def canvasToWorld(self, xpos, ypos):
"""Transform the given x/y canvas coordinates into the display
coordinate system.
"""
b = self.__displayCtx.bounds
width, height = self.GetSize()
# The first step is to invert the mouse
# coordinates w.r.t. the viewport.
#
# The canvas x axis corresponds to
# (-xhalf, xhalf), and the canvas y
# corresponds to (-yhalf, yhalf) -
# see routines.show3D.
xlen, ylen = glroutines.adjust(b.xlen, b.ylen, width, height)
xhalf = 0.5 * xlen
yhalf = 0.5 * ylen
# Pixels to viewport coordinates
xpos = xlen * (xpos / float(width)) - xhalf
ypos = ylen * (ypos / float(height)) - yhalf
# The second step is to transform from
# viewport coords into model-view coords.
# This is easy - transform by the inverse
# MV matrix.
#
# z=-1 because the camera is offset by 1
# on the depth axis (see __setViewport).
pos = np.array([xpos, ypos, -1])
xform = transform.invert(self.__viewMat)
pos = transform.transform(pos, xform)
return pos
def updateVertices(self, *a):
"""Called by :meth:`__init__`, and when certain display properties
change. (Re-)generates the mesh vertices, indices and normals (if
being displayed in 3D). They are stored as attributes called
``vertices``, ``indices``, and ``normals`` respectively.
"""
overlay = self.overlay
vertices = overlay.vertices
indices = overlay.indices
normals = self.overlay.vnormals
xform = self.opts.getCoordSpaceTransform()
if not np.all(np.isclose(xform, np.eye(4))):
vertices = transform.transform(vertices, xform)
if self.threedee:
nmat = transform.invert(xform).T
normals = transform.transform(normals, nmat, vector=True)
self.vertices = np.array(vertices, dtype=np.float32)
self.indices = np.array(indices.flatten(), dtype=np.uint32)
if self.threedee:
self.normals = np.array(normals, dtype=np.float32)
def draw3D(self, *args, **kwargs):
"""Calls the version dependent ``draw3D`` function. """
opts = self.opts
w, h = self.canvas.GetSize()
res = self.opts.resolution / 100.0
w = int(np.ceil(w * res))
h = int(np.ceil(h * res))
# Initialise and resize
# the offscreen textures
for rt in [self.renderTexture1, self.renderTexture2]:
if rt.getSize() != (w, h):
rt.setSize(w, h)
rt.bindAsRenderTarget()
gl.glClearColor(0, 0, 0, 0)
gl.glClear(gl.GL_COLOR_BUFFER_BIT | gl.GL_DEPTH_BUFFER_BIT)
rt.unbindAsRenderTarget()
if opts.resolution != 100:
gl.glViewport(0, 0, w, h)
# Do the render. Even though we're
# drawing off-screen, we need to
# enable depth-testing, otherwise
# depth values will not get written
# to the depth buffer!
with glroutines.enabled((gl.GL_DEPTH_TEST, gl.GL_CULL_FACE)):
gl.glPolygonMode(gl.GL_FRONT_AND_BACK, gl.GL_FILL)
gl.glFrontFace(gl.GL_CCW)
gl.glCullFace(gl.GL_BACK)
fslgl.glvolume_funcs.draw3D(self, *args, **kwargs)
# renderTexture1 should now
# contain the final result -
# draw it to the screen.
verts = np.array([[-1, -1, 0], [-1, 1, 0], [1, -1, 0], [1, -1, 0],
[-1, 1, 0], [1, 1, 0]],
dtype=np.float32)
invproj = transform.invert(self.canvas.getProjectionMatrix())
verts = transform.transform(verts, invproj)
if opts.resolution != 100:
w, h = self.canvas.GetSize()
gl.glViewport(0, 0, w, h)
with glroutines.enabled((gl.GL_DEPTH_TEST)):
self.renderTexture1.draw(verts, useDepth=True)
def draw(self, glType, vertices, indices=None, normals=None, vdata=None):
"""Called for 3D meshes, and :attr:`.MeshOpts.vertexData` is not
``None``. Loads and runs the shader program.
:arg glType: The OpenGL primitive type.
:arg vertices: ``(n, 3)`` array containing the line vertices to draw.
:arg indices: Indices into the ``vertices`` array. If not provided,
``glDrawArrays`` is used.
:arg normals: Vertex normals.
:arg vdata: ``(n, )`` array containing data for each vertex.
"""
shader = self.activeShader
if normals is not None: shader.setAtt('normal', normals)
if vdata is not None: shader.setAtt('vertexData', vdata.reshape(-1, 1))
if normals is not None:
# NOTE You are assuming here that the canvas
# view matrix is the GL model view matrix.
normalMatrix = self.canvas.viewMatrix
normalMatrix = transform.invert(normalMatrix).T
shader.setVertParam('normalMatrix', normalMatrix)
shader.loadAtts()
nvertices = vertices.shape[0]
vertices = vertices.ravel('C')
with glroutines.enabled((gl.GL_VERTEX_ARRAY)):
gl.glVertexPointer(3, gl.GL_FLOAT, 0, vertices)
if indices is None:
gl.glDrawArrays(glType, 0, nvertices)
else:
gl.glDrawElements(glType, indices.shape[0], gl.GL_UNSIGNED_INT,
indices.ravel('C'))
def __setViewport(self):
"""Called by :meth:`_draw`. Configures the viewport and calculates
the model-view trasformation matrix.
:returns: ``True`` if the viewport was successfully configured,
``False`` otherwise.
"""
width, height = self.GetScaledSize()
b = self.__displayCtx.bounds
blo = [b.xlo, b.ylo, b.zlo]
bhi = [b.xhi, b.yhi, b.zhi]
zoom = self.opts.zoom / 100.0
if width == 0 or height == 0:
return False
# We allow one dimension to be
# flat, so we can display 2D
# meshes (e.g. flattened surfaces)
if np.sum(np.isclose(blo, bhi)) > 1:
return False
# Generate the view and projection matrices
self.__genViewMatrix(width, height)
projmat, viewport = glroutines.ortho(blo, bhi, width, height, zoom)
self.__projMat = projmat
self.__viewport = viewport
self.__invViewProjMat = transform.concat(self.__projMat,
self.__viewMat)
self.__invViewProjMat = transform.invert(self.__invViewProjMat)
gl.glViewport(0, 0, width, height)
gl.glMatrixMode(gl.GL_PROJECTION)
gl.glLoadMatrixf(self.__projMat.ravel('F'))
gl.glMatrixMode(gl.GL_MODELVIEW)
gl.glLoadIdentity()
return True
def calculateRayCastSettings(self, view=None, proj=None):
"""Calculates various parameters required for 3D ray-cast rendering
(see the :class:`.GLVolume` class).
:arg view: Transformation matrix which transforms from model
coordinates to view coordinates (i.e. the GL view matrix).
:arg proj: Transformation matrix which transforms from view coordinates
to normalised device coordinates (i.e. the GL projection
matrix).
Returns a tuple containing:
- A vector defining the amount by which to move along a ray in a
single iteration of the ray-casting algorithm. This can be added
directly to the volume texture coordinates.
- A transformation matrix which transforms from image texture
coordinates into the display coordinate system.
.. note:: This method will raise an error if called on a
``GLImageObject`` which is managing an overlay that is not
associated with a :class:`.Volume3DOpts` instance.
"""
if view is None: view = np.eye(4)
if proj is None: proj = np.eye(4)
# In GL, the camera position
# is initially pointing in
# the -z direction.
eye = [0, 0, -1]
target = [0, 0, 1]
# We take this initial camera
# configuration, and transform
# it by the inverse modelview
# matrix
t2dmat = self.getTransform('texture', 'display')
xform = transform.concat(view, t2dmat)
ixform = transform.invert(xform)
eye = transform.transform(eye, ixform, vector=True)
target = transform.transform(target, ixform, vector=True)
# Direction that the 'camera' is
# pointing, normalied to unit length
cdir = transform.normalise(eye - target)
# Calculate the length of one step
# along the camera direction in a
# single iteration of the ray-cast
# loop. Multiply by sqrt(3) so that
# the maximum number of steps will
# be reached across the longest axis
# of the image texture cube.
rayStep = np.sqrt(3) * cdir / self.getNumSteps()
# A transformation matrix which can
# transform image texture coordinates
# into the corresponding screen
# (normalised device) coordinates.
# This allows the fragment shader to
# convert an image texture coordinate
# into a relative depth value.
#
# The projection matrix puts depth into
# [-1, 1], but we want it in [0, 1]
zscale = transform.scaleOffsetXform([1, 1, 0.5], [0, 0, 0.5])
xform = transform.concat(zscale, proj, xform)
return rayStep, xform
def draw3D(self, *args, **kwargs):
"""Calls the version dependent ``draw3D`` function. """
opts = self.opts
w, h = self.canvas.GetScaledSize()
res = self.opts.resolution / 100.0
sw = int(np.ceil(w * res))
sh = int(np.ceil(h * res))
# Initialise and resize
# the offscreen textures
for rt in [self.renderTexture1, self.renderTexture2]:
if rt.getSize() != (sw, sh):
rt.setSize(sw, sh)
with rt.bound():
gl.glClearColor(0, 0, 0, 0)
gl.glClear(gl.GL_COLOR_BUFFER_BIT | gl.GL_DEPTH_BUFFER_BIT)
if opts.resolution != 100:
gl.glViewport(0, 0, sw, sh)
# Do the render. Even though we're
# drawing off-screen, we need to
# enable depth-testing, otherwise
# depth values will not get written
# to the depth buffer!
#
# The glvolume_funcs.draw3D function
# will put the final render into
# renderTexture1
with glroutines.enabled((gl.GL_DEPTH_TEST, gl.GL_CULL_FACE)):
gl.glPolygonMode(gl.GL_FRONT_AND_BACK, gl.GL_FILL)
gl.glFrontFace(gl.GL_CCW)
gl.glCullFace(gl.GL_BACK)
fslgl.glvolume_funcs.draw3D(self, *args, **kwargs)
# Apply smoothing if needed. If smoothing
# is enabled, the final final render will
# be in renderTexture2
if opts.smoothing > 0:
self.smoothFilter.set(offsets=[1.0 / sw, 1.0 / sh])
self.smoothFilter.osApply(self.renderTexture1, self.renderTexture2)
# We now have the final result
# - draw it to the screen.
verts = np.array([[-1, -1, 0], [-1, 1, 0], [1, -1, 0], [1, -1, 0],
[-1, 1, 0], [1, 1, 0]],
dtype=np.float32)
invproj = transform.invert(self.canvas.projectionMatrix)
verts = transform.transform(verts, invproj)
if opts.resolution != 100:
gl.glViewport(0, 0, w, h)
with glroutines.enabled(gl.GL_DEPTH_TEST):
# If smoothing was not applied, rt1
# contains the final render. Otherwise,
# rt2 contains the final render, but rt1
# contains the depth information. So we
# need to # temporarily replace rt2.depth
# with rt1.depth.
if opts.smoothing > 0:
src = self.renderTexture2
olddep = self.renderTexture2.depthTexture
dep = self.renderTexture1.depthTexture
else:
src = self.renderTexture1
olddep = self.renderTexture1.depthTexture
dep = olddep
src.depthTexture = dep
src.draw(verts, useDepth=True)
src.depthTexture = olddep
def __setupTransforms(self):
"""Calculates transformation matrices between all of the possible
spaces in which the overlay may be displayed.
These matrices are accessible via the :meth:`getTransform` method.
"""
image = self.overlay
shape = np.array(image.shape[:3])
voxToIdMat = np.eye(4)
voxToPixdimMat = np.diag(list(image.pixdim[:3]) + [1.0])
voxToPixFlipMat = image.voxToScaledVoxMat
voxToWorldMat = image.voxToWorldMat
voxToWorldMat = transform.concat(self.displayXform, voxToWorldMat)
ds = self.displayCtx.displaySpace
# The reference transforms depend on the value of
# displaySpace
if ds == 'world':
voxToRefMat = voxToWorldMat
elif ds is self.overlay:
voxToRefMat = voxToPixFlipMat
else:
voxToRefMat = transform.concat(ds.voxToScaledVoxMat,
ds.worldToVoxMat, voxToWorldMat)
# When going from voxels to textures,
# we add 0.5 to centre the voxel (see
# the note on coordinate systems at
# the top of this file).
voxToTexMat = transform.scaleOffsetXform(tuple(1.0 / shape),
tuple(0.5 / shape))
idToVoxMat = transform.invert(voxToIdMat)
idToPixdimMat = transform.concat(voxToPixdimMat, idToVoxMat)
idToPixFlipMat = transform.concat(voxToPixFlipMat, idToVoxMat)
idToWorldMat = transform.concat(voxToWorldMat, idToVoxMat)
idToRefMat = transform.concat(voxToRefMat, idToVoxMat)
idToTexMat = transform.concat(voxToTexMat, idToVoxMat)
pixdimToVoxMat = transform.invert(voxToPixdimMat)
pixdimToIdMat = transform.concat(voxToIdMat, pixdimToVoxMat)
pixdimToPixFlipMat = transform.concat(voxToPixFlipMat, pixdimToVoxMat)
pixdimToWorldMat = transform.concat(voxToWorldMat, pixdimToVoxMat)
pixdimToRefMat = transform.concat(voxToRefMat, pixdimToVoxMat)
pixdimToTexMat = transform.concat(voxToTexMat, pixdimToVoxMat)
pixFlipToVoxMat = transform.invert(voxToPixFlipMat)
pixFlipToIdMat = transform.concat(voxToIdMat, pixFlipToVoxMat)
pixFlipToPixdimMat = transform.concat(voxToPixdimMat, pixFlipToVoxMat)
pixFlipToWorldMat = transform.concat(voxToWorldMat, pixFlipToVoxMat)
pixFlipToRefMat = transform.concat(voxToRefMat, pixFlipToVoxMat)
pixFlipToTexMat = transform.concat(voxToTexMat, pixFlipToVoxMat)
worldToVoxMat = transform.invert(voxToWorldMat)
worldToIdMat = transform.concat(voxToIdMat, worldToVoxMat)
worldToPixdimMat = transform.concat(voxToPixdimMat, worldToVoxMat)
worldToPixFlipMat = transform.concat(voxToPixFlipMat, worldToVoxMat)
worldToRefMat = transform.concat(voxToRefMat, worldToVoxMat)
worldToTexMat = transform.concat(voxToTexMat, worldToVoxMat)
refToVoxMat = transform.invert(voxToRefMat)
refToIdMat = transform.concat(voxToIdMat, refToVoxMat)
refToPixdimMat = transform.concat(voxToPixdimMat, refToVoxMat)
refToPixFlipMat = transform.concat(voxToPixFlipMat, refToVoxMat)
refToWorldMat = transform.concat(voxToWorldMat, refToVoxMat)
refToTexMat = transform.concat(voxToTexMat, refToVoxMat)
texToVoxMat = transform.invert(voxToTexMat)
texToIdMat = transform.concat(voxToIdMat, texToVoxMat)
texToPixdimMat = transform.concat(voxToPixdimMat, texToVoxMat)
texToPixFlipMat = transform.concat(voxToPixFlipMat, texToVoxMat)
texToWorldMat = transform.concat(voxToWorldMat, texToVoxMat)
texToRefMat = transform.concat(voxToRefMat, texToVoxMat)
self.__xforms['id', 'id'] = np.eye(4)
self.__xforms['id', 'pixdim'] = idToPixdimMat
self.__xforms['id', 'pixdim-flip'] = idToPixFlipMat
self.__xforms['id', 'affine'] = idToWorldMat
self.__xforms['id', 'reference'] = idToRefMat
self.__xforms['id', 'texture'] = idToTexMat
self.__xforms['pixdim', 'pixdim'] = np.eye(4)
self.__xforms['pixdim', 'id'] = pixdimToIdMat
self.__xforms['pixdim', 'pixdim-flip'] = pixdimToPixFlipMat
self.__xforms['pixdim', 'affine'] = pixdimToWorldMat
self.__xforms['pixdim', 'reference'] = pixdimToRefMat
self.__xforms['pixdim', 'texture'] = pixdimToTexMat
self.__xforms['pixdim-flip', 'pixdim-flip'] = np.eye(4)
self.__xforms['pixdim-flip', 'id'] = pixFlipToIdMat
self.__xforms['pixdim-flip', 'pixdim'] = pixFlipToPixdimMat
self.__xforms['pixdim-flip', 'affine'] = pixFlipToWorldMat
self.__xforms['pixdim-flip', 'reference'] = pixFlipToRefMat
self.__xforms['pixdim-flip', 'texture'] = pixFlipToTexMat
self.__xforms['affine', 'affine'] = np.eye(4)
self.__xforms['affine', 'id'] = worldToIdMat
self.__xforms['affine', 'pixdim'] = worldToPixdimMat
self.__xforms['affine', 'pixdim-flip'] = worldToPixFlipMat
self.__xforms['affine', 'reference'] = worldToRefMat
self.__xforms['affine', 'texture'] = worldToTexMat
self.__xforms['reference', 'reference'] = np.eye(4)
self.__xforms['reference', 'id'] = refToIdMat
self.__xforms['reference', 'pixdim'] = refToPixdimMat
self.__xforms['reference', 'pixdim-flip'] = refToPixFlipMat
self.__xforms['reference', 'affine'] = refToWorldMat
self.__xforms['reference', 'texture'] = refToTexMat
self.__xforms['texture', 'texture'] = np.eye(4)
self.__xforms['texture', 'id'] = texToIdMat
self.__xforms['texture', 'pixdim'] = texToPixdimMat
self.__xforms['texture', 'pixdim-flip'] = texToPixFlipMat
self.__xforms['texture', 'affine'] = texToWorldMat
self.__xforms['texture', 'reference'] = texToRefMat