Mailman 3 September 2012 - yt-users

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

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Variance in phase/profiles
by david collins 11 Apr '20

11 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.

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p.modify["point"]
by Elizabeth Tasker 05 Oct '12

05 Oct '12

Hi, I'm trying to add text to a particular point in my slice. I've got: position = na.array([20.2, 13.8, 16.0]) pc = PlotCollection(pf, center=position) p = pc.add_projection("Density", 2) p.set_width(2, 'kpc') for c in range(len(t1clouds)): r = abs(t1clouds[c]['position']-position) if r[0] < 1.0 and r[1] < 1.0: p.modify["point"](t1clouds[c]['position'], str(t1clouds[c]['track'])) p.modify["marker"](t1clouds[c]['position'], marker='o') pc.save("%s_tracking" % (fn)) But python complains with: TypeError: text() argument after ** must be a mapping, not NoneType Did I call the modifier incorrectly? Elizabeth

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eps writer with custom colormap
by Geoffrey So 29 Sep '12

29 Sep '12

Hi, this question is mainly for John Wise, While attempting to produce different plots for a paper, I wanted to create color and gray scale versions of the same plot, but since the background of most plots are white, a gray scale for 2D phase plot would either show the highest or lowest color as white and blend in with the background, so I made my own gray scale colormap according to the matplotlib manual. It works great for PlotCollection and I can make color/gray-scale-with-no-white-data images in png, but when I tried to use the same colormap with the eps writer, it complains about it in line 571 in yt/visualization/eps_writer.py Here's a sample script of what I used to generate my plots http://paste.yt-project.org/show/2739/ If I change the line 62 of the script from p.set_cmap(my_gray_cmap) to: p.set_cmap('jet') the error goes away. So PyX can take the matplotlib colormaps or have the same ones built-in. Is there a convenient way to get _cmap = plot.cmap.name to recognize custom colormaps? Or is there an easier solution to my problem of displaying gray scale data without using the white portion of the gray scale colorbar? Thanks in advance From G.S.

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Wireframe images
by Matthew Turk 25 Sep '12

25 Sep '12

Hi all, Has anybody had any luck adding wireframes to volume rendered images? I think it would be straightforward, although perhaps not easy/trivial, to do this on top of a volume rendered scene, but it would be nice if I could get it into the image proper. Any ideas? -Matt

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How do you make movies?
by Nathan Goldbaum 21 Sep '12

21 Sep '12

Hi all, I'm curious what sort of scripts, tools, and invocations thereof that people in the yt community use to stitch frames together into movies. It seems like there are a number of solutions to do this. It would be nice if we could gather some solutions for this process and put them in the documentation or on the website so that future users have a place to start when they're trying to make their first movies. For what it's worth, here's a script I just wrote to process a bunch of slices and projections dumped by a timeseries script: http://paste.yt-project.org/show/2703/ I've had good results with ffmpeg, although it's a pain to install and has an inflexible command line syntax to tell it to stitch together frames for a movie so I would love to hear of other solutions that don't use ffmpeg. Cheers, Nathan

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Re: How do you make movies?
by Markus Haider 19 Sep '12

19 Sep '12

Hi Nathan, I also use mencoder under Ubuntu 12.04, which I call through the following python script: ------------------------------------------------------- #!/usr/bin/python import os # where are the pictures? INPUTDIR ="./slices/slice_collection/" BASENAME ="Cluster_hdf5_plt_cnt_5363_" fps = '10' bitrate = '2048000' encode_opts=':mbd=2:mv0:trell:v4mv:cbp:vb_strategy=1:precmp=2:cmp=2:subcmp=2:preme=2:qns=2' FIELD ="Density" outputFile = './movies/'+FIELD+'_slice.avi' frameName=INPUTDIR+BASENAME+'*_Slice_x_'+FIELD+'.png' encodeCommand = 'mencoder mf://'+frameName+' -mf type=png:fps='+fps+' -ovc lavc -lavcopts vcodec=mpeg4:vbitrate='+bitrate+encode_opts+' -o '+outputFile os.system(encodeCommand) print 'Finished making video' ------------------------------------------------------- The only thing you have to make sure is that the slices are numbered with enough leading zeros, otherwise e.g. slice 100 will be inserted into the video before slice 11 Cheers, Markus

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Connected Sets
by Francia F. Riesco 19 Sep '12

19 Sep '12

Hello Everybody, I am writing you this time to ask if anybody has an example how to manipulate data. For instance, I am using contour_values, connected_sets = sphere.extract_connected_sets("Density", levels, mi, ma) print connected_sets[i] #{0: ExtractedRegionBase (redshift0058): _base_region=AMRSphere (redshift0058): center=[ 0.1005697 0.15871103 0.37831026], radius=0.0124657962771} and connected_sets is an array of dict of dicts, but I couldn't find any example of how manipulate a dict object. Thank in Advance -- Francia F.R.

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2D FLASH data again
by John Forbes 19 Sep '12

19 Sep '12

Hi all, I updated yt today, and a problem with my 2D FLASH data has arisen again. As of last week, all of my cells' z values were at pf.domain_left_edge[2], and all the dz values were 1. I think ideally I would want my z-values to be (upper + lower)/2, and my dz-values to be upper-lower, where by upper and lower I mean pf.domain_right_edge[2] and pf.domain_left_edge[2], respectively. So, things were working, just not in precisely the way I would have expected. With the current version of yt ( d77fb0031d39 ) , it appears that I get a range of z-values and dz-values, from 0 to upper/2, with dz = 2 z. These appear to be correlated with the refinement level. An example of what happens in this situation when I try to generate a slice plot is shown below. I also attempted to shift the center of the plot collection up by 1.0, but got the same set of errors. The file which I'm using in the session below is still available here: http://www.ucolick.org/~jforbes/cloud_hdf5_plt_cnt_0000 Thank you, John >>> from yt.mods import * >>> pf = load("cloud_hdf5_plt_cnt_0000") yt : [WARNING ] 2012-09-18 15:18:10,923 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2012-09-18 15:18:10,928 Parameters: current_time = 0.0 yt : [INFO ] 2012-09-18 15:18:10,928 Parameters: domain_dimensions = [ 8 32 1] yt : [INFO ] 2012-09-18 15:18:10,928 Parameters: domain_left_edge = [ -2.46854420e+22 0.00000000e+00 -2.46854420e+22] yt : [INFO ] 2012-09-18 15:18:10,928 Parameters: domain_right_edge = [ 2.46854420e+22 1.97483536e+23 2.46854420e+22] yt : [INFO ] 2012-09-18 15:18:10,929 Parameters: cosmological_simulation = 0.0 >>> pc=PlotCollection(pf) yt : [INFO ] 2012-09-18 15:18:43,245 Max Value is 1.67330e-26 at -430910425537109360640.0000000000000000 24248504855224609931264.0000000000000000 0.0000000000000000 in grid FLASHGrid_0649 ([8 8 1]) at level 10 (0, 7, 0) yt : [INFO ] 2012-09-18 15:18:43,245 Created plot collection with default plot-center = [-4.3091042553710936e+20, 2.424850485522461e+22, 0.0] >>> pc.add_slice("Density",2) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/jforbes/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py", line 431, in add_slice center=center, **field_parameters) File "/Users/jforbes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1045, in __init__ self._refresh_data() File "/Users/jforbes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 315, in _refresh_data self.get_data() File "/Users/jforbes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 830, in get_data self._generate_coords() File "/Users/jforbes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1079, in _generate_coords for grid in self._get_grids(): File "/Users/jforbes/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 898, in _get_grids return ObjectIterator(self, attr='_grids') File "/Users/jforbes/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 102, in __init__ raise YTNoDataInObjectError(pobj) yt.utilities.exceptions.YTNoDataInObjectError: The object requested has no data included in it. It may lie on a grid face. Try offsetting slightly. >>> dd=pf.h.all_data() >>> print dd['dz'].min(), dd['dz'].max(), dd['z'].min(), dd['z'].max() yt : [INFO ] 2012-09-18 15:19:27,137 Getting field dz from 3648 yt : [INFO ] 2012-09-18 15:19:28,476 Getting field z from 3648 0.0 2.4685442e+22 0.0 1.2342721e+22

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particle read error
by david collins 18 Sep '12

18 Sep '12

Hi, all-- I have a set of clumps that I've pickled to disk, now I've unpickled them and I'm trying to get some particle info. When I try to access the particle indices from the clump (in the error message, it's c1) it throws the following error. I do the same thing again, and it works fine (that is, access particle_index on the same c1, returns a reasonable looking particle list) I'm probably doing something dumb, do any of y'all see what it is? Thanks, d. File "p19_check_missing2.py", line 15, in <module> ind1 = c1['particle_index'] File "/Users/dccollins/yt2.0/DaveClump.py", line 80, in __getitem__ return self.data[request] File "/Users/dccollins/local2/src/yt-hg/yt/data_objects/data_containers.py", line 327, in __getitem__ self.get_data(key) File "/Users/dccollins/local2/src/yt-hg/yt/data_objects/data_containers.py", line 2525, in get_data self.particles.get_data(field) File "/Users/dccollins/local2/src/yt-hg/yt/data_objects/particle_io.py", line 62, in get_data if len(fields) == 1: return rvs[0] TypeError: 'NoneType' object is not subscriptable -- Sent from my computer.

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