[yt-users] error on volume rendering on zoom-in simulation

mohammad safarzadeh mtsafarzadeh at gmail.com
Wed Sep 4 13:34:44 PDT 2013


the off-axis plot is like this:
http://i.imgur.com/7fDuNTA.png
so no one has done volume rendering on DM only sims?
how can I provide a 3d view of the zoom in box ( if there are alternative
ways)?
Regards,

-Mohammad


On Wed, Sep 4, 2013 at 3:09 PM, Sam Skillman <samskillman at gmail.com> wrote:

> Hi Mohammad,
>
> I just filed an issue for this, as it has to do with taking the log of a
> field that has zeros/negatives.  There may not be a quick turnaround on
> fixing this issue, but I've assigned it to me. I have some thoughts on how
> to address this but it needs some more thinking.
>
>
> https://bitbucket.org/yt_analysis/yt/issue/647/volume-rendering-log-fields-zeros
>
>  Best,
> Sam
>
>
> On Wed, Sep 4, 2013 at 10:53 AM, Matthew Turk <matthewturk at gmail.com>wrote:
>
>> Hi Mohammad,
>>
>> I'm not really sure.  Try using an OffAxisProjectionPlot to see if it
>> looks like anything.  You should just be able to specify the
>> orientation and field, and it should give back a column density.
>>
>> -Matt
>>
>> On Wed, Sep 4, 2013 at 1:39 PM, mohammad safarzadeh
>> <mtsafarzadeh at gmail.com> wrote:
>> > I tried this, but I still get a blank black figure:
>> >
>> > import numpy as np
>> > from yt.mods import *
>> > from yt.analysis_modules.halo_finding.api import *
>> > Npixels=512
>> > L=[1,1,1]
>> > c_x =np.array( [ 0.5696202374 , 0.5330663554 , 0.4554251862 ])
>> > c_X =np.array( [ 0.5657944233 , 0.524785043 , 0.4587818409 ])
>> > for i in range(42,41,-1):
>> >         t1="RD00%s"%i
>> >         t2="RedshiftOutput00%s"%i
>> >         pf=load(t1+'/'+t2)
>> >
>> > W=1/pf["Mpc"]
>> > c=(c_x+c_X)/2.
>> > le=c-np.array(3*[2])/pf['Mpc']
>> > re=c+np.array(3*[2])/pf['Mpc']
>> >
>> > region=pf.h.region(c, le,re)
>> >
>> > region=pf.h.region(c, le,re,fields="particle_density" )
>> > mi,ma=region.quantities["Extrema"]("particle_density")[0]
>> > mi=-24
>> > ma=np.log10(ma)
>> > tf = ColorTransferFunction((mi,ma))
>> > tf.add_layers(5, w=0.02, colormap="spectral")
>> > cam=region.pf.h.camera(c, L, W, Npixels,
>> > tf,fields=["particle_density"],log_fields=True)
>> > cam.snapshot("%s_volume_rendered.png" % pf, clip_ratio=8.0)
>> >
>> > -Mohammad
>> >
>> >
>> > On Wed, Sep 4, 2013 at 1:13 PM, Matthew Turk <matthewturk at gmail.com>
>> wrote:
>> >>
>> >> Hi Mohammad,
>> >>
>> >> You have to tell the transfer function that you want some levels to
>> >> correspond to various colors.  An easy way to do that is with
>> >> tf.add_layers().  Otherwise, the transfer function is blank, and it
>> >> won't update the image as the rays traverse the domain.
>> >>
>> >> -Matt
>> >>
>> >> On Wed, Sep 4, 2013 at 1:04 PM, mohammad safarzadeh
>> >> <mtsafarzadeh at gmail.com> wrote:
>> >> > Hi,
>> >> > I am trying to do VR on a halo in my zoom-in region which is a dark
>> >> > matter
>> >> > only sim, but I get a black image when I try this:
>> >> >
>> >> > L=[1,1,1]
>> >> >
>> >> > W=1/pf["Mpc"]
>> >> >
>> >> > n [16]: mi,ma=region.quantities["Extrema"]("particle_density")[0]
>> >> >
>> >> >
>> >> > In [17]: mi
>> >> >
>> >> > Out[17]: 0.0
>> >> >
>> >> >
>> >> > In [18]: ma
>> >> >
>> >> > Out[18]: 4.5282895435060503e-24
>> >> >
>> >> >
>> >> > In [21]: np.log10(ma)
>> >> >
>> >> > Out[21]: -23.344065811694637
>> >> >
>> >> >
>> >> > mi=-24
>> >> >
>> >> > ma=np.log10(ma)
>> >> >
>> >> > tf = ColorTransferFunction((mi,ma))
>> >> >
>> >> > cam=region.pf.h.camera(c, L, W, Npixels,
>> >> > tf,fields=["particle_density"],log_fields=True)
>> >> >
>> >> >
>> >> > ImageArray([[[ 0.,  0.,  0.,  1.],
>> >> >
>> >> >         [ 0.,  0.,  0.,  1.],
>> >> >
>> >> >         [ 0.,  0.,  0.,  1.],
>> >> >
>> >> >         ...,
>> >> >
>> >> >         [ 0.,  0.,  0.,  1.],
>> >> >
>> >> >         [ 0.,  0.,  0.,  1.],
>> >> >
>> >> >         [ 0.,  0.,  0.,  1.]],
>> >> >
>> >> >
>> >> >        [[ 0.,  0.,  0.,  1.],
>> >> >
>> >> >         [ 0.,  0.,  0.,  1.],
>> >> >
>> >> >         [ 0.,  0.,  0.,  1.],
>> >> >
>> >> >         ...,
>> >> >
>> >> >         [ 0.,  0.,  0.,  1.],
>> >> >
>> >> >         [ 0.,  0.,  0.,  1.],
>> >> >
>> >> >         [ 0.,  0.,  0.,  1.]],….
>> >> >
>> >> >
>> >> > what is the mistake that I am doing?
>> >> >
>> >> >
>> >> > -Regards,
>> >> >
>> >> > Mohammad
>> >> >
>> >> >
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