Mailman 3 November 2011 - yt-users

ASCII Data in YT
by vishaalk＠umich.edu 10 Nov '11

10 Nov '11

Hi! I am an undergraduate student who is tasked with learning YT. I have gotten it to to work in command line and in the python shell with the given data set, but I am tasked with visualizing an ASCII data file of a single halo. Is it possible to import ASCII data sets with the load() function in the python shell? Also, to get my python shell working I have to input $ cd /src/yt-hg/tests instead of the cd $YT_DEST/src/yt-hg/tests suggested in the orientation session. Do you know why this might be? Thank you for your time. Sincerely, Vishaal Kalwani

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in-situ visualization possible with yt?
by Matthieu Dorier 09 Nov '11

09 Nov '11

Hello, I'm trying to make in-situ visualization available for a simulation, and I'm considering different softwares for that (VisIt, YT,...). I've never used YT, so my question is: is it possible to add some code in a simulation (written in C++) to have some kind of distributed rendering engine using YT, just like VisIt does with code-instrumentation? Thanks, Matthieu -- Matthieu Dorier ENS Cachan, antenne de Bretagne Département informatique et télécommunication http://perso.eleves.bretagne.ens-cachan.fr/~mdori307/wiki/

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Another data structure question
by Elizabeth Tasker 09 Nov '11

09 Nov '11

Hi, Another question about yt data structures. If I have: dd = pf.h.all_data() Then dd["Density"] contains all the density values in all the cells on all the grids? Given that, how does the indexing work? For instance: dd["Density"][100] is a single value, so have the grids and cells been numbered such that each cell in the simulation has a unique index? And if that's true, then dd["TotalEnergy"][100] is guaranteed to be the same cell? Finally, if I know the grid number and cell index of a cell I want to mark (e.g. via Sam's neighbour finding routine: grids, cis = kd.locate_neighbors_from_position(position) ), then can I work out what its uniform index will be such that I can then do: newfield = na.zeros(dd["x"].shape, dtype='float64') newfield[index] = value-of-my-choice ? Thank you! Elizabeth

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volume rendering rotate
by Stella Offner 08 Nov '11

08 Nov '11

Hi, I'm making a volume rendering movie and I'm encountering an issue with the rotate function. I'm iterating over a call to cam.rotate(angle, rot_vector=north), with a fixed angle and north vector. However, the output images rotate about that axis for a few frames and then switch north vectors and rotate about a different north. I'm using a yt version I installed a couple weeks ago, so its pretty up to date. Do you know what could be going on? for j in range(1,76): cam.rotate((3.14*2.0/75.0), rot_vector=[0, 0, 1]) vals = cam.snapshot() image_file = "%s_st%i_%i_%i_%i_box_%i.png" % (pf, star, xrot, yrot, zrot, ifile+j) write_bitmap(vals, image_file) Thanks, Stella

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basic question
by Elizabeth Tasker 08 Nov '11

08 Nov '11

Hi, I have a basic question about the way yt handles data (or maybe the way python functions handle data). If I have a function of the form: def _MyFunction(field, data): new_data = na.zeros(data["x"].shape, dtype='float64') ..... find xpos, ypos and zpos values of cells to be flagged as part of new_data for n in range(nflaggedcells): new_data[[data["x"] == xpos and data["y"] == ypos and data["z"] == zpos]] = 1.0 return new_data add_field("MyFunction", function=_MyFunction, validators=[ValidateSpatial(1, ["x", "y", "z"])]) pf = load('data') dd = pf.h.all_data() regions = dd["MyFunction"] Does yt call _MyFunction for each grid? So it runs through that routine many times, once per grid? If so, is there an alternative? One sweep through the function will --using Sam's KD tree-- find the positions on every grid that I want to mark. The only reason to put it in a function, as opposed to the main body, is so I can then use yt's slice and projection tools on the data set. I'd really like to create a new field I can use with add_slice that only is looped over a single time. I appreciate this line: for n in range(nflaggedcells): new_data[[data["x"] == xpos and data["y"] == ypos and data["z"] == zpos]] = 1.0 then won't work, but I can just store a list of the grids and cell numbers and mark up new_data using those instead. Does that make sense? Thanks! Elizabeth

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Some questions about plot and load
by Chao Shi 07 Nov '11

07 Nov '11

Hi everyone. I followed the yt Orientation Session and tried to load and plot parameter file moving7_0010 that comes with yt but encounter some errors. First I entered ~/yt-x86_64/bin where I can invoke yt by ./yt. The command "./yt stats ~/yt-x86_64/src/yt-hg/tests/DD0010/moving7_0010" and "./yt load ~/yt-x86_64/src/yt-hg/tests/DD0010/moving7_0010" works. Then I plotted the file by typing "./yt plot ~/yt-x86_64/src/yt-hg/tests/DD0010/moving7_0010". Then it showed at the last three lines that three .png files corresponding to density slices on x,y,z directions have been saved to ./frames. How can I make the image come out automatically after they were plotted? Then I tried to do this in python interpreter, ipython interface, and iyt respectively. In python and ipython, I first import yt by typing "from yt.mods import *", and then tried to load and plot the file moving7_0010. While I can load the file successfully, the interpreter told me that "plot" is not defined. So is the command "stats". However in iyt interface, load and plot are both ok but stats is not defined. I don't know whether such "errors" are normal or that I still miss some packages. All I know now is that yt is a library that can loaded in python. Right now I'm reading the tutorial of Python but haven't reach that far so I wonder if someone could explain a little bit about the relation between python, ipython, yt and iyt. Thanks very much! Chao

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Readline service not available
by Chao Shi 06 Nov '11

06 Nov '11

Hello everyone, I'm Chao, just started to learn how to use yt and python. After I installed yt following the instruction in the main page, when I invoke iyt or ipython, waring of "Readline Services not available on this platform" and "The auto-indent feature requires the readline library' came out. I'm using Ubuntu11.10 shipped with python2.7.2+ and when I run this version, readline is available. But I was installing yt, it seems that python2.7.1 was installed along with yt, and consequently ipython and iyt was built upon python2.7.1. I tried python2.7.1 and showed that the readline is not available, and so does iyt and ipython. I don't know whether multiple versions of python caused this problem and I don't know how to solve it. Can anyone give some guidance? I'm new to linux and I apologize if this problem is too obvious to experienced users. But I haven't found effective solution on google. Thanks, Chao

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Re: [yt-users] yt-users Digest, Vol 45, Issue 6
by Chao Shi 06 Nov '11

06 Nov '11

Good news guys, it works! Thanks very much for all of your advice. I first installed the new version as Jeff suggested and then installed realine by ./pip as Elisabeth and Casey said. I did followed the instruction before I updated yt to install readline under the right directory but and it said that readline was installed successfully but still didn't work. Now everything works:) Cheers, Chao On Sat, Nov 5, 2011 at 9:57 PM, <yt-users-request(a)lists.spacepope.org>wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. Readline service not available (Chao Shi) > 2. Re: Readline service not available (j s oishi) > 3. Re: Readline service not available (Elizabeth Tasker) > 4. Re: Readline service not available (Casey W. Stark) > 5. Fwd: Readline service not available (Chao Shi) > 6. Re: Fwd: Readline service not available (Casey W. Stark) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 5 Nov 2011 20:01:26 -0400 > From: Chao Shi <shichao116(a)gmail.com> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] Readline service not available > Message-ID: > <CA+P3+n-f-rMpGUs=h59LCS8o=Fbous_VypFBak+HxNAoE+7fNA(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hello everyone, > > I'm Chao, just started to learn how to use yt and python. > > After I installed yt following the instruction in the main page, when I > invoke iyt > or ipython, waring of "Readline Services not available on this platform" > and "The > auto-indent feature requires the readline library' came out. > > I'm using Ubuntu11.10 shipped with python2.7.2+ and when I run this > version, readline > is available. But I was installing yt, it seems that python2.7.1 was > installed along with yt, > and consequently ipython and iyt was built upon python2.7.1. I tried > python2.7.1 and > showed that the readline is not available, and so does iyt and ipython. I > don't know whether > multiple versions of python caused this problem and I don't know how to > solve it. Can > anyone give some guidance? I'm new to linux and I apologize if this problem > is > too obvious to experienced users. But I haven't found effective solution on > google. > > Thanks, > > Chao > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 2 > Date: Sat, 5 Nov 2011 17:30:50 -0700 > From: j s oishi <jsoishi(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Readline service not available > Message-ID: > <CAAOZTN_taMC3+fxCgSHsAAiZpDm-SRJqV1h=Ld7PC9twt9AyXQ(a)mail.gmail.com > > > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Chao, > > Welcome to yt! My apologies for this. By using the install script, you > get a complete python environment that is completely isolated from > your system. This means that you can be assured if something goes > wrong with the yt install, you haven't touched your system python at > all. As it happens, we just fixed this problem a few days ago, and it > hasn't propagated to the stable branch yet. Could you try to install > from the development branch, by downloading the install script from > > $ wget http://hg.yt-project.org/yt/raw/yt/doc/install_script.sh > $ bash install_script.sh > > instead? This should fix your problem straight away. As it happens, > Python 2.7.1 won't work on Ubuntu 11.10 very well at all. In the mean > time, I will migrate the updated install script from the development > branch to the stable branch. > > You can just delete the entire yt directory that you already > installed, and it will not interfere with anything. > > Again, welcome to yt! > > Jeff > > On Sat, Nov 5, 2011 at 5:01 PM, Chao Shi <shichao116(a)gmail.com> wrote: > > Hello everyone, > > I'm Chao, just started to learn how to use yt and python. > > After I installed yt following the instruction in the main page, when I > > invoke iyt > > or ipython, waring of "Readline Services not available on this platform" > and > > "The > > auto-indent feature requires the readline library' came out. > > I'm using Ubuntu11.10 shipped with python2.7.2+ and when I run this > version, > > readline > > is available. But I was installing yt, it seems?that python2.7.1 was > > installed along with yt, > > and consequently ipython and iyt was built upon python2.7.1. I tried > > python2.7.1 and > > showed that the readline is not available, and so does iyt and ipython. I > > don't know whether > > multiple versions of python caused this problem and I don't know how to > > solve it. Can > > anyone give some guidance? I'm new to linux and I apologize if this > problem > > is > > too obvious to experienced users. But I haven't found effective solution > on > > google. > > Thanks, > > Chao > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > > > ------------------------------ > > Message: 3 > Date: Sun, 6 Nov 2011 09:36:32 +0900 > From: Elizabeth Tasker <tasker(a)astro1.sci.hokudai.ac.jp> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Readline service not available > Message-ID: > <EFE4787E-6CE4-46A3-8610-F2B1DD0B8A29(a)astro1.sci.hokudai.ac.jp> > Content-Type: text/plain; charset=us-ascii > > Hi Chao, > > In case Jeff's solution doesn't work, try installing readline using "pip" > which is part of the yt package: > > ~/yt/bin/pip install readline > > For some reason, I get similar problems with readline even though it's > blatantly on the system already. > > Elizabeth > > > On 2011-11-06, at 9:01 AM, Chao Shi wrote: > > > Hello everyone, > > > > I'm Chao, just started to learn how to use yt and python. > > > > After I installed yt following the instruction in the main page, when I > invoke iyt > > or ipython, waring of "Readline Services not available on this platform" > and "The > > auto-indent feature requires the readline library' came out. > > > > I'm using Ubuntu11.10 shipped with python2.7.2+ and when I run this > version, readline > > is available. But I was installing yt, it seems that python2.7.1 was > installed along with yt, > > and consequently ipython and iyt was built upon python2.7.1. I tried > python2.7.1 and > > showed that the readline is not available, and so does iyt and ipython. > I don't know whether > > multiple versions of python caused this problem and I don't know how to > solve it. Can > > anyone give some guidance? I'm new to linux and I apologize if this > problem is > > too obvious to experienced users. But I haven't found effective solution > on google. > > > > Thanks, > > > > Chao > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > ------------------------------ > > Message: 4 > Date: Sat, 5 Nov 2011 18:13:04 -0700 > From: "Casey W. Stark" <caseywstark(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Readline service not available > Message-ID: > <CAPQaySUX31N2ECLEwpa5_686dtkAtoC2oXCqV9+cFC5yeCg6fw(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi all. > > Yeah, I've seen this a few times. GNU readline is installed by default on > Ubuntu, so you should be good there (you have to get it yourself on Macs). > The python package readline is the Python interface for GNU readline, see > http://docs.python.org/library/readline.html. So, even if you have python > readline installed on the default (system) python site-packages, you need > to install it again in your yt site-packages. > > Best, > Casey > > > On Sat, Nov 5, 2011 at 5:36 PM, Elizabeth Tasker < > tasker(a)astro1.sci.hokudai.ac.jp> wrote: > > > Hi Chao, > > > > In case Jeff's solution doesn't work, try installing readline using "pip" > > which is part of the yt package: > > > > ~/yt/bin/pip install readline > > > > For some reason, I get similar problems with readline even though it's > > blatantly on the system already. > > > > Elizabeth > > > > > > On 2011-11-06, at 9:01 AM, Chao Shi wrote: > > > > > Hello everyone, > > > > > > I'm Chao, just started to learn how to use yt and python. > > > > > > After I installed yt following the instruction in the main page, when I > > invoke iyt > > > or ipython, waring of "Readline Services not available on this > platform" > > and "The > > > auto-indent feature requires the readline library' came out. > > > > > > I'm using Ubuntu11.10 shipped with python2.7.2+ and when I run this > > version, readline > > > is available. But I was installing yt, it seems that python2.7.1 was > > installed along with yt, > > > and consequently ipython and iyt was built upon python2.7.1. I tried > > python2.7.1 and > > > showed that the readline is not available, and so does iyt and ipython. > > I don't know whether > > > multiple versions of python caused this problem and I don't know how to > > solve it. Can > > > anyone give some guidance? I'm new to linux and I apologize if this > > problem is > > > too obvious to experienced users. But I haven't found effective > solution > > on google. > > > > > > Thanks, > > > > > > Chao > > > _______________________________________________ > > > yt-users mailing list > > > yt-users(a)lists.spacepope.org > > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 5 > Date: Sat, 5 Nov 2011 21:19:52 -0400 > From: Chao Shi <shichao116(a)gmail.com> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] Fwd: Readline service not available > Message-ID: > <CA+P3+n_G3OsY8waot575wsw2vTqbKNRekYX0sLT3z4n8OLwkUA(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > BTW, I already tried the method in the FAQ > > http://yt-project.org/doc/faq.html#i-can-t-scroll-up-to-previous-commands-i… > , > but it still dosen't work. > > ---------- Forwarded message ---------- > From: Chao Shi <shichao116(a)gmail.com> > Date: Sat, Nov 5, 2011 at 8:01 PM > Subject: Readline service not available > To: yt-users(a)lists.spacepope.org > > > Hello everyone, > > I'm Chao, just started to learn how to use yt and python. > > After I installed yt following the instruction in the main page, when I > invoke iyt > or ipython, waring of "Readline Services not available on this platform" > and "The > auto-indent feature requires the readline library' came out. > > I'm using Ubuntu11.10 shipped with python2.7.2+ and when I run this > version, readline > is available. But I was installing yt, it seems that python2.7.1 was > installed along with yt, > and consequently ipython and iyt was built upon python2.7.1. I tried > python2.7.1 and > showed that the readline is not available, and so does iyt and ipython. I > don't know whether > multiple versions of python caused this problem and I don't know how to > solve it. Can > anyone give some guidance? I'm new to linux and I apologize if this problem > is > too obvious to experienced users. But I haven't found effective solution on > google. > > Thanks, > > Chao > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 6 > Date: Sat, 5 Nov 2011 18:50:52 -0700 > From: "Casey W. Stark" <caseywstark(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Fwd: Readline service not available > Message-ID: > <CAPQaySV-T7CATUrvguubUCKd=7vxb_+=9fohy6HAWWsU6P0erg(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Chao. > > Are you certain that this command installed readline to your yt python > environment? I'm not certain how pip determines which python site-packages > to install to, but I think it depends on PYTHONPATH/PYTHONHOME. Anyone know > about this? > > I recommend... > > $ source /path/to/yt/bin/activate > $ pip install readline > > You can check that it installed to the right place by navigating to > /path/to/yt/lib/python2.7/site-packages/ and seeing if the readline package > is there. If it is there and still doesn't work, then this is really > weird... > > Either way, we should fix this line of the docs because it assumes yt is > installed to ~/yt and it doesn't say anything about setting env vars or > using activate. Something like /path/to/yt? > > Best, > Casey > > > On Sat, Nov 5, 2011 at 6:19 PM, Chao Shi <shichao116(a)gmail.com> wrote: > > > BTW, I already tried the method in the FAQ > > > http://yt-project.org/doc/faq.html#i-can-t-scroll-up-to-previous-commands-i… > , > > but it still dosen't work. > > > > > > ---------- Forwarded message ---------- > > From: Chao Shi <shichao116(a)gmail.com> > > Date: Sat, Nov 5, 2011 at 8:01 PM > > Subject: Readline service not available > > To: yt-users(a)lists.spacepope.org > > > > > > Hello everyone, > > > > I'm Chao, just started to learn how to use yt and python. > > > > After I installed yt following the instruction in the main page, when I > > invoke iyt > > or ipython, waring of "Readline Services not available on this platform" > > and "The > > auto-indent feature requires the readline library' came out. > > > > I'm using Ubuntu11.10 shipped with python2.7.2+ and when I run this > > version, readline > > is available. But I was installing yt, it seems that python2.7.1 was > > installed along with yt, > > and consequently ipython and iyt was built upon python2.7.1. I tried > > python2.7.1 and > > showed that the readline is not available, and so does iyt and ipython. I > > don't know whether > > multiple versions of python caused this problem and I don't know how to > > solve it. Can > > anyone give some guidance? I'm new to linux and I apologize if this > > problem is > > too obvious to experienced users. But I haven't found effective solution > > on google. > > > > Thanks, > > > > Chao > > > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > End of yt-users Digest, Vol 45, Issue 6 > *************************************** >

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Re: [yt-users] Trouble with h5py + FLASH
by John ZuHone 03 Nov '11

03 Nov '11

Hi Nathan, You'd have to double-check with Matt, but as I recall we didn't design the yt interface to support FLASH2 data. Now, I wouldn't be surprised if it does for the most part, since the grid data is written in almost exactly the same format by design to ease people switching over to FLASH3. The particles, however, are a different story. In FLASH2, the particles are a composite HDF5 data structure of ints and doubles, whereas in FLASH3 they are a 2D array of doubles. In the latter case, simplicity was chosen over design sophistication. I know for a fact that yt only supports particle data in FLASH3. I'm looking at this file of yours now... I was not aware that the way compound data types work in HDF5 that you get Python dictionaries when you read them in. That is a lot simpler than what I have to do to read FLASH3 particles. In any case, I reproduce the error you get. If you add the lines del ParticleData del f after your "f.close()" call, I no longer get the error. This is what we had to do with the previous issue you mentioned. For some reason the FLASH files are sometimes a bit picky about having all objects allocated from the previous read deleted before accessing the file again. Best, John

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Re: [yt-users] Trouble with h5py + FLASH
by Nathan Goldbaum 02 Nov '11

02 Nov '11

Hello all, I'm currently trying to make an analysis script for a FLASH dataset using yt. I've had more or less smooth sailing so far; yt is a significant improvement over other freely available FLASH analysis tools. Unfortunately, I think I've run into a bug with how yt and h5py handle FLASH datasets. If I run the following script: http://paste.yt-project.org/show/1905/ I get the following shell output and traceback: http://paste.yt-project.org/show/1906/ This script needs a plot file from one of my simulations which you can download here. This is sort of a followup to an e-mail conversation I had with Matt where I pointed out that yt is unable to get particle data from my plot files - probably because they were produced by a version of FLASH that has been modified to convert tracer particles into sink particles. That's not such a big deal because I get the particle data directly using h5py. Unfortunately, this bug prevents me from accessing the particle data before I open the plot file using yt. This may follow up on a bug that John Zuhone noticed a while ago: http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2011-July/00170… Thanks for any help anyone can provide. Cheers, Nathan

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