Fellow yt users:
We at the yt development team want to make yt better for you, the user. We
have prepared a short survey to gain your valuable feedback to help us
understand what is working in yt and what is not. Could you please spare 2
minutes to fill out our survey below?
We plan to collect responses and make available a selection of results
by December
10, so please let us know what you think at the following URL:
http://goo.gl/forms/hRNryOWTPO
On behalf of the yt development team,
Cameron
--
Cameron Hummels
Postdoctoral Researcher
Steward Observatory
University of Arizona
http://chummels.org
New issue 946: Covering grid doesn't set "center" field parameter
https://bitbucket.org/yt_analysis/yt/issue/946/covering-grid-doesnt-set-c...
Kacper Kowalik:
This simple script:
```
#!python
import yt
ds = yt.load("Sedov_3d/sedov_hdf5_chk_0003")
data = ds.covering_grid(1, left_edge=ds.domain_left_edge, dims=[32,32,32])
data["radial_velocity"]
```
yields rather confusing traceback:
```
#!text
Traceback (most recent call last):
File "bug.py", line 4, in <module>
data["radial_velocity"]
File "yt/src/yt-my/yt/data_objects/data_containers.py", line 249, in __getitem__
self.get_data(f)
File "yt/src/yt-my/yt/data_objects/construction_data_containers.py", line 531, in get_data
if len(gen) > 0: self._generate_fields(gen)
File "yt/src/yt-my/yt/data_objects/data_containers.py", line 719, in _generate_fields
fd = self._generate_field(field)
File "yt/src/yt-my/yt/data_objects/data_containers.py", line 286, in _generate_field
tr = self._generate_fluid_field(field)
File "yt/src/yt-my/yt/data_objects/data_containers.py", line 306, in _generate_fluid_field
rv = finfo(gen_obj)
File "yt/src/yt-my/yt/fields/derived_field.py", line 184, in __call__
dd = self._function(self, data)
File "yt/src/yt-my/yt/fields/vector_operations.py", line 109, in _radial
theta = data['index', 'spherical_theta']
File "yt/src/yt-my/yt/data_objects/data_containers.py", line 249, in __getitem__
self.get_data(f)
File "yt/src/yt-my/yt/data_objects/construction_data_containers.py", line 531, in get_data
if len(gen) > 0: self._generate_fields(gen)
File "yt/src/yt-my/yt/data_objects/data_containers.py", line 719, in _generate_fields
fd = self._generate_field(field)
File "yt/src/yt-my/yt/data_objects/data_containers.py", line 286, in _generate_field
tr = self._generate_fluid_field(field)
File "yt/src/yt-my/yt/data_objects/data_containers.py", line 306, in _generate_fluid_field
rv = finfo(gen_obj)
File "yt/src/yt-my/yt/fields/derived_field.py", line 184, in __call__
dd = self._function(self, data)
File "yt/src/yt-my/yt/fields/geometric_fields.py", line 104, in _spherical_theta
coords = get_periodic_rvec(data)
File "yt/src/yt-my/yt/fields/field_functions.py", line 51, in get_periodic_rvec
coords = obtain_rvec(data)
File "yt/utilities/lib/geometry_utils.pyx", line 89, in yt.utilities.lib.geometry_utils.obtain_rvec (yt/utilities/lib/geometry_utils.c:2228)
TypeError: 'NoneType' object has no attribute '__getitem__'
```
`covering_grid` should either set sane default for *center* or fields using `ValidateParameter()` should catch this earlier and more gracefully.
New issue 945: Adding multiple sets of annotations to a slice is slow
https://bitbucket.org/yt_analysis/yt/issue/945/adding-multiple-sets-of-an...
Daniel Fenn:
If I open a large dataset and create a slice, then add density contours, followed by text annotations, the text annotations take a very long time to add.
If I add the text annotations before adding the contours, it's much faster.
If I add multiple sets of density contours, each set takes progressively longer.
Nathan Goldbaum has suggested that implementing caching would alleviate the issue.
Responsible: yt_analysis
New issue 944: Slices of fields that need ghost zones are slow for patch AMR data
https://bitbucket.org/yt_analysis/yt/issue/944/slices-of-fields-that-need...
Nathan Goldbaum:
On my laptop, the following script:
```
#!python
import yt
import time
def test(field):
slc = yt.SlicePlot(ds, 2, field)
if __name__ == "__main__":
ds = yt.load("GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150")
ds.periodicity = (True, True, True)
setup = "from __main__ import test"
t0 = time.time()
test('density')
tden = time.time() - t0
t0 = time.time()
test('velocity_divergence')
tdiv = time.time() - t0
print tden, tdiv
```
shows that it takes about 3.5 seconds to do the density slice and 63 seconds to do the velocity_divergence slice.
I've been looking over the field list:
http://yt-project.org/docs/dev/reference/field_list.html#field-list
At the bottom of that page, we list the fields specific to each
frontend/code. I'd like to make the presentation for each frontend a
table, with columns for the name, units, what its aliases to, and whether
it is a particle -- these are what we currently list, and perhaps show the
display name. Showing it as a table for each frontend would be more
compact than the list, and I think it would be clearer for people to read.
Before I hack the script that writes that page, I wanted to see if there
are any objections.
Also, a minor point, there is a _dynamical_time() field which I assume is
the free-fall timescale assuming uniform density throughout the collapse.
I've always seen a '32' not '16' in the denominator (see, e.g. Carroll &
Ostlie, Eq. 12.26 or Kippenhahn & Weigert Eq. 27.10).
--
Michael Zingale
Associate Professor
Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY
11794-3800
*phone*: 631-632-8225
*e-mail*: Michael.Zingale(a)stonybrook.edu
*web*: http://www.astro.sunysb.edu/mzingale
Hi gang,
I got an inquiry about using the PlotWindow plot show() method outside of the notebook. How hard would it be to extend this to other matplotlib backends, so that a window pops up on the screen when you want to see a plot, but aren't in the notebook?
Obviously matplotlib does this already, so it's a matter of figuring out how to get it hooked up.
Best,
John Z
Sent from John ZuHone's iPad
Hi all,
If anyone has some time this week, it would be great if you could take a
look at the latest docs builds:
http://tests.yt-project.org/job/yt-docs-3.0/395/console
Some of the recipes seem to be triggering tracebacks and the total docs
build time now regularly exceeds the 200 min timeout. It would be great if
we could bring the total docs build time down - I bet there are a few
recipes that are dominating the build time.
Thanks for your help getting yt 3.1 out the door.
-Nathan
Hi all,
Cameron and I were chatting, and it looks like only 5/19 of the
analysis modules have tests. I think it would be really valuable to
have tests -- even failing ones -- so that we can start finishing the
job of porting to yt-3.0 all of the analysis modules.
So what do you think -- should we start writing some tests designed to fail?
-Matt
New issue 941: CutRegionSelector doesn't work with some data types
https://bitbucket.org/yt_analysis/yt/issue/941/cutregionselector-doesnt-w...
Nathan Goldbaum:
It turns out the `CutRegionSelector` I recently added doesn't work so well for FLASH data:
```
#!python
import yt
ds = yt.load("GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150")
dd = ds.all_data()
dd = dd.cut_region("obj['density'] > 1e-27")
slc = yt.SlicePlot(ds, 2, 'density', data_source=dd)
slc.set_zlim('density', 1e-30, 1e-25)
slc.set_figure_size(5)
slc.save()
```
This is happening because `CutRegionSelector` is using a fragile exact comparison between floats. It does this to take advantage of an efficient hashing algorithm, but it looks like this comes at the cost of maintaining bitwise identicality between two different ways of calculating cell positions.
The fix is either:
1. Figure out why the FLASH cell position fields are not bitwise identical to the cell positions calculated inside `SelectorObject.fill_mask`. It seems Enzo data is unaffected by the round-off artifacts we see with FLASH data, so we know that means it is possible to rely on the cell positions matching exactly at some level.
2. Use a more forgiving data structure to retrieve matching cell positions. A KD-tree seems like a natural choice, but I'm unsure if there's a ready-to-use KD-tree library available.
Responsible: ngoldbaum
