Mailman 3 জুলাই 2015 - AstroPy

ValueError in vstacking tables
by Brian Cherinka 5 অক্টোবর, 2015

5 অক্টোবর, 2015

Hi, I’m trying to vstack (vertically stack) two Astropy tables with different numbers of columns. The tables appear to stack correctly without error. However, upon attempting to index a row in the table, it throws me this error <repr(<astropy.table.row.Row at 0x10c72ed50>) failed: ValueError: setting an array element with a sequence.> I’m not trying to do anything fancy with mixed columns, or Quantities. Just stackin’ two good ol’ natural Tables together. One table has 84 columns, and another has 57, which are all a part of the 84 in the first table. At first glance I would guess it’s a mismatch in the dtypes of a particular column that I’m trying to merge. However, the columns all have the same dtype, format, and they are in the same order. I get no messages regarding any kind of merge errors. Any ideas on this? Thanks, Brian P.S. Full print of traceback below table3 = vstack([table1, table3],join_type=‘outer’) print table3[0] --------------------------------------------------------------------------- ValueError Traceback (most recent call last) <ipython-input-278-a0c75e8d3ef3> in <module>() ----> 1 print tmp3[0] /Users/Brian/anaconda/lib/python2.7/site-packages/astropy/table/row.pyc in __repr__(self) 176 def __repr__(self): 177 return "<{3} {0} of table\n values={1!r}\n dtype={2}>".format( --> 178 self.index, self.as_void(), self.dtype, self.__class__.__name__) 179 180 /Users/Brian/anaconda/lib/python2.7/site-packages/numpy/ma/core.pyc in __repr__(self) 5699 return self._data.__repr__() 5700 m = tuple(m) -> 5701 if not any(m): 5702 return self._data.__repr__() 5703 p = masked_print_option /Users/Brian/anaconda/lib/python2.7/site-packages/numpy/ma/core.pyc in __call__(self, a, *args, **params) 6089 method = getattr(MaskedArray, method_name, None) 6090 if method is not None: -> 6091 return method(MaskedArray(a), *args, **params) 6092 # Still here ? OK, let's call the corresponding np function 6093 method = getattr(np, method_name) /Users/Brian/anaconda/lib/python2.7/site-packages/numpy/ma/core.pyc in __new__(cls, data, mask, dtype, copy, subok, ndmin, fill_value, keep_mask, hard_mask, shrink, **options) 2649 """ 2650 # Process data............ -> 2651 _data = np.array(data, dtype=dtype, copy=copy, subok=True, ndmin=ndmin) 2652 _baseclass = getattr(data, '_baseclass', type(_data)) 2653 # Check that we're not erasing the mask.......... ValueError: setting an array element with a sequence. --------------------------------------- Brian Cherinka, Ph.D Dunlap Institute for Astronomy & Astrophysics University of Toronto Toronto, ON, Canada M5S 3H4 phone: 416-978-7299 email: cherinka(a)di.utoronto.ca ----------------------------------------

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Changing dtype when copying masked table throws TypeError
by Gregory Simonian 25 আগস্ট, 2015

25 আগস্ট, 2015

Hi all, I have a Table with several columns which were read in as strings because they had a combination of numeric and non-numeric characters. After cleaning out the non-numeric characters, I'd like to convert the dtype of the column from string to int. Looking at the astropy documentation for modifying tables [0], under the caveats section it states: "The data type for a column cannot be changed in place. In order to do this you must make a copy of the table with the column type changed appropriately." So I try making a new table (the table is small, so I don't mind the temporary memory hit), but I run into the error: "TypeError: Cannot set fill value of string with array of dtype int64" When checking the fill value of the column (which is masked from the reader), it's 'N/A', which makes sense that it wouldn't work. But when I change it to '0', I still get the same problem. I managed to find a minimal working example as: import numpy as np t = Table({'a': ['1']}, masked=True) t['a'].set_fill_value('0') u = Table(t, names=['a'], dtype=[np.int]) > TypeError: Cannot set fill value of string with array of dtype int64 When debugging the exception, it seems like the Table constructor doesn't convert the fill value of masked tables when generating a new table, which seems to defeat the ability to change the dtype of masked columns. I was wondering if other people have run by this, and if there's a more straightforward way of changing the dtype of a column. This is with Astropy 1.0.3 on Python 2.7.10 through Anaconda on CentOS 6.6. When checking to see if this was reported, I ran into issue #3809 [1], which might end up being the ultimate solution to my problem. It seems like a workaround would be: temp_column = np.ma.asanyarray(t['a'], np.int) del(t['a']) t['a'] = temp_column Thanks! Gregory Simonian [0]http://docs.astropy.org/en/stable/table/modify_table.html#caveats [1] https://github.com/astropy/astropy/issues/3809

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[ANN] SunPy 0.6 Released
by Stuart Mumford 31 জুলাই, 2015

31 জুলাই, 2015

Hello all, I am very happy to tell you that the long in the works 0.6.0 release of the SunPy library has arrived. This release has been 'in the oven' for well over a year, and is full of rather major changes. The major changes in this release are: * Most functions throughout the SunPy code base now expect Astropy Quantity objects, and return Astropy Quantity objects. * Python 2.6 support has ended, we do not expect this release to work under Python 2.6. * Sample data has been removed from SunPy but helpers for downloading sample data have been added to sunpy.data. * TimeRange has a new property based API, e.g. start and end are now properties. * SunPy colormaps are now registered with matplotlib, allowing their use from imshow and similar functions after the import of sunpy.cm. * Solar rotation calculation functionality has been added, along with functionality to de-rotate MapCubes. While there have been lots of changes, it is the move to Astropy Units throughout the code base that will require most users to update their code, if you wish to learn more about Astropy Units see: http://docs.astropy.org/en/latest/units/ You can install this release using either pip or conda. If you have a scientific python environment already configured, run: pip install sunpy or: pip install --upgrade sunpy if you have anaconda you need to add the sunpy and astropy channels to your conda config: conda config --add channels sunpy --add channels astropy and then run: conda install sunpy for more information about installing sunpy see our installation documentation: http://docs.sunpy.org/en/stable/guide/installation/index.html This release consists of 1,341 commits from 29 different people and 13 new contributors! The people who have contributed to this release are: Stuart Mumford Daniel Ryan Steven Christe Jack Ireland Brigitta Sipocz * Asish Panda Andrew Inglis Albert Y. Shih Rishabh Sharma David Perez-Suarez Rajul Srivastava Andrew Leonard Ruben De Visscher * Dumindu Buddhika * Goran Cetusic * Jongyeob Park * ChloÃ© Guennou * Ishtyaq Habib * Nabil Freij Simon Liedtke Abigail Stevens * Alex Hamilton * Ambar Mehrotra * Erik M. Bray * Jaylen Wimbish * Juan Camilo Buitrago-Casas * Larry Manley Norbert Gyenge Rishabh Mishra * Happy Pythoning, Stuart Mumford

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where are the binary installers?
by John Wainwright 29 জুলাই, 2015

29 জুলাই, 2015

Hi there. I'd like to run Astropy on a Windows machine connected to an imaging rig but cannot find the binary installers mentioned in several places as being on the PyPi page <https://pypi.python.org/pypi/astropy/> for Astropy. Can someone point me at the binary installers? Thanks very much!! John.

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Visibility plot with the list of coords
by Ilya Yakunin 28 জুলাই, 2015

28 জুলাই, 2015

Hi! I'd like to plot observability curves for list of the objects of my interest. Following this example https://astropy.readthedocs.org/en/v1.0.3/coordinates/observing-example.html I created coords list using SkyCoord: >>>coords = SkyCoord(data[:,2], data[:,3], unit=(u.deg,u.deg)) which contains more than 300 objects. And then, when I'm trying to transform equatorial coords to horizontal I get: >>>from astropy.coordinates import get_sun >>>delta_midnight = np.linspace(-12, 12, 1000)*u.hour >>>times = midnight + delta_midnight >>>altazframe = AltAz(obstime=times, location=bta_location) >>>sunaltazs = get_sun(times).transform_to(altazframe) >>>coordaltazs = coords.transform_to(altazframe) Traceback (most recent call last): File "testing", line 38, in <module> corraaltazs = coords.transform_to(altazframe) File "/usr/lib/python2.7/dist-packages/astropy/coordinates/sky_coordinate.py", line 348, in transform_to new_coord = trans(self.frame, generic_frame) File "/usr/lib/python2.7/dist-packages/astropy/coordinates/transformations.py", line 920, in __call__ curr_coord = t(curr_coord, curr_toframe) File "/usr/lib/python2.7/dist-packages/astropy/coordinates/transformations.py", line 708, in __call__ res = self.func(fromcoord, toframe) File "/usr/lib/python2.7/dist-packages/astropy/coordinates/builtin_frames/icrs_cirs_transforms.py", line 41, in icrs_to_cirs cirs_ra, cirs_dec = erfa.atciq(i_ra, i_dec, 0, 0, px, 0, astrom) File "/usr/lib/python2.7/dist-packages/astropy/_erfa/core.py", line 22306, in atciq broadcast = numpy.broadcast(numpy.int32(0.0), numpy.int32(0.0), rc_in, dc_in, pr_in, pd_in, px_in, rv_in, astrom_in) ValueError: shape mismatch: objects cannot be broadcast to a single shape But when I use a single string from coords list (say, coords[20] ) everything goes well. Looks like transform_to() waits for a single SkyCoord object but I have a list. Is there any way to convert and plot several objects on one plot? Thanks for the any help! -- Cheers, Ilya

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ANN: yt-3.2 released
by John ZuHone 24 জুলাই, 2015

24 জুলাই, 2015

We are proud to announce the release of yt 3.2! yt (http://yt-project.org <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 <http://yt-project.org/docs/dev/visualizing/plots.html#particle-plots> 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 <http://yt-project.org/docs/dev/examining/loading_data.html#halo-catalog-data> to learn how to load halo catalogs as regular yt datasets. Custom colormaps can now be easily defined and added - see here <http://yt-project.org/docs/dev/visualizing/colormaps/index.html> 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 <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 <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/ <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/ <https://www.enthought.com/products/canopy/>) WinPython (http://winpython.sourceforge.net/ <http://winpython.sourceforge.net/>) Mac OS X x86_64: Enthought Canopy Python (https://www.enthought.com/products/canopy/ <https://www.enthought.com/products/canopy/>) Homebrew Python (http://brew.sh/ <http://brew.sh/>) Python.org <http://python.org/> Python Mac OS X’s system Python MacPorts Python (https://www.macports.org/ <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 <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 <http://yt-project.org/> and the documentation for yt-3.2 at http://yt-project.org/docs/3.2 <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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New astropython.org site preview
by Aldcroft, Thomas 23 জুলাই, 2015

23 জুলাই, 2015

This summer we have been fortunate to have a very talented Google Summer of Code student, Aman Jhunjhunwala, working to create a brand new astropython.org site from scratch. In addition to writing all the code, Aman has also brought a fresh design look and many cool ideas to the project. The primary driver is to make a modern site that would engage the community and succeed in having a broad base of contributors to the site content. To that end the site allows contributions from anyone who authenticates via Github, Google, or Facebook. By default all such content will be moderated before appearing on the live site, but there is also a category for trusted users that can post directly. During the preview phase moderation is disabled, so you can post at will! The preview version is available at: http://amanjhunjhunwala.pythonanywhere.com/ At this time we are opening the site for a preview in order to get feedback from the AstroPython community regarding the site including: Overall concept, in particular whether the site design will be conducive to broad base of contributors. Would you want to post? Are the authentication options obvious and sufficient? General site organization and ease of navigating How easily can you find information? Visual design and aesthetics Other features, e.g. a Q&A forum? Accessibility Ease of posting Bugs Code review (https://github.com/x-calibre/astropython) Security We highly encourage you to post content in any / all of the categories. You can either try to play nice and use things as we intended, or do stress testing and try to break it. All posts will show up immediately, so please do act responsibly in terms of the actual content you post. As you find issues or have comments, please first check the site github repo to see if it is already known: https://github.com/x-calibre/astropython/issues Ideally put your comments into github. For most of the broad review categories above I have already created a placeholder issue starting with [DISCUSS]. Also, if you'd rather not use github then just send to me directly at taldcroft(a)gmail.com. Best regards, Tom Aldcroft, Aman Jhunjhunwala, Jean Connelly, and Tom Robitaille

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Fwd: [matplotlib-devel] Call for new style defaults
by Erik Tollerud 15 জুলাই, 2015

15 জুলাই, 2015

Hello all, I thought the message below from the matplotlib mailing lists might be of interest to those in our community with strong opinions about plotting styles. In the next few months there will be a 2.0 release of matplotlib, which will primarily feature new defaults plotting styles (including a new colormap). The window for community input on these defaults is 1 month, so if you want a say in the new defaults, now's the time, or forever hold your peace (at least until 3.0). ---------- Forwarded message ---------- From: Thomas Caswell <tcaswell(a)gmail.com> Date: Sun, Jul 12, 2015 at 12:11 PM Subject: [matplotlib-devel] Call for new style defaults To: "matplotlib-devel(a)lists.sourceforge.net" < matplotlib-devel(a)lists.sourceforge.net>, " matplotlib-announce(a)lists.sourceforge.net" < matplotlib-announce(a)lists.sourceforge.net>, Matplotlib Users < matplotlib-users(a)lists.sourceforge.net> Hello all, Following much discussion, we are changing the default color map and styles in the upcoming 2.0 release! The new default color map will be 'viridis' (aka option D). I recommend everyone watch Nathaniel Smith and Stéfan van der Walt's talk from SciPy2015 introducing the new color map and providing an introduction to the math of color perception: https://www.youtube.com/watch?v=xAoljeRJ3lU We are soliciting proposals to change any and all other visual defaults (including adding new rcParams as needed). If you have a proposal please create a PR or issue with the changes to `rcsetup.py` and `matplotlibrc.template` implementing the changes by August 9, 2015 (1 month from now). Do not worry about updating any failing tests. At the end, Micheal Droettboom and I will decide on the new defaults. A 'classic' style will be provided so reverting to the current default values will be a single line of python (`mpl.style.use('classic')`). Please distribute this as widely as possible. We only want to do this once and want to get feedback from as many users as possible. Thomas Caswell PS jet is harmful to you and those around you See https://github.com/matplotlib/matplotlib/pull/4622 for an example proposal PR. ------------------------------------------------------------------------------ Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ _______________________________________________ Matplotlib-devel mailing list Matplotlib-devel(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel -- Erik T

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Python in Astronomy 2015 proceedings
by Thomas Robitaille 15 জুলাই, 2015

15 জুলাই, 2015

Hi everyone, Back in April, we held a workshop entitled 'Python in Astronomy' at the Lorentz center in Leiden, and due to space constraints, a number of people were not able to attend the workshop, but we promised that we would make available as much as possible from the meeting. We are now happy to announce the availability of the 'proceedings' for the Python in Astronomy 2015 workshop, which you can find on the following page: http://python-in-astronomy.github.io This includes a document summarizing all the unconference sessions, videos of most of the talks, the slides for many of the talks, a collection of links shared during the conference, links to blog posts, photos, and a Twitter archive. Note that the unproceedings document as well as the talk slides are both citable, since they are available on Zenodo, so they have a DOI (you can find BibTex entries on the Zenodo pages). Let us know if you have any questions about any of the proceedings! The organizing committee: Pauline Barmby Eric Jeschke Sarah Kendrew Stuart Mumford Magnus Persson Thomas Robitaille

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ImportError: cannot import name _compiler
by Steffen Brinkmann 13 জুলাই, 2015

13 জুলাই, 2015

Hello, I just installed locally with $ python setup.py install --user Now when I import astropy, I get >>> In [1]: import astropy --------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-1-d192094ef7da> in <module>() ----> 1 import astropy /disk1/brinkmann/code/astropy-1.0.3/astropy/__init__.py in <module>() 323 log = _init_log() 324 --> 325 _initialize_astropy() 326 327 from .utils.misc import find_api_page /disk1/brinkmann/code/astropy-1.0.3/astropy/__init__.py in _initialize_astropy() 236 237 try: --> 238 from .utils import _compiler 239 except ImportError: 240 if is_astropy_source_dir: ImportError: cannot import name _compiler <<< what did I miss? Cheers, Steffen

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