yt-dev March 2014

yt-dev@python.org

20 participants
58 discussions

Issue #806: Covering grid does not respect field_parameters (yt_analysis/yt)

by Matthew Turk

New issue 806: Covering grid does not respect field_parameters https://bitbucket.org/yt_analysis/yt/issue/806/covering-grid-does-not-respe… Matthew Turk: Currently, the mechanism by which fields are chunked and whatnot in the covering grid does not respect passing field parameters down to the `_data_source`. Responsible: MatthewTurk

7 years, 7 months

Datadex

by Matthew Turk

Hi all, I just saw this neat project on the Mozilla Science Lab etherpad for their call this week: http://datadex.io/ I think we should consider exploring it as a replacement for the data hub, once our AWS time goes away. Anybody feel like spinning up an instance? -Matt

7 years, 7 months

Change the default plot size?

by Nathan Goldbaum

Hi all, I recently opened a PR that fixes a number of bugs in yt's plotting code. Hopefully this will fix many common visual issues that show up in yt plots. As part of the PR I decided to change the default size of yt plots from 8 inches to 6. My justification is that the current default will create a plot that overflows an IPython notebook output cell, particularly on small displays. The PR is here: https://bitbucket.org/yt_analysis/yt/pull-request/723/fixing-some-longstand… The discussion about the figure size is here: https://bitbucket.org/yt_analysis/yt/pull-request/723/fixing-some-longstand… As I mention in the PR description I'm willing to back down on this change if the consensus is that this is a bad idea. Matt has already come out against the change, but before I revert it I wanted to bring it up here and get opinions from other people. Thanks for your help :) -Nathan

7 years, 7 months

Issue #805: Install requirements don't mention "setuptools" (yt_analysis/yt)

by Erik Schnetter

New issue 805: Install requirements don't mention "setuptools" https://bitbucket.org/yt_analysis/yt/issue/805/install-requirements-dont-me… Erik Schnetter: I just followed the instructions on <http://yt-project.org/#getyt> to download and install yt. I installed the prerequisites listed after the paragraph {{{ To build yt, you will first need to install a number of Python and C libraries that yt uses for key functionality }}} but I still received an error message {{{ $ python setup.py develop Traceback (most recent call last): File "setup.py", line 9, in <module> import setuptools ImportError: No module named setuptools }}} I found that installing the package "py27-setuptools" (I am using OS X with MacPorts) helped. I suggest you list "setuptools" as prerequisite as well.

7 years, 7 months

SciPy abstract submission

by Matthew Turk

Hi everyone, The (nominal) due date for submissions for SciPy2014 is next Friday: https://conference.scipy.org/scipy2014/ . I think we should aim to have a strong presence there -- I've heard from a couple people they plan to be there, which is *awesome*. For various reasons, I am only going to be traveling to the yt workshop in Santa Cruz and SciPy for a little while, so I am planning to be there the entire duration. There are a few things I think we should consider: * A joint talk introducing yt 3.0, where everyone in attendance either participates in the talk or acts as ambassadors. I want this to be submitted to the general track. I do not have any particular interest in acting as the primary presenter. * Sprints! For sure. * Possibly a talk submitted to the astro track about domain-specific stuff, like Hilary's spectrum generator, or John's Chandra generator, or the integration with Rockstar, or even AGORA. * We should participate in the WSSSPE workshop, which will be on Thursday afternoon. Looks like right now I'll be co-chairing this. * We may consider submitting a poster in addition, which emphasizes things like outreach using yt. Here are my drafts of the sprint and talk abstracts. You should be able to provide comments on them by right-clicking. If you want direct edit privs, let me know. https://docs.google.com/document/d/15BakPzOLdN6IIjx3jDFyD4Jg01ing1uQ9nIgKFy… Options I think we should pass on: * yt-centric tutorial: we will get to the point that I think this is a good idea, but I don't think we'd get enough people signing up for it. * yt-BOF. It might be worthwhile to consider setting up a BOF for data analysis of spatial data, though. (Not just GIS.) I will be submitting a talk about ZeroPy as well. -Matt

7 years, 7 months

species naming

by Matthew Turk

Hi all, Just wanted to make sure everyone had an opportunity to comment on and look at these pull requests: https://bitbucket.org/yt_analysis/yt/pull-request/719/adding-some-species-h… https://bitbucket.org/yt_analysis/ytep/pull-request/34/proposed-names-for-s… They propose new naming schemes for species fields, and then implement them for Enzo. You can see the translation table in the enzo/fields.py file. -Matt

7 years, 7 months

Issue #804: Querying for index properties before the index is generated fails (yt_analysis/yt)

by Nathan Goldbaum

New issue 804: Querying for index properties before the index is generated fails https://bitbucket.org/yt_analysis/yt/issue/804/querying-for-index-propertie… Nathan Goldbaum: The following IPython session illustrates the issue: ``` #!python [goldbaum@hyades CenOstriker_feedback]$ yt load DD0002/DD0002 yt : [INFO ] 2014-03-14 11:20:36,955 Parameters: current_time = 0.00200008999 yt : [INFO ] 2014-03-14 11:20:36,955 Parameters: domain_dimensions = [64 64 64] yt : [INFO ] 2014-03-14 11:20:36,955 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2014-03-14 11:20:36,956 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2014-03-14 11:20:36,956 Parameters: cosmological_simulation = 0.0 Python 2.7.6 |Anaconda 1.8.0 (64-bit)| (default, Nov 11 2013, 10:47:18) Type "copyright", "credits" or "license" for more information. IPython 2.0.0-dev -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object', use 'object??' for extra details. In [1]: ds.derived_field_list --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) /home/goldbaum/yt-hg/yt/mods.pyc in <module>() ----> 1 ds.derived_field_list AttributeError: 'EnzoDataset' object has no attribute 'derived_field_list' In [2]: ds.index yt : [INFO ] 2014-03-14 11:20:56,557 Gathering a field list (this may take a moment.) yt : [INFO ] 2014-03-14 11:20:57,316 Loading field plugins. yt : [INFO ] 2014-03-14 11:20:57,317 Loaded angular_momentum (6 new fields) yt : [INFO ] 2014-03-14 11:20:57,317 Loaded astro (12 new fields) yt : [INFO ] 2014-03-14 11:20:57,317 Loaded cosmology (18 new fields) yt : [INFO ] 2014-03-14 11:20:57,318 Loaded fluid (53 new fields) yt : [INFO ] 2014-03-14 11:20:57,318 Loaded fluid_vector (84 new fields) yt : [INFO ] 2014-03-14 11:20:57,319 Loaded geometric (99 new fields) yt : [INFO ] 2014-03-14 11:20:57,320 Loaded local (99 new fields) yt : [INFO ] 2014-03-14 11:20:57,320 Loaded magnetic_field (105 new fields) Out[2]: <yt.frontends.enzo.data_structures.EnzoHierarchy at 0x5485190> In [3]: ds.derived_field_list Out[3]: [('all', 'ParticleMass'), ('all', 'ParticleMassMsun'), ** snip ** In [4]: ```

7 years, 7 months

Issue #803: Particle filters cannot be added without referencing pf.h first. (yt_analysis/yt)

by Britton Smith

New issue 803: Particle filters cannot be added without referencing pf.h first. https://bitbucket.org/yt_analysis/yt/issue/803/particle-filters-cannot-be-a… Britton Smith: In the experimental bookmark, adding particle filters fails unless you specifically reference pf.h first. For example, the following script: http://paste.yt-project.org/show/4379/ results in this ``` #!python Traceback (most recent call last): File "test.py", line 12, in <module> pf.add_particle_filter("co_star") File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 373, in add_particle_filter used = self._setup_filtered_type(f) File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 386, in _setup_filtered_type if not filter.available(self.derived_field_list): AttributeError: 'EnzoDataset' object has no attribute 'derived_field_list' ``` However, this script works fine: http://paste.yt-project.org/show/4380/ The only difference is the addition of "pf.h" to line 12.

7 years, 7 months

Re: [yt-dev] Question about vorticity and divergence plots

by 吳佳鴻

Hi Matt, I already sent an email which has the subject “About YT Divergence and Vorticity Plots from Jia-hung” to your gmail account. In the email, it includes my data and my several frontend files. Any suggestion is welcome and thank you in advance for the help. Sincerely, -Jia-Hung -----------------Previous------------------------------------------- Hi Jia-Hung, Interesting. With cell-centered data, it ought to produce correct results. Would you be able to send me a small sample dataset (off-list) and I can take a look? Or feel free to stop by our hangout at 11AM Eastern and I can try it out there. -Matt On Wed, Mar 5, 2014 at 1:31 PM, 吳佳鴻 <r00222055 at ntu.edu.tw<http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org>> wrote: > Hi Matt, > > > > I am sorry that somehow my mailbox could not receive the mail successfully, > so I copy and paste the previous discussion at the bottom of this email. I > think my data is cell-centered, and I give YT my velocity field in the name > of ["velx", "vely", "velz"]. Is there anything wrong? > > > > Jia-Hung > > > > > > --------------------------------------previous > ------------------------------------------ > > Hi Jia-Hung, > > > > Are values stored as face-centered or cell-centered in your output? > > > > -Matt > > > > On Wed, Mar 5, 2014 at 5:21 AM, 吳佳鴻 <r00222055 at ntu.edu.tw<http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org>> wrote: > >> Dear all, > >> > >> > >> > >> I’m new to YT. I encountered a problem when trying to plot the > >> divergence and vorticity of a velocity field with an octree data > >> structure similar to FLASH. > >> > >> > >> > >> I put a cylindrically symmetric velocity field into YT. So far I could > >> get Velocity Magnitude Plot correctly and the Velocity vector looks > >> also fine (see the attachment). However, the VorticityMagnitude and > >> DivV plots have a offset toward the top right corner. I was wondering >> where I did it wrong. > >> Any suggestion will be welcome, and thanks for the help in advance. > >> > >> > >> > >> Sincerely, > >> > >> Jia-Hung > >> > >> > >> > >> > >> > >> > >> _______________________________________________ > >> yt-dev mailing list > >> yt-dev at lists.spacepope.org<http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org> > >> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org > >> > > _______________________________________________ > > yt-dev mailing list > > yt-dev at lists.spacepope.org<http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org> > > http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org > > > > > > > _______________________________________________ > yt-dev mailing list > yt-dev at lists.spacepope.org<http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org> > http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >

7 years, 7 months

Cleaning up my bookmarks

by Matthew Turk

Hi all, Now that all the main differences and changes and whatnot are merged in, I've decided to clean up my bookmarks. In case anybody else wants to do the same, here's my procedure. First, I collected all the names of non-head bookmarks: hg log -r "bookmark() and not head()" --template "{bookmarks}\n" > b1 I also backed up the full log output, just in case: hg log -r "bookmark() and not head()" > b1 I edited this because there were a few I didn't want to delete. Then, I deleted the rest: for bm in `cat b1`; do hg bookmark --delete ${bm} ; done for bm in `cat b1`; do hg push -B ${bm} ; done Note that there's probably a way to do it in a single pass with multiple -B arguments, but I didn't. -Matt

7 years, 7 months

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yt-dev March 2014