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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> >> >
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> >
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> >
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