Mailman 3 January 2014 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman 15 Aug '22

15 Aug '22

Hi All, I was curious if anyone has had any luck porting .ply files generated with yt into Blender with colors? It seems to port in the surfaces just fine, but they are a uniform color. From what I can gather, Blender imports .ply files with face color instead of vertex so I tried the surf.export_ply routine with "face" instead of "vertex" for sample_type, but no luck ("vertex" doesn't work either). Let me know if I can provide any more useful info. Thanks for any help, -J

3 2

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

8 14

Variance in phase/profiles
by david collins 12 Apr '20

12 Apr '20

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

6 8

Notebook server question
by Andrew Myers 19 Apr '14

19 Apr '14

Hello yt users, I have a (perhaps naive) ssh question related to the yt notebook. I would like to run a yt notebook server on machine A. However, machine A cannot be directly accessed via ssh from the wider internet. Instead, I must first ssh into machine B, and then ssh from B to A. Machine B cannot run the notebook server itself. Does anyone know how I can configure things - perhaps by using a more complicated ssh tunnel command - so I that access a notebook server running on machine A through machine B? Thanks, Andrew

4 5

change size of phase plot
by Stephanie Tonnesen 15 Apr '14

15 Apr '14

Hi all, I am trying to make my phase plots smaller so they can fit more nicely into a paper. Alternatively, I would be fine with upping the font size so when I shrink them you can read the axes. I found advise on how to do this for slices, but not for phase_objects. pc = PlotCollection(pf) tracerp25 = alld.cut_region(["grid['specific_scalar[0]'] > 0.5", "grid['z'] < 0.192","grid['z'] > -0.192","grid['cyl_RCode'] < 1.2"]) pc.add_phase_object(tracerp25,["Density","z-velocity","CellMassSolar"],weight=None,x_bins=50,y_bins=50,y_bounds = [-4e7,8e7],x_bounds=[5e-28,5e-23],x_log=True,y_log=False) Any help is much appreciated! Thanks, Stephanie

4 17

Light Cone Projection
by Pengfei Chen 02 Mar '14

02 Mar '14

Hi all, I downloaded the example script of light cone projectoin( http://yt-project.org/doc/cookbook/cosmological_analysis.html#light-cone-pr…) to my laptop and changed the Enzo simulation parameter file and redshifts. But when I ran it the following error occurred: File "light_cone_projection.py", line 19, in <module> find_outputs=False) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py", line 158, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/cosmology_splice.py", line 44, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/convenience.py", line 131, in simulation find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 81, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/data_objects/time_series.py", line 343, in __init__ self._parse_parameter_file() File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 273, in _parse_parameter_file param, vals = (i.strip() for i in line.split("=")) ValueError: need more than 1 value to unpack Does the parameters "near_redshift" and "far_redshift" in LightCone need to be the same with "CosmologyFinalRedshift" and "CosmologyInitialRedshift" in enzo parameter file? Does anyone know how to solve this? Thank you all! Pengfei

2 10

Two Point Correlation Function in yt 3.0 with RAMSES
by David Sullivan 03 Feb '14

03 Feb '14

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 P.S Sorry if this gets duplicated as I accidentally tried to send this with an unregistered e-mail

2 1

chemical species abundances discrepancy
by poetaste＠gmail.com 02 Feb '14

02 Feb '14

Hi Guys, I did a simple test with enzo and I tried to plot a radial profile of the chemical species fractions with YT. The problem is that if I use the YT function which intrinsically plot the fraction for a species, let's say H2I_Fraction (as usual), and compare this with a direct evaluation of the mass fraction: data['H2I_Density']/data['Density'] I obtain some slightly different results, mostly at large radii. Anyone might explain this discrepancy!? This happens with all the species. Thank you in advance Stefano

5 16

More PhasePlots questions
by Stephanie Tonnesen 31 Jan '14

31 Jan '14

Hi everyone! I have a few more PhasePlots questions. 1) I would like to force my axes to be a particular range. I am looking at several times in my simulation, and the length of the stripped tail increases, so different PhasePlots end up with different height above the disk x-axis ranges, which makes comparison more annoying. 2) I would like for the last tick label to be blank--to not print out on the figure (in the attachment, I would like for '100' to not be there). 3) On a slightly different note, I want the bin size to be bigger. The PhasePlots look very streaky, see attached. I will paste my current set of commands for making my PhasePlot. Thanks for any help! Stephanie plot = PhasePlot(tracerp25,"zkpc","zvelocity8",["CellMassMsun"],weight_field=None,fontsize=19)#,x_bounds=[3e-28,5e-23],y_bounds=[-0.7,1.2]) plot.set_log("zkpc",False) plot.set_log("zvelocity8",False) plot.set_zlim("CellMassMsun",1e4,1e9) plot.set_figure_size(3) ax = plot.plots['CellMassMsun'].axes ax.set_ylabel(r'z-velocity (10$^8$ cm/s)',fontsize=10) ax.set_xlabel(r'Height above disk (kpc)',fontsize=10) print r'z-velocity (10$^8$ cm/s)' for label in ax.xaxis.get_ticklabels(): #label.set_color('red') label.set_rotation(35) label.set_fontsize(11) for label in ax.yaxis.get_ticklabels(): label.set_fontsize(10) plot.save()

2 2

Trouble with SciPy Install
by Nathan Butcher 30 Jan '14

30 Jan '14

Hello, I am trying to install yt with SciPy on Michigan State University's HPCC system and am running into errors that I cannot resolve by following the instructions in the install script. I have tried uncommenting each of the NUMPY_ARGS statements and had no success. I have attached the log file from my most recent installation attempt as the error message is long. My guess is that it has to do with the "recompile with -fPIC" message but I cannot figure out what that means. Can anybody explain what this error message means and how to resolve it. Thank you, Nathan Butcher

5 8

Mailing list issues
by Matthew Turk 30 Jan '14

30 Jan '14

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

1 0

ProjectionTransferFunction with Camera
by Munier Azzam Salem 29 Jan '14

29 Jan '14

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

2 3

Two Point Correlation Function in yt 3.0 with RAMSES
by David Sullivan 29 Jan '14

29 Jan '14

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

1 0

size of a modified boundary.hdf Enzo file
by Jean-Claude Passy 28 Jan '14

28 Jan '14

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

2 2

Perspective Camera / Spherical Projections
by Munier Azzam Salem 28 Jan '14

28 Jan '14

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

2 1

plotting program
by Kathy Eastwood 28 Jan '14

28 Jan '14

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

2 2

Re: [yt-users] RAMSES halo profiling error
by David Sullivan 27 Jan '14

27 Jan '14

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

1 0

RAMSES halo profiling error
by David Sullivan 27 Jan '14

27 Jan '14

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

2 1

Error with important of AbsorptionSpectrum
by Devin Silvia 27 Jan '14

27 Jan '14

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

3 4

Profile plots
by John ZuHone 24 Jan '14

24 Jan '14

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.

2 1

Trouble with SciPy install
by Nathan Butcher 24 Jan '14

24 Jan '14

Hello, I am trying to install yt with SciPy on Michigan State University's HPCC system and am running into errors that I cannot resolve by following the instructions in the install script. I have tried uncommenting each of the NUMPY_ARGS statements and had no success. I have attached the log file from my most recent installation attempt as the error message is long. My guess is that it has to do with the "recompile with -fPIC" message in lines 75202 and 75205 but I cannot figure out what that means. Can anybody explain what this error message means and how to resolve it. Thank you, Nathan Butcher

1 0

building fKDpy.so manually
by Remudin Mekuria 24 Jan '14

24 Jan '14

Hi all, While trying to run the attached script from "yt-cookbook" to get halo mass function, I am getting NameError: global name 'fKD' is not defined. It looks like I am tied up already, since I can't do "yt update" on the top of my manual installation. If I am not wrong, it looks to me that I have to build fKDpy.so, may you help me on how to do that. Thank you in advance for your kindest help. Cheers, Remudin ==================== yt : [INFO ] 2014-01-24 15:32:41,413 Building kd tree for 2097152 particles... Traceback (most recent call last): File "mass_function.py", line 15, in <module> hp = amods.halo_profiler.HaloProfiler("/home/remudin/gas_plus_dm_uni_adia_simulation/RD0003/RedshiftOutput0003") File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_profiler/multi_halo_profiler.py", line 305, in __init__ self._load_halo_data() File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_profiler/multi_halo_profiler.py", line 983, in _load_halo_data self._run_hop(hop_file) File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_profiler/multi_halo_profiler.py", line 1140, in _run_hop **self.halo_finder_kwargs) File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/halo_objects.py", line 2305, in __init__ premerge=premerge, tree=self.tree) File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/halo_objects.py", line 1670, in __init__ HaloList.__init__(self, data_source, dm_only) File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/halo_objects.py", line 1059, in __init__ self._run_finder() File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/halo_objects.py", line 1698, in _run_finder tree=self.tree) File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py", line 63, in __init__ self._chain_hop() File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py", line 1526, in _chain_hop self._init_kd_tree() File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py", line 341, in _init_kd_tree fKD.dens = np.zeros(self.size, dtype='float64', order='F') NameError: global name 'fKD' is not defined ================================== ................................ ................................. Remudin Reshid; MEKURIA, School of Physics, Wits University, 1 Jan Smuts Ave, Braamfontein, WITS 2050 Johannesburg, South Africa ................................ ................................. <table width="100%" border="0" cellspacing="0" cellpadding="0" style="width:100%;"> <tr> <td align="left" style="text-align:justify;"><font face="arial,sans-serif" size="1" color="#999999"><span style="font-size:11px;">This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorised signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. </span></font></td> </tr> </table

1 0

Release of pywwt 0.1.0, a Python interface to the World Wide Telescope Windows Client
by John ZuHone 24 Jan '14

24 Jan '14

Hi all, Apologies for the spam, but I thought maybe the yt-users list would be good place to find some interest in this new library I wrote, pywwt: http://www.jzuhone.com/pywwt pywwt is a Python interface for the Microsoft World Wide Telescope (WWT, http://www.worldwidetelescope.org) Windows client, using the Layer Control API (LCAPI). The LCAPI provides an interface to WWT’s Layer Manager by sending data and information in the form of strings over HTTP. pywwt provides a straightforward Python interface to make these calls, enabling the control of WWT from scripts or an IPython notebook. Most importantly, it enables the passing of data created within a Python environment to WWT. The upshot of this is that particle data that can be loaded into yt can be passed off to a World Wide Telescope client running on a Windows machine, either the same host or a host on the same network. To see an example IPython notebook (complete with an example video!), visit: http://www.jzuhone.com/pywwt/pywwt_example.html pywwt requires the following packages: • NumPy • Matplotlib • AstroPy • Beautiful Soup 4 • Requests • Dateutil pywwt can be installed from pip: pip install pywwt or download the source from http://github.com/jzuhone/pywwt and install: python setup.py install My use cases are limited, and I'd be interested in what others could do with it, so if you are interested please fork the code and help develop! Best, John Z

2 2

NotImplementedError
by Yong Zheng 23 Jan '14

23 Jan '14

Hi, I newly installed yt in my laptop, but ran into an error call "NotImplementedError" when I tried to use 'pixelize_healpix' which used to work fine in my another computer, the whole message is as followed: img2d,count = pixelize_healpix(NP, img1d, resolution, resolution, rotation) File "grid_traversal.pyx", line 1127, in yt.utilities.lib.grid_traversal.pixelize_healpix (yt/utilities/lib/grid_traversal.c:14555) NotImplementedError Can any of you help to explain why this happens here? How can I fix it? Thanks for your help! Yong

2 1

Surface plot from FITS data cube
by Mairan Teodoro 22 Jan '14

22 Jan '14

Hi yt-users! I'm new to yt and Python (I'm an IDL guy). Currently, I'm using VisIt to visualize my FITS data cube. However, since I'm wandering through the fields of Python, I would really like to use yt as my default visualization tool. Having said that, I would like to ask if somebody out there has some piece of code to read a FITS data cube into a Python array (I know how to do this already) and use yt to visualize it and make iso-surface plots (like the ones I've attached to this message). I went through the yt manual examples (especially the volume plot sections) but all I've got was some kind of blurred blotch (see figure "UniformGridData_volume_rendered.png"). Any help would be very appreciated. Best regards! m. --Dr. Mairan Teodoro NASA Goddard Space Flight Center 8800 Greenbelt Rd. Greenbelt, MD 20771 USA Bldg. 34, Rm. 321 301-286-6321 Code 667 http://asd.gsfc.nasa.gov/Mairan.Teodoro http://etacar2014.wikidot.com

2 1

Another clump finder error
by Caroline Van Borm 22 Jan '14

22 Jan '14

Hi all, Sorry to bother you again, but I have another problem with the clump finder. I have been able to run the script to find the clumps, wrote them to a text file, and saved the clump object using <pf.h.save_object(master_clump, 'myclumps')>. However, when I try to read the object back in and get the lowest clumps using master_clump = pf.h.load_object('myclumps') leaf_clumps = get_lowest_clumps(master_clump) I get an error saying: Traceback (most recent call last): File "./findclumps.py", line 66, in <module> leaf_clumps = get_lowest_clumps(master_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 209, in get_lowest_clumps if clump.children is None or len(clump.children) == 0: AttributeError: 'NoneType' object has no attribute 'children' Does this happen because the clump object didn't actually get saved? And how can I check whether it did or not? Thanks again! Cheers, Caroline

4 4

Setting x and y limits in PhasePlot
by Devin Silvia 21 Jan '14

21 Jan '14

Hi all, I'm currently running into and issue where I can't seem to figure out how to control the x and y limits of my axes in a PhasePlot. Is this possible? Or do I need to go the PlotCollection route? Thanks! Devin -- Devin W. Silvia Research Associate Department of Physics and Astronomy Michigan State University www.devinsilvia.com

2 1

yt-installation failed on getting pip
by Remudin Mekuria 20 Jan '14

20 Jan '14

Dear YT-users, My installation of yt on Ubuntu machine failed up on getting pip. I have tried to test the source of the problem first by installing pip as "sudo apt-get install python-pip". And I have pip installed. It turn out to be the same even when i do again "bash install_script.sh". Then, I also tried to verify these is not a network connection problem as it is saying in the error message"error: Download error for https://pypi.python.org/packages/source/p/pip/pip-1.5.tar.gz: Tunnel connection failed: 407 Proxy Authentication Required". I will be glad to receive your help on these. Cheers, Remudin ################ ################ ################ ################ ...... Installing Python. This may take a while, but don't worry. yt loves you. Installing mercurial-2.8 Setting YT_DIR=/home/remudin/yt-x86_64/src/yt-hg/ Installing distribute Installing pip ******************************************** FAILURE REPORT: ******************************************** Processing dependencies for distribute==0.6.32 Finished processing dependencies for distribute==0.6.32 After install bootstrap. Creating /home/remudin/yt-x86_64/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg-info Creating /home/remudin/yt-x86_64/lib/python2.7/site-packages/setuptools.pth Searching for pip Reading http://pypi.python.org/simple/pip/ Best match: pip 1.5 Downloading https://pypi.python.org/packages/source/p/pip/pip-1.5.tar.gz#md5=6969b8a8ad… error: Download error for https://pypi.python.org/packages/source/p/pip/pip-1.5.tar.gz: Tunnel connection failed: 407 Proxy Authentication Required ******************************************** ******************************************** Failure. Check /home/remudin/yt-x86_64/yt_install.log. The last 10 lines are above. ################ ################ ################ ################ ................................ ................................. Remudin Reshid; MEKURIA, School of Physics, Wits University, 1 Jan Smuts Ave, Braamfontein, WITS 2050 Johannesburg, South Africa ................................ ................................. <table width="100%" border="0" cellspacing="0" cellpadding="0" style="width:100%;"> <tr> <td align="left" style="text-align:justify;"><font face="arial,sans-serif" size="1" color="#999999"><span style="font-size:11px;">This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorised signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. </span></font></td> </tr> </table

2 1

Does anybody have a sample script for plotting a time-series of images from frb's?
by Kathy Eastwood 17 Jan '14

17 Jan '14

Hi, everybody I've been working off the example scripts on the yt website, and can't quite seem to do what I want to do. I want to plot something like 20 tall/skinny images in a horizontal row, and label the time steps below, and put the colorbar vertically. I am constrained to using frb's because my images are not square. I have managed to make a plot with three such images, although I haven't managed to put in the time step labels, and there is white space between the images. But it was very much brute force -- I had to create a separate set of axes for each image. All the example scripts that use frb's use the "get_multi_plot" inside yt, whereas the only example of a time series in the image plots uses the AxesGrid from matplotlib. I have not managed to make the AxesGrid work with an frb. There is also a non-image-plotting example in the bootcamp of using "TimeSeriesData" to go through a lot of files, which would be great, but I have not been able to figure out how to translate that into what I need. If anybody has a sample script of something vaguely similar to this, I would really appreciate it! 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

4 3

Clump finder error
by Caroline Van Borm 16 Jan '14

16 Jan '14

Hi all, I have a problem with the clump finder. When I try to run it on my dataset (Enzo data), using a script that mostly follows the find_clumps.py from the yt docs, I get the following, very long, error: Traceback (most recent call last): File "./findclumps.py", line 44, in <module> find_clumps(master_clump, c_min, c_max, step) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 191, in find_clumps elif (child._isValid()): File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 145, in _isValid self.function_value = eval(self.function) File "<string>", line 1, in <module> File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 94, in __call__ return self._call_func_unlazy(args, kwargs) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 119, in _call_func_unlazy retval = self.func(self._data_source, *args, **kwargs) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 378, in _IsBound mass_to_use = data["TotalMass"] File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 332, in __getitem__ self.get_data(key) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 2618, in get_data if self._generate_field(field): File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 362, in _generate_field self[field] = self.pf.field_info[field](self) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 395, in __call__ dd = self._function(self, data) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/universal_fields.py", line 444, in _TotalMass return (data["Density"]+data["particle_density"]) * data["CellVolume"] File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 332, in __getitem__ self.get_data(key) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 2618, in get_data if self._generate_field(field): File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 359, in _generate_field self._generate_field_in_grids(field, ngt_exception.ghost_zones) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 369, in _generate_field_in_grids grid[field] = self.__touch_grid_field(grid, field) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 95, in save_state tr = func(self, grid, field, *args, **kwargs) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 373, in __touch_grid_field return grid[field] File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 157, in __getitem__ self.get_data(key) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 200, in get_data self._generate_field(field) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 145, in _generate_field self[field] = self.pf.field_info[field](self) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 395, in __call__ dd = self._function(self, data) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/universal_fields.py", line 998, in _pdensity if data["particle_position_x"].size == 0: return blank File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 157, in __getitem__ self.get_data(key) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 200, in get_data self._generate_field(field) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 145, in _generate_field self[field] = self.pf.field_info[field](self) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 396, in __call__ dd *= self._convert_function(data) TypeError: unsupported operand type(s) for *=: 'NoneType' and 'float' The main difference is that for the function passed to Clump, I'm using 'self.data.quantities["IsBound"](truncate=True,include_thermal_energy=True) > 1.0' to find gravitationally bound objects. When I run the clump finder on my data with a function that keeps clumps based on the number of cells, it works fine. I also tried running the script on the IsolatedGalaxy dataset as demonstrated in the docs. This works fine too, also when the function is set to the one mentioned above. Anyone knows what's going on here? Btw, my yt version is b118390aa42c. Thanks! Cheers, Caroline

3 5

draw axes triad in volume rendering
by Michael Zingale 13 Jan '14

13 Jan '14

Is there a yt way to add an axes triad (like in VisIt -- just a simple indicator of the direction for +x, +y, +z) to a volume render image? Also on those lines, when I draw a box for the domain with cam.draw_domain(im), is there a way to get it to add ticks and labels to the box? Thanks, Mike -- 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

2 1

LightRay Objection Creation - Index Error
by Claire Kopenhafer 13 Jan '14

13 Jan '14

Hello out there, I'm trying to create a LightRay object for an enzo sim. I get this error message: Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/data/codes/yt-x86_64/src/yt-hg/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py", line 117, in __init__ redshift_data=redshift_data) File "/data/codes/yt-x86_64/src/yt-hg/yt/analysis_modules/cosmological_observation/cosmology_splice.py", line 119, in create_cosmology_splice cosmology_splice.append({'time': self.simulation[0].current_time, File "/data/codes/yt-x86_64/src/yt-hg/yt/data_objects/time_series.py", line 117, in __getitem__ o = self._pre_outputs[key] IndexError: list index out of range The nearest and farthest redshift are both 0, which is the current redshift of the dataset I was given. This may or may not have any bearing on the problem. Thanks for the help! -Claire Kopenhafer

3 2

Rotations in off_axis_projection
by James Guillochon 10 Jan '14

10 Jan '14

Hi everyone, I have a 3D simulation FLASH that I wish to rotate and then project using YT. I know the transformation matrix needed to rotate the domain such that the projection is correct, depicted in this image: http://i.imgur.com/AOmY6Ao.png. In the image, the dashed lines are the original coordinate system, where the original "north_vector" is the red dashed line, and the original "normal_vector" is a green dashed line that points out of the plane (not visible). The rotated coordinates are shown by the solid lines. The transformation matrix A is: A = 0.0478113 -0.345249 0.937292 0.912293 -0.367011 -0.181724 -0.406737 -0.863774 -0.297421 My question is what should I set "normal_vector" and "north_vector" to to get the proper projection. I tried just doing A.normal and A.north, but the projection I get is not correct. I've also tried multiplying by A_inverse, or just multiplying normal and/or north by A (or A_inverse), and setting the other vector to a trivial direction (such as [0,0,1]), but none of these projections seem to be correct. Another thing I have tried is opening the data in Visit and rotating the domain manually, taking note of what Visit calls the "view normal" and the "up vector". The "up vector" matches the "north vector" I calculate using A.north, but the "view normal" does not match A.normal. Does anyone know the proper way to go about this? Thanks! - James -- James Guillochon Einstein Fellow at the Harvard-Smithsonian CfA jguillochon(a)cfa.harvard.edu

3 2

YT Error on trestles
by Munier Azzam Salem 10 Jan '14

10 Jan '14

Hey Guys, I've just tried installing yt on trestles for the first time (vanilla install of dev version, with scipy and rockstar included). The install seemed to go well, but when I tried to import the modules, it appeared some dependencies were missing: *>>> from yt.mods import ** *Traceback (most recent call last):* * File "<stdin>", line 1, in <module>* * File "/home/msalem/src/yt-x86_64/src/yt-hg/yt/mods.py", line 25, in <module>* * import numpy as na # For historical reasons* * File "/home/msalem/src/yt-x86_64/lib/python2.7/site-packages/numpy/__init__.py", line 137, in <module>* * import add_newdocs* * File "/home/msalem/src/yt-x86_64/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>* * from numpy.lib import add_newdoc* * File "/home/msalem/src/yt-x86_64/lib/python2.7/site-packages/numpy/lib/__init__.py", line 13, in <module>* * from polynomial import ** * File "/home/msalem/src/yt-x86_64/lib/python2.7/site-packages/numpy/lib/polynomial.py", line 17, in <module>* * from numpy.linalg import eigvals, lstsq, inv* * File "/home/msalem/src/yt-x86_64/lib/python2.7/site-packages/numpy/linalg/__init__.py", line 48, in <module>* * from linalg import ** * File "/home/msalem/src/yt-x86_64/lib/python2.7/site-packages/numpy/linalg/linalg.py", line 23, in <module>* * from numpy.linalg import lapack_lite* *ImportError: libquadmath.so.0: cannot open shared object file: No such file or directory* Any insights here? thanks! Munier -- Munier A. Salem // 845.489.6450

2 1

yt-3.0 issues with FLASH
by Alex Bogert 08 Jan '14

08 Jan '14

http://yt-project.org/data/ I ran into an error with the GalaxyClusterMerger example file on the yt-project site. I was attempting to use a covering grid on the data to sub-sample densities. This is with yt-3.0 . Here is the code and error: http://pastie.org/8611073 Thanks, Alex

2 1

Removing Yt and reversing changes to system.
by k.grisdale＠surrey.ac.uk 06 Jan '14

06 Jan '14

Hi, I want to remove yt from my system and reverse the changes that yt made to my python install. What is the best way to achieve this? Thanks Kearn (I am using a Mac with Mavericks incase that is needed)

2 1

YT parallel error
by John Regan 02 Jan '14

02 Jan '14

Hi All, I've started to see a strange error in a simple enough parallel computation. I can reproduce it with the script below but with some other scripts where the code is embedded it runs fine so it may be a race condition. from yt.mods import * pf = load("/wrk/regan/H2/Ctrl/DD0035/Data0035") v, c = pf.h.find_max("Density") print v, c Thanks in advance for any help! Cheers, John Error: Traceback (most recent call last): P001 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at 0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid EnzoGrid_1214 at level 18 (3, 3, 2) Traceback (most recent call last): File "ptest.py", line 5, in <module> P003 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at 0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid EnzoGrid_1214 at level 18 (3, 3, 2) File "ptest.py", line 5, in <module> Traceback (most recent call last): File "ptest.py", line 5, in <module> P002 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at 0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid EnzoGrid_1214 at level 18 (3, 3, 2) Traceback (most recent call last): P004 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at 0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid EnzoGrid_1214 at level 18 (3, 3, 2) Traceback (most recent call last): File "ptest.py", line 5, in <module> P005 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at 0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid EnzoGrid_1214 at level 18 (3, 3, 2) Traceback (most recent call last): File "ptest.py", line 5, in <module> P006 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at 0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid EnzoGrid_1214 at level 18 (3, 3, 2) Traceback (most recent call last): File "ptest.py", line 5, in <module> Traceback (most recent call last): File "ptest.py", line 5, in <module> Traceback (most recent call last): File "ptest.py", line 5, in <module> File "ptest.py", line 5, in <module> v, c = pf.h.find_max("Density") v, c = pf.h.find_max("Density") v, c = pf.h.find_max("Density") v, c = pf.h.find_max("Density") File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max v, c = pf.h.find_max("Density") File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max v, c = pf.h.find_max("Density") File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max v, c = pf.h.find_max("Density") v, c = pf.h.find_max("Density") v, c = pf.h.find_max("Density") File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels) mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels) File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 66, in find_max_cell_location mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels) File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 66, in find_max_cell_location File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 66, in find_max_cell_location mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels)

3 4