Mailman 3 December 2013 - yt-users

sliceplot and frb problems
by Kathy Eastwood 06 Dec '13

06 Dec '13

Dear (very helpful) yt folk: I have been struggling with trying to make a slice plot of some FLASH data that is an odd size; the volume is 1 kpc square in x and y, and 40 kpc tall in z. The grid sizes vary widely, as expected. I have two questions: one, I would like to understand the odd behavior that I get with regular SlicePLots, and I would like some help using the FixedResolutionBuffer, which I *suspect* is the way I want to go, but I have not been able to make it work. I am using the newest version of yt (upgraded this morning!) on Mac OS 10.7.5. The SlicePlot weirdnesses: from yt.mods import * %matplotlib inline import matplotlib.pyplot as plt import matplotlib.image as mpimg import matplotlib.colorbar as cb import numpy as np pf = load("Strat_Box_hdf5_plt_cnt_0064") #First try a 20 kpc tall box slc = SlicePlot(pf, 'x', 'Density',center='c',width=((1,"kpc"),(20.0,"kpc"))) slc.annotate_title('This is a Density plot') slc.save('test_20kpc.png') slc.show() #Please see plot at http://i.imgur.com/N65CNfU.png #Now try a 5 kpc tall plot slc = SlicePlot(pf, 'x', 'Density',center='c',width=((1,"kpc"),(5.0,"kpc"))) slc.annotate_title('This is a Density plot') slc.save('test_5kpc.png') slc.show() #Please see plot at http://i.imgur.com/L1YORNK.png ; note that it seems to filling #a different part of the plotting "window" #Now try a 2 kpc tall plot slc = SlicePlot(pf, 'x', 'Density',center='c',width=((1,"kpc"),(2.0,"kpc"))) slc.annotate_title('This is a Density plot') slc.save('test_2kpc.png') slc.show() #Please see plot at http://i.imgur.com/Bq1WaIP.png ; note that it seems to filling #even MORE of the plotting "window", but that the density labels were cut off a bit. OK, now the part that doesn't work. After reading, I decided that an frb must be the way to go, so I tried frb = FixedResolutionBuffer(slc, (0.0, 1.0, 0.0, 1.0), (1024,1024)) plt.imshow(frb['Density']) plt.savefig('test_figure.png') and I get the following error. Note: I also tried slc.to_frb and that didn't work either. ---------------------------------------------------------------------------AttributeError Traceback (most recent call last)<ipython-input-17-e68719d58ae4> in <module>()----> 1 frb = FixedResolutionBuffer(slc, (0.0, 1.0, 0.0, 1.0), (1024,1024)) 2 plt.imshow(frb['Density']) 3 plt.savefig('test_figure.png') 4 5 /Users/kde/yt-x86_64/src/yt-hg/yt/visualization/fixed_resolution.pyc in __init__(self, data_source, bounds, buff_size, antialias, periodic) 89 self.antialias = antialias 90 self.data = {}---> 91 self.axis = data_source.axis 92 self.periodic = periodic 93 AttributeError: 'SlicePlot' object has no attribute 'axis' THanks in advance for any help. cheers 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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HaloProfiler Troubles
by Claire Kopenhafer 06 Dec '13

06 Dec '13

Hello, my name is Claire. Recently, I've been having some very odd trouble with HaloProfiler. When I try to initiate HaloProfiler, it cannot open HopAnalysis.out, even when I feed it the full file path. This has happened on two different systems, but only with one particular data set! HaloProfiler then goes on to run HaloFinder, which would be totally cool except that that fails, too. Parallel_hop_interface.py cannot open fKD. Any ideas? Thanks!! -Claire

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EPS Multiplot
by John Regan 06 Dec '13

06 Dec '13

Hi All, Not sure whether this is currently possible but I'd like to create a multiplot eps figure containing a selection of projections. I first of all create my list of OffAxisProjectionPlots (proj) and then call ep = eps.multiplot(1, 2, proj, bare_axes=True). where proj is a list of plot_window objects. I'm using the YT dev branch and it's falling over with the error: Traceback (most recent call last): File "OffAxisProjection_MultiPlot.py", line 64, in <module> ep = eps.multiplot(1, 2, proj, bare_axes=True) File "/homeappl/home/regan/appl_taito/YT/Dev/yt-x86_64/src/yt-hg/yt/visualization/eps_writer.py", line 934, in multiplot d.insert_image_yt(yt_plots[index], pos=(xpos, ypos)) File "/homeappl/home/regan/appl_taito/YT/Dev/yt-x86_64/src/yt-hg/yt/visualization/eps_writer.py", line 424, in insert_image_yt plot.refresh() File "/homeappl/home/regan/appl_taito/YT/Dev/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", line 32, in newfunc args[0]._recreate_frb() File "/homeappl/home/regan/appl_taito/YT/Dev/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 266, in _recreate_frb periodic=self._periodic) File "/homeappl/home/regan/appl_taito/YT/Dev/yt-x86_64/src/yt-hg/yt/visualization/fixed_resolution.py", line 96, in __init__ h.plots.append(weakref.proxy(self)) ReferenceError: weakly-referenced object no longer exists If anyone knows what's happening let me know. Thanks in advance! John

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empty plot issue
by Kathy Eastwood 06 Dec '13

06 Dec '13

Hi, helpful folks. Another issue I have been struggling with, which is similar to this thread http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-May/003652… I am working on some FLASH data with the current version of yt using MacOS 10.7.5. Using this exact same data set, I managed to create some nice phaseplots using spheres centered on the densest spot. However, I now want to make some plots for a much larger volume of scientific interest... Here is the code from yt.mods import * %matplotlib inline import matplotlib.pyplot as plt import numpy as np pf = load("Strat_Box_hdf5_plt_cnt_0064") pc = PlotCollection(pf, [0.5, 0.5, 0.5]) plane = pf.h.region([0.5,0.5,0.5],[0.0,0.0,0.4],[1.0,1.0,0.6]) pc.save("plane_cnt_0064") I then get the following error ValueError: Data has no positive values, and therefore can not be log-scaled Following the advice in the thread listed above, John Wise suggested "For your "empty" plot, do you have any gas with densities between 1e-26 and 1e-27 g/cm^3 in this sphere? If there's no gas in this range, then CellVolume will be zero and will give you that error message when it tries to take the log of CellVolume. If you want to manually inspect the CellVolume field, you can print out the following variable pc.plots[-1].data['CellVolume'] which will give you the CellVolume as a function of the x-variable for the last plot you have added to your PlotCollection." The writer did not respond in the next thread, so I'm not sure if this worked. But when I try it, I get the following: KeyError Traceback (most recent call last)<ipython-input-18-71f93f9e2cb6> in <module>()----> 1 pc.plots[-1].data["CellVolume"] /Users/kde/yt-x86_64/src/yt-hg/yt/data_objects/profiles.pyc in __getitem__(self, key) 160 # This raises a KeyError if it doesn't exist 161 # This is because we explicitly want to add all fields--> 162 return self.field_data[key] 163 164 def __setitem__(self, key, value): KeyError: 'CellVolume' Even though CellVolume is explicitly listed in my list of derived fields... Also, I did try the same command for Density rather than CellVolume, and the numbers were in the e-24 g cm-3 range...in fact, all the numbers were exactly the same. So I don't know if I've screwed up my data container somehow, or if the density values really are too low? any ideas? thanks SO much 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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HaloProfiler troubles
by Claire Kopenhafer 05 Dec '13

05 Dec '13

Hello, my name is Claire. Recently, I've been having some very odd trouble with HaloProfiler. When I try to initiate HaloProfiler, it cannot open HopAnalysis.out, even when I feed it the full file path. This has happened on two different systems, but only with one particular data set! HaloProfiler then goes on to run HaloFinder, which would be totally cool except that that fails, too. Parallel_hop_interface.py cannot open fKD. Any ideas? Thanks!!

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Temporary IPython nbviewer replacement
by Nathan Goldbaum 05 Dec '13

05 Dec '13

Hi all, The IPython nbviewer web service has been having spotty uptime and errors lately. If you need to look at a notebook and find yourself unable to use nbviewer, try this URL instead: http://nbtest.herokuapp.com/ This is a test version of nbviewer that includes some fixes that haven't found their way into nbviewer proper yet. Use it just like nbviewer - for example by appending a url: http://nbtest.herokuapp.com/url/hub.yt-project.org/notebooks/3d1f4e7258a147… Hopefully within the next week or two nbviewer should be back up to full steam. -Nathan

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healpix_aitoff_proj
by Yong Zheng 04 Dec '13

04 Dec '13

Hi, I am currently trying to use healpix_aitoff_proj to make all sky map with the current stable version. But I am wondering if HEALpix will be back in the latest version (2.6) since it is currently noted as 'removed' in the document... Thanks! Best, Yong

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Image/Data Interpolation
by John Regan 04 Dec '13

04 Dec '13

Hi All, I'm not sure if anything like this exists in YT. I'd like to interpolate between images from different snapshots so as to make multiple images (e.g. projections) between two snapshots. The best way to do this is probably at the field level I imagine. Is there a way in YT to access the image array that is used to produce the projections? Or maybe there is a better way in YT? Any suggestions/pointers much appreciated! Cheers, John

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getting the average density inside a data container
by k.grisdale＠surrey.ac.uk 03 Dec '13

03 Dec '13

Hi yt Users I am trying to create a data container that is a cube from which I can extract the average density of the gas inside the cube. I am using Ramses data. When I create a data container using: p6 = load("output_00006/info_00006.txt", fields = ["Density","x-velocity", "y-velocity", "z-velocity", "Pressure"]) cen = [0, 0, 0] box = p6.h.region(cen, 0.2/p6['cm'], 0.3/p6['cm’]) print box["Density”] I get this error: TypeError: 'float' object has no attribute ‘__getitem__' I have tried creating a sphere as a data container and this works for the Density, but then when I try to take the AverageDensity in the sphere: sphere = p6.h.sphere(cen, 0.7/p6['cm’]) print sphere['AveragedDensity’] I get this error: enerationInProgress Traceback (most recent call last) <ipython-input-28-574d78c4fb5c> in <module>() ----> 1 print sphere['AveragedDensity'] /Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key) 187 return self.field_data[f] 188 else: --> 189 self.get_data(f) 190 # Note that this is less succinct so that we can account for the case 191 # when there are, for example, no elements in the object. /Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields) 514 return 515 elif self._locked == True: --> 516 raise GenerationInProgress(fields) 517 # At this point, we want to figure out *all* our dependencies. 518 fields_to_get = self._identify_dependencies(fields_to_get) Any idea what I am doing wrong or if there is another way to go about this? Thanks Kearn

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2.6.1 point release
by Matthew Turk 03 Dec '13

03 Dec '13

Hi all, Because of a regression in phase plots in yt 2.6, we've just rolled out a point release of yt 2.6.1. If you have been using phase plots, or want to use them in the future, we recommend upgrading. If you're using the "stable" branch already from source, just run "yt update". -Matt

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