I found a post about 3D data in YT ,
http://astrobiased.com/3d-data-vis-in-yt.html , very interesting. I am
working with spectral cubes from PMAS Spectrograph (at 3.5m CAHA
telescope). Thus, I tried to use it. I am newbie with python, but I was
able to install everything :-)
However I get an error message when loading the data into yt's data
structure (script http://paste.yt-project.org/show/3182/ ):
ERROR: ValueError: total size of new array must be unchanged
astropy: [ERROR ] 2013-02-20 10:46:53,395 ValueError: total size of new
array must be unchanged
Traceback (most recent call last):
File "3d_viewer.py", line 9, in <module>
pf = load_uniform_grid(data, cube.shape, 9e16)
line 490, in load_uniform_grid
grid_dimensions = domain_dimensions.reshape(nprocs,3).astype("int32")
ValueError: total size of new array must be unchanged
I have uploaded the cube to: http://bolidox.fis.ucm.es/~alex/YT_cube/ .
FITS seems to be quite ok according to the FITS validator. And the 'cube'
object is well loaded, I guess.
Have you had this problem? Cheers,
I have downloaded several ART files and parameters like current redshift or
omega lambda are okay but the current time = 4.38272802952e+17 looks very
suspicious. This may be the reason why I got an error when I try to print_stats
I also think this error is the reason why I got wrong units. By the way, I
know ART time code unit is negative and reached zero at the present time. Any
yt has been installed and I have already done some tests. I can load data from
ART but I have run into some problems. At this moment, I have a couple of
questions. One of the things that yt can do is to find the maximum of the
density field and give you the coordenates of it. The web page says that
coordinates are in code units which I guess are yt units, [0,1] in any
direction. If this is so, the maximum found by yt does not agree with the one
I found with ifrit. A second point is that when I try to compute the
"AngularMomentumVector" inside a sphere it gives me an error (with Enzo test
data I don't have this problem):
line 316, in __call__
dd = self._function(self, data)
TypeError: _x_velocity() takes exactly 1 argument (2 given)
As this years conference communications co-chair, it is my extreme pleasure
to announce the *SciPy 2013 conference from June 24th - 29th in sunny
Austin, Texas, USA.* Please see our
website<http://conference.scipy.org/scipy2013/about.php>(or below) for
A call for presentations, tutorials, and papers will be coming out very
soon. Please make sure to sign up on our mailing list<http://eepurl.com/dyoeL>,
follow us on twitter <https://twitter.com/SciPy2013>, or Google
that you don't miss out on any important updates. I sincerely hope that you
can attend this year and make 2013 the best year for SciPy yet!
SciPy 2013 Conference Announcement
SciPy 2013, the twelfth annual Scientific Computing with Python conference,
be held this June 24th-29th in Austin, Texas. SciPy is a community
the advancement of scientific computing through open source Python software
mathematics, science, and engineering. The annual SciPy Conference allows
participants from academic, commercial, and governmental organizations to
their latest projects, learn from skilled users and developers, and
The conference consists of two days of tutorials by followed by two days of
presentations, and concludes with two days of developer sprints on projects
interest to the attendees.
This year we are happy to announce two specialized tracks run in parallel to
the general conference:
In recent years, Python's machine learning libraries rapidly matured with a
flurry of new libraries and cutting-edge algorithm implement and development
occurring within Python. As Python makes these algorithms more accessible,
machine learning algorithm application has spread across disciplines.
your favorite machine learning library or how it has been used as an
tool in your work!
Over recent years, the Open Science movement has stoked a renewed
of the importance of reproducible research. The goals of this movement
improving the dissemination of progress, prevent fraud through
enable deeper/wider development and collaboration. This track is to
discuss the tools
and methods used to achieve reproducible scientific computing.
Introduced in 2012, mini-symposia are held to discuss scientific
computing applied to a specific scientific domain/industry during a
half afternoon after the general conference. Their goal is to promote
industry specific libraries and tools, and gather people with similar
interests for discussions.
Mini-symposia on the following topics will take place this year:
- Meteorology, climatology, and atmospheric and oceanic science
- Astronomy and astrophysics
- Medical imaging
Multiple interactive half-day tutorials will be taught by community experts.
The tutorials provide conceptual and practical coverage of tools that have
broad interest at both an introductory or advanced level. This year, a
third track will be added, targeting specifically programmers with no
prior knowledge of scientific python.
A hackathon environment is setup for attendees to work on the core SciPy
packages or their own personal projects. The conference is an opportunity
developers that are usually physically separated to come together and
highly productive sessions. It is also an occasion for new community
members to introduce themselves and recieve tips from community
experts. This year, some of the sprints will be scheduled and
announced ahead of the conference.
Birds-of-a-Feather (BOF) Sessions
Birds-of-a-Feather sessions are self-organized discussions that run
the main conference. The BOFs sessions cover primary, tangential, or
topics in an interactive, discussion setting. This year, some of the
BOF sessions will be scheduled and announced ahead of the conference.
- March 18th: Presentation abstracts, poster, tutorial submission
deadline. Application for sponsorship deadline.
- April 15th: Speakers selected
- April 22nd: Sponsorship acceptance deadline
- May 1st: Speaker schedule announced
- May 5th: Paper submission deadline
- May 6th: Early-bird registration ends
- June 24th-29th: 2 days of tutorials, 2 days of conference, 2 days of
We look forward to a very exciting conference and hope to see you all at
The SciPy2013 organization team:
* Andy Terrel, Co-chair
* Jonathan Rocher, Co-chair
* Katy Huff, Program Committee co-chair
* Matt McCormick, Program Committee co-chair
* Dharhas Pothina, Tutorial co-chair
* Francesc Alted, Tutorial co-chair
* Corran Webster, Sprint co-chair
* Peter Wang, Sprint co-chair
* Matthew Turk, BoF co-chair
* Jarrod Millman, Proceeding co-chair
* Stéfan van der Walt, Proceeding co-chair
* Anthony Scopatz, Communications co-chair
* Majken Tranby, Communications co-chair
* Jeff Daily, Financial Aid co-chair
* John Wiggins, Financial Aid co-chair
* Leah Jones, Operations chair
* Brett Murphy, Sponsor chair
* Bill Cowan, Financial chair
Dear List --
I had some build issues with yt on OpenSuSE 12.2 which likely affect users of >12.1 Python apparently builds critical components into
and then looks for them in:
resulting in this failure when the script tried to build distribute.
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
Traceback (most recent call last):
File "/UBC-O/erosolo/yt-x86_64/lib/python2.7/site.py", line 563, in <module>
File "/UBC-O/erosolo/yt-x86_64/lib/python2.7/site.py", line 545, in main
known_paths = addusersitepackages(known_paths)
File "/UBC-O/erosolo/yt-x86_64/lib/python2.7/site.py", line 278, in addusersitepackages
user_site = getusersitepackages()
File "/UBC-O/erosolo/yt-x86_64/lib/python2.7/site.py", line 253, in getusersitepackages
user_base = getuserbase() # this will also set USER_BASE
File "/UBC-O/erosolo/yt-x86_64/lib/python2.7/site.py", line 243, in getuserbase
USER_BASE = get_config_var('userbase')
File "/UBC-O/erosolo/yt-x86_64/lib/python2.7/sysconfig.py", line 521, in get_config_var
File "/UBC-O/erosolo/yt-x86_64/lib/python2.7/sysconfig.py", line 420, in get_config_vars
File "/UBC-O/erosolo/yt-x86_64/lib/python2.7/sysconfig.py", line 288, in _init_posix
IOError: invalid Python installation: unable to open /UBC-O/erosolo/yt-x86_64/lib/python2.7/config/Makefile (No such file or directory)
I patched the problem by symbolically linking the lib64/python2.7 files into the lib/python2.7 directories and re-executing the script. Is there a better approach to this fail?
Asst. Prof. of Physics and Astronomy
University of British Columbia Okanagan
3333 University Way, Kelowna BC V1V 1V7 Canada
(250) 807-9623 - erik.rosolowsky(a)ubc.ca
i am trying to set up ENZO environment using Intel compilers and not default gcc, gfort, etc
I am using install_script.sh script.
Does somebody know how to change the choice of a compiler that will be used in order to
build HDF5, Python, etc needed for ENZO compilation.
Thanks in advance,
Hi yt user,
This question mostly goes to John Wise (maybe not).
I try to use eps_writer module in the yt to generate a high-quality .eps
I attempt to make four phase plot (rho-T) from four different times (i.e.
four different data output)
But, I got the following error message:
File "Phase_eps.py", line 39, in <module>
ep = eps.multiplot_yt(2,2,pc)
line 1010, in multiplot_yt
"x ncol(%d)." % (len(plot_col.plots), nrow, ncol)
TypeError: not all arguments converted during string formatting
It look that there is a problem when I over write PlotCollection object for
four different data output (or maybe not).
How can I solve the issue?
I paste my script at http://paste.yt-project.org/show/3112/ .
In addition, I would like to get more information/document about eps_writer.
For example, I would like to write the time of four phase respectively.
Where can I get the information about it?
Thank you in advance,
Jun-Hwan Choi, Ph.D.
Department of Physics and Astronomy, University of Kentucky
Tel: (859) 897-6737 Fax: (859) 323-2846
Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi
I am new to YT and I was trying to install YT using the install script. And it fails with the following error:
I have cut and pasted lines of the log:
Installing Python. This may take a while, but don't worry. YT loves you.
Installing mercurial-2.2.2 (arguments: 'mercurial-2.2.2')
File "/home/labuser/exp_ib_tests/yt-x86_64/lib/python2.7/tarfile.py", line 744, in readnormal
File "/home/labuser/exp_ib_tests/yt-x86_64/lib/python2.7/gzip.py", line 252, in read
File "/home/labuser/exp_ib_tests/yt-x86_64/lib/python2.7/gzip.py", line 299, in _read
File "/home/labuser/exp_ib_tests/yt-x86_64/lib/python2.7/gzip.py", line 338, in _read_eof
IOError: CRC check failed 0x900b50a1 != 0x35489988L
Failure. Check /home/labuser/exp_ib_tests/yt-x86_64/yt_install.log. The last 10 lines are above.
Any help would be great!
Hello YT users,
A couple of years ago, Sam Skillman (email chain attached) asked about
support for saving derived fields to the disk, so we don't have to
re-compute expensive fields over and over again. Did this functionality
ever make it into yt? I'm working on something where this would be very
useful, so if not I might have a go at implementing myself.
---------- Forwarded message ----------
From: Sam Skillman <samskillman(a)gmail.com>
Date: Tue, Jan 11, 2011 at 9:40 AM
Subject: [Yt-dev] saving derived fields
I've started dealing with a lot of time-consuming derived fields and am
wondering if there is already support for writing derived fields back to
the raw data files (e.g. .cpu files). If not, any thoughts on doing so?
Yt-dev mailing list
I'd like to take a phase diagram and convert it to a simple array to
plot alongside some other nifty stuff in matplotlib.
A couple questions related to this aim (feel free to ignore ones that
1. Since I can add a phase object to a plot collection, is there a
way to convert a plot collection (or piece of it?) to a fixed resolution
2. Data objects made with pf.h.FUNCTION seem to be pass-able to the
fixed resolution buffer function. Is there a way to create phase plots this
way, instead of with plot collections?
3. Objects like simple line profiles have simple arrays living
inside them. Is there a simple 2D array I can pull out of the phase plot
Munier A. Salem // 845.489.6450