[yt-users] volume rendering handedness

[Nathan Goldbaum]

Hi Mike,

At this point, if yt isn't using a right-handed coordinate system
somewhere, it's a bug.

If I remember correctly, save_annotated does a transpose on the image
before saving it to disk - that might be the source of one of your
workarounds?

The orientation of volume rendering cameras is controlled via the
Orientation class.  You might want to poke around in there to see what it
does - it might be the source of the left-handedness.

I don't think anyone has gone through in detail to make sure the volume
rendering orientation is consistent in all cases.  It would be a major help
to do that.

-Nathan


On Tue, Jul 22, 2014 at 9:00 AM, Michael Zingale <
michael.zingale at stonybrook.edu> wrote:

> I've been having trouble understanding the parameters that specify the
> orientation of the camera for volume rendering.  To help, I made a test
> dataset.  On [-1,1]^3, there is a sphere at the origin, a single cube on
> the +x axis, two cubes on the +y axis, and three cubes on the +z axis.
>  When I do a simple volume-render, I see this:
>
> http://bender.astro.sunysb.edu/random/yt-test.png
>
> Note that it looks left-handed.
>
> I've attached my script.  There are a few hacks that I needed to do that I
> don't completely understand.  In particular, if I turn on the
> coordinate_vectors, the image is blank.  I've seen this a lot.  Also, I had
> to make the north vector negative of what I would think.
>
> Mike
>
> --
>
> #!/usr/bin/env python
>
> import matplotlib
> matplotlib.use('agg')
>
> # this example comes from
> # http://yt-project.org/doc/visualizing/volume_rendering.html
>
> import math
> import sys
> import pylab
>
> from yt.mods import *
> import yt.visualization.volume_rendering.api as vr
>
> def doit(plotfile):
>
>     ds = load(plotfile)
>
>     cm = "gist_rainbow"
>
>
>     field = ('gas', 'density')
>     use_log = False
>     vals = [0.1, 1]
>     sigma = 0.1
>
>     dd = ds.h.all_data()
>
>     ds.field_info[field].take_log = use_log
>
>
>     mi = min(vals)
>     ma = max(vals)
>
>     if use_log:
>         mi, ma = np.log10(mi), np.log10(ma)
>
>
>     # Instantiate the ColorTransferfunction.
>     tf =  vr.ColorTransferFunction((mi, ma))
>
>     # Set up the camera parameters: center, looking direction, width,
> resolution
>     c = np.array([0.0, 0.0, 0.0])
>     L = np.array([1.0, 1.0, 1.0])
>     L = np.array([1.0, 1.0, 1.2])
>     W = 1.5*ds.domain_width
>     N = 720
>
>     north=[0.0,0.0,-1.0]
>
>     for v in vals:
>         if (use_log):
>             tf.sample_colormap(math.log10(v), sigma**2, colormap=cm) #,
> alpha=0.2)
>         else:
>             tf.sample_colormap(v, sigma**2, colormap=cm) #, alpha=0.2)
>
>
>     # alternate attempt
>     ds.periodicity = (True, True, True)
>
>     # Create a camera object
>     cam = vr.Camera(c, L, W, N, transfer_function=tf, ds=ds,
>                     no_ghost=False, #data_source=reg,
>                     north_vector=north,
>                     fields = [field], log_fields = [use_log])
>
>     #cam.rotate(3.0*np.pi/2., rot_vector=rot_vector)
>
>
>     # make an image
>     im = cam.snapshot()
>
>
>     # add an axes triad -- note if we do this, we HAVE to do draw
>     # domain, otherwise the image is blank (likely a bug)
>     #cam.draw_coordinate_vectors(im)
>
>     # add the domain box to the image:
>     nim = cam.draw_domain(im)
>
>     # increase the contrast -- for some reason, the enhance default
>     # to save_annotated doesn't do the trick (likely a bug)
>     max_val = im[:,:,:3].std() * 4.0
>     nim[:,:,:3] /= max_val
>
>     f = pylab.figure()
>
>     pylab.text(0.2, 0.85, "{:.3g} s".format(float(ds.current_time.d)),
>                transform=f.transFigure, color="white")
>
>     cam._render_figure = f
>
>     # save annotated -- this added the transfer function values,
>     # but this messes up our image size defined above
>     cam.save_annotated("yt-test.png", nim,
>                        dpi=145, clear_fig=False)
>
>
>
> if __name__ == "__main__":
>
>     # Choose a field
>     plotfile = ""
>
>
>     try: plotfile = sys.argv[1]
>     except: sys.exit("ERROR: no plotfile specified")
>
>     doit(plotfile)
>
>
>
> --
> Michael Zingale
> Associate Professor
>
> Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY
> 11794-3800
> *phone*:  631-632-8225
> *e-mail*: Michael.Zingale at stonybrook.edu
> *web*: http://www.astro.sunysb.edu/mzingale
>
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