yt-users August 2015

yt-users@python.org

34 participants
37 discussions

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.

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

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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 30 Aug '15

30 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

3 8

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

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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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yt-users August 2015