[yt-users] volume rendering handedness
Michael Zingale
michael.zingale at stonybrook.edu
Tue Jul 22 10:07:21 PDT 2014
I'll look deeper -- thanks for the pointer. I created this test dataset
specifically to make it easier to look at handedness. There are a few
quirks that may be related to all of this (such as the
draw_coordinate_vectors stuff) that I will also try to hunt down.
On Tue, Jul 22, 2014 at 12:37 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:
> 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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>>
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--
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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