[yt-users] volume rendering handedness

Michael Zingale michael.zingale at stonybrook.edu
Wed Jul 23 07:07:54 PDT 2014


ok, the following change makes things good for me, but I'd like others to
comment.

in camera.py: show_mpl, I change the

origin='upper'

to

origin='lower'

then I set the north vector as my intuition suggests, (0,0,1) to be +z, and
the plot has the right orientation and handedness.

(There is a separate issues still the sometimes using
draw_coordinate_vector() erases the image, but when I can get it to show,
it has the right handedness too).  Here's another plot from actual data
(uploaded to the yt data page) showing things that look right to me:

http://bender.astro.sunysb.edu/random/xrb_vol_radvel.png



On Tue, Jul 22, 2014 at 3:50 PM, Michael Zingale <
michael.zingale at stonybrook.edu> wrote:

> so that swapaxes(0,1) in save_annotated is needed -- otherwise the plot is
> sideways.  Looks like we need a flip as well though.
>
>
> 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
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>>
>>
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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
>



-- 
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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