Mailman 3 August 2012 - yt-users

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

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Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

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p.modify["point"]
by Elizabeth Tasker 05 Oct '12

05 Oct '12

Hi, I'm trying to add text to a particular point in my slice. I've got: position = na.array([20.2, 13.8, 16.0]) pc = PlotCollection(pf, center=position) p = pc.add_projection("Density", 2) p.set_width(2, 'kpc') for c in range(len(t1clouds)): r = abs(t1clouds[c]['position']-position) if r[0] < 1.0 and r[1] < 1.0: p.modify["point"](t1clouds[c]['position'], str(t1clouds[c]['track'])) p.modify["marker"](t1clouds[c]['position'], marker='o') pc.save("%s_tracking" % (fn)) But python complains with: TypeError: text() argument after ** must be a mapping, not NoneType Did I call the modifier incorrectly? Elizabeth

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Changing na => np internally
by Matthew Turk 10 Sep '12

10 Sep '12

Hi all, There's been quite a bit of discussion on yt-dev about changing the internal convention in yt of using "na" for numpy (which originally stood for "numarray") to "np", which is the commonly used shorthand. We'll keep around "na" in the yt.mods namespace, which means your scripts should *not* need any adjustment. But, if you have made a number of substantial changes to the internals of yt in your version, any updates after this change is made may pose problems and may need to be hand-modified. If you'd like to contribute to the discussion (we're waiting until next week to make the switch) please do so on yt-dev or here. This change, which touches many many files, was not decided on lightly and we're trying to ensure that the transition is smooth without any external effects. Here's the thread: http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2012-August/00235… (Note that tomorrow starts a new archive month, so you might need to switch the URL for any new messages after today.) Again, this should not pose any issues for you unless you have modified yt internals. If you have done so and would like help updating, please reply to this message or contact yt-dev. Best, Matt

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Cylindrical coordinate fields
by Matthew Turk 31 Aug '12

31 Aug '12

Hi all, Just as a heads up, if you are on the development branch and have been using fields that used the field_parameter "height", this has been changed to fit better with other areas of the code and is now the field_parameter "normal". Thanks to Mike Kuhlen for fixing up our cylindrical coordinates fields! Relevant changeset: https://bitbucket.org/yt_analysis/yt/changeset/edc2b99212bd100a4357083f3f36… -Matt

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Fortran kD Tree Setup and Clumps
by Francia F. Riesco 30 Aug '12

30 Aug '12

Everybody good afternoon, about Fortran kD Tree Setup, just to keep thread with my fix. 1) I downloaded the YT-DEV version and it didn't fix my problem. However, when I downloaded Forthon-0.8.7.tgz it did the trick. 2) Now I want to talk about another issue that I am getting. This time is with clumps. I am using an enzo data, with the code example in the YT documentation. this is my code: ----- import sys from yt.mods import * # set up our namespace from yt.analysis_modules.level_sets.api import * import yt.frontends.enzo.api yt.frontends.enzo.api.EnzoHierarchy._bn = "%s.grid.cpu%%04i" fn = "/astro/data/redshift0058/redshift0058" # parameter file to load field = "Density" step = 10.0 pf = load(fn) # load data c = [0.403290331 , 0.471765608 , 0.461319029] r = [0.411690331 , 0.480165608 , 0.469719029] l = [0.394890331 , 0.463365608 , 0.452919029] data_source = pf.h.region(c,l,r) c_min = 10**na.floor(na.log10(data_source[field]).min() ) c_max = 10**na.floor(na.log10(data_source[field]).max()+1) master_clump = Clump(data_source, None, field) find_clumps(master_clump, c_min, c_max, step) f = open('%s_clump_hierarchy.txt' % pf,'w') write_clump_hierarchy(master_clump, 0, f) f.close() f = open('%s_clumps.txt' % pf,'w') write_clumps(master_clump,0,f) f.close() --------- and I got the follow error. Traceback (most recent call last): File "/astro/py/clump.py", line 34, in <module> find_clumps(master_clump, c_min, c_max, step) File "/astro/yt-dev/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 181, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/astro/yt-dev/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 181, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/astro/yt-dev/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 190, in find_clumps elif (child._isValid()): File "/astro/yt-dev/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 144, in _isValid self.function_value = eval(self.function) File "<string>", line 1, in <module> File "/astro/yt-dev/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 94, in __call__ return self._call_func_unlazy(args, kwargs) File "/astro/yt-dev/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 119, in _call_func_unlazy retval = self.func(self._data_source, *args, **kwargs) File "/astro/yt-dev/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 360, in _IsBound thermal = (data["ThermalEnergy"] * mass_to_use).sum() File "/astro/yt-dev/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 327, in __getitem__ self.get_data(key) File "/astro/yt-dev/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 2536, in get_data if self._generate_field(field): File "/astro/yt-dev/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 359, in _generate_field self[field] = self.pf.field_info[field](self) File "/astro/yt-dev/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 316, in __call__ dd = self._function(self, data) File "/astro/yt-dev/yt-x86_64/src/yt-hg/yt/frontends/enzo/fields.py", line 134, in _ThermalEnergy return data["TotalEnergy"] File "/astro/yt-dev/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 327, in __getitem__ self.get_data(key) File "/astro/yt-dev/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 2536, in get_data if self._generate_field(field): File "/astro/yt-dev/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 363, in _generate_field raise KeyError(field) KeyError: 'TotalEnergy' I did it with the whole data (it took forever), however, I got the same exactly error. Anybody has an advice?? -- Francia F.R.

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Fortran kD Tree Setup
by Francia F. Riesco 29 Aug '12

29 Aug '12

Dear All, First, thank you for the previous help that I got from the ML. Now I have another issue. Traceback (most recent call last): File "/astro/py/halo_finder.py", line 14, in <module> hp = HP.HaloProfiler(fn, halo_list_file='HopAnalysis.out') File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_profiler/multi_halo_profiler.py", line 310, in __init__ self._load_halo_data() File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_profiler/multi_halo_profiler.py", line 967, in _load_halo_data self._run_hop(hop_file) File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_profiler/multi_halo_profiler.py", line 1124, in _run_hop **self.halo_finder_kwargs) File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/halo_objects.py", line 2268, in __init__ premerge=premerge, tree=self.tree) File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/halo_objects.py", line 1639, in - Ignored: __init__ HaloList.__init__(self, data_source, dm_only) File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/halo_objects.py", line 1067, in __init__ self._run_finder() File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/halo_objects.py", line 1667, in _run_finder tree=self.tree) File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py", line 73, in __init__ self._chain_hop() File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py", line 1536, in _chain_hop self._init_kd_tree() File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py", line 351, in _init_kd_tree fKD.dens = na.zeros(self.size, dtype='float64', order='F') NameError: global name 'fKD' is not defined I tried to install Fortran kD Tree Setup http://yt-project.org/doc/analysis_modules/running_halofinder.html?highligh… But I got the follow error. Using Forthon () Forthon -F gfortran --compile_first fKD_source --no2underscores --with-numpy --fopt "-O3" fKD fKD_source.f90 Usage: Forthon [options] pkgname [extra Fortran or C files to be compiled or objects to link] [options for distutils] Forthon: error: no such option: --with-numpy make: *** [fKD] Error 2 X-Riesco-Francia:kdtree friesco$ sudo make Using Forthon () Forthon -F gfortran --compile_first fKD_source --no2underscores --with-numpy --fopt "-O3" fKD fKD_source.f90 Usage: Forthon [options] pkgname [extra Fortran or C files to be compiled or objects to link] [options for distutils] Forthon: error: no such option: --with-numpy make: *** [fKD] Error 2 I am using Mac IOS Lion 10.7.4 and the latest YT build Thank in Advance

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SciPy and YT problem
by roberto iaconi 28 Aug '12

28 Aug '12

Dear YT users, I have a problem in installing the SciPy library when using YT python, what happens is that: -when installing from packages, also after activating yt (i.e. through the command sudo apt-get install python-scipy) I get the confirmation that SciPy is correctly installed but i cannot import it in YT python, since probably the installation is connected to the system python instead. -when installing from source (by downloading the packages) I get a lot of errors concerning missing libraries (mainly blas and atlas). I installed them and added the paths to a "site.cfg" file, but I am still getting the same error. Also, I appended the system SciPy path through the sys.path.append() function, in this way I can succesfully import SciPy, but I cannot import any sublibrary such as SciPy.optimize (which is the one I particularly need). By browsing the YT Mailing List I found a user with a similar problem (http://lists.spacepope.org/htdig.cgi/yt-users-spacepope.org/2011-July/00169…), but there are no suggestions in reply. I would like to ask if there is a way to get SciPy installed under YT or make it available to be included. Cheers, Roberto

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XSPEC issue
by Eric Hallman 24 Aug '12

24 Aug '12

John, as of right now, I have just "successfully" built XSPEC for Lion, with the patch applied that Matt pointed me to for Python. I had no errors in the build, and I'll attempt to use it shortly and let you know off-line if anything fails. Cheers, Eric The other problem is that XSPEC doesn't do 64-bit builds on Mac because of X11, or so they say. If you can get it to work please let me know. I tried this earlier this week with no luck. John ZuHone Laboratory for High-Energy Astrophysics NASA/Goddard Space Flight Center 8800 Greenbelt Rd., Code 662 Greenbelt, MD 20771 (w) 301-286-2531 (m) 773-758-0172 jzuhone(a)gmail.com john.zuhone(a)nasa.gov On Aug 24, 2012, at 5:02 PM, Eric Hallman <hallman13(a)gmail.com> wrote: Matt, thanks for the heads up. I made the patch and am trying to rebuild. Thanks! Eric Matt wrote: Hi Eric, Looks like this is known for non-framework builds of Python on OSX. (We don't build it Framework-wise because it caused a bunch of problems in the past and mainly only allowed usage of a few native widgets.) Here is a patch you can apply and then rebuild Python with to (possibly) get it to work: http://bugs.python.org/issue1602133 -Matt On Fri, Aug 24, 2012 at 4:46 PM, Eric Hallman <hallman13(a)gmail.com> wrote: Hello, I know this is not a yt specific issue, however it involves an interaction of the yt installed python and XSPEC. Maybe some of you on this list have done an XSPEC install on Mac OS X (Lion in this case) and run into this. At link time during the build of XSPEC, it gives the following error: Undefined symbols for architecture x86_64: "_environ", referenced from: _initposix in libpython2.7.a(posixmodule.o) ld: symbol(s) not found for architecture x86_64 Originally on my Mac, XSPEC tried to build 32-bit, and failed with python linkages (since python is 64 bit in the yt install build). Once I went to 64-bit, this was the only remaining error. Does anyone have ideas? Thanks! Eric Hallman _______________________________________________ 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

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XSPEC issue
by Eric Hallman 24 Aug '12

24 Aug '12

Matt, thanks for the heads up. I made the patch and am trying to rebuild. Thanks! Eric Matt wrote: Hi Eric, Looks like this is known for non-framework builds of Python on OSX. (We don't build it Framework-wise because it caused a bunch of problems in the past and mainly only allowed usage of a few native widgets.) Here is a patch you can apply and then rebuild Python with to (possibly) get it to work: http://bugs.python.org/issue1602133 -Matt On Fri, Aug 24, 2012 at 4:46 PM, Eric Hallman <hallman13(a)gmail.com> wrote: Hello, I know this is not a yt specific issue, however it involves an interaction of the yt installed python and XSPEC. Maybe some of you on this list have done an XSPEC install on Mac OS X (Lion in this case) and run into this. At link time during the build of XSPEC, it gives the following error: Undefined symbols for architecture x86_64: "_environ", referenced from: _initposix in libpython2.7.a(posixmodule.o) ld: symbol(s) not found for architecture x86_64 Originally on my Mac, XSPEC tried to build 32-bit, and failed with python linkages (since python is 64 bit in the yt install build). Once I went to 64-bit, this was the only remaining error. Does anyone have ideas? Thanks! Eric Hallman _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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yt-users August 2012