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@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@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@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@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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