Mailman 3 March 2012 - yt-users

getting all the data in a subgrid
by Jean-Claude Passy 08 Mar '12

08 Mar '12

Hi all, As far as I understand, a: ------------------------------------ region = pf.h.region(...) density = region["Density"] ------------------------------------ will return the density field without considering cells that have subcells. How can I access ALL the data stored in the hdf5 file? I have tried to use ------------------------------------ grid = pf.h.grids[i] rhogrid = grid.get_data("Density") ------------------------------------ but I would like to get a 1D array. Thanks for you help, JC

2 2

find_max error
by Stella Offner 06 Mar '12

06 Mar '12

Hi, I'm working with an undergrad student doing Orion data analysis using the most recent stable version of yt (he attended the recent yt workshop - yea!). However, he is encountering this error with his yt installation: File "slicePJ.py", line 18, in <module> c = pf.h.find_max("Density") #this involves finding the max density File "/usr/local/yt/yt-x86_64/src/yt-hg/yt/data_objects/ static_output.py", line 172, in hierarchy self, data_style=self.data_style) File "/usr/local/yt/yt-x86_64/src/yt-hg/yt/frontends/orion/ data_structures.py", line 131, in __init__ self._setup_field_list() File "/usr/local/yt/yt-x86_64/src/yt-hg/yt/frontends/orion/ data_structures.py", line 365, in _setup_field_list for field in self.field_info: AttributeError: 'OrionHierarchy' object has no attribute 'field_info' I can't reproduce this error on any of my own yt installations with the data (although my versions are a bit older). His script (below) is pretty straight forward and successfully loads the data first. Any ideas? from yt.mods import * from yt.funcs import * import particles import fields """ The next section is taken from the yt cookbook as a basic test to make sure I can get everything to work """ fn = "p1a09025" pf = load(fn) pf = load(fn) # load data pc = PlotCollection(pf) # defaults to center at most dense point pc.add_slice("Density", 0) # 0 = x-axis pc.add_slice("Density", 1) # 1 = y-axis pc.add_slice("Density", 2) # 2 = z-axis #pc.set_width(1.5, 'mpc') # change width of all plots in pc #I have commented this line from the cookbook version pc.save(fn) # save all plots """ Below are commented versions of older efforts, working off from what I did at the yt workshop """ #dd = pf.h.all_data() #c = pf.h.find_max("Density") #this involves finding the max density #pc = PlotCollection(pf) #recentering # commenented out the( ,c ) in the argument to test if #p1 = pc.add_slice("Temperature", 2) #p2 = pc.add_projection("Density", 2, "Density") #pc.set_width(0.1, "unitary") #pc.set_cmap("cool") Thanks! Stella

2 2

Feature Requests
by Matthew Turk 06 Mar '12

06 Mar '12

Hi all, Just a reminder: feature requests can (and *should*) be submitted to the BitBucket issue tracker here: https://bitbucket.org/yt_analysis/yt/issues/new This will help yt-dev track where there are deficiencies, things that can be corrected, and places for improvement -- even big, gigantic long-reaching features. :) Best, Matt

1 0

Reading in Potential Field
by meecegre＠msu.edu 03 Mar '12

03 Mar '12

Hi Everyone, I'm trying to use yt to calculate the spin parameter of a halo generated by Enzo. I have enzo writing out the potential using the -g flag, but when yt reads in the field, it isn't able to figure out the units or recognize it as a known field. Also, yt is keeping the potential data in code units, rather than converting to CGS. When I make a plot of the potential, the plot says that the units are unknown. When I load the dataset into yt, the relavant output is yt : [INFO ] 2012-03-01 17:10:20,349 Adding unknown field PotentialField to list of fields I discussed this probelm with Brian O'Shea and Britton Smith. Not sure if anyone else has run into this issue. -- Greg Meece

3 2

Strange artifacts in volume rendering movie made using parallel_objects
by Nathan Goldbaum 01 Mar '12

01 Mar '12

Hi all, I'm running into some weird issues when I try to make a time series volume rendering movie using parallel_objects. The script I'm running is pasted here: http://paste.yt-project.org/show/2206/ And the resulting movie is located here: http://ucolick.org/~goldbaum/files/volume.avi The movie is stitched together using ffmpeg but i've confirmed that the artifacts are present in the individual frames. This is not due to my use of the enhance script since the artifacts appear in the raw frames and in fact the movie was stitched together using the raw frames. I don't see any artifacts when I volume render individual frames in serial. I'm doing one processor per file parallelism. Thanks for your help with this - I know there's a cool looking movie buried in there somewhere. Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum(a)ucolick.org http://www.ucolick.org/~goldbaum

3 5

Kraken yt/dev import error
by Britton Smith 29 Feb '12

29 Feb '12

Hi, The yt/dev and yt/dev-local modules on Kraken are giving errors when trying to do 'from yt.mods import *'. Just doing that give the following error: http://paste.yt-project.org/show/5A6G4lAjr7UE2y1wsLNQ I get the exact same thing with both of those two modules. Thanks! Britton

3 4