Mailman 3 August 2015 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman 15 Aug '22

15 Aug '22

Hi All, I was curious if anyone has had any luck porting .ply files generated with yt into Blender with colors? It seems to port in the surfaces just fine, but they are a uniform color. From what I can gather, Blender imports .ply files with face color instead of vertex so I tried the surf.export_ply routine with "face" instead of "vertex" for sample_type, but no luck ("vertex" doesn't work either). Let me know if I can provide any more useful info. Thanks for any help, -J

3 2

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

8 14

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.

6 8

EnzoDatasetInMemory not working in parallel
by Britton Smith 24 Feb '16

24 Feb '16

Hi all, I've recently been trying to use yt's inline analysis functionality with Enzo and am having some difficultly getting it to work in parallel. I am using the development tip of yt. In serial, everything works fine, but in parallel, I get the following error: http://paste.yt-project.org/show/5694/ It seems that the issue is that yt is not correctly identifying which grids are available on a given processory for the EnzoDatasetInMemory object. Does anyone have an idea of how to fix this? Has anyone else seen this? For reference, my user_script is just this: import yt from yt.frontends.enzo.api import EnzoDatasetInMemory def main(): ds = EnzoDatasetInMemory() ad = ds.all_data() print ad.quantities.total_quantity("cell_mass") Thanks for any help, Britton

3 9

stitching data sets together
by Jonah Miller 03 Sep '15

03 Sep '15

Hi Everyone, I have data for a simulation in spherical coordinates that I wish to input into yt and visualize using the generic reader tools. However, the simulation is broken up into six volumes, each of which is a solid angle that makes up part of a sphere. Unfortunately, stitching together the arrays of data produces a lot of redundancies, there's no easy way to include all of it in a single array without including the same data points several times. So what I'd like is a way to feed in each solid angle as an individual data set, but visualize all six datasets on a single plot. Is this possible? Thanks in advance for your help! Best, Jonah MIller

2 6

problem with units
by alex volioths 03 Sep '15

03 Sep '15

Hello everyone, I've been practicing with the example "Creating a X-ray observation from an in-memory dataset" from here http://yt-project.org/doc/analyzing/analysis_modules/photon_simulator.html However even with simple copy and paste after defining the photons I get this error message: File "/usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 685, in runfile execfile(filename, namespace) File "/usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 78, in execfile builtins.execfile(filename, *where) File "/home/afi/Documents/X_ray_sim/X_mock.py", line 75, in <module> exp_time, thermal_model, center="c") File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/analysis_modules/photon_simulator/photon_simulator.py", line 330, in from_scratch photons = photon_model(data_source, parameters) File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/analysis_modules/photon_simulator/photon_models.py", line 140, in __call__ kT_bins = np.linspace(kT_min, max(my_kT_max, kT_max), num=n_kT+1) File "/usr/lib/python2.7/dist-packages/numpy/core/function_base.py", line 87, in linspace step = (stop-start)/float((num-1)) File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/units/yt_array.py", line 745, in __sub__ ro = sanitize_units_add(self, right_object, "subtraction") File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/units/yt_array.py", line 134, in sanitize_units_add raise YTUnitOperationError(op_string, inp.units, dimensionless) YTUnitOperationError: The subtraction operator for YTArrays with units (keV) and (1) is not well defined. Any ideas? I am new to yt and i can't see something wrong. Thnak you Alex Creating a X-ray observation from an in-memory datasetCreating a X-ray observation from an in-memory dataset

2 12

color bar limits
by Guido granda muñoz 29 Aug '15

29 Aug '15

Hello, I'm wondering how can I get the color bar limits of a projection plot in the new yt version, I managed to do it in the old 2.5 version in this way: ********************************************************************** fn =data[i] title =titles[i] pro =fn.h.proj(axis,field,center=fn.domain_center) proj =fn.h.proj(0,field,weight_field=field,center=fn.domain_center) pro_frb =pro.to_frb((25./h, "Mpc"), 2000) axs1[i] =plt.subplot(2,2,i+1) Image=axs1[i].imshow(pro_frb[field],origin='lower',norm=LogNorm(),extent=(-12.5/h,12.5/h,-12.5/h,12.5/h)) vmin_0,vmax_0 = Image.get_clim() *********************************************************************** I tried to find out something similar with the new yt.ProjectionPlot( ) without success, Could you please help me? Kind Regards, -- Guido

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Re: [yt-users] [FLASH-USERS] ANN: yt-3.2 released
by Alexander Heger 27 Aug '15

27 Aug '15

Dear John, I just tried the new version of yt. Installation worked! But going through the demo notebooks, already "3)_Simple_Visualization" fails on the first plot. Error trace below. I ma not really sure why the first error occurs as the font is installed, but the second error is a bug with trying to decode a string (you can decode bytes type and encode strings in python3), the last one seems strange why it would look for a font in the current directory. I also note that the notebook is still python 2 - so all the print statements don't work. I am happy to share my notebooks with these fixed if I can get them to run. -Alexander --------------------------------------------------------------------------- KeyError Traceback (most recent call last) /home/alex/Python/lib/python3.4/site-packages/matplotlib/dviread.py in __getitem__(self, texname) 706 try: --> 707 result = self._font[texname] 708 except KeyError: KeyError: 'cmsy10' During handling of the above exception, another exception occurred: AttributeError Traceback (most recent call last) /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in print_pdf(self, filename, **kwargs) 2484 bbox_inches_restore=_bbox_inches_restore) -> 2485 self.figure.draw(renderer) 2486 renderer.finalize() /home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs) 58 before(artist, renderer) ---> 59 draw(artist, renderer, *args, **kwargs) 60 after(artist, renderer) /home/alex/Python/lib/python3.4/site-packages/matplotlib/figure.py in draw(self, renderer) 1084 for zorder, a, func, args in dsu: -> 1085 func(*args) 1086 /home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs) 58 before(artist, renderer) ---> 59 draw(artist, renderer, *args, **kwargs) 60 after(artist, renderer) /home/alex/Python/lib/python3.4/site-packages/matplotlib/axes/_base.py in draw(self, renderer, inframe) 2109 for zorder, a in dsu: -> 2110 a.draw(renderer) 2111 /home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs) 58 before(artist, renderer) ---> 59 draw(artist, renderer, *args, **kwargs) 60 after(artist, renderer) /home/alex/Python/lib/python3.4/site-packages/matplotlib/axis.py in draw(self, renderer, *args, **kwargs) 1118 for tick in ticks_to_draw: -> 1119 tick.draw(renderer) 1120 /home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs) 58 before(artist, renderer) ---> 59 draw(artist, renderer, *args, **kwargs) 60 after(artist, renderer) /home/alex/Python/lib/python3.4/site-packages/matplotlib/axis.py in draw(self, renderer) 248 if self.label1On: --> 249 self.label1.draw(renderer) 250 if self.label2On: /home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs) 58 before(artist, renderer) ---> 59 draw(artist, renderer, *args, **kwargs) 60 after(artist, renderer) /home/alex/Python/lib/python3.4/site-packages/matplotlib/text.py in draw(self, renderer) 637 renderer.draw_tex(gc, x, y, clean_line, --> 638 self._fontproperties, angle, mtext=mtext) 639 else: /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in draw_tex(self, gc, x, y, s, prop, angle, ismath, mtext) 1823 if dvifont.texname not in self.file.dviFontInfo: -> 1824 psfont = self.tex_font_mapping(dvifont.texname) 1825 self.file.dviFontInfo[dvifont.texname] = Bunch( /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in tex_font_mapping(self, texfont) 1530 dviread.PsfontsMap(dviread.find_tex_file('pdftex.map')) -> 1531 return self.tex_font_map[texfont] 1532 /home/alex/Python/lib/python3.4/site-packages/matplotlib/dviread.py in __getitem__(self, texname) 708 except KeyError: --> 709 result = self._font[texname.decode('ascii')] 710 fn, enc = result.filename, result.encoding AttributeError: 'str' object has no attribute 'decode' During handling of the above exception, another exception occurred: FileNotFoundError Traceback (most recent call last) /home/alex/Python/lib/python3.4/site-packages/IPython/core/formatters.py in __call__(self, obj) 339 method = _safe_get_formatter_method(obj, self.print_method) 340 if method is not None: --> 341 return method() 342 return None 343 else: /home/alex/Python/lib/python3.4/site-packages/yt/visualization/plot_container.py in newfunc(*args, **kwargs) 75 if hasattr(args[0], 'run_callbacks'): 76 args[0].run_callbacks() ---> 77 rv = f(*args, **kwargs) 78 return rv 79 return newfunc /home/alex/Python/lib/python3.4/site-packages/yt/visualization/plot_container.py in _repr_html_(self) 642 ret = '' 643 for field in self.plots: --> 644 img = base64.b64encode(self.plots[field]._repr_png_()).decode() 645 ret += r'<img style="max-width:100%%;max-height:100%%;" ' \ 646 r'src="data:image/png;base64,{0}"><br>'.format(img) /home/alex/Python/lib/python3.4/site-packages/yt/visualization/base_plot_types.py in _repr_png_(self) 165 canvas = FigureCanvasAgg(self.figure) 166 f = BytesIO() --> 167 canvas.print_figure(f) 168 f.seek(0) 169 return f.read() /home/alex/Python/lib/python3.4/site-packages/matplotlib/backend_bases.py in print_figure(self, filename, dpi, facecolor, edgecolor, orientation, format, **kwargs) 2209 orientation=orientation, 2210 bbox_inches_restore=_bbox_inches_restore, -> 2211 **kwargs) 2212 finally: 2213 if bbox_inches and restore_bbox: /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in print_pdf(self, filename, **kwargs) 2489 file.endStream() 2490 else: # we opened the file above; now finish it off -> 2491 file.close() 2492 2493 /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in close(self) 523 self.endStream() 524 # Write out the various deferred objects --> 525 self.writeFonts() 526 self.writeObject(self.alphaStateObject, 527 dict([(val[0], val[1]) /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in writeFonts(self) 623 # a normal TrueType font 624 matplotlib.verbose.report('Writing TrueType font', 'debug') --> 625 realpath, stat_key = get_realpath_and_stat(filename) 626 chars = self.used_characters.get(stat_key) 627 if chars is not None and len(chars[1]): /home/alex/Python/lib/python3.4/site-packages/matplotlib/cbook.py in __call__(self, path) 1020 stat_key = realpath 1021 else: -> 1022 stat = os.stat(realpath) 1023 stat_key = (stat.st_ino, stat.st_dev) 1024 result = realpath, stat_key FileNotFoundError: [Errno 2] No such file or directory: '/home/alex/yt/doc/source/quickstart/cmsy10' <yt.visualization.plot_window.ProjectionPlot at 0x7fb8225470b8> On 25 July 2015 at 05:48, John ZuHone <jzuhone(a)space.mit.edu> wrote: > We are proud to announce the release of yt 3.2! > > yt (http://yt-project.org) is an open source, community-developed toolkit > for analysis and visualization of volumetric data of all types, with a > particular emphasis on astrophysical simulations and nuclear engineering > simulations. > > Major enhancements > > Particle-Only Plots - a series of new plotting functions for visualizing > particle data. See here for more information. > Late-stage beta support for Python 3 - unit tests and answer tests pass for > all the major frontends under python 3.4, and yt should now be mostly if not > fully usable. Because many of the yt developers are still on Python 2 at > this point, this should be considered a “late stage beta” as there may be > remaining issues yet to be identified or worked out. > Now supporting Gadget Friend-of-Friends/Subfind catalogs - see here to learn > how to load halo catalogs as regular yt datasets. > Custom colormaps can now be easily defined and added - see here to learn > how! > Now supporting Fargo3D data > Performance improvements throughout the code base for memory and speed > > > Minor enhancements > > Various updates to the following frontends: ART, Athena, Castro, Chombo, > Gadget, GDF, Maestro, Pluto, RAMSES, Rockstar, SDF, Tipsy > Numerous documentation updates > Generic hexahedral mesh pixelizer > Adding annotate_ray() callback for plots > AbsorptionSpectrum returned to full functionality and now using faster SciPy > Voigt profile > Add a color_field argument to annotate_streamline > Smoothing lengths auto-calculated for Tipsy Datasets > Adding SimulationTimeSeries support for Gadget and OWLS. > Generalizing derived quantity outputs to all be YTArrays or lists of > YTArrays as appropriate > Star analysis returned to full functionality > FITS image writing refactor > Adding gradient fields on the fly > Adding support for Gadget Nx4 metallicity fields > Updating value of solar metal mass fraction to be consistent with Cloudy. > Gadget raw binary snapshot handling & non-cosmological simulation units > Adding support for LightRay class to work with Gadget+Tipsy > Add support for subclasses of frontends > Dependencies updated > Serialization for projections using minimal representation > Adding Grid visitors in Cython > Improved semantics for derived field units > Add a yaw() method for the PerspectiveCamera + switch back to LHS > Adding annotate_clear() function to remove previous callbacks from a plot > Added documentation for hexahedral mesh on website > Speed up nearest neighbor evaluation > Add a convenience method to create deposited particle fields > UI and docs updates for 3D streamlines > Ensure particle fields are tested in the field unit tests > Allow a suffix to be specified to save() > Add profiling using airspeed velocity > Various plotting enhancements and bugfixes > Use hglib to update > Various minor updates to halo_analysis toolkit > Docker-based tests for install_script.sh > Adding support for single and non-cosmological datasets to LightRay > Adding the Pascal unit > Add weight_field to PPVCube > FITS reader: allow HDU in auxiliary > Fixing electromagnetic units > Specific Angular Momentum [xyz] computed relative to a normal vector > > > Bugfixes > > Adding ability to create union fields from alias fields > Small fix to allow enzo AP datasets to load in parallel when no APs present > Use proper cell dimension in gradient function. > Minor memory optimization for smoothed particle fields > Fix thermal_energy for Enzo HydroMethod==6 > Make sure annotate_particles handles unitful widths properly > Improvements for add_particle_filter and particle_filter > Specify registry in off_axis_projection's image finalization > Apply fix for particle momentum units to the boxlib frontend > Avoid traceback in "yt version" when python-hglib is not installed > Expose no_ghost from export_sketchfab down to _extract_isocontours_from_grid > Fix broken magnetic_unit attribute > Fixing an off-by-one error in the set x/y lim methods for profile plots > Providing better error messages to PlotWindow callbacks > Updating annotate_timestamp to avoid auto-override > Updating callbacks to consistently define coordinate system > Fixing species fields for OWLS and tipsy > Fix extrapolation for vertex-centered data > Fix periodicity check in FRBs > Rewrote project_to_plane() in PerspectiveCamera for draw_domain() > Fix intermittent failure in test_add_deposited_particle_field > Improve minorticks for a symlog plot with one-sided data > Fix smoothed covering grid cell computation > Absorption spectrum generator now 3.0 compliant > Fix off-by-one-or-more in particle smallest dx > Fix dimensionality mismatch error in covering grid > Fix curvature term in cosmology calculator > Fix geographic axes and pixelization > Ensure axes aspect ratios respect the user-selected plot aspect ratio > Avoid clobbering field_map when calling profile.add_fields > Fixing the arbitrary grid deposit code > Fix spherical plotting centering > Make the behavior of to_frb consistent with the docstring > Ensure projected units are initialized when there are no chunks. > Removing "field already exists" warnings from the Owls and Gadget frontends > Various photon simulator bugs > Fixed use of LaTeX math mode > Fix upload_image > Enforce plot width in CSS when displayed in a notebook > Fix cStringIO.StringIO -> cStringIO in png_writer > Add some input sanitizing and error checking to covering_grid initializer > Fix for geographic plotting > Use the correct filename template for single-file OWLS datasets. > Fix Enzo IO performance for 32 bit datasets > Adding a number density field for Enzo MultiSpecies=0 datasets. > Fix RAMSES block ordering > Fix ART star particle masses to correctly reflect current and initial mass > Updating ragged array tests for NumPy 1.9.1 > Force returning lists for HDF5FileHandler > > > Coming Soon! > > The next major release of yt will be version 3.3, which is slated to include > an overhaul of the volume rendering system and support for analyzing and > visualizing unstructured mesh data. > > Standard Installation Methods > > As with previous releases, you can install yt from source using one of the > following methods. > > 1) From the install script (http://yt-project.org/#getyt ): > > Note, many of the dependencies have been updated since version 3.1. If you > previously installed yt from the install script, it is advised that you > re-install yt from scratch. > > # Installation > > $ wget http://bitbucket.org/yt_analysis/yt/raw/stable/doc/install_script.sh > $ bash install_script.sh > > # Update > > $ yt update > > 2) From pip (source or binary wheel, see below for more details): > > # Installation > > $ pip install yt > > # Update > > $ pip install -U yt > > 3) From the Anaconda Python Distribution > (https://store.continuum.io/cshop/anaconda/): > > # Installation > > $ conda install yt > > # Update > > $ conda update yt > > Note that it might take a day or two for the conda package to be updated. > > If you are on the “stable” branch, updating will bring you from yt 3.1 to > 3.2, incorporating all > changes since 3.1, whereas if you are on the “dev” or “yt” branch, only the > changes since > your last update should be incorporated. > > Installing Binary Packages via pip > > New to this release is the ability to install binary packages (“wheels”) > using pip on Windows and Mac OS X (64-bit only for both). This has the > advantage of not needing to install yt from source using a proper compiler > setup, which has caused occasional problems on both of these platforms and > prevented us from installing yt easily on other Python distributions. > > We have so far been able to install and run the binary distribution via pip > on the following platforms and Python stacks: > > Note that it might take a day or two for the pip wheels to be updated. > > Windows x86_64: > > Enthought Canopy Python (https://www.enthought.com/products/canopy/) > WinPython (http://winpython.sourceforge.net/) > > > Mac OS X x86_64: > > Enthought Canopy Python (https://www.enthought.com/products/canopy/) > Homebrew Python (http://brew.sh/) > Python.org Python > Mac OS X’s system Python > MacPorts Python (https://www.macports.org/) > > > This is somewhat experimental, so other distributions may work (or not), > please submit bug reports or successes to the mailing list or to the > Bitbucket issues page (http://bitbucket.org/yt_analysis/yt/issues). > > All distributions are recommended to be Python v. 2.7, although with yt 3.2 > there is late-stage beta support for Python 3.4. The requirements for > installing yt via this method are the same as from source: > > NumPy > h5py > HDF5 > SymPy > Matplotlib > IPython (not required, but strongly recommended) > > > To install a new version of yt on one of these platforms, simply do > > $ pip install yt > > and you should get the binary distribution automatically. Also, if your > python installation is system-wide (e.g., the Mac system Python) you might > need to run pip with administrator privileges. > > For more information, including more installation instructions, links to > community resources, and information on contributing to yt’s development, > please see the yt homepage at http://yt-project.org and the documentation > for yt-3.2 at http://yt-project.org/docs/3.2. > > yt is the product of a large community of developers and users and we are > extraordinarily grateful for and proud of their contributions. Please > forward this announcement on to any interested parties. > > As always, if you have any questions, concerns, or run into any trouble > updating please don't hesitate to send a message to the mailing list or stop > by our IRC channel. > > All the best, > The yt development team

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Problem installing yt on NASA Pleiades
by Eli Visbal 27 Aug '15

27 Aug '15

Hello, I am a postdoc at Columbia University fairly new to yt and am having trouble installing it on the NASA Pleiades supercomputer. I was hoping that someone else has figured this out before and could help me. I tried running the yt install script obtained with: wget http://bitbucket.org/yt_analysis/yt/raw/stable/doc/install_script.sh When I attempt to run this script, it crashes giving the error message copied below. I believe it may be related to the version of ssl on Pleiades. Any help would be greatly appreciated. Thank you! Best, Eli Visbal ----------------------------------------------------------------- ... Installing HDF5 Installing SQLite3 Installing Python 2. This may take a while, but don't worry. yt loves you. Installing setuptools-18.0.1 Installing mercurial-3.4 Cloning yt Setting YT_DIR=/u/evisbal/yt-x86_64/src/yt-hg/ Installing pip ******************************************** FAILURE REPORT: ******************************************** File "/home1/evisbal/yt-x86_64/lib/python2.7/site-packages/mercurial/url.py", line 346, in connect **sslutil.sslkwargs(self.ui, host)) File "/home1/evisbal/yt-x86_64/lib/python2.7/site-packages/mercurial/sslutil.py", line 36, in ssl_wrap_socket sslcontext.options &= ssl.OP_NO_SSLv2 & ssl.OP_NO_SSLv3 ValueError: can't clear options before OpenSSL 0.9.8m abort: repository /u/evisbal/yt-x86_64/src/yt-hg/ not found! 2015-08-26 14:01:04 URL:https://bootstrap.pypa.io/get-pip.py [1412744/1412744] -> "get-pip.py" [1] Collecting pip Could not find a version that satisfies the requirement pip (from versions: ) No matching distribution found for pip ******************************************** ********************************************

2 4

Problem with Units in a Derived Field
by Jared Coughlin 26 Aug '15

26 Aug '15

Hello! I have a gadget snapshot for which the standard internal energy block has been replaced by one containing the temperature. I'm trying to calculate a derived field for the neutral hydrogen number density, but I'm getting an error when I try to do ds.add_field(): http://paste.yt-project.org/show/5833/ However, I get an error about being unable to add quantities with differing units: http://paste.yt-project.org/show/5834/ The docs say not to do any unit conversion because that is apparently taken care of behind the scenes, so I didn't. I was just wondering if there was a way around this? Thanks! -Jared

4 16

Arch Linux Packages
by Stuart Mumford 25 Aug '15

25 Aug '15

Hello, I have uploaded new Arch Linux AUR yt packages for both Python 2 and Python 3. https://aur.archlinux.org/packages/python-yt/ https://aur.archlinux.org/packages/python2-yt/ For the Python 2 package I have appended a '2' to all the executable scripts so you can have both Python 2 and Python 3 versions installed along side one another. Any feedback and bug reports are welcome. Sorry it took a while after the 3.2 release, blame my impending release of Thesis 0.1. Stuart

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Re: [yt-users] [FLASH-USERS] ANN: yt-3.2 released
by Alexander Heger 25 Aug '15

25 Aug '15

Dear John, I just tried the new version of yt. Installation worked! But going through the demo notebooks, already "3)_Simple_Visualization" fails on the first plot. Error trace below. I ma not really sure why the first error occurs as the font is installed, but the second error is a bug with trying to decode a string (you can decode bytes type and encode strings in python3), the last one seems strange why it would look for a font in the current directory. I also note that the notebook is still python 2 - so all the print statements don't work. I am happy to share my notebooks with these fixed if I can get them to run. -Alexander --------------------------------------------------------------------------- KeyError Traceback (most recent call last) /home/alex/Python/lib/python3.4/site-packages/matplotlib/dviread.py in __getitem__(self, texname) 706 try: --> 707 result = self._font[texname] 708 except KeyError: KeyError: 'cmsy10' During handling of the above exception, another exception occurred: AttributeError Traceback (most recent call last) /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in print_pdf(self, filename, **kwargs) 2484 bbox_inches_restore=_bbox_inches_restore) -> 2485 self.figure.draw(renderer) 2486 renderer.finalize() /home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs) 58 before(artist, renderer) ---> 59 draw(artist, renderer, *args, **kwargs) 60 after(artist, renderer) /home/alex/Python/lib/python3.4/site-packages/matplotlib/figure.py in draw(self, renderer) 1084 for zorder, a, func, args in dsu: -> 1085 func(*args) 1086 /home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs) 58 before(artist, renderer) ---> 59 draw(artist, renderer, *args, **kwargs) 60 after(artist, renderer) /home/alex/Python/lib/python3.4/site-packages/matplotlib/axes/_base.py in draw(self, renderer, inframe) 2109 for zorder, a in dsu: -> 2110 a.draw(renderer) 2111 /home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs) 58 before(artist, renderer) ---> 59 draw(artist, renderer, *args, **kwargs) 60 after(artist, renderer) /home/alex/Python/lib/python3.4/site-packages/matplotlib/axis.py in draw(self, renderer, *args, **kwargs) 1118 for tick in ticks_to_draw: -> 1119 tick.draw(renderer) 1120 /home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs) 58 before(artist, renderer) ---> 59 draw(artist, renderer, *args, **kwargs) 60 after(artist, renderer) /home/alex/Python/lib/python3.4/site-packages/matplotlib/axis.py in draw(self, renderer) 248 if self.label1On: --> 249 self.label1.draw(renderer) 250 if self.label2On: /home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs) 58 before(artist, renderer) ---> 59 draw(artist, renderer, *args, **kwargs) 60 after(artist, renderer) /home/alex/Python/lib/python3.4/site-packages/matplotlib/text.py in draw(self, renderer) 637 renderer.draw_tex(gc, x, y, clean_line, --> 638 self._fontproperties, angle, mtext=mtext) 639 else: /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in draw_tex(self, gc, x, y, s, prop, angle, ismath, mtext) 1823 if dvifont.texname not in self.file.dviFontInfo: -> 1824 psfont = self.tex_font_mapping(dvifont.texname) 1825 self.file.dviFontInfo[dvifont.texname] = Bunch( /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in tex_font_mapping(self, texfont) 1530 dviread.PsfontsMap(dviread.find_tex_file('pdftex.map')) -> 1531 return self.tex_font_map[texfont] 1532 /home/alex/Python/lib/python3.4/site-packages/matplotlib/dviread.py in __getitem__(self, texname) 708 except KeyError: --> 709 result = self._font[texname.decode('ascii')] 710 fn, enc = result.filename, result.encoding AttributeError: 'str' object has no attribute 'decode' During handling of the above exception, another exception occurred: FileNotFoundError Traceback (most recent call last) /home/alex/Python/lib/python3.4/site-packages/IPython/core/formatters.py in __call__(self, obj) 339 method = _safe_get_formatter_method(obj, self.print_method) 340 if method is not None: --> 341 return method() 342 return None 343 else: /home/alex/Python/lib/python3.4/site-packages/yt/visualization/plot_container.py in newfunc(*args, **kwargs) 75 if hasattr(args[0], 'run_callbacks'): 76 args[0].run_callbacks() ---> 77 rv = f(*args, **kwargs) 78 return rv 79 return newfunc /home/alex/Python/lib/python3.4/site-packages/yt/visualization/plot_container.py in _repr_html_(self) 642 ret = '' 643 for field in self.plots: --> 644 img = base64.b64encode(self.plots[field]._repr_png_()).decode() 645 ret += r'<img style="max-width:100%%;max-height:100%%;" ' \ 646 r'src="data:image/png;base64,{0}"><br>'.format(img) /home/alex/Python/lib/python3.4/site-packages/yt/visualization/base_plot_types.py in _repr_png_(self) 165 canvas = FigureCanvasAgg(self.figure) 166 f = BytesIO() --> 167 canvas.print_figure(f) 168 f.seek(0) 169 return f.read() /home/alex/Python/lib/python3.4/site-packages/matplotlib/backend_bases.py in print_figure(self, filename, dpi, facecolor, edgecolor, orientation, format, **kwargs) 2209 orientation=orientation, 2210 bbox_inches_restore=_bbox_inches_restore, -> 2211 **kwargs) 2212 finally: 2213 if bbox_inches and restore_bbox: /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in print_pdf(self, filename, **kwargs) 2489 file.endStream() 2490 else: # we opened the file above; now finish it off -> 2491 file.close() 2492 2493 /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in close(self) 523 self.endStream() 524 # Write out the various deferred objects --> 525 self.writeFonts() 526 self.writeObject(self.alphaStateObject, 527 dict([(val[0], val[1]) /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in writeFonts(self) 623 # a normal TrueType font 624 matplotlib.verbose.report('Writing TrueType font', 'debug') --> 625 realpath, stat_key = get_realpath_and_stat(filename) 626 chars = self.used_characters.get(stat_key) 627 if chars is not None and len(chars[1]): /home/alex/Python/lib/python3.4/site-packages/matplotlib/cbook.py in __call__(self, path) 1020 stat_key = realpath 1021 else: -> 1022 stat = os.stat(realpath) 1023 stat_key = (stat.st_ino, stat.st_dev) 1024 result = realpath, stat_key FileNotFoundError: [Errno 2] No such file or directory: '/home/alex/yt/doc/source/quickstart/cmsy10' <yt.visualization.plot_window.ProjectionPlot at 0x7fb8225470b8> On 25 July 2015 at 05:48, John ZuHone <jzuhone(a)space.mit.edu> wrote: > We are proud to announce the release of yt 3.2! > > yt (http://yt-project.org) is an open source, community-developed toolkit > for analysis and visualization of volumetric data of all types, with a > particular emphasis on astrophysical simulations and nuclear engineering > simulations. > > Major enhancements > > Particle-Only Plots - a series of new plotting functions for visualizing > particle data. See here for more information. > Late-stage beta support for Python 3 - unit tests and answer tests pass for > all the major frontends under python 3.4, and yt should now be mostly if not > fully usable. Because many of the yt developers are still on Python 2 at > this point, this should be considered a “late stage beta” as there may be > remaining issues yet to be identified or worked out. > Now supporting Gadget Friend-of-Friends/Subfind catalogs - see here to learn > how to load halo catalogs as regular yt datasets. > Custom colormaps can now be easily defined and added - see here to learn > how! > Now supporting Fargo3D data > Performance improvements throughout the code base for memory and speed > > > Minor enhancements > > Various updates to the following frontends: ART, Athena, Castro, Chombo, > Gadget, GDF, Maestro, Pluto, RAMSES, Rockstar, SDF, Tipsy > Numerous documentation updates > Generic hexahedral mesh pixelizer > Adding annotate_ray() callback for plots > AbsorptionSpectrum returned to full functionality and now using faster SciPy > Voigt profile > Add a color_field argument to annotate_streamline > Smoothing lengths auto-calculated for Tipsy Datasets > Adding SimulationTimeSeries support for Gadget and OWLS. > Generalizing derived quantity outputs to all be YTArrays or lists of > YTArrays as appropriate > Star analysis returned to full functionality > FITS image writing refactor > Adding gradient fields on the fly > Adding support for Gadget Nx4 metallicity fields > Updating value of solar metal mass fraction to be consistent with Cloudy. > Gadget raw binary snapshot handling & non-cosmological simulation units > Adding support for LightRay class to work with Gadget+Tipsy > Add support for subclasses of frontends > Dependencies updated > Serialization for projections using minimal representation > Adding Grid visitors in Cython > Improved semantics for derived field units > Add a yaw() method for the PerspectiveCamera + switch back to LHS > Adding annotate_clear() function to remove previous callbacks from a plot > Added documentation for hexahedral mesh on website > Speed up nearest neighbor evaluation > Add a convenience method to create deposited particle fields > UI and docs updates for 3D streamlines > Ensure particle fields are tested in the field unit tests > Allow a suffix to be specified to save() > Add profiling using airspeed velocity > Various plotting enhancements and bugfixes > Use hglib to update > Various minor updates to halo_analysis toolkit > Docker-based tests for install_script.sh > Adding support for single and non-cosmological datasets to LightRay > Adding the Pascal unit > Add weight_field to PPVCube > FITS reader: allow HDU in auxiliary > Fixing electromagnetic units > Specific Angular Momentum [xyz] computed relative to a normal vector > > > Bugfixes > > Adding ability to create union fields from alias fields > Small fix to allow enzo AP datasets to load in parallel when no APs present > Use proper cell dimension in gradient function. > Minor memory optimization for smoothed particle fields > Fix thermal_energy for Enzo HydroMethod==6 > Make sure annotate_particles handles unitful widths properly > Improvements for add_particle_filter and particle_filter > Specify registry in off_axis_projection's image finalization > Apply fix for particle momentum units to the boxlib frontend > Avoid traceback in "yt version" when python-hglib is not installed > Expose no_ghost from export_sketchfab down to _extract_isocontours_from_grid > Fix broken magnetic_unit attribute > Fixing an off-by-one error in the set x/y lim methods for profile plots > Providing better error messages to PlotWindow callbacks > Updating annotate_timestamp to avoid auto-override > Updating callbacks to consistently define coordinate system > Fixing species fields for OWLS and tipsy > Fix extrapolation for vertex-centered data > Fix periodicity check in FRBs > Rewrote project_to_plane() in PerspectiveCamera for draw_domain() > Fix intermittent failure in test_add_deposited_particle_field > Improve minorticks for a symlog plot with one-sided data > Fix smoothed covering grid cell computation > Absorption spectrum generator now 3.0 compliant > Fix off-by-one-or-more in particle smallest dx > Fix dimensionality mismatch error in covering grid > Fix curvature term in cosmology calculator > Fix geographic axes and pixelization > Ensure axes aspect ratios respect the user-selected plot aspect ratio > Avoid clobbering field_map when calling profile.add_fields > Fixing the arbitrary grid deposit code > Fix spherical plotting centering > Make the behavior of to_frb consistent with the docstring > Ensure projected units are initialized when there are no chunks. > Removing "field already exists" warnings from the Owls and Gadget frontends > Various photon simulator bugs > Fixed use of LaTeX math mode > Fix upload_image > Enforce plot width in CSS when displayed in a notebook > Fix cStringIO.StringIO -> cStringIO in png_writer > Add some input sanitizing and error checking to covering_grid initializer > Fix for geographic plotting > Use the correct filename template for single-file OWLS datasets. > Fix Enzo IO performance for 32 bit datasets > Adding a number density field for Enzo MultiSpecies=0 datasets. > Fix RAMSES block ordering > Fix ART star particle masses to correctly reflect current and initial mass > Updating ragged array tests for NumPy 1.9.1 > Force returning lists for HDF5FileHandler > > > Coming Soon! > > The next major release of yt will be version 3.3, which is slated to include > an overhaul of the volume rendering system and support for analyzing and > visualizing unstructured mesh data. > > Standard Installation Methods > > As with previous releases, you can install yt from source using one of the > following methods. > > 1) From the install script (http://yt-project.org/#getyt ): > > Note, many of the dependencies have been updated since version 3.1. If you > previously installed yt from the install script, it is advised that you > re-install yt from scratch. > > # Installation > > $ wget http://bitbucket.org/yt_analysis/yt/raw/stable/doc/install_script.sh > $ bash install_script.sh > > # Update > > $ yt update > > 2) From pip (source or binary wheel, see below for more details): > > # Installation > > $ pip install yt > > # Update > > $ pip install -U yt > > 3) From the Anaconda Python Distribution > (https://store.continuum.io/cshop/anaconda/): > > # Installation > > $ conda install yt > > # Update > > $ conda update yt > > Note that it might take a day or two for the conda package to be updated. > > If you are on the “stable” branch, updating will bring you from yt 3.1 to > 3.2, incorporating all > changes since 3.1, whereas if you are on the “dev” or “yt” branch, only the > changes since > your last update should be incorporated. > > Installing Binary Packages via pip > > New to this release is the ability to install binary packages (“wheels”) > using pip on Windows and Mac OS X (64-bit only for both). This has the > advantage of not needing to install yt from source using a proper compiler > setup, which has caused occasional problems on both of these platforms and > prevented us from installing yt easily on other Python distributions. > > We have so far been able to install and run the binary distribution via pip > on the following platforms and Python stacks: > > Note that it might take a day or two for the pip wheels to be updated. > > Windows x86_64: > > Enthought Canopy Python (https://www.enthought.com/products/canopy/) > WinPython (http://winpython.sourceforge.net/) > > > Mac OS X x86_64: > > Enthought Canopy Python (https://www.enthought.com/products/canopy/) > Homebrew Python (http://brew.sh/) > Python.org Python > Mac OS X’s system Python > MacPorts Python (https://www.macports.org/) > > > This is somewhat experimental, so other distributions may work (or not), > please submit bug reports or successes to the mailing list or to the > Bitbucket issues page (http://bitbucket.org/yt_analysis/yt/issues). > > All distributions are recommended to be Python v. 2.7, although with yt 3.2 > there is late-stage beta support for Python 3.4. The requirements for > installing yt via this method are the same as from source: > > NumPy > h5py > HDF5 > SymPy > Matplotlib > IPython (not required, but strongly recommended) > > > To install a new version of yt on one of these platforms, simply do > > $ pip install yt > > and you should get the binary distribution automatically. Also, if your > python installation is system-wide (e.g., the Mac system Python) you might > need to run pip with administrator privileges. > > For more information, including more installation instructions, links to > community resources, and information on contributing to yt’s development, > please see the yt homepage at http://yt-project.org and the documentation > for yt-3.2 at http://yt-project.org/docs/3.2. > > yt is the product of a large community of developers and users and we are > extraordinarily grateful for and proud of their contributions. Please > forward this announcement on to any interested parties. > > As always, if you have any questions, concerns, or run into any trouble > updating please don't hesitate to send a message to the mailing list or stop > by our IRC channel. > > All the best, > The yt development team

1 0

Derived Field Mass Unit Errors
by Madison Fitzgerald 25 Aug '15

25 Aug '15

Hello, I’ve been working on a project where I created derived fields to represent inflowing and outflowing gas in the galaxy. In doing so, I’ve run into a strange issue where yt wants my derived field for inflowing/outflowing mass (cell mass) to be dimensionless, but it will scale graphs as though the units are grams (original script found here: http://paste.yt-project.org/show/5829/ <http://paste.yt-project.org/show/5829/>). However, this makes it difficult to work with the data, so I’ve tried to give units in the derived field function (g and Msun), but I receive errors similar to this (http://paste.yt-project.org/show/5830/ <http://paste.yt-project.org/show/5830/>). If I try to change the specified unit within the mass function in the script to g or Msun, I receive this error when I try to plot instead (http://paste.yt-project.org/show/5831/ <http://paste.yt-project.org/show/5831/>). I’m working with yt through miniconda, so I have yt version 3.2, no changeset, on a Mac with OS X 10.10.4. Any suggestions? Thank you, Madison Fitzgerald Astrophysics | Lyman Briggs College Women’s & Gender Studies | College of Arts & Letters LGBTQ and Sexuality Studies Specialization Women in Science, President Undergraduate Teaching Assistant Undergraduate Research Assistant Department of Physics and Astronomy Honors College Michigan State University

2 2

Vorticity field with FLASH
by Markus Haider 21 Aug '15

21 Aug '15

Hi, I was trying to calculate the vorticity for a flash dataset. I selected a region using center = (ad.quantities.min_location('gpot')[2],ad.quantities.min_location('gpot')[3],ad.quantities.min_location('gpot')[4]) LE = center-width.in_units('code_length')/2. CN = int(width/dx) Roi = ds.covering_grid(level=level_max,left_edge=LE, dims=[CN,CN,CN]) Then, for this region I wanted to compute the vorticity using Roi["gas","vorticity_x"] This resulted in the following error: http://paste.yt-project.org/show/5824/ Thanks for your help, Cheers, Markus

4 4

ProfilePlot error: weakly-referenced object no longer exists
by Mateusz Ruszkowski 21 Aug '15

21 Aug '15

Hi, I am trying to plot two profiles on one plot and adjust xlim. I am getting the following error message: Traceback (most recent call last): File "test.py", line 17, in <module> plot.set_xlim([0.1, 1.0]) File "/home/mateuszr/my_yt/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", line 62, in newfunc rv = f(*args, **kwargs) File "/home/mateuszr/my_yt/yt-x86_64/src/yt-hg/yt/visualization/profile_plotter.py", line 547, in set_xlim extrema=extrema, units=units) File "/home/mateuszr/my_yt/yt-x86_64/src/yt-hg/yt/data_objects/profiles.py", line 1436, in create_profile bin_fields = data_source._determine_fields(bin_fields) File "/home/mateuszr/my_yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 552, in _determine_fields finfo = self.ds._get_field_info(ftype, fname) ReferenceError: weakly-referenced object no longer exists --------------------------------------------------- I am using the following script: import yt profiles = [] labels = [] for i in range(0,2,1): print i ds=yt.load("./sedov_hdf5_chk_%04i"%i) my_data = ds.sphere(ds.domain_center, 1.0) sim_time = ds.current_time profiles.append(yt.create_profile(my_data, "radius", fields=["density"], weight_field="cell_volume", n_bins=32)) labels.append("t= %.0f" % sim_time) plot = yt.ProfilePlot.from_profiles(profiles, labels=labels) plot.set_xlim([0.1, 1.0]) plot.save() ------------------------------------------------------ I am using the following yt version: Version = 3.3-dev Changeset = 603eab147248 (yt) tip ------------------------------------------------------- Data = standard Flash Sedov test. Any idea what I may be doing wrong? Thanks, Mateusz

3 3

Absorption Spectrum from Gadget snapshot problem
by Jared Coughlin 20 Aug '15

20 Aug '15

Hello! I have a custom gadget snapshot distributed onto four files, and I'm trying to make an absorption spectrum from a LOS through the middle of the box parallel to the x-axis. To this end, I have done: lr = LightRay(fname, load_kwargs={'unit_base' : my_unit_base, 'field_spec' : my_field_def}) lr.make_light_ray(start_position=[0.0, 25000.0, 25000.0], end_position=[50000.0, 25000.0, 25000.0], solution_filename='lrsol.txt', data_filename='lr.h5', fields=['temperature', 'density'], get_los_velocity=True) sp = AbsorptionSpectrum(4862.4, 4949.04, 3000) my_label = 'HI Lya' field = 'H_number_density' wavelength = 1215.67 f_value = 4.164E-01 gamma = 6.265E+08 mass = 1.00794 sp.add_line(my_label, field, wavelength, f_value, gamma, mass, label_threshold=1e10) wl, flux = sp.make_spectrum('lr.h5', output_file='spectrum.txt', line_list_file='lines.txt', use_peculiar_velocity=True) And I get the error: KeyError: "Unable to open object (Object 'h_number_density' doesn't exist)" I didn't post the traceback because it's kind of long. I have two questions. First: When calling make_light_ray and passing it fields, do I need to pass it H_number_density? Second: Does yt read in those fields from the gadget snapshot, or does it calculate them from the data in the snapshot (for example, a standard gadget snapshot does not write the temperature, but rather the internal energy)? Thanks! -Jared

3 5

convert arbitrary particle based quantities to cloud-in-cell mesh
by Brendan Griffen 19 Aug '15

19 Aug '15

Hi, I'm looking to convert particle based quantities into a uniform grid based quantity (arepo data is input). So say I have a collection of gas elements with some density rho and x,y,z positions. I want to construct an 256^3 mesh representing the cells in a mesh. x,y,z,rho --> cic mesh where the values at i,j,k is the smoothed density are created by the cic algorithm Now, generalising this more, can I have rho to be any quantity? So now say I have star particles which similarly have x,y,z but I want to distribute their luminosity. Again, I want to do it for say the gas velocity field as well. Is there any general functionality for converting particle quantities to mesh quantites in yt with the deposit all_cic functionality? I have a basic code for just x,y,z particle data and distributing that based on density to a cic (see below) ad = pf.all_data() level = int(math.log(ndim,2)) cg = pf.covering_grid(level=level, left_edge=[0,0,0],dims=[ndim,ndim,ndim]) arr = cg['deposit', 'all_cic'], but I'm not sure what to do for the other variables. Any help is appreciated in advance. Thanks. Brendan

4 5

Gadget snapshot read Problem
by Jared Coughlin 19 Aug '15

19 Aug '15

Hello! I have two questions: the first is related to saving new field specs, and the second is related to reading in the file itself. I was following along with the documentation that describes saving new field specs, and I defined a new field spec as (it should be noted that my extra columns are for both gas and star particles, and I was unsure as to how to tell yt that it applied for both types, so I made a best guess): my_field_def = ("Coordinates", "Velocities", "ParticleIDs", "Mass", ("InternalEnergy", "Gas"), ("Density", "Gas"), ("SmoothingLength", "Gas"), ("RII", "Stars"), ("RIa", "Stars"), ("StellarAge", "Stars"), ("C", "Gas", "Stars"), ("O", "Gas", "Stars"), ("Ca", "Gas", "Stars"), ("Cr", "Gas", "Stars"), ("Mn", "Gas", "Stars"), ("Fe", "Gas", "Stars"), ) And a unit base: unit_base = {'UnitLength_in_cm' : 3.085678e+21, 'UnitMass_in_g' : 1.989e+43, 'UnitVelocity_in_cm_per_s' : 1.0e+5} Firstly, when I tried to add my custom field definition to the gadget_field_specs by doing: from yt.frontends.sph.definitions import gadget_field_specs I get the error: Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named definitions Just wondering what I was doing wrong? Also, when I try to load in the snapshot, I am doing: fname = 'snapshot_000.0' ds = yt.GadgetDataset(fname, unit_base=unit_base, field_spec=my_field_def) ds.index ad = ds.all_data() pz = yt.ProjectionPlot(ds, 'z', ('gas', 'density')) pz.show() The output is: yt : [INFO ] 2015-08-18 17:24:45,103 Calculating time from 2.500e-01 to be 6.950e+16 seconds yt : [INFO ] 2015-08-18 17:24:45,144 Parameters: current_time = 6.95032608578e+16 s yt : [INFO ] 2015-08-18 17:24:45,144 Parameters: domain_dimensions = [2 2 2] yt : [INFO ] 2015-08-18 17:24:45,144 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2015-08-18 17:24:45,145 Parameters: domain_right_edge = [ 50000. 50000. 50000.] yt : [INFO ] 2015-08-18 17:24:45,145 Parameters: cosmological_simulation = 1 yt : [INFO ] 2015-08-18 17:24:45,145 Parameters: current_redshift = 3.00000005201 yt : [INFO ] 2015-08-18 17:24:45,145 Parameters: omega_lambda = 0.726 yt : [INFO ] 2015-08-18 17:24:45,145 Parameters: omega_matter = 0.274 yt : [INFO ] 2015-08-18 17:24:45,145 Parameters: hubble_constant = 0.702 yt : [INFO ] 2015-08-18 17:24:45,146 Allocating for 4.194e+06 particles yt : [INFO ] 2015-08-18 17:24:45,664 Identified 3.077e+05 octs Traceback (most recent call last): File "yt_test_script.py", line 72, in <module> ds.index File "/home/user/Research/Tools/yt/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 321, in index self, dataset_type=self.dataset_type) File "/home/user/Research/Tools/yt/yt-x86_64/src/yt-hg/yt/geometry/particle_geometry_handler.py", line 53, in __init__ super(ParticleIndex, self).__init__(ds, dataset_type) File "/home/user/Research/Tools/yt/yt-x86_64/src/yt-hg/yt/geometry/geometry_handler.py", line 65, in __init__ self._detect_output_fields() File "/home/user/Research/Tools/yt/yt-x86_64/src/yt-hg/yt/geometry/particle_geometry_handler.py", line 125, in _detect_output_fields fl, _units = self.io._identify_fields(dom) File "/home/user/Research/Tools/yt/yt-x86_64/src/yt-hg/yt/frontends/gadget/io.py", line 208, in _identify_fields field, req = field ValueError: too many values to unpack The snapshot I'm trying to load is a 128^3 50Mpc snapshot distributed onto 4 files and the error occurs on a call to ds.index, if that helps. Thank you! -Jared

4 9

Camera Annotation
by John Regan 19 Aug '15

19 Aug '15

Hi All, Just wondering if there is a way to annotate a volume render with scale lines, text etc? From (quickly) looking at the source it looks like the annotate function only adds a colorbar and doesn't have the flexibility to add other labels? Cheers, John

2 1

How to take log of a user defined field ?
by Reju Sam John 18 Aug '15

18 Aug '15

Hi, I have a user defined field with the following definition. def _epsilon(field, data): return (4.0/3.0)*(data['vShock']/data["VelocityMagnitude"]) add_field("epsilon", function=_epsilon, take_log=False, units=r" " ) Now I would like take ln(1 + data["epsilon"]). I am trying with the following definition. Is this the correct way of doing this ? def _lnepsilon(field, data): return 1 + data["epsilon"] add_field("lnepsilon", function=_lnepsilon, *take_log=True*, units=r" " ) Thank you -- Reju Sam John

2 2

How to get Cell Velocity ?
by Reju Sam John 18 Aug '15

18 Aug '15

Hi all, How to get Cell Velocity from Enzo data? Thank You. -- Reju Sam John

2 2

Installation query
by Sushilkumar 14 Aug '15

14 Aug '15

HI yt I am trying to install yt on my laptop and I got an error which mentioned checking the yt_install.log. But because the file is so extensive I am unable to locate the error. Could you help me with the same? I can email the the yt_install.log file if you need it Thanks in advance -- *SK2* *"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*

2 1

gradient field in yt3
by Yuan Li 13 Aug '15

13 Aug '15

Hi all: I am having trouble creating a gradient field in yt3. What I want is the gradient of logP, where logP is defined as: @derived_field(name="logP",units="") def _logP(field,data): return numpy.log(numpy.array(data["gas","pressure"])) Then I add the gradient field: pf.add_gradient_fields(("gas","logP")) which seems to work and I can find it in pf.derived_field_list. But if I try to use it, I get this error message: yt.units.unit_object.UnitParseError: Cannot parse for unit data from '()'. Please supply an expression of only Unit, Symbol, Pow, and Mulobjects. Is this because logP does not have a unit? Also, I had another unrelated question about the gradient fields: Can I add the gradient fields globally instead of to a specific dataset? Thanks! Yuan

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volume rendering colorbar issue
by Stephanie Tonnesen 12 Aug '15

12 Aug '15

Hi yt-users, My last attempt was too big to make it to the user list, so I will try again! I am trying to make a volume rendering using --- Version = 3.2-dev Changeset = dc2467c4eae7 (yt) tip --- and basically following this example: http://bender.astro.sunysb.edu/random/vol_rotate.py My problem is that the units are wonky on my colorbar. I input them in my transfer function as cgs, and the peaks seem to be in the right place based on my input range and sample values. Can I get the colorbar to present the density values in cgs? You can see the colorbar and the code attached. Oh, I had to add in the line matplotlib.use('pdf') because I was getting a _tkinter can't find your screen error everytime I tried to add the colorbar. I think it was a matplotlib with my computer problem. Thanks! Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes(a)gmail.com

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display of 2D cylindrical slice
by Slavin, Jonathan 11 Aug '15

11 Aug '15

Hi, As I mentioned in an earlier message, I'm doing FLASH simulations in 2D cylindrical symmetry (r-z). When I use SlicePlot in an ipython notebook, the correct labels for the axes are used but they are incorrectly centered about 0 - when both r and z should start at 0 and go to 36 pc. It's especially odd in that the INFO message printed indicates the correct limits. I suppose I should report that as a bug, but I also wondered about how to change the plotting limits. It seems that the yt.SlicePlot object does not have a set_xlim or set_ylim method. Does anyone know how to do that? Jon -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

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