Mailman 3 January 2014 - yt-users

Mailing list issues
by Matthew Turk Jan. 29, 2014

Jan. 29, 2014

Hi all, We were having some mailing list issues earlier in the day, but I have been assured they are now fixed. So if you're seeing this, and got a bounce earlier, the clog seems to have been resolved. Sorry about that. -Matt

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ProjectionTransferFunction with Camera
by Munier Azzam Salem Jan. 29, 2014

Jan. 29, 2014

Hey Guys, I'm trying to get simple projections, but using the Camera interface, to allow skewed perspectives. I've tried simply allowing the camera to use the default ProjectionTransferFunction, in lieu of prettier color transfer functions ... this seems to yield an all-black image. I've also tried explicitly setting it's bounds (both with log and non-log limits). This doesn't seem to help. I see this issue came up about a year ago here<http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-January/00…> . My script's included below. I'm tempted to just tweak my inputs to the color trasnfer function to mimic a simple projection. thanks! Munier My script: *from yt.mods import ** *import yt.visualization.volume_rendering.api as vr* *from yt.visualization.volume_rendering.transfer_functions import ProjectionTransferFunction as PTF* *pf = load("DD0179/DD0179")* *field = 'Density'* *use_log = True* *# Find the bounds in log space of for your field* *dd = pf.h.all_data()* *limits = np.array(dd.quantities["Extrema"](field)[0]) * pf.units['cm']* *#if use_log:* *# limits = np.log(limits)* *# Set up the camera parameters: center, looking direction, width, resolution* *c = np.array([.333]*3)* *L = np.array([1.0, 1.0, 1.0])* *W = 0.3 / pf["unitary"]* *N = 1028* *# Create a camera object* *cam = vr.Camera(c, L, W, (N,N), transfer_function=PTF(limits),pf=pf)* *im = cam.snapshot('density.png')* -- Munier A. Salem // 845.489.6450

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Two Point Correlation Function in yt 3.0 with RAMSES
by David Sullivan Jan. 29, 2014

Jan. 29, 2014

Hi all, I’m trying to compute the two point halo correlation function for RAMSES data using the code found at http://yt-project.org/docs/2.6/analyzing/analysis_modules/two_point_functio… (I’ve already run HOP and written to HopAnalysis.out). I get an error saying ‘add_tree’ is not defined, but yt.utilities.kdtree is imported and build properly. Is this feature working in version 3.0? Many thanks, David

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size of a modified boundary.hdf Enzo file
by Jean-Claude Passy Jan. 28, 2014

Jan. 28, 2014

Hi all, I realize this is rather a question for the HDF group, but I was wondering if anyone had an explanation for what I am seeing. I would like to restart an Enzo simulation with different BCs on the root grid. Therefore, I created a new data.boundary.hdf with this very simple script: Aside from the different values in BoundaryDimensionType.X, the two files look completely identical to me (same datasets, attributes, types, sizes,…). However, I don't understand why the new file is about twice as big as the original one: ------------------------------------------------------------------------------- [15:42:09] Obiwan:$ du -sh CE0010.boundary*hdf 344K CE0010.boundary-new.hdf 176K CE0010.boundary.hdf ------------------------------------------------------------------------------- This is probably something simple, but I could not figure it out. Any suggestion would be much appreciated! Script is attached and the hdf files can be found there: https://dl.dropboxusercontent.com/u/19410190/CE0010.boundary.hdf https://dl.dropboxusercontent.com/u/19410190/CE0010.boundary-new.hdf Thanks a lot, JC

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Perspective Camera / Spherical Projections
by Munier Azzam Salem Jan. 28, 2014

Jan. 28, 2014

Hey Guys, I'm running a simulation of the Large Magellanic Clouds and would like to produce projections of the system as would be seen from the solar neighborhood (i.e., actual observations!). I'm thus looking to create projections in spherical coordinates from a point that happens to lie a factor of unity beyond my simulation box. I believe the camera objects can help me out here and I've messed around with all_sky plots. But the PerspectiveCamera class looks particularly useful. Unfortunately I could find any documentation for this class. Anyone have some advice on how to use this? thanks! Munier -- Munier A. Salem // 845.489.6450

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plotting program
by Kathy Eastwood Jan. 28, 2014

Jan. 28, 2014

hi, helpful folks I am once again very confused, and would appreciate any help. I am still trying to make a plot which contains frb's created from datafiles at different time steps. This is what I have that I think should work, and doesn't: from yt.mods import * %matplotlib inline import matplotlib.pyplot as plt import matplotlib.colorbar as cb from matplotlib.colors import LogNorm import numpy as np ts = TimeSeriesData.from_filenames("Strat_Box_hdf5_plt_cnt_01*") print len(ts) #just checking num = len(ts) for index, val in enumerate(ts): print "%s = %s" % (index, val) #again, just checking that this does what I think orient = 'vertical' fig, axes, colorbars = get_multi_plot( num, 1, colorbar=orient, bw = 6) plots = [] for i, fn in enumerate(ts): pf = load(fn) # load data sl = pf.h.slice(0, pf.domain_center[0],fields=["Density","Temperature"] ) frb = sl.to_frb( (1.0, 'kpc'), (4096,1024),height=(4.0, 'kpc')) dens_axes = [axes[0][i]] for ax in dens_axes: ax.xaxis.set_visible(False) ax.yaxis.set_visible(False) plots = [dens_axes[0].imshow(frb["Density"], origin='lower', norm=LogNorm())] These are the errors that I get; TypeError Traceback (most recent call last)<ipython-input-6-cd09eb0aaf88> in <module>() 1 for i, fn in enumerate(ts):----> 2 pf = load(fn) # load data 3 sl = pf.h.slice(0, pf.domain_center[0],fields=["Density","Temperature"] ) 4 frb = sl.to_frb( (1.0, 'kpc'), (4096,1024),height=(4.0, 'kpc')) 5 dens_axes = [axes[0][i]] /Users/kde/yt-x86_64/src/yt-hg/yt/convenience.pyc in load(*args, **kwargs) 65 try: 66 from yt.data_objects.time_series import TimeSeriesData---> 67 ts = TimeSeriesData.from_filenames(*args, **kwargs) 68 return ts 69 except YTOutputNotIdentified: /Users/kde/yt-x86_64/src/yt-hg/yt/data_objects/time_series.pyc in from_filenames(cls, filenames, parallel, **kwargs) 263 filenames = glob.glob(filenames) 264 filenames.sort()--> 265 obj = cls(filenames[:], parallel = parallel, **kwargs) 266 return obj 267 /Users/kde/yt-x86_64/src/yt-hg/yt/data_objects/static_output.pyc in __getitem__(self, key) 146 for d in [self.units, self.time_units, self.parameters, \ 147 self.conversion_factors]:--> 148 if key in d: return d[key] 149 raise KeyError(key) 150 TypeError: unhashable type thanks kathy -- Kathy DeGioia Eastwood, Ph.D. Professor of Physics and Astronomy Northern Arizona University Flagstaff, AZ 86011-6010 Ph: 928-523-7159 FX: 928-523-1371 Kathy.Eastwood(a)nau.edu deliveries: 602 S. Humphreys St., Bldg 19 Rm 209

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Re: [yt-users] RAMSES halo profiling error
by David Sullivan Jan. 27, 2014

Jan. 27, 2014

Hi Matthew, Many thanks for your help, just pulled your changes and the issue is now resolved. The last remaining call to _grids shouldn’t be a problem for me right now. Thanks for the speedy response! David

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RAMSES halo profiling error
by David Sullivan Jan. 27, 2014

Jan. 27, 2014

Hi all. I’m having some issues following the yt halo mass function example here: http://yt-project.org/docs/2.5/analysis_modules/hmf_howto.html for RAMSES data. The halo finder works, but I get the following error when trying to run the profiler: AttributeError: 'RAMSESGeometryHandler' object has no attribute ‘grids. I searched through the users archive but didn’t find anything. Appreciate any help (I’m using yt 3.0). Many thanks, David Sullivan

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Error with important of AbsorptionSpectrum
by Devin Silvia Jan. 27, 2014

Jan. 27, 2014

Hi all, I recently used conda to install yt, but when I try to import AbsorptionSpectrum, I get this error: http://paste.yt-project.org/show/4246/ I'm not familiar with particle_trajectories, but is this something that is actually needed by AbsorptionSpectrum? If not, should it even being trying to import that? Any thoughts/help are, as always, appreciated. Cheers, Devin -- Devin W. Silvia Research Associate Department of Physics and Astronomy Michigan State University www.devinsilvia.com

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Profile plots
by John ZuHone Jan. 24, 2014

Jan. 24, 2014

When using create_profile and ProfilePlot, how do I make it so that the y-axis for the field is in logscale? It looks like it sets log or linear by default based on the field's log property.

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