[yt-users] volume rendering handedness

Chris Malone chris.m.malone at gmail.com
Wed Jul 23 08:03:32 PDT 2014


My intuition agrees with yours, but I don't know if that change will break
anything else.  If the VR is touched in the test suite (is it?) then maybe
it would be best to issue a pull request.


On Wed, Jul 23, 2014 at 8:07 AM, Michael Zingale <
michael.zingale at stonybrook.edu> wrote:

> 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
>>>>
>>>> _______________________________________________
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>>>> 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
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
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