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Commit a97234e8 authored by Paul McCarthy's avatar Paul McCarthy
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TensorImage now derives from the Nifti1 class, rather than the Image 

class. Associated changes to RGB/Line/Vector code so they support
TensorImage overlays. More changes need to be made, methinks.
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fsl/data/tensorimage.py
+ 7
− 14
View file @ a97234e8
......@@ -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'])
......
fsl/fsleyes/displaycontext/display.py
+ 1
− 1
View file @ a97234e8
......@@ -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
......
fsl/fsleyes/gl/gl14/gllinevector_funcs.py
+ 8
− 7
View file @ a97234e8
......@@ -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]
......
fsl/fsleyes/gl/gl14/glrgbvector_funcs.py
+ 1
− 1
View file @ a97234e8
......@@ -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)
......
fsl/fsleyes/gl/gl21/gllinevector_funcs.py
+ 6
− 8
View file @ a97234e8
......@@ -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)
......
fsl/fsleyes/gl/gl21/glrgbvector_funcs.py
+ 1
− 1
View file @ a97234e8
......@@ -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)
......
fsl/fsleyes/gl/gllabel.py
+ 5
− 0
View file @ a97234e8
......@@ -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:
......
fsl/fsleyes/gl/gllinevector.py
+ 19
− 5
View file @ a97234e8
......@@ -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
......
fsl/fsleyes/gl/globject.py
+ 4
− 13
View file @ a97234e8
......@@ -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
......
fsl/fsleyes/gl/glrgbvector.py
+ 25
− 10
View file @ a97234e8
......@@ -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.
......
fsl/fsleyes/gl/gltensor.py
+ 8
− 2
View file @ a97234e8
......@@ -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)
......
fsl/fsleyes/gl/glvector.py
+ 25
− 13
View file @ a97234e8
......@@ -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)
......
fsl/fsleyes/gl/glvolume.py
+ 4
− 0
View file @ a97234e8
......@@ -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)
......
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