Mailman 3 December 2014 - yt-dev

Issue #950: get_smallest_appropriate_unit is defined twice (yt_analysis/yt)
by John ZuHone Dec. 8, 2014

Dec. 8, 2014

New issue 950: get_smallest_appropriate_unit is defined twice https://bitbucket.org/yt_analysis/yt/issue/950/get_smallest_appropriate_uni… John ZuHone: `get_smallest_appropriate_unit` is defined as a method of `Dataset`, but there is also a version of it in `yt.visualization.plot_modifications`. Worse yet, the answers don't agree. I ran the following script: ``` #!python import yt from yt.visualization.plot_modifications import get_smallest_appropriate_unit parameters = {"length_unit":(1.0,"Mpc"), "time_unit":(1.0,"Myr"), "mass_unit":(1.0e14,"Msun")} ds = yt.load("MHDSloshing/virgo_low_res.0054.vtk", parameters=parameters) print "domain width = ", ds.domain_width[0].in_units("Mpc") print "from Dataset method = ", ds.get_smallest_appropriate_unit(ds.domain_width[0]) print "from plot_modifications = ", get_smallest_appropriate_unit(ds, ds.domain_width[0]) ``` which gives: ``` #! domain width = 4.0 Mpc from Dataset method = pc from plot_modifications = Mpc ``` I have seen other bizarre behavior of this nature as well. We should remove this duplication, in favor of the version in `plot_modifications`, since it seems to give the more sensible result. I can work on a PR. Responsible: jzuhone

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Issue #949: Halo analysis cookbook notebook fails (yt_analysis/yt)
by Nathan Goldbaum Dec. 6, 2014

Dec. 6, 2014

New issue 949: Halo analysis cookbook notebook fails https://bitbucket.org/yt_analysis/yt/issue/949/halo-analysis-cookbook-noteb… Nathan Goldbaum: >From the current docs build: ``` #!python INFO:root:Cell returned INFO:root:Running cell: # Define a virial radius for the halo. hc.add_callback("virial_quantities", ["radius"], profile_storage = "virial_quantities_profiles") INFO:root:Cell returned INFO:root:Running cell: hc.add_callback('delete_attribute','virial_quantities_profiles') INFO:root:Cell returned INFO:root:Running cell: hc.add_callback('sphere', radius_field='radius_200', factor=5, field_parameters=dict(virial_radius=('quantity', 'radius_200'))) INFO:root:Cell returned INFO:root:Running cell: hc.add_callback('profile', 'virial_radius', [('gas','temperature')], storage='virial_profiles', weight_field='cell_mass', accumulation=False, output_dir='profiles') INFO:root:Cell returned INFO:root:Running cell: # Save the profiles hc.add_callback("save_profiles", storage="virial_profiles", output_dir="profiles") INFO:root:Cell returned INFO:root:Running cell: hc.create() /home/xarth/yt-x86_64/lib/python2.7/site-packages/numpy/ma/core.py:790: RuntimeWarning: invalid value encountered in less_equal return umath.less_equal(x, self.critical_value) INFO:root:Cell raised uncaught exception: --------------------------------------------------------------------------- YTFieldNotFound Traceback (most recent call last) <ipython-input-12-76041198ce66> in <module>() ----> 1 hc.create() /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/analysis_modules/halo_analysis/halo_catalog.pyc in create(self, save_halos, save_catalog, njobs, dynamic) 295 296 """ --> 297 self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic) 298 299 def load(self, save_halos=True, save_catalog=False, njobs=-1, dynamic=False): /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/utilities/parallel_tools/parallel_analysis_interface.pyc in barrierize(*args, **kwargs) 273 def barrierize(*args, **kwargs): 274 if not parallel_capable: --> 275 return func(*args, **kwargs) 276 mylog.debug("Entering barrier before %s", func.func_name) 277 comm = _get_comm(args) /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/analysis_modules/halo_analysis/halo_catalog.pyc in _run(self, save_halos, save_catalog, njobs, dynamic) 387 for action_type, action in self.actions: 388 if action_type == "callback": --> 389 action(new_halo) 390 elif action_type == "filter": 391 halo_filter = action(new_halo) /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/analysis_modules/halo_analysis/halo_callbacks.pyc in __call__(self, halo) 54 55 def __call__(self, halo): ---> 56 self.function(halo, *self.args, **self.kwargs) 57 return True 58 /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/analysis_modules/halo_analysis/halo_callbacks.pyc in profile(halo, bin_fields, profile_fields, n_bins, extrema, logs, weight_field, accumulation, fractional, storage, output_dir) 224 my_profile = create_profile(halo.data_object, bin_fields, profile_fields, n_bins=n_bins, 225 extrema=extrema, logs=logs, weight_field=weight_field, --> 226 accumulation=accumulation, fractional=fractional) 227 228 prof_store = dict([(field, my_profile[field]) \ /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/profiles.pyc in create_profile(data_source, bin_fields, fields, n_bins, extrema, logs, units, weight_field, accumulation, fractional) 1307 1308 """ -> 1309 bin_fields = data_source._determine_fields(bin_fields) 1310 fields = ensure_list(fields) 1311 if len(bin_fields) == 1: /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/data_containers.pyc in _determine_fields(self, fields) 496 else: 497 fname = field --> 498 finfo = self.ds._get_field_info("unknown", fname) 499 if finfo.particle_type: 500 ftype = self._current_particle_type /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/static_output.pyc in _get_field_info(self, ftype, fname) 485 self._last_finfo = self.field_info[(ftype, fname)] 486 return self._last_finfo --> 487 raise YTFieldNotFound((ftype, fname), self) 488 489 def _setup_classes(self): YTFieldNotFound: Could not find field '('all', 'virial_radius')' in RedshiftOutput0006. ``` Ping @brittonsmith @hegan.

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yt 3.1 release
by Nathan Goldbaum Dec. 6, 2014

Dec. 6, 2014

Hi all, We have a working docs build, yay!! Even better, it now only takes an hour and 20 minutes to finish due to the new parallel reading capabilities in sphinx 1.3! The build is here: http://yt-project.org/docs/dev/ It would be great to get eyes on it, especially with an eye towards broken formatting, typos and bugs in example scripts. Now that the docs build is working, I think we're in shape to do a release. There will still probably be bugfixes doc fixes, and performance improvements incoming, but I don't think we should merge in any new features until we do the release. There are also some open pull requests, it would be great if we got eyes on them and started merging them in. We had tests shut off for a little while the other day while we resolved issues with the docs build, so if you notice a PR where tests weren't run, poke me or kacper and we can trigger a new build. We could probably also do an official release candidate, but I'm not sure how useful that will be given our normal distribution channels. What do you all think about cutting a release Monday Dec. 15? -Nathan

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Issue #948: FITSProjection fails with ValueError: 'code_length' did not parse as fits unit (yt_analysis/yt)
by Kacper Kowalik Dec. 5, 2014

Dec. 5, 2014

New issue 948: FITSProjection fails with ValueError: 'code_length' did not parse as fits unit https://bitbucket.org/yt_analysis/yt/issue/948/fitsprojection-fails-with-va… Kacper Kowalik: Following script: ``` #!python import yt from yt.utilities.fits_image import FITSProjection ds = yt.load("MHDSloshing/virgo_low_res.0054.vtk", parameters={"length_unit": (1.0, "Mpc"), "mass_unit": (1.0e14, "Msun"), "time_unit": (1.0, "Myr")}) prj_fits = FITSProjection(ds, "z", ["temperature"], weight_field="density") ``` yields ``` #!text Traceback (most recent call last): File "foo.py", line 8, in <module> prj_fits = FITSProjection(ds, "z", ["temperature"], weight_field="density") File "yt/utilities/fits_image.py", line 474, in __init__ image_res=image_res) File "yt/utilities/fits_image.py", line 358, in construct_image w.wcs.cunit = cunit File "/usr/lib64/python2.7/site-packages/astropy/units/core.py", line 1735, in __call__ raise ValueError(msg) ValueError: 'code_length' did not parse as fits unit: At col 0, Unit u'code_length' not supported by the FITS standard. ``` I'm using *astropy-0.4* and *yt* rev: 09a0a10893ef Responsible: jzuhone

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Issue #947: Consistent field naming for spherical and cylindrical fields (yt_analysis/yt)
by Cameron Hummels Dec. 2, 2014

Dec. 2, 2014

New issue 947: Consistent field naming for spherical and cylindrical fields https://bitbucket.org/yt_analysis/yt/issue/947/consistent-field-naming-for-… Cameron Hummels: The issue of consistent field naming came up in Pull Request #1308, and further discussion occurred on the yt development sprint for yt 3.1 on 12.2.14. Right now there are two somewhat inconsistent field naming schemes associated with non-cartesian position and velocity fields. In particles, we have these: *Cartesian* ``` #!python ('all', 'particle_position_x') ('all', 'particle_position_y') ('all', 'particle_position_z') ('all', 'particle_velocity_x') ('all', 'particle_velocity_y') ('all', 'particle_velocity_z') ``` *Spherical* ``` #!python (‘all’, ‘particle_spherical_position_phi’) (‘all’, ‘particle_spherical_position_radius’) (‘all’, ‘particle_spherical_position_theta’) (‘all’, ‘particle_spherical_velocity_phi’) (‘all’, ‘particle_spherical_velocity_radius’) (‘all’, ‘particle_spherical_velocity_theta’) ``` and (after PR #1308): *Cylindrical* ``` #!python (‘all’, ‘particle_cylindrical_position_z’) (‘all’, ‘particle_cylindrical_position_radius’) (‘all’, ‘particle_cylindrical_position_theta’) (‘all’, ‘particle_cylindrical_velocity_z’) (‘all’, ‘particle_cylindrical_velocity_radius’) (‘all’, ‘particle_cylindrical_velocity_theta’) ``` For gas fields, we have these: *Cartesian* ``` #!python (‘index’, ‘x’) (‘index’, ‘y’) (‘index’, ‘z’) (‘gas’, ‘velocity_x’) (‘gas’, ‘velocity_y’) (‘gas’, ‘velocity_z’) ``` *Spherical* ``` #!python (‘index’, ‘spherical_phi’) (‘index’, ‘spherical_r’) (‘index’, ‘spherical_theta’) (‘gas’, ‘radial_velocity’) (‘gas’, ‘radial_velocity_absolute’) (‘gas’, ‘tangential_velocity’) (‘gas’, ‘tangential_over_velocity_magnitude’) ``` *Cylindrical* ``` #!python (‘index’, ‘cylindrical_r’) (‘index’, ‘cylindrical_theta’) (‘index’, ‘cylindrical_z’) (‘gas’, ‘cylindrical_radial_velocity’) (‘gas’, ‘cylindrical_radial_velocity_absolute’) (‘gas’, ‘cylindrical_tangential_velocity’) (‘gas’, ‘cylindrical_tangential_velocity_absolute’) ``` I would like to propose that we make new spherical and cylindrical gas fields that follow a similar naming convention to the explicit form of the particle fields. To make sure we're backwards compatible, we can just make field aliases from the field names above to the new fields. Or in the case of 'tangential_velocity' (and 'cylindrical_tangential_velocity'), it can remain, since it seem like the superposition of phi_velocity and theta_velocity.

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Hangout 3pm EST / 12 pm PST to discuss version 3.1
by John ZuHone Dec. 2, 2014

Dec. 2, 2014

Hi folks, I created a Hangout for us to talk about 3.1 this afternoon at 3 pm Eastern: https://plus.google.com/u/0/events/cs6ng7s6o3ue81pvattu3mpglko?authkey=CK6l… <https://plus.google.com/u/0/events/cs6ng7s6o3ue81pvattu3mpglko?authkey=CK6l…> If you’re not on the list I set up please request an invite from me. Best, John

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Parallel segmentation algorithm
by Matthew Turk Dec. 2, 2014

Dec. 2, 2014

An absolutely *fascinating* paper: http://arxiv.org/abs/1412.0510 This is similar, but not identical, to our contour finder, which is also a parallel segmentation algorithm, but without any of the watershed analysis or noise removal. (h/t John Wise's astro-ph blog)

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3.1 today?
by John ZuHone Dec. 2, 2014

Dec. 2, 2014

Hi all, It’s Dec. 1st, and we previously discussed a 3.1 release today. Is everyone OK with doing that? Currently there are 18 open pull requests, with a couple that contain bug fixes: https://bitbucket.org/yt_analysis/yt/pull-request/1320/owls-bug-fix-for-fil… <https://bitbucket.org/yt_analysis/yt/pull-request/1320/owls-bug-fix-for-fil…> https://bitbucket.org/yt_analysis/yt/pull-request/1311/bugfix-first-pass-at… <https://bitbucket.org/yt_analysis/yt/pull-request/1311/bugfix-first-pass-at…> If there are any others that need review, we should do that today. Also, if anyone thinks we need more time, we should discuss that as well. I have some as-of-yet un-PRed stuff that is important, but it can wait, because it should get a proper review and I don’t want to hold things up if we are ready and want to stay on schedule. Best, John

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