def add_volume(self,
volume,
cmap='afmhot_r',
alpha=1,
add_colorbar=True,
**kwargs):
"""
Renders intensitdata from a 3D numpy array as a lego volumetric actor.
:param volume: np 3D array with number of dimensions = those of the 100um reference space.
:param cmap: str with name of colormap to use
:param alpha: float, transparency
:param add_colorbar: if True a colorbar is added to show the values of the colormap
"""
# Parse kwargs
line_width = kwargs.pop('line_width', 1)
if cmap == 'random' or not cmap or cmap is None:
cmap = get_random_colormap()
# Get vmin and vmax threshold for visualisation
vmin = kwargs.pop('vmin', 0.000001)
vmax = kwargs.pop('vmax', np.nanmax(volume))
# Check values
if np.max(volume) > vmax:
print(
"While rendering mapped projection some of the values are above the vmax threshold."
+ "They will not be displayed." +
f" vmax was {vmax} but found value {round(np.max(volume), 5)}."
)
if vmin > vmax:
raise ValueError(
f'The vmin threhsold [{vmin}] cannot be larger than the vmax threshold [{vmax}'
)
if vmin < 0: vmin = 0
# Get 'lego' actor
vol = Volume(volume)
lego = vol.legosurface(vmin=vmin, vmax=vmax, cmap=cmap)
# Scale and color actor
lego.alpha(alpha).lw(line_width).scale(self.voxel_size)
lego.cmap = cmap
# Add colorbar
if add_colorbar:
lego.addScalarBar(vmin=vmin,
vmax=vmax,
horizontal=1,
c='k',
pos=(0.05, 0.05),
titleFontSize=40)
# Add to scene
actor = self.scene.add_vtkactor(lego)
return actor
iteration = 4
size = 3**iteration
voxels = np.ones((size, size, size))
def iterate(length, x, y, z):
nl = length // 3
if nl < 1: return
margin = (nl - 1) // 2
voxels[z - margin:z + margin + 1, y - margin:y + margin + 1, :] = 0
voxels[z - margin:z + margin + 1, :, x - margin:x + margin + 1] = 0
voxels[:, y - margin:y + margin + 1, x - margin:x + margin + 1] = 0
for ix, iy, iz in np.ndindex((3, 3, 3)):
if (1 if ix != 1 else 0) + (1 if iy != 1 else 0) + (1 if iz != 1 else
0) != 2:
iterate(nl, x + (ix - 1) * nl, y + (iy - 1) * nl,
z + (iz - 1) * nl)
iterate(size, size // 2, size // 2, size // 2)
print('voxels min, max =', np.min(voxels), np.max(voxels))
vol = Volume(voxels)
lego = vol.legosurface(-0.1, 1.1, cmap='afmhot_r')
show(vol, lego, N=2, bg='w')