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
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.
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
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
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
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
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
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
********************************************
********************************************
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
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
