def plot_proj_shell(ms,
use_sym=True,
use_sphere=True,
same_color=False,
rad=0.025,
opacity=1.0,
ofile=None,
ores=(300, 300)):
"""
Plot each shell
Parameters
----------
ms: list of numpy.ndarray
bvecs for each bvalue
use_sym: boolean
Plot symmetrical vectors
use_sphere: boolean
rendering of the sphere
same_color: boolean
use same color for all shell
rad: float
radius of each point
opacity: float
opacity for the shells
ofile: str
output filename
ores: tuple
resolution of the output png
Return
------
"""
global vtkcolors
if len(ms) > 10:
vtkcolors = fury.colormap.distinguishable_colormap(nb_colors=len(ms))
scene = window.Scene()
scene.SetBackground(1, 1, 1)
if use_sphere:
sphere = get_sphere('symmetric724')
shape = (1, 1, 1, sphere.vertices.shape[0])
fid, fname = mkstemp(suffix='_odf_slicer.mmap')
odfs = np.memmap(fname, dtype=np.float64, mode='w+', shape=shape)
odfs[:] = 1
odfs[..., 0] = 1
affine = np.eye(4)
sphere_actor = actor.odf_slicer(odfs,
affine,
sphere=sphere,
colormap='winter',
scale=1.0,
opacity=opacity)
scene.add(sphere_actor)
for i, shell in enumerate(ms):
if same_color:
i = 0
pts_actor = actor.point(shell, vtkcolors[i], point_radius=rad)
scene.add(pts_actor)
if use_sym:
pts_actor = actor.point(-shell, vtkcolors[i], point_radius=rad)
scene.add(pts_actor)
window.show(scene)
if ofile:
window.snapshot(scene, fname=ofile + '.png', size=ores)
def test_odf_slicer(interactive=False):
sphere = get_sphere('symmetric362')
shape = (11, 11, 11, sphere.vertices.shape[0])
fid, fname = mkstemp(suffix='_odf_slicer.mmap')
print(fid)
print(fname)
odfs = np.memmap(fname, dtype=np.float64, mode='w+', shape=shape)
odfs[:] = 1
affine = np.eye(4)
scene = window.Scene()
mask = np.ones(odfs.shape[:3])
mask[:4, :4, :4] = 0
odfs[..., 0] = 1
odf_actor = actor.odf_slicer(odfs,
affine,
mask=mask,
sphere=sphere,
scale=.25,
colormap='blues')
fa = 0. * np.zeros(odfs.shape[:3])
fa[:, 0, :] = 1.
fa[:, -1, :] = 1.
fa[0, :, :] = 1.
fa[-1, :, :] = 1.
fa[5, 5, 5] = 1
k = 5
I, J, _ = odfs.shape[:3]
fa_actor = actor.slicer(fa, affine)
fa_actor.display_extent(0, I, 0, J, k, k)
scene.add(odf_actor)
scene.reset_camera()
scene.reset_clipping_range()
odf_actor.display_extent(0, I, 0, J, k, k)
odf_actor.GetProperty().SetOpacity(1.0)
if interactive:
window.show(scene, reset_camera=False)
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr, find_objects=True)
npt.assert_equal(report.objects, 11 * 11)
scene.clear()
scene.add(fa_actor)
scene.reset_camera()
scene.reset_clipping_range()
if interactive:
window.show(scene)
mask[:] = 0
mask[5, 5, 5] = 1
fa[5, 5, 5] = 0
fa_actor = actor.slicer(fa, None)
fa_actor.display(None, None, 5)
odf_actor = actor.odf_slicer(odfs,
None,
mask=mask,
sphere=sphere,
scale=.25,
colormap='blues',
norm=False,
global_cm=True)
scene.clear()
scene.add(fa_actor)
scene.add(odf_actor)
scene.reset_camera()
scene.reset_clipping_range()
if interactive:
window.show(scene)
scene.clear()
scene.add(odf_actor)
scene.add(fa_actor)
odfs[:, :, :] = 1
mask = np.ones(odfs.shape[:3])
odf_actor = actor.odf_slicer(odfs,
None,
mask=mask,
sphere=sphere,
scale=.25,
colormap='blues',
norm=False,
global_cm=True)
scene.clear()
scene.add(odf_actor)
scene.add(fa_actor)
scene.add(actor.axes((11, 11, 11)))
for i in range(11):
odf_actor.display(i, None, None)
fa_actor.display(i, None, None)
if interactive:
window.show(scene)
for j in range(11):
odf_actor.display(None, j, None)
fa_actor.display(None, j, None)
if interactive:
window.show(scene)
# with mask equal to zero everything should be black
mask = np.zeros(odfs.shape[:3])
odf_actor = actor.odf_slicer(odfs,
None,
mask=mask,
sphere=sphere,
scale=.25,
colormap='blues',
norm=False,
global_cm=True)
scene.clear()
scene.add(odf_actor)
scene.reset_camera()
scene.reset_clipping_range()
if interactive:
window.show(scene)
npt.assert_raises(IOError,
actor.odf_slicer,
odfs,
None,
mask=None,
sphere=sphere,
scale=.25,
colormap=None,
norm=False,
global_cm=True)
# colormap=None and global_cm=False results in directionally encoded colors
scene.clear()
scene.add(odf_actor)
scene.add(fa_actor)
odfs[:, :, :] = 1
odf_actor = actor.odf_slicer(odfs,
None,
mask=None,
sphere=sphere,
scale=.25,
colormap=None,
norm=False,
global_cm=False)
report = window.analyze_scene(scene)
npt.assert_equal(report.actors, 1)
npt.assert_equal(report.actors_classnames[0], 'vtkLODActor')
del odf_actor
odfs._mmap.close()
del odfs
os.close(fid)
os.remove(fname)
def test_sh():
from dipy.sims.voxel import multi_tensor, multi_tensor_odf, sticks_and_ball
from dipy.data import get_sphere, get_fnames
from dipy.core.gradients import gradient_table
from dipy.io.gradients import read_bvals_bvecs
_, fbvals, fbvecs = get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
gtab = gradient_table(bvals, bvecs)
d = 0.0015
S, sticks = sticks_and_ball(gtab,
d=d,
S0=1,
angles=[(0, 0), (30, 30)],
fractions=[60, 40],
snr=None)
print(S)
print(sticks)
mevals = np.array([[0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]])
angles = [(0, 0), (60, 0)]
fractions = [50, 50]
sphere = get_sphere('repulsion724')
sphere = sphere.subdivide(2)
odf = multi_tensor_odf(sphere.vertices, mevals, angles, fractions)
print(odf)
ren = window.Scene()
odf_actor = actor.odf_slicer(odf[None, None, None, :],
sphere=sphere,
colormap='plasma')
# odf_actor.RotateX(90)
ren.add(odf_actor)
# window.show(ren)
odf_test_dec= \
"""
// Constants, see here: http://en.wikipedia.org/wiki/Table_of_spherical_harmonics
#define k01 0.2820947918 // sqrt( 1/PI)/2
#define k02 0.4886025119 // sqrt( 3/PI)/2
#define k03 1.0925484306 // sqrt( 15/PI)/2
#define k04 0.3153915652 // sqrt( 5/PI)/4
#define k05 0.5462742153 // sqrt( 15/PI)/4
#define k06 0.5900435860 // sqrt( 70/PI)/8
#define k07 2.8906114210 // sqrt(105/PI)/2
#define k08 0.4570214810 // sqrt( 42/PI)/8
#define k09 0.3731763300 // sqrt( 7/PI)/4
#define k10 1.4453057110 // sqrt(105/PI)/4
// unrolled version of the above
float SH_0_0( in vec3 s ) { vec3 n = s.zxy; return k01; }
float SH_1_0( in vec3 s ) { vec3 n = s.zxy; return -k02*n.y; }
float SH_1_1( in vec3 s ) { vec3 n = s.zxy; return k02*n.z; }
float SH_1_2( in vec3 s ) { vec3 n = s.zxy; return -k02*n.x; }
float SH_2_0( in vec3 s ) { vec3 n = s.zxy; return k03*n.x*n.y; }
float SH_2_1( in vec3 s ) { vec3 n = s.zxy; return -k03*n.y*n.z; }
float SH_2_2( in vec3 s ) { vec3 n = s.zxy; return k04*(3.0*n.z*n.z-1.0); }
float SH_2_3( in vec3 s ) { vec3 n = s.zxy; return -k03*n.x*n.z; }
float SH_2_4( in vec3 s ) { vec3 n = s.zxy; return k05*(n.x*n.x-n.y*n.y); }
float SH_3_0( in vec3 s ) { vec3 n = s.zxy; return -k06*n.y*(3.0*n.x*n.x-n.y*n.y); }
float SH_3_1( in vec3 s ) { vec3 n = s.zxy; return k07*n.z*n.y*n.x; }
float SH_3_2( in vec3 s ) { vec3 n = s.zxy; return -k08*n.y*(5.0*n.z*n.z-1.0); }
float SH_3_3( in vec3 s ) { vec3 n = s.zxy; return k09*n.z*(5.0*n.z*n.z-3.0); }
float SH_3_4( in vec3 s ) { vec3 n = s.zxy; return -k08*n.x*(5.0*n.z*n.z-1.0); }
float SH_3_5( in vec3 s ) { vec3 n = s.zxy; return k10*n.z*(n.x*n.x-n.y*n.y); }
float SH_3_6( in vec3 s ) { vec3 n = s.zxy; return -k06*n.x*(n.x*n.x-3.0*n.y*n.y); }
vec3 map( in vec3 p )
{
vec3 p00 = p - vec3( 0.00, 2.5,0.0);
vec3 p01 = p - vec3(-1.25, 1.0,0.0);
vec3 p02 = p - vec3( 0.00, 1.0,0.0);
vec3 p03 = p - vec3( 1.25, 1.0,0.0);
vec3 p04 = p - vec3(-2.50,-0.5,0.0);
vec3 p05 = p - vec3(-1.25,-0.5,0.0);
vec3 p06 = p - vec3( 0.00,-0.5,0.0);
vec3 p07 = p - vec3( 1.25,-0.5,0.0);
vec3 p08 = p - vec3( 2.50,-0.5,0.0);
vec3 p09 = p - vec3(-3.75,-2.0,0.0);
vec3 p10 = p - vec3(-2.50,-2.0,0.0);
vec3 p11 = p - vec3(-1.25,-2.0,0.0);
vec3 p12 = p - vec3( 0.00,-2.0,0.0);
vec3 p13 = p - vec3( 1.25,-2.0,0.0);
vec3 p14 = p - vec3( 2.50,-2.0,0.0);
vec3 p15 = p - vec3( 3.75,-2.0,0.0);
float r, d; vec3 n, s, res;
#ifdef SHOW_SPHERES
#define SHAPE (vec3(d-0.35, -1.0+2.0*clamp(0.5 + 16.0*r,0.0,1.0),d))
#else
#define SHAPE (vec3(d-abs(r), sign(r),d))
#endif
d=length(p00); n=p00/d; r = SH_0_0( n ); s = SHAPE; res = s;
d=length(p01); n=p01/d; r = SH_1_0( n ); s = SHAPE; if( s.x<res.x ) res=s;
d=length(p02); n=p02/d; r = SH_1_1( n ); s = SHAPE; if( s.x<res.x ) res=s;
d=length(p03); n=p03/d; r = SH_1_2( n ); s = SHAPE; if( s.x<res.x ) res=s;
d=length(p04); n=p04/d; r = SH_2_0( n ); s = SHAPE; if( s.x<res.x ) res=s;
d=length(p05); n=p05/d; r = SH_2_1( n ); s = SHAPE; if( s.x<res.x ) res=s;
d=length(p06); n=p06/d; r = SH_2_2( n ); s = SHAPE; if( s.x<res.x ) res=s;
d=length(p07); n=p07/d; r = SH_2_3( n ); s = SHAPE; if( s.x<res.x ) res=s;
d=length(p08); n=p08/d; r = SH_2_4( n ); s = SHAPE; if( s.x<res.x ) res=s;
d=length(p09); n=p09/d; r = SH_3_0( n ); s = SHAPE; if( s.x<res.x ) res=s;
d=length(p10); n=p10/d; r = SH_3_1( n ); s = SHAPE; if( s.x<res.x ) res=s;
d=length(p11); n=p11/d; r = SH_3_2( n ); s = SHAPE; if( s.x<res.x ) res=s;
d=length(p12); n=p12/d; r = SH_3_3( n ); s = SHAPE; if( s.x<res.x ) res=s;
d=length(p13); n=p13/d; r = SH_3_4( n ); s = SHAPE; if( s.x<res.x ) res=s;
d=length(p14); n=p14/d; r = SH_3_5( n ); s = SHAPE; if( s.x<res.x ) res=s;
d=length(p15); n=p15/d; r = SH_3_6( n ); s = SHAPE; if( s.x<res.x ) res=s;
return vec3( res.x, 0.5+0.5*res.y, res.z );
}
vec3 intersect( in vec3 ro, in vec3 rd )
{
vec3 res = vec3(1e10,-1.0, 1.0);
float maxd = 10.0;
float h = 1.0;
float t = 0.0;
vec2 m = vec2(-1.0);
for( int i=0; i<200; i++ )
{
if( h<0.001||t>maxd ) break;
vec3 res = map( ro+rd*t );
h = res.x;
m = res.yz;
t += h*0.3;
}
if( t<maxd && t<res.x ) res=vec3(t,m);
return res;
}
vec3 calcNormal( in vec3 pos )
{
vec3 eps = vec3(0.001,0.0,0.0);
return normalize( vec3(
map(pos+eps.xyy).x - map(pos-eps.xyy).x,
map(pos+eps.yxy).x - map(pos-eps.yxy).x,
map(pos+eps.yyx).x - map(pos-eps.yyx).x ) );
}
"""
odf_test_impl = \
"""
// camera matrix
vec3 ww = vec3(0.0,0.0,0.0); //MCDCMatrix (2);
vec3 uu = vec3(0.0,0.0,0.0); //MCDCMatrix (0);
vec3 vv = vec3(0.0,0.0,0.0); //MCDCMatrix (1);
vec3 tot = vec3(0.0);
vec2 p = (-vec2(0.5, 0.5) + (2.0*point,0)) / 0.5;
vec3 ro = vec3(0.0,0.0,0.0);
// create view ray
vec3 rd = normalize( p.x*uu + p.y*vv + 2.0*ww );
// background
vec3 col = vec3(0.3) * clamp(1.0-length(point)*0.5,0.0,1.0);
// raymarch
vec3 tmat = intersect(ro,rd);
if( tmat.y>-0.5 )
{
// geometry
vec3 pos = ro + tmat.x*rd;
vec3 nor = calcNormal(pos);
vec3 ref = reflect( rd, nor );
// material
vec3 mate = 0.5*mix( vec3(1.0,0.6,0.15), vec3(0.2,0.4,0.5), tmat.y );
float occ = clamp( 2.0*tmat.z, 0.0, 1.0 );
float sss = pow( clamp( 1.0 + dot(nor,rd), 0.0, 1.0 ), 1.0 );
// lights
vec3 lin = 2.5*occ*vec3(1.0,1.00,1.00)*(0.6+0.4*nor.y);
lin += 1.0*sss*vec3(1.0,0.95,0.70)*occ;
// surface-light interacion
col = mate.xyz * lin;
}
// gamma
col = pow( clamp(col,0.0,1.0), vec3(0.4545) );
tot += col;
fragOutput0 = vec4( tot, 1.0 );
"""
scene = window.Scene()
scene.background((0.8, 0.8, 0.8))
centers = np.array([[2, 0, 0], [0, 0, 0], [-2, 0, 0]])
# np.random.rand(3, 3) * 3
# colors = np.array([[255, 0, 0], [0, 255, 0], [0, 0, 255]])
colors = np.random.rand(3, 3) * 255
scale = 1 # np.random.rand(3) * 5
# https://www.shadertoy.com/view/MstXWS
# https://www.shadertoy.com/view/XsX3R4
fs_dec = \
"""
uniform mat4 MCDCMatrix;
uniform mat4 MCVCMatrix;
float sdRoundBox( vec3 p, vec3 b, float r )
{
vec3 q = abs(p) - b;
return length(max(q,0.0)) + min(max(q.x,max(q.y,q.z)),0.0) - r;
}
float sdEllipsoid( vec3 p, vec3 r )
{
float k0 = length(p/r);
float k1 = length(p/(r*r));
return k0*(k0-1.0)/k1;
}
float sdCylinder(vec3 p, float h, float r)
{
vec2 d = abs(vec2(length(p.xz),p.y)) - vec2(h,r);
return min(max(d.x,d.y),0.0) + length(max(d,0.0));
}
float sdSphere(vec3 pos, float r)
{
float d = length(pos) - r;
return d;
}
float map( in vec3 pos)
{
float d = sdSphere(pos-0.5, .2);
float d1 = sdCylinder(pos+0.5, 0.05, .5);
float d2 = sdEllipsoid(pos + vec3(-0.5,0.5,0), vec3(0.2,0.3,0.5));
float d3 = sdRoundBox(pos + vec3(0.5,-0.5,0), vec3(0.2,0.1,0.3), .05);
//.xy
return min(min(min(d, d1), d2), d3);
}
vec3 calcNormal( in vec3 pos )
{
vec2 e = vec2(0.0001,0.0);
return normalize( vec3(map(pos + e.xyy) - map(pos - e.xyy ),
map(pos + e.yxy) - map(pos - e.yxy),
map(pos + e.yyx) - map(pos - e.yyx)
)
);
}
float castRay(in vec3 ro, vec3 rd)
{
float t = 0.0;
for(int i=0; i < 100; i++)
{
vec3 pos = ro + t * rd;
vec3 nor = calcNormal(pos);
float h = map(pos);
if (h < 0.001) break;
t += h;
if (t > 20.0) break;
}
return t;
}
"""
fake_sphere = \
"""
vec3 uu = vec3(MCVCMatrix[0][0], MCVCMatrix[1][0], MCVCMatrix[2][0]); // camera right
vec3 vv = vec3(MCVCMatrix[0][1], MCVCMatrix[1][1], MCVCMatrix[2][1]); // camera up
vec3 ww = vec3(MCVCMatrix[0][2], MCVCMatrix[1][2], MCVCMatrix[2][2]); // camera direction
vec3 ro = MCVCMatrix[3].xyz * mat3(MCVCMatrix); // camera position
// create view ray
vec3 rd = normalize( point.x*-uu + point.y*-vv + 7*ww);
vec3 col = vec3(0.0);
float t = castRay(ro, rd);
if (t < 20.0)
{
vec3 pos = ro + t * rd;
vec3 nor = calcNormal(pos);
vec3 sun_dir = vec3(MCVCMatrix[0][2], MCVCMatrix[1][2], MCVCMatrix[2][2]); //normalize()
float dif = clamp( dot(nor, sun_dir), 0.0, 1.0);
//vec3 sun_dif = normalize()
col = color * dot(color,nor); // (color + diffuseColor + ambientColor + specularColor)*nor.zzz;//vec3(1.0);
fragOutput0 = vec4(col, 1.0);
}
else{
//fragOutput0 = vec4(0,1,0, 1.0);
discard;
}
/*float radius = 1.;
if(len > radius)
{discard;}
//err, lightColor0 vertexColorVSOutput normalVCVSOutput, ambientIntensity; diffuseIntensity;specularIntensity;specularColorUniform;
float c = len;
fragOutput0 = vec4(c,c,c, 1);
vec3 normalizedPoint = normalize(vec3(point.xy, sqrt(1. - len)));
vec3 direction = normalize(vec3(1., 1., 1.));
float df = max(0, dot(direction, normalizedPoint));
float sf = pow(df, 24);
fragOutput0 = vec4(max(df * color, sf * vec3(1)), 1);*/
"""
billboard_actor = actor.billboard(centers,
colors=colors.astype(np.uint8),
scale=scale,
fs_dec=fs_dec,
fs_impl=fake_sphere)
scene.add(billboard_actor)
scene.add(actor.axes())
scene.camera_info()
matrix = scene.camera().GetViewTransformMatrix()
mat = np.zeros((4, 4))
for i in range(4):
for j in range(4):
mat[i, j] = matrix.GetElement(i, j)
print(mat)
print(np.dot(-mat[:3, 3], mat[:3, :3])) # camera position
window.show(scene)
###############################################################################
# Now, we create a slicer for each orientation to display a slice in
# the middle of the volume and we add them to a `scene`.
# Change these values to test various parameters combinations.
scale = 0.5
norm = False
colormap = None
radial_scale = True
opacity = 1.0
global_cm = False
# ODF slicer for axial slice
odf_actor_z = actor.odf_slicer(sh, affine=affine, sphere=sphere_low,
scale=scale, norm=norm,
radial_scale=radial_scale, opacity=opacity,
colormap=colormap, global_cm=global_cm,
B_matrix=B_low)
# ODF slicer for coronal slice
odf_actor_y = actor.odf_slicer(sh, affine=affine, sphere=sphere_low,
scale=scale, norm=norm,
radial_scale=radial_scale, opacity=opacity,
colormap=colormap, global_cm=global_cm,
B_matrix=B_low)
odf_actor_y.display_extent(0, grid_shape[0] - 1, grid_shape[1]//2,
grid_shape[1]//2, 0, grid_shape[2] - 1)
# ODF slicer for sagittal slice
odf_actor_x = actor.odf_slicer(sh, affine=affine, sphere=sphere_low,
scale=scale, norm=norm,
def test_odf_slicer(interactive=False):
# Prepare our data
sphere = get_sphere('repulsion100')
shape = (11, 11, 11, sphere.vertices.shape[0])
odfs = np.ones(shape)
affine = np.array([[2.0, 0.0, 0.0, 3.0],
[0.0, 2.0, 0.0, 3.0],
[0.0, 0.0, 2.0, 1.0],
[0.0, 0.0, 0.0, 1.0]])
mask = np.ones(odfs.shape[:3], bool)
mask[:4, :4, :4] = False
# Test that affine and mask work
odf_actor = actor.odf_slicer(odfs, sphere=sphere, affine=affine, mask=mask,
scale=.25, colormap='blues')
k = 2
I, J, _ = odfs.shape[:3]
odf_actor.display_extent(0, I - 1, 0, J - 1, k, k)
scene = window.Scene()
scene.add(odf_actor)
scene.reset_camera()
scene.reset_clipping_range()
if interactive:
window.show(scene, reset_camera=False)
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr, find_objects=True)
npt.assert_equal(report.objects, 11 * 11 - 16)
# Test that global colormap works
odf_actor = actor.odf_slicer(odfs, sphere=sphere, mask=mask, scale=.25,
colormap='blues', norm=False, global_cm=True)
scene.clear()
scene.add(odf_actor)
scene.reset_camera()
scene.reset_clipping_range()
if interactive:
window.show(scene)
# Test that the most basic odf_slicer instanciation works
odf_actor = actor.odf_slicer(odfs)
scene.clear()
scene.add(odf_actor)
scene.reset_camera()
scene.reset_clipping_range()
if interactive:
window.show(scene)
# Test that odf_slicer.display works properly
scene.clear()
scene.add(odf_actor)
scene.add(actor.axes((11, 11, 11)))
for i in range(11):
odf_actor.display(i, None, None)
if interactive:
window.show(scene)
for j in range(11):
odf_actor.display(None, j, None)
if interactive:
window.show(scene)
# With mask equal to zero everything should be black
mask = np.zeros(odfs.shape[:3])
odf_actor = actor.odf_slicer(odfs, sphere=sphere, mask=mask,
scale=.25, colormap='blues',
norm=False, global_cm=True)
scene.clear()
scene.add(odf_actor)
scene.reset_camera()
scene.reset_clipping_range()
if interactive:
window.show(scene)
# global_cm=True with colormap=None should raise an error
npt.assert_raises(IOError, actor.odf_slicer, odfs, sphere=sphere,
mask=None, scale=.25, colormap=None, norm=False,
global_cm=True)
# Dimension mismatch between sphere vertices and number
# of SF coefficients will raise an error.
npt.assert_raises(ValueError, actor.odf_slicer, odfs, mask=None,
sphere=get_sphere('repulsion200'), scale=.25)
# colormap=None and global_cm=False results in directionally encoded colors
odf_actor = actor.odf_slicer(odfs, sphere=sphere, mask=None,
scale=.25, colormap=None,
norm=False, global_cm=False)
scene.clear()
scene.add(odf_actor)
scene.reset_camera()
scene.reset_clipping_range()
if interactive:
window.show(scene)
# Test that SH coefficients input works
B = sh_to_sf_matrix(sphere, return_inv=False)
odfs = np.zeros((11, 11, 11, B.shape[0]))
odfs[..., 0] = 1.0
odf_actor = actor.odf_slicer(odfs, sphere=sphere, B_matrix=B)
scene.clear()
scene.add(odf_actor)
scene.reset_camera()
scene.reset_clipping_range()
if interactive:
window.show(scene)
# Dimension mismatch between sphere vertices and dimension of
# B matrix will raise an error.
npt.assert_raises(ValueError, actor.odf_slicer, odfs, mask=None,
sphere=get_sphere('repulsion200'))
# Test that constant colormap color works. Also test that sphere
# normals are oriented correctly. Will show purple spheres with
# a white contour.
odf_contour = actor.odf_slicer(odfs, sphere=sphere, B_matrix=B,
colormap=(255, 255, 255))
odf_contour.GetProperty().SetAmbient(1.0)
odf_contour.GetProperty().SetFrontfaceCulling(True)
odf_actor = actor.odf_slicer(odfs, sphere=sphere, B_matrix=B,
colormap=(255, 0, 255), scale=0.4)
scene.clear()
scene.add(odf_contour)
scene.add(odf_actor)
scene.reset_camera()
scene.reset_clipping_range()
if interactive:
window.show(scene)
# Test that we can change the sphere on an active actor
new_sphere = get_sphere('symmetric362')
new_B = sh_to_sf_matrix(new_sphere, return_inv=False)
odf_actor.update_sphere(new_sphere.vertices, new_sphere.faces, new_B)
if interactive:
window.show(scene)
del odf_actor
del odfs
def test_manifest_standard(interactive=False):
scene = window.Scene() # Setup scene
# Setup surface
surface_actor = _generate_surface()
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(surface_actor)
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 1)
scene.clear() # Reset scene
# Contour from roi setup
data = np.zeros((50, 50, 50))
data[20:30, 25, 25] = 1.
data[25, 20:30, 25] = 1.
affine = np.eye(4)
surface = actor.contour_from_roi(data, affine, color=np.array([1, 0, 1]))
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(surface)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 1)
scene.clear() # Reset scene
# Contour from label setup
data = np.zeros((50, 50, 50))
data[5:15, 1:10, 25] = 1.
data[25:35, 1:10, 25] = 2.
data[40:49, 1:10, 25] = 3.
color = np.array([[255, 0, 0, 0.6],
[0, 255, 0, 0.5],
[0, 0, 255, 1.0]])
surface = actor.contour_from_label(data, color=color)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(surface)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 3)
scene.clear() # Reset scene
# Streamtube setup
data1 = np.array([[0, 0, 0], [1, 1, 1], [2, 2, 2.]])
data2 = data1 + np.array([0.5, 0., 0.])
data = [data1, data2]
colors = np.array([[1, 0, 0], [0, 0, 1.]])
tubes = actor.streamtube(data, colors, linewidth=.1)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(tubes)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 2)
scene.clear() # Reset scene
# ODF slicer setup
if have_dipy:
from dipy.data import get_sphere
from tempfile import mkstemp
sphere = get_sphere('symmetric362')
shape = (11, 11, 11, sphere.vertices.shape[0])
fid, fname = mkstemp(suffix='_odf_slicer.mmap')
odfs = np.memmap(fname, dtype=np.float64, mode='w+', shape=shape)
odfs[:] = 1
affine = np.eye(4)
mask = np.ones(odfs.shape[:3])
mask[:4, :4, :4] = 0
odfs[..., 0] = 1
odf_actor = actor.odf_slicer(odfs, affine, mask=mask, sphere=sphere,
scale=.25, colormap='blues')
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
k = 5
I, J, _ = odfs.shape[:3]
odf_actor.display_extent(0, I, 0, J, k, k)
odf_actor.GetProperty().SetOpacity(1.0)
scene.add(odf_actor)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 11 * 11)
scene.clear() # Reset scene
# Tensor slicer setup
if have_dipy:
from dipy.data import get_sphere
sphere = get_sphere('symmetric724')
evals = np.array([1.4, .35, .35]) * 10 ** (-3)
evecs = np.eye(3)
mevals = np.zeros((3, 2, 4, 3))
mevecs = np.zeros((3, 2, 4, 3, 3))
mevals[..., :] = evals
mevecs[..., :, :] = evecs
affine = np.eye(4)
scene = window.Scene()
tensor_actor = actor.tensor_slicer(mevals, mevecs, affine=affine,
sphere=sphere, scale=.3)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
_, J, K = mevals.shape[:3]
tensor_actor.display_extent(0, 1, 0, J, 0, K)
scene.add(tensor_actor)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 4)
scene.clear() # Reset scene
# Point setup
points = np.array([[0, 0, 0], [0, 1, 0], [1, 0, 0]])
colors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
opacity = 0.5
points_actor = actor.point(points, colors, opacity=opacity)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(points_actor)
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 3)
scene.clear() # Reset scene
# Sphere setup
xyzr = np.array([[0, 0, 0, 10], [100, 0, 0, 25], [200, 0, 0, 50]])
colors = np.array([[1, 0, 0, 0.3], [0, 1, 0, 0.4], [0, 0, 1., 0.99]])
opacity = 0.5
sphere_actor = actor.sphere(centers=xyzr[:, :3], colors=colors[:],
radii=xyzr[:, 3], opacity=opacity)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(sphere_actor)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 3)
scene.clear() # Reset scene
# Advanced geometry actors setup (Arrow, cone, cylinder)
xyz = np.array([[0, 0, 0], [50, 0, 0], [100, 0, 0]])
dirs = np.array([[0, 1, 0], [1, 0, 0], [0, 0.5, 0.5]])
colors = np.array([[1, 0, 0, 0.3], [0, 1, 0, 0.4], [1, 1, 0, 1]])
heights = np.array([5, 7, 10])
actor_list = [[actor.cone, {'directions': dirs, 'resolution': 8}],
[actor.arrow, {'directions': dirs, 'resolution': 9}],
[actor.cylinder, {'directions': dirs}]]
for act_func, extra_args in actor_list:
aga_actor = act_func(centers=xyz, colors=colors[:], heights=heights,
**extra_args)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(aga_actor)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 3)
scene.clear()
# Basic geometry actors (Box, cube, frustum, octagonalprism, rectangle,
# square)
centers = np.array([[4, 0, 0], [0, 4, 0], [0, 0, 0]])
colors = np.array([[1, 0, 0, 0.4], [0, 1, 0, 0.8], [0, 0, 1, 0.5]])
directions = np.array([[1, 1, 0]])
scale_list = [1, 2, (1, 1, 1), [3, 2, 1], np.array([1, 2, 3]),
np.array([[1, 2, 3], [1, 3, 2], [3, 1, 2]])]
actor_list = [[actor.box, {}], [actor.cube, {}], [actor.frustum, {}],
[actor.octagonalprism, {}], [actor.rectangle, {}],
[actor.square, {}]]
for act_func, extra_args in actor_list:
for scale in scale_list:
scene = window.Scene()
bga_actor = act_func(centers=centers, directions=directions,
colors=colors, scales=scale, **extra_args)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(bga_actor)
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
msg = 'Failed with {}, scale={}'.format(act_func.__name__, scale)
npt.assert_equal(report.objects, 3, err_msg=msg)
scene.clear()
# Cone setup using vertices
centers = np.array([[0, 0, 0], [20, 0, 0], [40, 0, 0]])
directions = np.array([[0, 1, 0], [1, 0, 0], [0, 0, 1]])
colors = np.array([[1, 0, 0, 0.3], [0, 1, 0, 0.4], [0, 0, 1., 0.99]])
vertices = np.array([[0.0, 0.0, 0.0], [0.0, 10.0, 0.0],
[10.0, 0.0, 0.0], [0.0, 0.0, 10.0]])
faces = np.array([[0, 1, 3], [0, 1, 2]])
cone_actor = actor.cone(centers=centers, directions=directions,
colors=colors[:], vertices=vertices, faces=faces)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(cone_actor)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 3)
scene.clear() # Reset scene
# Superquadric setup
centers = np.array([[8, 0, 0], [0, 8, 0], [0, 0, 0]])
colors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
directions = np.random.rand(3, 3)
scales = [1, 2, 3]
roundness = np.array([[1, 1], [1, 2], [2, 1]])
sq_actor = actor.superquadric(centers, roundness=roundness,
directions=directions,
colors=colors.astype(np.uint8),
scales=scales)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(sq_actor)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 3)
scene.clear() # Reset scene
# Label setup
text_actor = actor.label("Hello")
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(text_actor)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 5)
scene.clear() # Reset scene
# Texture setup
arr = (255 * np.ones((512, 212, 4))).astype('uint8')
arr[20:40, 20:40, :] = np.array([255, 0, 0, 255], dtype='uint8')
tp2 = actor.texture(arr)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(tp2)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 1)
scene.clear() # Reset scene
# Texture on sphere setup
arr = 255 * np.ones((810, 1620, 3), dtype='uint8')
rows, cols, _ = arr.shape
rs = rows // 2
cs = cols // 2
w = 150 // 2
arr[rs - w: rs + w, cs - 10 * w: cs + 10 * w] = np.array([255, 127, 0])
tsa = actor.texture_on_sphere(arr)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(tsa)
scene.reset_camera()
scene.reset_clipping_range()
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr)
npt.assert_equal(report.objects, 1)
# NOTE: From this point on, these actors don't have full support for PBR
# interpolation. This is, the test passes but there is no evidence of the
# desired effect.
"""
# Setup slicer
data = (255 * np.random.rand(50, 50, 50))
affine = np.eye(4)
slicer = actor.slicer(data, affine, value_range=[data.min(), data.max()])
slicer.display(None, None, 25)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(slicer)
"""
"""
# Line setup
data1 = np.array([[0, 0, 0], [1, 1, 1], [2, 2, 2.]])
data2 = data1 + np.array([0.5, 0., 0.])
data = [data1, data2]
colors = np.array([[1, 0, 0], [0, 0, 1.]])
lines = actor.line(data, colors, linewidth=5)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(lines)
"""
"""
# Scalar bar setup
lut = actor.colormap_lookup_table(
scale_range=(0., 100.), hue_range=(0., 0.1), saturation_range=(1, 1),
value_range=(1., 1))
sb_actor = actor.scalar_bar(lut, ' ')
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(sb_actor)
"""
"""
# Axes setup
axes = actor.axes()
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(axes)
"""
"""
# Peak slicer setup
_peak_dirs = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]], dtype='f4')
# peak_dirs.shape = (1, 1, 1) + peak_dirs.shape
peak_dirs = np.zeros((11, 11, 11, 3, 3))
peak_dirs[:, :, :] = _peak_dirs
peak_actor = actor.peak_slicer(peak_dirs)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(peak_actor)
"""
"""
# Dots setup
points = np.array([[0, 0, 0], [0, 1, 0], [1, 0, 0]])
dots_actor = actor.dots(points, color=(0, 255, 0))
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(dots_actor)
"""
"""
# Text3D setup
msg = 'I \nlove\n FURY'
txt_actor = actor.text_3d(msg)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(txt_actor)
"""
"""
# Figure setup
arr = (255 * np.ones((512, 212, 4))).astype('uint8')
arr[20:40, 20:40, 3] = 0
tp = actor.figure(arr)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(tp)
"""
"""
# SDF setup
centers = np.array([[2, 0, 0], [0, 2, 0], [0, 0, 0]]) * 11
colors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
directions = np.array([[0, 1, 0], [1, 0, 0], [0, 0, 1]])
scales = [1, 2, 3]
primitive = ['sphere', 'ellipsoid', 'torus']
sdf_actor = actor.sdf(centers, directions=directions, colors=colors,
primitives=primitive, scales=scales)
material.manifest_standard(surface_actor, ambient_level=.3,
diffuse_level=.25)
scene.add(sdf_actor)
"""
# NOTE: For these last set of actors, there is not support for PBR
# interpolation at all.
"""
# Billboard setup
centers = np.array([[0, 0, 0], [5, -5, 5], [-7, 7, -7], [10, 10, 10],
[10.5, 11.5, 11.5], [12, -12, -12], [-17, 17, 17],
[-22, -22, 22]])
colors = np.array([[1, 1, 0], [0, 0, 0], [1, 0, 1], [0, 0, 1], [1, 1, 1],
[1, 0, 0], [0, 1, 0], [0, 1, 1]])
scales = [6, .4, 1.2, 1, .2, .7, 3, 2]
"""
fake_sphere = \
"""
float len = length(point);
float radius = 1.;
if (len > radius)
discard;
vec3 normalizedPoint = normalize(vec3(point.xy, sqrt(1. - len)));
vec3 direction = normalize(vec3(1., 1., 1.));
float df_1 = max(0, dot(direction, normalizedPoint));
float sf_1 = pow(df_1, 24);
fragOutput0 = vec4(max(df_1 * color, sf_1 * vec3(1)), 1);
"""
"""
billboard_actor = actor.billboard(centers, colors=colors, scales=scales,
fs_impl=fake_sphere)
material.manifest_pbr(billboard_actor)
scene.add(billboard_actor)
"""
if interactive:
window.show(scene)
def plot_an_odf_slice(odf_4d, full_sphere, background_data, tile_size,
filename, centroid, axis, camera_distance, subtract_iso,
mask_image):
view_up = [(0., 0., 1.), (0., 0., 1.), (0., -1., 0.)]
# Adjust the centroid so it's only a single slice
slicenum = int(np.round(centroid)[axis])
centroid[axis] = 0
position = centroid.copy()
position[axis] = position[axis] + camera_distance
# Roll if viewing an axial slice
roll = 3 if axis == 2 else 0
position[1] = position[1] - roll
# Ensure the dimensions reflect that there is only one slice
new_shape = list(odf_4d.shape)
new_shape[axis] = 1
image_shape = new_shape[:3]
if axis == 0:
odf_slice = odf_4d[slicenum, :, :, :].reshape(new_shape)
image_slice = background_data[slicenum, :, :].reshape(image_shape)
elif axis == 1:
odf_slice = odf_4d[:, slicenum, :, :].reshape(new_shape)
image_slice = background_data[:, slicenum, :].reshape(image_shape)
elif axis == 2:
odf_slice = odf_4d[:, :, slicenum, :].reshape(new_shape)
image_slice = background_data[:, :, slicenum].reshape(image_shape)
# Tile to get the whole ODF
odf_slice = np.tile(odf_slice, (1, 1, 1, 2))
if subtract_iso:
odf_slice = odf_slice - odf_slice.min(3, keepdims=True)
# Make graphics objects
odf_actor = actor.odf_slicer(odf_slice,
sphere=full_sphere,
colormap=None,
scale=0.6,
mask=image_slice)
image_actor = actor.slicer(image_slice,
opacity=0.6,
interpolation='nearest')
image_size = (tile_size, tile_size)
scene = window.Scene()
scene.add(image_actor)
scene.add(odf_actor)
xfov_min, xfov_max = 0, new_shape[0] - 1
yfov_min, yfov_max = 0, new_shape[1] - 1
zfov_min, zfov_max = 0, new_shape[2] - 1
odf_actor.display_extent(xfov_min, xfov_max, yfov_min, yfov_max, zfov_min,
zfov_max)
image_actor.display_extent(xfov_min, xfov_max, yfov_min, yfov_max,
zfov_min, zfov_max)
scene.set_camera(focal_point=tuple(centroid),
position=tuple(position),
view_up=view_up[axis])
window.record(scene,
out_path=filename,
reset_camera=False,
size=image_size)
scene.clear()