ # assume that the overlay is the vector image.
+ if isinstance(image, tensorimage.TensorImage): vecImage = image.V1()
+ else: vecImage = image
+
+ glvector.GLVector.__init__(self, image, display, vectorImage=vecImage)
fslgl.gllinevector_funcs.init(self)
def update(*a):
self.onUpdate()
- self.displayOpts.addListener(
- 'lineWidth', self.name, update, weak=False)
+ self.displayOpts.addListener('lineWidth',
+ self.name,
+ update,
+ weak=False)
+ self.vectorImage.addListener('data',
+ self.name,
+ update,
+ weak=False)
def destroy(self):
@@ -78,6 +91,7 @@ class GLLineVector(glvector.GLVector):
function, and calls the :meth:`.GLVector.destroy` method.
"""
self.displayOpts.removeListener('lineWidth', self.name)
+ self.vectorImage.removeListener('data', self.name)
fslgl.gllinevector_funcs.destroy(self)
glvector.GLVector.destroy(self)
@@ -247,7 +261,7 @@ class GLLineVertices(object):
"""
opts = glvec.displayOpts
- image = glvec.image
+ image = glvec.vectorImage
# Extract a sub-sample of the vector image
# at the current display resolution
diff --git a/fsl/fsleyes/gl/globject.py b/fsl/fsleyes/gl/globject.py
index 1b0687f8338b2c7cf571b5d77e2c39a0878344d3..4eb8aacb38c0315371e8c5fd8ad5caebff928f05 100644
--- a/fsl/fsleyes/gl/globject.py
+++ b/fsl/fsleyes/gl/globject.py
@@ -314,7 +314,7 @@ class GLSimpleObject(GLObject):
class GLImageObject(GLObject):
"""The ``GLImageObject`` class is the base class for all GL representations
- of :class:`.Image` instances.
+ of :class:`.Nifti1` instances.
"""
def __init__(self, image, display):
@@ -323,7 +323,8 @@ class GLImageObject(GLObject):
This constructor adds the following attributes to this instance:
=============== =======================================================
- ``image`` A reference to the :class:`.Image` being displayed.
+ ``image`` A reference to the :class:`.Nifti1` overlay being
+ displayed.
``display`` A reference to the :class:`.Display` instance
associated with the ``image``.
``displayOpts`` A reference to the :class:`.DisplayOpts` instance,
@@ -331,7 +332,7 @@ class GLImageObject(GLObject):
is assumed to be a sub-class of :class:`.ImageOpts`.
=============== =======================================================
- :arg image: The :class:`.Image` instance
+ :arg image: The :class:`.Nifti1` instance
:arg display: An associated :class:`.Display` instance.
"""
@@ -341,18 +342,9 @@ class GLImageObject(GLObject):
self.display = display
self.displayOpts = display.getDisplayOpts()
- self.image.addListener('data', self.name, self.__imageDataChanged)
-
log.memory('{}.init ({})'.format(type(self).__name__, id(self)))
- def __imageDataChanged(self, *a):
- """Called when the :attr:`.Image.data` changes. Calls
- :meth:`GLObject.onUpdate`.
- """
- self.onUpdate()
-
-
def __del__(self):
"""Prints a log message."""
log.memory('{}.del ({})'.format(type(self).__name__, id(self)))
@@ -363,7 +355,6 @@ class GLImageObject(GLObject):
implementation. It clears references to the :class:`.Image`,
:class:`.Display`, and :class:`.DisplayOpts` instances.
"""
- self.image.removeListener('data', self.name)
self.image = None
self.display = None
self.displayOpts = None
diff --git a/fsl/fsleyes/gl/glrgbvector.py b/fsl/fsleyes/gl/glrgbvector.py
index b995085b0362f9a8469736215709ba696d0dac7e..fcdd272cc10de35c605759dc76fce3291fd20a14 100644
--- a/fsl/fsleyes/gl/glrgbvector.py
+++ b/fsl/fsleyes/gl/glrgbvector.py
@@ -12,6 +12,7 @@ vector :class:`.Image` overlays in RGB mode.
import numpy as np
import OpenGL.GL as gl
+import fsl.data.tensorimage as tensorimage
import fsl.fsleyes.gl as fslgl
import fsl.fsleyes.gl.glvector as glvector
@@ -60,17 +61,31 @@ class GLRGBVector(glvector.GLVector):
def __init__(self, image, display):
"""Create a ``GLRGBVector``.
- :arg image: The :class:`.Image` instance.
+ :arg image: An :class:`.Image` or :class:`.TensorImage` instance.
:arg display: The associated :class:`.Display` instance.
"""
- glvector.GLVector.__init__(self, image, display, self.__prefilter)
+ # If the overlay is a TensorImage, use the
+ # V1 image is the vector data. Otherwise,
+ # assume that the overlay is the vector image.
+ if isinstance(image, tensorimage.TensorImage): vecImage = image.V1()
+ else: vecImage = image
+
+ glvector.GLVector.__init__(self,
+ image,
+ display,
+ prefilter=np.abs,
+ vectorImage=vecImage)
+
fslgl.glrgbvector_funcs.init(self)
self.displayOpts.addListener('interpolation',
self.name,
self.__interpChanged)
-
+ self.vectorImage.addListener('data',
+ self.name,
+ self.__dataChanged)
+
def destroy(self):
"""Must be called when this ``GLRGBVector`` is no longer needed.
@@ -91,13 +106,6 @@ class GLRGBVector(glvector.GLVector):
self.__setInterp()
- def __prefilter(self, data):
- """This method is passed to :meth:`.GLVector.__init__` as the
- ``prefilter`` parameter. It removes the sign from the given data.
- """
- return np.abs(data)
-
-
def __setInterp(self):
"""Updates the interpolation setting on the :class:`.ImageTexture`
that contains the vector :class:`.Image` being displayed.
@@ -109,7 +117,14 @@ class GLRGBVector(glvector.GLVector):
self.imageTexture.set(interp=interp)
+
+ def __dataChanged(self, *a):
+ """Called when the :attr:`.Image.data` of the vector image
+ changes. Calls :meth:`.GLObject.onUpdate`.
+ """
+ self.onUpdate()
+
def __interpChanged(self, *a):
"""Called when the :attr:`.RGBVectorOpts.interpolation` property
changes. Updates the :class:`.ImageTexture` interpolation.
diff --git a/fsl/fsleyes/gl/gltensor.py b/fsl/fsleyes/gl/gltensor.py
index 1be569b2c5daba93bd4e8874cb3869c5211492d9..ee76085e95c539746750a5b4564715d3232e1801 100644
--- a/fsl/fsleyes/gl/gltensor.py
+++ b/fsl/fsleyes/gl/gltensor.py
@@ -5,8 +5,11 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
+
import logging
+import numpy as np
+
import glvector
import fsl.fsleyes.gl as fslgl
@@ -18,8 +21,11 @@ class GLTensor(glvector.GLVector):
def __init__(self, image, display):
- glvector.GLVector.__init__(self, image, display)
-
+ glvector.GLVector.__init__(self,
+ image,
+ display,
+ prefilter=np.abs,
+ vectorImage=image.V1())
fslgl.gltensor_funcs.init(self)
diff --git a/fsl/fsleyes/gl/glvector.py b/fsl/fsleyes/gl/glvector.py
index 5a8ea15b39d51535b7b80261261eaf3352ef88c3..7a905fa1bd65537c9a57a4061318c20a183bf8d7 100644
--- a/fsl/fsleyes/gl/glvector.py
+++ b/fsl/fsleyes/gl/glvector.py
@@ -51,7 +51,7 @@ class GLVector(globject.GLImageObject):
"""
- def __init__(self, image, display, prefilter=None):
+ def __init__(self, image, display, prefilter=None, vectorImage=None):
"""Create a ``GLVector`` object bound to the given image and display.
Initialises the OpenGL data required to render the given image.
@@ -64,19 +64,29 @@ class GLVector(globject.GLImageObject):
instances, so the textures and geometry can be updated when
necessary.
- :arg image: An :class:`.Image` object.
+ :arg image: An :class:`.Nifti1` object.
- :arg display: A :class:`.Display` object which describes how the
- image is to be displayed.
-
- :arg prefilter: An optional function which filters the data before it
- is stored as a 3D texture. See :class:`.ImageTexture`.
- Whether or not this function is provided, the data is
- transposed so that the fourth dimension is the fastest
- changing.
+ :arg display: A :class:`.Display` object which describes how the
+ image is to be displayed.
+
+ :arg prefilter: An optional function which filters the data before it
+ is stored as a 3D texture. See
+ :class:`.ImageTexture`. Whether or not this function
+ is provided, the data is transposed so that the
+ fourth dimension is the fastest changing.
+
+ :arg vectorImage: Optional. If ``None``, the ``image`` is assumed to
+ be a 4D :class:`.Image` instance which contains
+ the vector data. If this is not the case, the
+ ``vectorImage`` parameter can be used to specify
+ an ``Image`` instance which does contain the
+ vector data.
"""
- if not image.is4DImage() or image.shape[3] != 3:
+ if vectorImage is None:
+ vectorImage = image
+
+ if len(vectorImage.shape) != 4 or vectorImage.shape[3] != 3:
raise ValueError('Image must be 4 dimensional, with 3 volumes '
'representing the XYZ vector angles')
@@ -84,6 +94,7 @@ class GLVector(globject.GLImageObject):
name = self.name
+ self.vectorImage = vectorImage
self.xColourTexture = textures.ColourMapTexture('{}_x'.format(name))
self.yColourTexture = textures.ColourMapTexture('{}_y'.format(name))
self.zColourTexture = textures.ColourMapTexture('{}_z'.format(name))
@@ -225,7 +236,8 @@ class GLVector(globject.GLImageObject):
opts = self.displayOpts
prefilter = self.prefilter
- texName = '{}_{}'.format(type(self).__name__, id(self.image))
+ vecImage = self.vectorImage
+ texName = '{}_{}'.format(type(self).__name__, id(vecImage))
if self.imageTexture is not None:
glresources.delete(self.imageTexture.getTextureName())
@@ -248,7 +260,7 @@ class GLVector(globject.GLImageObject):
texName,
textures.ImageTexture,
texName,
- self.image,
+ vecImage,
nvals=3,
normalise=True,
prefilter=realPrefilter)
diff --git a/fsl/fsleyes/gl/glvolume.py b/fsl/fsleyes/gl/glvolume.py
index 227a2042945ecf92e28cdf9c5228ca38a333bf82..aadf49cf05b052edbf70fb863a1a4f110b8a8080 100644
--- a/fsl/fsleyes/gl/glvolume.py
+++ b/fsl/fsleyes/gl/glvolume.py
@@ -186,6 +186,7 @@ class GLVolume(globject.GLImageObject):
display properties are changed.
"""
+ image = self.image
display = self.display
opts = self.displayOpts
lName = self.name
@@ -234,6 +235,7 @@ class GLVolume(globject.GLImageObject):
opts .addListener('resolution', lName, imageUpdate, weak=False)
opts .addListener('interpolation', lName, imageUpdate, weak=False)
opts .addListener('transform', lName, update, weak=False)
+ image .addListener('data', lName, update, weak=False)
# Save a flag so the removeDisplayListeners
# method knows whether it needs to de-register
@@ -258,6 +260,7 @@ class GLVolume(globject.GLImageObject):
were added by :meth:`addDisplayListeners`.
"""
+ image = self.image
display = self.display
opts = self.displayOpts
@@ -276,6 +279,7 @@ class GLVolume(globject.GLImageObject):
opts .removeListener( 'resolution', lName)
opts .removeListener( 'interpolation', lName)
opts .removeListener( 'transform', lName)
+ image .removeListener( 'data', lName)
if self.__syncListenersRegistered:
opts.removeSyncChangeListener('volume', lName)