def test_normalise(seed):
vectors = -100 + 200 * np.random.random((200, 3))
def parallel(v1, v2):
v1 = v1 / affine.veclength(v1)
v2 = v2 / affine.veclength(v2)
return np.isclose(np.dot(v1, v2), 1)
for v in vectors:
vtype = random.choice((list, tuple, np.array))
v = vtype(v)
vn = affine.normalise(v)
vl = affine.veclength(vn)
assert np.isclose(vl, 1.0)
assert parallel(v, vn)
# normalise should also be able
# to do multiple vectors at once
results = affine.normalise(vectors)
lengths = affine.veclength(results)
pars = np.zeros(200)
for i in range(200):
v = vectors[i]
r = results[i]
pars[i] = parallel(v, r)
assert np.all(np.isclose(lengths, 1))
assert np.all(pars)
def calcVertexNormals(vertices, indices, fnormals):
"""Calculates vertex normals for the mesh described by ``vertices``
and ``indices``.
:arg vertices: A ``(n, 3)`` array containing the mesh vertices.
:arg indices: A ``(m, 3)`` array containing the mesh triangles.
:arg fnormals: A ``(m, 3)`` array containing the face/triangle normals.
:returns: A ``(n, 3)`` array containing normals for every vertex in
the mesh.
"""
vnormals = np.zeros((vertices.shape[0], 3), dtype=float)
# TODO make fast. I can't figure
# out how to use np.add.at to
# accumulate the face normals for
# each vertex.
for i in range(indices.shape[0]):
v0, v1, v2 = indices[i]
vnormals[v0, :] += fnormals[i]
vnormals[v1, :] += fnormals[i]
vnormals[v2, :] += fnormals[i]
# normalise to unit length
return affine.normalise(vnormals)
def needsFixing(vertices, indices, fnormals, loBounds, hiBounds):
"""Determines whether the triangle winding order, for the mesh described by
``vertices`` and ``indices``, needs to be flipped.
If this function returns ``True``, the given ``indices`` and ``fnormals``
need to be adjusted so that all face normals are facing outwards from the
centre of the mesh. The necessary adjustments are as follows::
indices[:, [1, 2]] = indices[:, [2, 1]]
fnormals = fnormals * -1
:arg vertices: A ``(n, 3)`` array containing the mesh vertices.
:arg indices: A ``(m, 3)`` array containing the mesh triangles.
:arg fnormals: A ``(m, 3)`` array containing the face/triangle normals.
:arg loBounds: A ``(3, )`` array contaning the low vertex bounds.
:arg hiBounds: A ``(3, )`` array contaning the high vertex bounds.
:returns: ``True`` if the ``indices`` and ``fnormals`` need to be
adjusted, ``False`` otherwise.
"""
# Define a viewpoint which is
# far away from the mesh.
camera = loBounds - (hiBounds - loBounds)
# Find the nearest vertex
# to the viewpoint
dists = np.sqrt(np.sum((vertices - camera) ** 2, axis=1))
ivert = np.argmin(dists)
vert = vertices[ivert]
# Get all the triangles
# that this vertex is in
# and their face normals
itris = np.where(indices == ivert)[0]
norms = fnormals[itris, :]
# Calculate the angle between each
# normal, and a vector from the
# vertex to the camera. If more than
# 50% of the angles are negative
# (== more than 90 degrees == the
# face is facing away from the
# camera), assume that we need to
# flip the triangle winding order.
angles = np.dot(norms, affine.normalise(camera - vert))
return ((angles >= 0).sum() / len(itris)) < 0.5
def calculateRayCastSettings(self, viewmat):
"""Calculates a camera direction and ray casting step vector, based
on the given view matrix.
"""
d2tmat = self.getTransform('display', 'texture')
xform = affine.concat(d2tmat, viewmat)
cdir = np.array([0, 0, 1])
cdir = affine.transform(cdir, xform, vector=True)
cdir = affine.normalise(cdir)
# sqrt(3) so the maximum number
# of samplews is taken along the
# diagonal of a cube
rayStep = np.sqrt(3) * cdir / self.numSteps
return cdir, rayStep
def calcFaceNormals(vertices, indices):
"""Calculates face normals for the mesh described by ``vertices`` and
``indices``.
:arg vertices: A ``(n, 3)`` array containing the mesh vertices.
:arg indices: A ``(m, 3)`` array containing the mesh triangles.
:returns: A ``(m, 3)`` array containing normals for every triangle in
the mesh.
"""
v0 = vertices[indices[:, 0]]
v1 = vertices[indices[:, 1]]
v2 = vertices[indices[:, 2]]
fnormals = np.cross((v1 - v0), (v2 - v0))
fnormals = affine.normalise(fnormals)
return np.atleast_2d(fnormals)
def planeEquation2(origin, normal):
"""Calculates the equation of a plane equation from a normal vector
and a single point on the plane.
Returns a ``numpy`` array containing four values, the coefficients of the
equation:
See also :func:`planeEquation`.
"""
normal = affine.normalise(normal)
ax, by, cz = np.array(origin) * normal
eqn = np.zeros(4, dtype=np.float64)
eqn[:3] = normal
eqn[3] = -np.sum((ax, by, cz))
return eqn
def get3DClipPlane(self, planeIdx):
"""A convenience method which calculates a point-vector description
of the specified clipping plane. ``planeIdx`` is an index into the
:attr:`clipPosition`, :attr:`clipAzimuth`, and
:attr:`clipInclination`, properties.
Returns the clip plane at the given ``planeIdx`` as an origin and
normal vector, in the display coordinate system..
"""
pos = self.clipPosition[ planeIdx]
azimuth = self.clipAzimuth[ planeIdx]
incline = self.clipInclination[planeIdx]
b = self.bounds
pos = pos / 100.0
azimuth = azimuth * np.pi / 180.0
incline = incline * np.pi / 180.0
xmid = b.xlo + 0.5 * b.xlen
ymid = b.ylo + 0.5 * b.ylen
zmid = b.zlo + 0.5 * b.zlen
centre = [xmid, ymid, zmid]
normal = [0, 0, -1]
rot1 = affine.axisAnglesToRotMat(incline, 0, 0)
rot2 = affine.axisAnglesToRotMat(0, 0, azimuth)
rotation = affine.concat(rot2, rot1)
normal = affine.transformNormal(normal, rotation)
normal = affine.normalise(normal)
offset = (pos - 0.5) * max((b.xlen, b.ylen, b.zlen))
origin = centre + normal * offset
return origin, normal
CUBE_TRIANGLES_CCW[:, [1, 2]] = CUBE_TRIANGLES_CCW[:, [2, 1]]
CUBE_CCW_FACE_NORMALS = np.array([
[ 0, 0, -1], [ 0, 0, -1],
[ 0, 0, 1], [ 0, 0, 1],
[ 0, -1, 0], [ 0, -1, 0],
[ 0, 1, 0], [ 0, 1, 0],
[-1, 0, 0], [-1, 0, 0],
[ 1, 0, 0], [ 1, 0, 0],
])
CUBE_CCW_VERTEX_NORMALS = np.zeros((8, 3))
for i in range(8):
faces = np.where(CUBE_TRIANGLES_CCW == i)[0]
CUBE_CCW_VERTEX_NORMALS[i] = CUBE_CCW_FACE_NORMALS[faces].sum(axis=0)
CUBE_CCW_VERTEX_NORMALS = affine.normalise(CUBE_CCW_VERTEX_NORMALS)
def test_mesh_create():
verts = np.array(CUBE_VERTICES)
tris = np.array(CUBE_TRIANGLES_CCW)
mesh = fslmesh.Mesh(tris, vertices=verts)
print(str(mesh))
assert mesh.name == 'mesh'
assert mesh.dataSource is None
assert mesh.nvertices == 8
assert np.all(np.isclose(mesh.vertices, verts))
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 = affine.concat(view, t2dmat)
ixform = affine.invert(xform)
eye = affine.transform(eye, ixform, vector=True)
target = affine.transform(target, ixform, vector=True)
# Direction that the 'camera' is
# pointing, normalied to unit length
cdir = affine.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 = affine.scaleOffsetXform([1, 1, 0.5], [0, 0, 0.5])
xform = affine.concat(zscale, proj, xform)
return rayStep, xform
def _pickModeLeftMouseDown(self, ev, canvas, mousePos, canvasPos):
"""Called on mouse down events in ``pick`` mode.
Updates the :attr:`DisplayContext.location` property.
"""
from fsl.data.mesh import Mesh
displayCtx = self.displayCtx
ovl = displayCtx.getSelectedOverlay()
if ovl is None:
return
# The canvasPos is located on the near clipping
# plane (see Scene3DCanvas.canvasToWorld).
# We also need the corresponding point on the
# far clipping plane.
farPos = canvas.canvasToWorld(mousePos[0], mousePos[1], near=False)
# For non-mesh overlays, we select a point which
# is in between the near/far clipping planes.
if not isinstance(ovl, Mesh):
posDir = farPos - canvasPos
dist = affine.veclength(posDir)
posDir = affine.normalise(posDir)
midPos = canvasPos + 0.5 * dist * posDir
self.displayCtx.location.xyz = midPos
else:
opts = self.displayCtx.getOpts(ovl)
rayOrigin = canvasPos
rayDir = affine.normalise(farPos - canvasPos)
# transform location from display into model space
rayOrigin = opts.transformCoords(rayOrigin, 'display', 'mesh')
rayDir = opts.transformCoords(rayDir,
'display',
'mesh',
vector=True)
loc, tri = ovl.rayIntersection([rayOrigin], [rayDir],
vertices=True)
if len(loc) == 0:
return
loc = loc[0]
tri = ovl.indices[int(tri[0]), :]
# The rayIntersection method gives us a
# point on one of the mesh triangles -
# we want the vertex on that triangle
# which is nearest to the intersection.
triVerts = ovl.vertices[tri, :]
triDists = affine.veclength(loc - triVerts)
vertIdx = np.argsort(triDists)[0]
loc = ovl.vertices[tri[vertIdx], :]
loc = opts.transformCoords(loc, 'mesh', 'display')
self.displayCtx.location.xyz = loc