Mailman 3 May 2014 - yt-users

specify bounds before constructing octree
by Desika Narayanan May 12, 2014

May 12, 2014

Hi Team YT, I have a gadget snapshot that I'd like to specify a sub-region of before constructing an octree, so that the octree built is only over the specified [xmin,xmax], [ymin,ymax],[zmin,zmax] subregion of the original sanpshot? Something just after pf=load(...) presumably is what I want in: http://paste.yt-project.org/show/4606/ though maybe prior to the loading itself? thanks, desika

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Error importing yt.mods
by Sam Geen May 9, 2014

May 9, 2014

Hi, I've downloaded the latest version of the yt-3.0 branch, and have run into some import errors. I've numbered them 1) and 2) below. 1) is "ImportError: No module named owls_subfind.api" and 2) is a problem locating yt.utilities. I've deleted the yt egg file and downloaded a clean cloned version, and the errors persist. Any ideas? Thanks! Sam --- 1) ------ In [1]: import yt.mods yt : [DEBUG ] 2014-05-09 16:07:19,697 Set log level to 0 yt : [DEBUG ] 2014-05-09 16:07:22,067 Registering: Dataset as <class 'yt.data_objects.static_output.Dataset'> yt : [DEBUG ] 2014-05-09 16:07:22,145 Registering: ARTDataset as <class 'yt.frontends.art.data_structures.ARTDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,149 Registering: ARTIODataset as <class 'yt.frontends.artio.data_structures.ARTIODataset'> yt : [DEBUG ] 2014-05-09 16:07:22,152 Registering: AthenaDataset as <class 'yt.frontends.athena.data_structures.AthenaDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,161 Registering: BoxlibDataset as <class 'yt.frontends.boxlib.data_structures.BoxlibDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,161 Registering: OrionDataset as <class 'yt.frontends.boxlib.data_structures.OrionDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,161 Registering: CastroDataset as <class 'yt.frontends.boxlib.data_structures.CastroDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,161 Registering: MaestroDataset as <class 'yt.frontends.boxlib.data_structures.MaestroDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,161 Registering: NyxDataset as <class 'yt.frontends.boxlib.data_structures.NyxDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,165 Registering: ChomboDataset as <class 'yt.frontends.chombo.data_structures.ChomboDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,165 Registering: Orion2Dataset as <class 'yt.frontends.chombo.data_structures.Orion2Dataset'> yt : [DEBUG ] 2014-05-09 16:07:22,174 Registering: EnzoDataset as <class 'yt.frontends.enzo.data_structures.EnzoDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,174 Registering: EnzoDatasetInMemory as <class 'yt.frontends.enzo.data_structures.EnzoDatasetInMemory'> yt : [DEBUG ] 2014-05-09 16:07:22,174 Registering simulation: Enzo as <class 'yt.frontends.enzo.simulation_handling.EnzoSimulation'> yt : [DEBUG ] 2014-05-09 16:07:22,178 Registering: FITSDataset as <class 'yt.frontends.fits.data_structures.FITSDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,314 Registering: FLASHDataset as <class 'yt.frontends.flash.data_structures.FLASHDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,317 Registering: GDFDataset as <class 'yt.frontends.gdf.data_structures.GDFDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,321 Registering: HaloCatalogDataset as <class 'yt.frontends.halo_catalogs.halo_catalog.data_structures.HaloCatalogDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,324 Registering: RockstarDataset as <class 'yt.frontends.halo_catalogs.rockstar.data_structures.RockstarDataset'> --------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-1-fcd62da66eec> in <module>() ----> 1 import yt.mods /home/samgeen/.local/lib/python2.7/site-packages/yt-3.0dev-py2.7-linux-x86_64.egg/yt/__init__.pyc in <module>() 124 125 from yt.frontends.api import _frontend_container --> 126 frontends = _frontend_container() 127 128 from yt.frontends.stream.api import \ /home/samgeen/.local/lib/python2.7/site-packages/yt-3.0dev-py2.7-linux-x86_64.egg/yt/frontends/api.pyc in __init__(self) 39 for frontend in _frontends: 40 _mod = "yt.frontends.%s.api" % frontend ---> 41 setattr(self, frontend, importlib.import_module(_mod)) /home/samgeen/lib/python2.7/importlib/__init__.pyc in import_module(name, package) 35 level += 1 36 name = _resolve_name(name[level:], package, level) ---> 37 __import__(name) 38 return sys.modules[name] /home/samgeen/.local/lib/python2.7/site-packages/yt-3.0dev-py2.7-linux-x86_64.egg/yt/frontends/halo_catalogs/api.py in <module>() 25 RockstarFieldInfo 26 ---> 27 from .owls_subfind.api import \ 28 OWLSSubfindDataset, \ 29 IOHandlerOWLSSubfindHDF5, \ ImportError: No module named owls_subfind.api 2) --- In [3]: import yt --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-3-59dfcfe9846c> in <module>() ----> 1 import yt /home/samgeen/.local/lib/python2.7/site-packages/yt-3.0dev-py2.7-linux-x86_64.egg/yt/__init__.py in <module>() 97 from yt.utilities.logger import ytLogger as mylog 98 ---> 99 import yt.utilities.physical_constants as physical_constants 100 import yt.units as units 101 from yt.units.yt_array import YTArray, YTQuantity AttributeError: 'module' object has no attribute 'utilities' ----

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Fwd: [astropy-dev] Lorentz Center Workshop on "Python in Astronomy"
by Matthew Turk May 8, 2014

May 8, 2014

---------- Forwarded message ---------- From: Thomas Robitaille <thomas.robitaille(a)gmail.com> Date: Thu, May 8, 2014 at 7:45 AM Subject: [astropy-dev] Lorentz Center Workshop on "Python in Astronomy" To: astropy-dev <astropy-dev(a)googlegroups.com>, astropy <astropy(a)scipy.org> Hi everyone, Back in December last year I forwarded a call for proposals for workshops at the Lorentz center to this list, and a few of us subsequently put in an application to hold a Python Astronomy workshop. We are now very happy to report that a "Python in Astronomy" workshop has been accepted and will take place at the Lorentz center in Leiden on 20-24 April 2015. This workshop aims to bring together researchers, Python developers, users, and educators, and will include presentations, tutorials, unconference sessions, and coding sprints. In addition to sharing information about the state-of-the art of Python Astronomy packages, the workshop will also focus on improving interoperability between astronomical Python packages, providing training for new contributors, and developing a common set of educational materials for Python in Astronomy. The meeting is therefore not only aimed at current developers, but also users and educators. A formal website and announcement will come later this year, but we wanted to share this with you now so that you can keep the dates free if you are interested in participating. In the mean time, you can already sign up to receive future announcements about the workshop at the following page: http://python-in-astronomy.github.io Please feel free to spread the word to others that this is happening and get them to sign up to the announcement list. We are very excited about the opportunity to hold this workshop, and we hope to see many of you there! The organizing committee: Thomas Robitaille Pauline Barmby Eric Jeschke Stuart Mumford Magnus Persson -- You received this message because you are subscribed to the Google Groups "astropy-dev" group. To unsubscribe from this group and stop receiving emails from it, send an email to astropy-dev+unsubscribe(a)googlegroups.com. For more options, visit https://groups.google.com/d/optout.

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Particle only plots
by Jeremy Ritter May 7, 2014

May 7, 2014

Hello yt, Is there an easy way to plot only particles? What I would like to do is plot a z-axis projection of particle x/y positions, with no background data loaded from the grid. I only see examples for annotate_particles() on top of another plot, but I don't want to unnecessarily load grid data. Thanks! -Jeremy

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Everybody using yt-3.0, turn around
by Matthew Turk May 7, 2014

May 7, 2014

Hi all, Just wanted to drop a note to let you know that we've switched the coordinate system in yt-3.0's mainline to be right-handed. https://bitbucket.org/yt_analysis/yt/pull-request/864/switch-to-right-hande… This should only affect projections and slices along the y axis. According to my understanding of the terms and vocabulary of heraldic coats-of-arms, this makes yt 33% less "sinister." -Matt

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Boundary of the data container
by Junhwan Choi (최준환) May 7, 2014

May 7, 2014

Hi yt users, I have one basic question about the membership of the data container. For example, I make a sphere data container and try to estimate the total enclosed mass of the sphere. However one of the refined cell (grid) is partially enclosed in the sphere. Does the yt add entire cell (grid) mass into the sphere mass or estimate the volume fraction of the cell mass and add only this partial mass? This question can be also applied for the density profile (r vs density). What happen one cell extends to multiple binning point? I would like to clarify my yt analysis. Thanks in advance, Junhwan

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Re: [yt-users] Parallel Broadcasting in yt
by Claire Kopenhafer May 7, 2014

May 7, 2014

mpi_bcast was what I was looking for! Thank you -Claire On Tue, May 6, 2014 at 2:05 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. Parallel Broadcasting in yt (Claire Kopenhafer) > 2. Re: Parallel Broadcasting in yt (Britton Smith) > 3. fractional keyword in profile plot (Chang-Goo Kim) > 4. total mass (Chang-Goo Kim) > 5. Re: total mass (Matthew Turk) > > > ---------- Forwarded message ---------- > From: Claire Kopenhafer <clairekope(a)gmail.com> > To: yt-users(a)lists.spacepope.org > Cc: > Date: Mon, 5 May 2014 15:56:29 -0400 > Subject: [yt-users] Parallel Broadcasting in yt > Hello all, > > I've got a code that reads in a dictionary from file and then operates on > it, and I'd like to run it in parallel. My best thought is to have the root > process read in the dict and then broadcast it to all the rest, but I am > not sure how best to do this within yt. Any suggestions? Thanks! > > -Claire > > > ---------- Forwarded message ---------- > From: Britton Smith <brittonsmith(a)gmail.com> > To: Discussion of the yt analysis package <yt-users(a)lists.spacepope.org> > Cc: > Date: Mon, 5 May 2014 16:50:06 -0400 > Subject: Re: [yt-users] Parallel Broadcasting in yt > Hi Claire, > > You might want to have a look at the function called mpi_bcast > in yt/utilities/parallel_tools/parallel_analysis_interface.py. This should > do a standard mpi broadcast from the root process to all of the > subprocesses. Alternatively, if the dictionary is something that can be > loaded in in parts by each of the processors and then combined, you might > also want to check par_combine_object in the same file. > > Britton > > > On Mon, May 5, 2014 at 3:56 PM, Claire Kopenhafer <clairekope(a)gmail.com>wrote: > >> Hello all, >> >> I've got a code that reads in a dictionary from file and then operates on >> it, and I'd like to run it in parallel. My best thought is to have the root >> process read in the dict and then broadcast it to all the rest, but I am >> not sure how best to do this within yt. Any suggestions? Thanks! >> >> -Claire >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> > > > ---------- Forwarded message ---------- > From: Chang-Goo Kim <cgkim(a)astro.princeton.edu> > To: Discussion of the yt analysis package <yt-users(a)lists.spacepope.org> > Cc: > Date: Tue, 6 May 2014 13:43:39 -0400 > Subject: [yt-users] fractional keyword in profile plot > Hi all, > > I tried to draw PDFs using ProfilePlot with "fractional" keyword. But, it > returned unit incompatibility. I have looked at the code, and realized that > the fractional keyword makes field_data dimensionless, while it tried to > return data with units of original data. I think it must be easy to fix. > Error message is attached below. > > Thanks, > > Chang-Goo > > ---------------------------------------------------------------------------YTUnitConversionError Traceback (most recent call last)<ipython-input-137-18016774c3d0> in <module>()----> 1 pdf=ProfilePlot(dd,"temp",['cell_mass','cell_volume'],weight_field=None,fractional=True) 2 pdf.show() > /u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/visualization/profile_plotter.pyc in __init__(self, data_source, x_field, y_fields, weight_field, n_bins, accumulation, fractional, label, plot_spec, profiles) 216 self.plot_spec = [self.plot_spec.copy() for p in self.profiles] 217 --> 218 self._setup_plots() 219 220 def save(self, name=None): > /u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/visualization/profile_plotter.pyc in _setup_plots(self) 309 self.axes = AxesContainer(self.figures) 310 for i, profile in enumerate(self.profiles):--> 311 for field, field_data in profile.items(): 312 self.axes[field].plot(np.array(profile.x), 313 np.array(field_data), > /u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/data_objects/profiles.pyc in items(self) 854 855 def items(self):--> 856 return [(k,self[k]) for k in self.field_data.keys()] 857 858 def __iter__(self): > /u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/data_objects/profiles.pyc in __getitem__(self, field) 851 raise KeyError(field) 852 else:--> 853 return self.field_data[fname].in_units(self.field_units[fname]) 854 855 def items(self): > /u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/units/yt_array.pyc in in_units(self, units) 358 359 """--> 360 new_units = self._unit_repr_check_same(units) 361 conversion_factor = self.units.get_conversion_factor(new_units) 362 > /u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/units/yt_array.pyc in _unit_repr_check_same(self, units) 315 if not self.units.same_dimensions_as(units): 316 raise YTUnitConversionError(--> 317 self.units, self.units.dimensions, units, units.dimensions) 318 319 return units > YTUnitConversionError: Unit dimensionalities do not match. Tried to convert between dimensionless (dim 1) and code_length**3 (dim (length)**3). > > > > > > ---------- Forwarded message ---------- > From: Chang-Goo Kim <cgkim(a)astro.princeton.edu> > To: Discussion of the yt analysis package <yt-users(a)lists.spacepope.org> > Cc: > Date: Tue, 6 May 2014 13:50:47 -0400 > Subject: [yt-users] total mass > Hi all again, > > I tried to find mass fraction of each temperature component, but I got > inconsistent results as below: > > == > > dd=pf.all_data() > > > > hot=dd.cut_region(["obj['temperature'] >= 1.e4"]) > > wnm=dd.cut_region(["obj['temperature'] < 1.e4"]) > > > > print dd.quantities.total_mass() > > print wnm.quantities.total_mass()+hot.quantities.total_mass() > > > > 2.88677799841e+38 g > 2.91575727709e+38 g > > == > > I can't understand why those two are different. Have any idea? > > Chang-Goo > > > > ---------- Forwarded message ---------- > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package <yt-users(a)lists.spacepope.org> > Cc: > Date: Tue, 6 May 2014 13:53:45 -0400 > Subject: Re: [yt-users] total mass > Hi Chang-Goo, > > On Tue, May 6, 2014 at 1:50 PM, Chang-Goo Kim <cgkim(a)astro.princeton.edu> > wrote: > > Hi all again, > > > > I tried to find mass fraction of each temperature component, but I got > > inconsistent results as below: > > > > == > > > > dd=pf.all_data() > > > > > > > > hot=dd.cut_region(["obj['temperature'] >= 1.e4"]) > > > > wnm=dd.cut_region(["obj['temperature'] < 1.e4"]) > > > > > > > > print dd.quantities.total_mass() > > > > print wnm.quantities.total_mass()+hot.quantities.total_mass() > > > > The total_mass includes particle fields, which will be incorrectly cut > by the cut_region. We're trying to figure out a way to make this > clearer, but you should get identical results if you use the > .total_quantity("cell_mass") function. This was the subject of a > recent bug report and discussion, as well: > > > https://bitbucket.org/yt_analysis/yt/issue/812/derived-quantities-on-cut_re… > > I thought we'd had a pull request discussion, too, but I can't find it > right now. > > -Matt > > > > > > > 2.88677799841e+38 g > > 2.91575727709e+38 g > > > > == > > > > I can't understand why those two are different. Have any idea? > > > > Chang-Goo > > > > > > _______________________________________________ > > 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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fractional keyword in profile plot
by Chang-Goo Kim May 6, 2014

May 6, 2014

Hi all, I tried to draw PDFs using ProfilePlot with "fractional" keyword. But, it returned unit incompatibility. I have looked at the code, and realized that the fractional keyword makes field_data dimensionless, while it tried to return data with units of original data. I think it must be easy to fix. Error message is attached below. Thanks, Chang-Goo ---------------------------------------------------------------------------YTUnitConversionError Traceback (most recent call last)<ipython-input-137-18016774c3d0> in <module>()----> 1 pdf=ProfilePlot(dd,"temp",['cell_mass','cell_volume'],weight_field=None,fractional=True) 2 pdf.show() /u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/visualization/profile_plotter.pyc in __init__(self, data_source, x_field, y_fields, weight_field, n_bins, accumulation, fractional, label, plot_spec, profiles) 216 self.plot_spec = [self.plot_spec.copy() for p in self.profiles] 217 --> 218 self._setup_plots() 219 220 def save(self, name=None): /u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/visualization/profile_plotter.pyc in _setup_plots(self) 309 self.axes = AxesContainer(self.figures) 310 for i, profile in enumerate(self.profiles):--> 311 for field, field_data in profile.items(): 312 self.axes[field].plot(np.array(profile.x), 313 np.array(field_data), /u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/data_objects/profiles.pyc in items(self) 854 855 def items(self):--> 856 return [(k,self[k]) for k in self.field_data.keys()] 857 858 def __iter__(self): /u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/data_objects/profiles.pyc in __getitem__(self, field) 851 raise KeyError(field) 852 else:--> 853 return self.field_data[fname].in_units(self.field_units[fname]) 854 855 def items(self): /u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/units/yt_array.pyc in in_units(self, units) 358 359 """--> 360 new_units = self._unit_repr_check_same(units) 361 conversion_factor = self.units.get_conversion_factor(new_units) 362 /u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/units/yt_array.pyc in _unit_repr_check_same(self, units) 315 if not self.units.same_dimensions_as(units): 316 raise YTUnitConversionError(--> 317 self.units, self.units.dimensions, units, units.dimensions) 318 319 return units YTUnitConversionError: Unit dimensionalities do not match. Tried to convert between dimensionless (dim 1) and code_length**3 (dim (length)**3).

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total mass
by Chang-Goo Kim May 6, 2014

May 6, 2014

Hi all again, I tried to find mass fraction of each temperature component, but I got inconsistent results as below: == dd=pf.all_data() hot=dd.cut_region(["obj['temperature'] >= 1.e4"]) wnm=dd.cut_region(["obj['temperature'] < 1.e4"]) print dd.quantities.total_mass() print wnm.quantities.total_mass()+hot.quantities.total_mass() 2.88677799841e+38 g 2.91575727709e+38 g == I can't understand why those two are different. Have any idea? Chang-Goo

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Parallel Broadcasting in yt
by Claire Kopenhafer May 5, 2014

May 5, 2014

Hello all, I've got a code that reads in a dictionary from file and then operates on it, and I'd like to run it in parallel. My best thought is to have the root process read in the dict and then broadcast it to all the rest, but I am not sure how best to do this within yt. Any suggestions? Thanks! -Claire

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Profile of a projected quantity?
by Nathan Goldbaum May 5, 2014

May 5, 2014

Hi all, Is there a way for me to find a profile using a projection as a data source? In particular, I'd like to find a radial profile of a surface density in a disk galaxy simulation. I think I could do this by histogramming a fixed resolution buffer created by a projection data source but is that the only way to do it? I'd prefer for my data pipeline to look identical for computing profiles and in all other cases I'm using a Profile1D object to find things like the cumulative mass or the average density as a function of radius. Thanks for your help with this! -Nathan

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Problem importing yt.mods
by Saqib Nawaz May 5, 2014

May 5, 2014

hello everyone, i am new to enzo. I am tyrying to make a phase plot from a.py script. but i am getting following errors. from: can't read /var/mail/yt.mods ./a.py: line 4: syntax error near unexpected token `(' ./a.py: line 4: `pf = load("IsolatedGalaxy/galaxy0030")' Is yt is not activated right? yt_install.log file is also attached. thanks in advance Saqib

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installation problem.
by oleg burgueño May 5, 2014

May 5, 2014

i been having a problem trying to install the 3.0 version of yt. It appears that some file or files are missing. i would appreciate any help in the matter, thank you

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Axis labels and text annotations
by Jeremy Ritter May 4, 2014

May 4, 2014

Hello, I'm relatively new to YT. Creating great looking plots seems to be really easy, but setting axis labels and other text labels (timestamps) has proven to be quite challenging. I'm creating some phase plots with the latest stable version (2.6 I think), and I would like for variables to have proper names, e.g. "Number Density" instead of "NumberDensity". I first tried changing the labels using the axes object set_xlabel/set_ylabel methods, but that removes the units and doesn't accept latex style commands for making my own units. It also appears to change the font style. Then I tried creating derived fields with the proper names including spaces, but it seems that the labels get squished, having all spaces removed when it prints the label. Filename output still has the spaces in the variable name. What is the easiest way to set publication quality axis labels with units in v2.6? My other problem seems to be that I'm unable to use any of the annotation callbacks with a phase plot. Is this true? I just want to add a timestamp, for which I've already created the string, e.g. "5.35 Myr". Thanks! -Jeremy

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Freeprocessing
by tom fogal April 30, 2014

April 30, 2014

Hi all, I'm Tom; new here, but I've been lurking on #yt (and #enzo) for a while now. My group and I created an in situ visualization tool that we're calling "Freeprocessing", and a few of you helped me hook it up to yt for a publication. Thanks for all your help---that paper was recently accepted! :-) Now that the edits are in, I'd like to delve into the problem deeper and hopefully expand on the 'proof of concept' we had used in the paper. If you could give it a try, I'd love to get people's thoughts on future directions, or even just issues we could address. More info on the website: https://tfogal.github.io/freeprocessing/ I'm "tfogal" on freenode/#yt and would love to chat with some of you there, but email works if you're not the IRC type. Thanks! -tom

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