Volume scalar bar

[teteraf]

First of all congratulations for the great work you do with Mayavi!
I have been trying to visualise a volume using Maximum Intensity Projection and cannot get the scalar bar depicted properly unless I kind of "update" the source. In the example at the end, the scalar bar appears just black. A workaround I have found is to change the name of the dataset (see last code line).
I have seen this behaviour on Windows 7 (Enthought Canopy 1.1.0 64 bit) and on Ubuntu 12.04 64 bit (Mayavi 4.0.0, VTK 5.8.0, Python 2.7.3).
Do you know why does this happen and if there is any other way of solving it?
In addition, is it possible to create a colorbar that also displays the alpha channel?

Thanks in advance!

# Testing lut and transparency for a given Volume
import numpy as np
x, y, z = np.ogrid[-.5:.5:200j, -.5:.5:200j, -.5:.5:200j]
r = np.sqrt(x**2 + y**2 + z**2)
# Generalized Laguerre polynomial (3, 2)
L = -r**3/6 + 5./2*r**2 - 10*r + 6
# Spherical harmonic (3, 2)
Y = (x+y*1j)**2*z/r**3
Phi = L*Y*np.exp(-r)*r**2
# Defining array for ColorTransferFunction
clr=np.array([[0,0,0,0],
  [abs(Phi).max()*0.5,0.9,0,0],
  [abs(Phi).max(),1,0.9,0]])
# Defining opacity array
opct=np.array([[0,0],
  [abs(Phi).max()*0.5,0.5],
  [abs(Phi).max(),1]])
clr=clr.transpose()
opct=opct.transpose()
# Visualize it with mlab.volume
from mayavi import mlab
mlab.figure(1, fgcolor=(1, 1, 1), bgcolor=(0, 0, 0))
# We create a scalar field with the module of Phi as the scalar
src = mlab.pipeline.scalar_field(np.abs(Phi))
vuf = mlab.pipeline.volume(src)
vuf.volume_mapper.lock_sample_distance_to_input_spacing = True
vuf.volume_mapper.blend_mode = 'maximum_intensity'

# Changing the ctf: 
from tvtk.util.ctf import ColorTransferFunction
# ctf.add_rgb_point(value, r, g, b) # r, g, and b are float between 0 and 1
# ctf.add_hsv_point(value, h, s, v)
ctf = ColorTransferFunction()
for n in range(np.shape(clr)[1]):
    aux=np.squeeze(clr[:,n])
    ctf.add_rgb_point(aux[0],aux[1],aux[2],aux[3])

vuf._volume_property.set_color(ctf)
vuf._ctf = ctf
vuf.update_ctf = True

# Changing the otf:
from tvtk.util.ctf import PiecewiseFunction
# otf.add_point(value, opacity)
otf = PiecewiseFunction()
for n in range(np.shape(opct)[1]):
    aux=np.squeeze(opct[:,n])
    otf.add_point(aux[0],aux[1])
vuf._otf = otf
vuf._volume_property.set_scalar_opacity(otf)
ctf.range = [abs(Phi).min(), abs(Phi).max()]

vuf.lut_manager.show_scalar_bar = True
# src.scalar_name='Phi' # Uncomment to get it to work 

[stefanoborini]

Confirmed. Investigating.

[stefanoborini]

I am puzzled because the LUT is apparently keeping the default hue (red-blue gradient) even when the correct gradient is shown. it's not touched and yet it's the only source for the widget. There is some mechanism at work that I still haven't found.

[stefanoborini]

The Volume Module appears to be installing a VolumeProperty to the LUT where all color values are zero. Probably uninitialized _volume_property?

[stefanoborini]

After investigation, I don't think this is a bug. The main problem is that you are accessing members that are considered private, but in any case the issue is that you are replacing the CTF on the Volume. The VolumeProperty has an internal CTF that never gets updated. Internally, we keep this consistent, but manipulating it from the outside you obtain strange results.

@prabhuramachandran any comment?