[yt-users] Problem in simple volume rendering (yt-users Digest, Vol 36, Issue 18)
Kuo-Chuan Pan
kpan2 at astro.illinois.edu
Thu Feb 24 11:24:53 PST 2011
Dear Matt,
Thank you very much for your quick reply.
1. The balck_center I found is
back_center = [-0.28306926 -0.1132277 -0.39629696]
2. The physical size I used is from -8.2605e11 cm to 8.2605e11 cm (same for x,y,z directions)
The domain is correctly printing when running my yt script
yt INFO 2011-02-24 13:08:20,186 Parameters: domain_left_edge = [ -8.26050000e+11 -8.26050000e+11 -8.26050000e+11]
yt INFO 2011-02-24 13:08:20,186 Parameters: domain_right_edge = [ 8.26050000e+11 8.26050000e+11 8.26050000e+11]
3. I set the width = 1 as used in the example code.
(all value are the same as the example code, except center, c=[0.,0.,0.] and the datafile is the Flash output file)
Thank you very much for your kindly assistance.
Best,
Kuo-Chuan
I have got some warning from yt, but I think that may not relate to my problem.
The whole output are listed as bellow:
[kpan2 at taranaki yt-scripts]$ ./ShowPlots.py
yt WARNING 2011-02-24 13:21:00,791 Setting 1.0 in code units to be 1.0 cm
yt WARNING 2011-02-24 13:21:00,793 No time units. Setting 1.0 = 1 second.
yt INFO 2011-02-24 13:21:00,794 Parameters: current_time = 5635.73778789
yt ERROR 2011-02-24 13:21:00,794 Missing domain_dimensions in parameter file definition!
yt INFO 2011-02-24 13:21:00,794 Parameters: domain_left_edge = [ -8.26050000e+11 -8.26050000e+11 -8.26050000e+11]
yt INFO 2011-02-24 13:21:00,794 Parameters: domain_right_edge = [ 8.26050000e+11 8.26050000e+11 8.26050000e+11]
yt INFO 2011-02-24 13:21:00,795 Parameters: cosmological_simulation = 0.0
yt WARNING 2011-02-24 13:21:00,795 Setting 1.0 in code units to be 1.0 cm
yt WARNING 2011-02-24 13:21:00,795 No time units. Setting 1.0 = 1 second.
Warning: invalid value encountered in sqrt
Warning: invalid value encountered in sqrt
Adding gaussian at -5.8560788466 with width 0.02 and colors (0.2867691866508944, 0.015686274509803921, 0.031372549019607843, 0.01)
Adding gaussian at -4.32198464433 with width 0.02 and colors (0.23702881439314105, 0.20784313725490194, 0.41568627450980389, 0.025118864315095794)
Adding gaussian at -2.78789044206 with width 0.02 and colors (0.40392156862745099, 0.40392156862745099, 0.80784313725490198, 0.063095734448019331)
Adding gaussian at -1.25379623979 with width 0.02 and colors (0.59607843137254901, 0.59607843137254901, 0.59115561118064242, 0.15848931924611143)
Adding gaussian at 0.280297962486 with width 0.02 and colors (0.792156862745098, 0.792156862745098, 0.21568627450980413, 0.39810717055349731)
Adding gaussian at 1.81439216476 with width 0.02 and colors (0.98431372549019602, 0.98431372549019602, 0.94080651128375881, 1.0)
THIS MANY GRIDS! 0| | ETA: --:--:--
Partitioning 100% |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00
KC>>> back_center = [ 0.21693074 0.3867723 0.10370304]
KC>>> bricks = []
KC>>> LE = []
Traceback (most recent call last):
File "./ShowPlots.py", line 161, in <module>
test.plotVR()
File "./ShowPlots.py", line 126, in plotVR
vp.ray_cast()
File "/home/kpan2/softwares/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/software_sampler.py", line 111, in ray_cast
LE = na.array(LE) - self.back_center
ValueError: shape mismatch: objects cannot be broadcast to a single shape
Exception AttributeError: "'NoneType' object has no attribute 'chdir'" in <bound method ShowPlots.__del__ of <__main__.ShowPlots instance at 0x17bb3200>> ignored
PS. (the lines with "KC>>>" are my debug outputs )
On Feb 24, 2011, at 1:11 PM, yt-users-request at lists.spacepope.org wrote:
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> Today's Topics:
>
> 1. Problem in simple volume rendering (Kuo-Chuan Pan)
> 2. Re: Problem in simple volume rendering (Matthew Turk)
> 3. Forthon and yt installation problems. (Andrew Davis)
> 4. Re: Forthon and yt installation problems. (Matthew Turk)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 24 Feb 2011 04:12:18 -0600
> From: Kuo-Chuan Pan <kpan2 at astro.illinois.edu>
> To: yt-users at lists.spacepope.org
> Subject: [yt-users] Problem in simple volume rendering
> Message-ID: <7301A4B8-2601-4AFB-960D-D6CAC55F6D29 at astro.illinois.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Sir/Madam,
>
> I am new in yt and trying to visualize my FLASH simulation data (3D) with volume rendering.
> I followed the cookbook in:
>
> http://hg.enzotools.org/cookbook/raw-file/tip/recipes/simple_volume_rendering.py
>
> However I got an error message:
>
> File "/home/kpan2/softwares/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/software_sampler.py", line 110, in ray_cast
> LE = na.array(LE) - self.back_center
> ValueError: shape mismatch: objects cannot be broadcast to a single shape
>
> I looked the software_sampler.py file and found all LE, RE, self.bricks are empty lists ( = []), but self.back_center is not and correct.
> I guess there are some problems when setting self.bricks.
>
> If anyone has any suggestions, I would be very happy to hear.
> Thank you.
>
> Best regards,
> Kuo-Chuan
>
> ------------------------------
>
> Message: 2
> Date: Thu, 24 Feb 2011 07:49:45 -0500
> From: Matthew Turk <matthewturk at gmail.com>
> To: Discussion of the yt analysis package
> <yt-users at lists.spacepope.org>
> Cc: Kuo-Chuan Pan <kpan2 at astro.illinois.edu>
> Subject: Re: [yt-users] Problem in simple volume rendering
> Message-ID:
> <AANLkTi=MeytZo=-7ENNgHs7KTeGmemtrT32CYUGYpep1 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Kuo-Chuan,
>
> Sorry to hear it didn't work for you! Do you think you could help us
> out with a bit more information, and then we'll see if we can get it
> working for you?
>
> * What is the exact value of back_center that you find?
> * What is the physical size of your domain?
> * What is the width you supplied to the volume_rendering object?
>
> It might also be easier if you could try it with the "Camera"
> interface as described here:
>
> http://yt.enzotools.org/doc/visualizing/volume_rendering.html#volume-rendering-camera
>
> That should allow for a bit more flexibility in describing the scene,
> and may help us narrow down the error.
>
> Best wishes,
>
> Matt
>
> On Thu, Feb 24, 2011 at 5:12 AM, Kuo-Chuan Pan <kpan2 at astro.illinois.edu> wrote:
>> Dear Sir/Madam,
>>
>> I am new in yt and trying to visualize my FLASH simulation data (3D) with volume rendering.
>> I followed the cookbook in:
>>
>> ? ?http://hg.enzotools.org/cookbook/raw-file/tip/recipes/simple_volume_rendering.py
>>
>> However I got an error message:
>>
>> ?File "/home/kpan2/softwares/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/software_sampler.py", line 110, in ray_cast
>> ? ?LE = na.array(LE) - self.back_center
>> ValueError: shape mismatch: objects cannot be broadcast to a single shape
>>
>> I looked the software_sampler.py file and found all LE, RE, self.bricks are empty lists ( = []), but self.back_center is not and correct.
>> I guess there are some problems when setting self.bricks.
>>
>> If anyone has any suggestions, I would be very happy to hear.
>> Thank you.
>>
>> Best regards,
>> Kuo-Chuan
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 24 Feb 2011 11:44:37 -0500
> From: Andrew Davis <andrew.davis at yale.edu>
> To: yt-users at lists.spacepope.org
> Subject: [yt-users] Forthon and yt installation problems.
> Message-ID: <20110224114437.djff25pj404cc8sg at www.mail.yale.edu>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi folks,
>
> I'm updating my yt to the latest version, and so I'm just starting from scratch
> in installing everything on a local cluster. I am running into errors, however
> with the install script (line 479). When running the script, I get the
> following output regarding Forthon:
>
> Installing Forthon-0.8.4 (arguments: 'Forthon-0.8.4')
> Doing yt update, wiping local changes and updating to branch stable
> Installing yt
> install_script.sh: line 479: cd: yt/utilities/kdtree: No such file or directory
> Failure. Check /home/ajd53/YT_NEW/yt-x86_64/yt_install.log.
>
> I haven't been able to find any directory called yt/utilities, which is probably
> why it can't find it.
> At the end of the yt_install.log file, I see the following error, which doesn't
> seem to be related to the install error at first glance:
>
> abort: data/doc/install_script.sh.i at 908327e16660: no match found!
> /home/ajd53/YT_NEW/yt-x86_64/bin/python2.6: can't open file 'setup.py': [Errno
> 2] No such file or directory
>
> Any thoughts?
>
> Thanks,
> andrew
>
>
> *************************************************************
> ** Andrew J. Davis andrew.davis at yale.edu **
> ** Dept. of Astronomy 203-432-5119 **
> ** Yale University www.astro.yale.edu/adavis **
> *************************************************************
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 24 Feb 2011 11:51:38 -0500
> From: Matthew Turk <matthewturk at gmail.com>
> To: Discussion of the yt analysis package
> <yt-users at lists.spacepope.org>
> Subject: Re: [yt-users] Forthon and yt installation problems.
> Message-ID:
> <AANLkTinvoEfjmRD1n80kk4=Ppmab9M3rGWdViwY_ta3z at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Andrew,
>
> Sorry about the problem -- this looks like an issue with our hg
> server; I don't believe it's directly with Forthon. There's something
> up with the webserver, so you should be able to do this:
>
> cd /home/ajd53/YT_NEW/yt-x86_64/src
> rm -rf yt-hg
> /home/ajd53/YT_NEW/yt-x86_64/bin/hg clone --pull --uncompressed
> http://hg.enzotools.org/yt ./yt-hg
>
> and that *should* get you the full set of yt, and then re-run the
> install script with no modifications. Please let me know if that
> doesn't work.
>
> -Matt
>
> PS The webserver for serving hg has been an issue for a while now, and
> I'm embarrassed by the problem. I had hoped to move us to a different
> host several weeks ago, but we've been trying to get the username
> "yt." I think I need to give up that particular goal and settle for
> something different. I'll have an update on this soon.
>
> On Thu, Feb 24, 2011 at 11:44 AM, Andrew Davis <andrew.davis at yale.edu> wrote:
>> Hi folks,
>>
>> I'm updating my yt to the latest version, and so I'm just starting from scratch
>> in installing everything on a local cluster. ?I am running into errors, however
>> with the install script (line 479). ?When running the script, I get the
>> following output regarding Forthon:
>>
>> Installing Forthon-0.8.4 (arguments: 'Forthon-0.8.4')
>> Doing yt update, wiping local changes and updating to branch stable
>> Installing yt
>> install_script.sh: line 479: cd: yt/utilities/kdtree: No such file or directory
>> Failure. ?Check /home/ajd53/YT_NEW/yt-x86_64/yt_install.log.
>>
>> I haven't been able to find any directory called yt/utilities, which is probably
>> why it can't find it.
>> At the end of the yt_install.log file, I see the following error, which doesn't
>> seem to be related to the install error at first glance:
>>
>> abort: data/doc/install_script.sh.i at 908327e16660: no match found!
>> /home/ajd53/YT_NEW/yt-x86_64/bin/python2.6: can't open file 'setup.py': [Errno
>> 2] No such file or directory
>>
>> Any thoughts?
>>
>> Thanks,
>> andrew
>>
>>
>> *************************************************************
>> ** ?Andrew J. Davis ? ? ? ? ? ? andrew.davis at yale.edu ? ? ?**
>> ** ?Dept. of Astronomy ? ? ? ? ?203-432-5119 ? ? ? ? ? ? ? **
>> ** ?Yale University ? ? ? ? ? ? www.astro.yale.edu/adavis ?**
>> *************************************************************
>>
>>
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>
>
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>
> End of yt-users Digest, Vol 36, Issue 18
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