Issue #950: get_smallest_appropriate_unit is defined twice (yt_analysis/yt)
by John ZuHone
New issue 950: get_smallest_appropriate_unit is defined twice
https://bitbucket.org/yt_analysis/yt/issue/950/get_smallest_appropriate_u...
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
4 years, 3 months
Issue #949: Halo analysis cookbook notebook fails (yt_analysis/yt)
by Nathan Goldbaum
New issue 949: Halo analysis cookbook notebook fails
https://bitbucket.org/yt_analysis/yt/issue/949/halo-analysis-cookbook-not...
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.
4 years, 3 months
yt 3.1 release
by Nathan Goldbaum
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
4 years, 3 months
Issue #948: FITSProjection fails with ValueError: 'code_length' did not parse as fits unit (yt_analysis/yt)
by Kacper Kowalik
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-...
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
4 years, 3 months
Issue #947: Consistent field naming for spherical and cylindrical fields (yt_analysis/yt)
by Cameron Hummels
New issue 947: Consistent field naming for spherical and cylindrical fields
https://bitbucket.org/yt_analysis/yt/issue/947/consistent-field-naming-fo...
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.
4 years, 3 months
Parallel segmentation algorithm
by Matthew Turk
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)
4 years, 3 months
