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 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 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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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-z... Best, Sam On Wed, Sep 4, 2013 at 10:53 AM, Matthew Turk 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 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 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 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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Hi Mohammad, On Wed, Sep 4, 2013 at 4:34 PM, mohammad safarzadeh wrote:

the off-axis plot is like this: http://i.imgur.com/7fDuNTA.png so no one has done volume rendering on DM only sims?

No, probably not in the way you're describing. You might try creating a new field that floors to 1e-30 or something. That should be a hotfix for now; you could do something like: @derived_field(name = "SomethingMeaningful") def my_field(field, data): tr = data["particle_density"].copy() np.maximum(tr, 1e-30, tr) return tr and then render that field instead. But one issue that comes up often is that the results of applying a continuous transfer function to a discontinuous field (and one that is actually a realization of a discrete distribution!) is pretty tricky, and more advanced than what we usually do. In the future we hope to provide flexible mechanisms for smoothing kernels (which aren't even necessarily the best way to do this), but as it stands rendering particle_density will probably produce not very good looking results.

how can I provide a 3d view of the zoom in box ( if there are alternative ways)?

When you say 3d, I think you mean that you want something that shows the structure both behind and in front, in a way of showing the structure inside. The onion-peel approach does this, but you may be able to communicate the information you're looking for just using OffAxisProjection itself. -Matt

Regards,

-Mohammad

On Wed, Sep 4, 2013 at 3:09 PM, Sam Skillman 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-z...

Best, Sam

On Wed, Sep 4, 2013 at 10:53 AM, Matthew Turk 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 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 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 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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