Mailman 3 August 2013 - 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

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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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broke yt trying to update
by Stephanie Tonnesen 29 Aug '13

29 Aug '13

Dear all, After a pretty long (few month) hiatus, I just tried to update my yt and seem to have broken it. Now my desktop is frozen so I can't cut and paste the long outputs, but it boils down to: >yt update The current version of the code is: ___ 0be45301e0eb (yt) tip ___ This version CAN be automatically updated. .... added 1740 changesets with 3520 changes to 355 files (+1 heads) Updating the repository 126 files updates, 0 files merged, 0 files removed, 0 files unresolved BROKEN: See /u/stonnes/Installs/yt-x86_64/src/yt-hg/yt_updater.log So I looked at that and the first thing it had was: pulling from https://bitbucket.org/yt_analysis/yt/ (run 'hg update' to get a working copy) So I ran hg update and then it failed and said I had no module named write_array When I start python2.7 and type >> from yt.mods import * I get the same error (no module write_array) Any advice would be appreciated! Thanks, Stephanie

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Re: [yt-users] yt-users Digest, Vol 66, Issue 42
by Renyue Cen 26 Aug '13

26 Aug '13

Hi, Thanks. I am not even plotting using MATLAB or alike. I just want to read in the data in Fortran to look at it in some detail, so I think that my (j,i) switched way should work. Just to make sure. Renyue On Aug 26, 2013, at 1:50 PM, yt-users-request(a)lists.spacepope.org wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. Re: pc.add_phase_object(source,[x,y,z],?) (Geoffrey So) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 25 Aug 2013 11:46:23 -0700 > From: Geoffrey So <gsiisg(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] pc.add_phase_object(source,[x,y,z],?) > Message-ID: > <CAM-dO+Bw4g+V4QDsNt1s2vCbnpG8Q4-X8amrwmKnvZFu90skCA(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > I usually use something similar to > http://paste.yt-project.org/show/3816/ > to use yt to bin the data then use matplotlib to make the plot of the 2D > profile for more customization options. > If you compare the test1.....png and test2.png, you should see they are > using the same data range, the 2D profile is transposed to switch x,y and > origin set at (0,0). > > hope it's something you can use. > > From > G.S. > > > On Sun, Aug 25, 2013 at 9:34 AM, Renyue Cen <cen(a)astro.princeton.edu> wrote: > >> Hi Matt, >> >> so if I just read in data filename like: >> >> do j=1,50 >> do i=1,50 >> read(1,*)column(i),row(j),Z(j,i) >> enddo >> enddo >> >> will that correct Z exactly? >> >> Renyue >> >> On Aug 25, 2013, at 12:28 PM, Matthew Turk <matthewturk(a)gmail.com> wrote: >> >>> Hi Renyue, >>> >>> Yup, it's column/row switched from what one might expect. But, the >>> bins written out should correspond. >>> >>> -Matt >>> >>> On Sun, Aug 25, 2013 at 10:38 AM, Renyue Cen <cen(a)astro.princeton.edu> >> wrote: >>>> Hi, >>>> >>>> When I do >>>> >> plotdata=pc.add_phase_object(source,["FieldX","FieldY","QuantityZ"],weight >> = None,..) >>>> plotdata.data_write_out(filename) >>>> >>>> It seems that the QuantityZ written out in file filename is transposed >> with respect to >>>> x-y plane of the plot plotted by pc.add_phase_object(). >>>> >>>> Has anyone encountered this? >>>> If anyone wants script and actual file to help me, I can send to you. >>>> >>>> Thanks, >>>> Renyue >>>> >>>> _______________________________________________ >>>> yt-users mailing list >>>> yt-users(a)lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >

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yt volume render/AMRKDtree help
by Renyue Cen 25 Aug '13

25 Aug '13

Hi, I did some simple volume rendering with the following script: volume2 = AMRKDTree(pf, fields=["Dark_Matter_Density"], no_ghost=False, tree_type="domain", le=c-0.5*WW, re=c+0.5*WW) cam = pf.h.camera(c, L, W, N, tf, volume=volume2, no_ghost=False, north_vector=L, steady_north=True) cam.snapshot(fn="%s_iso-DMdensity-%3.3d.png" % (filenameTHIS, j)) I got rather strange results in that the pictures look symmetric, which I am pretty sure can not be true. I attach the obtained plot. Note that I am using KD tree and using 32 cores. Your help at your earliest convenience is appreciated. Best, Renyue

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Announcing: yt 2.5.5
by Matthew Turk 23 Aug '13

23 Aug '13

Hi all, We're proud to release yt version 2.5.5. This is an unscheduled point release that includes all bug fixes identified and fixed since the release of 2.5.4 on July 2nd. We missed our scheduled release date a bit, and have continued to push off a 2.6 as development on the 2.x branch winds down. Additions, changes and bug fixes include: * New absorption spectrum analysis module with documentation * Fix for volume rendering on the command line * map_to_colormap will no longer return out-of-bounds errors * Fixes for dds in covering grid calculations * Library searching for build process is now more reliable * Unit fix for "VorticityGrowthTimescale" field * Pyflakes stylistic fixes * Adding ability to draw lines with Grey Opacity in volume rendering * Updated physical constants to reflect 2010 CODATA data * Number density added to FLASH * Dependency updates (including IPython 1.0) * Many fixes for Athena frontend * Radius and ParticleRadius now work for reduced-dimensionality datasets * Source distributions now work again! * Better notebook support for yt plots * Athena data now 64 bits everywhere * Grids displays on plots are now shaded to reflect the level of refinement * show_colormaps() is a new function for displaying all known colormaps * PhasePlotter by default now adds a colormap. If you are using the stable branch of yt from an installation script, you can upgrade using "yt update" or "yt update --all" to upgrade your full dependency stack. If you are using the development branch, you may already have these fixes. A tarball of this release has been uploaded to the Python Package Index (PyPI). yt releases often feature contributions from many individuals; this release includes first time contributions from John Forbes, Noel Scudder and Hilary Egan. Documentation for this release can be found at: http://yt-project.org/docs/dev/ Thanks very much, Matt, on behalf of the yt development team

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Colorbar on Phase Plots
by Patrick Rieser 22 Aug '13

22 Aug '13

Hi all, does anybody have an idea how to get a colorbar to show up for the zfield (weight=none) with the PhasePlotter? I am using log scaling and I'd like to have the colorbar for the zfield logarithmic as well. I used the PhasePlotter as described at the following page: http://yt-project.org/doc/visualizing/manual_plotting.html#phase-plots Just to be clear, what I'd like to have is something like this (just on the right side of the plot): http://matplotlib.org/examples/api/colorbar_only.html Best wishes, Patrick.

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Announcing: yt 3.0 alpha 3
by Matthew Turk 22 Aug '13

22 Aug '13

Hi everyone, We're proud to announce the third ALPHA release of yt 3.0. yt has recently transitioned to a time-based release plan ( https://ytep.readthedocs.org/en/latest/YTEPs/YTEP-0008.html ) and this is the third scheduled alpha of 3.0, although we've grossly missed the estimated date of July 15. No date for a "final" release has yet been set, but there will likely be several more alphas before that time. The yt 2.5 codebase, and further updates in the 2.x series, will be supported for a considerable amount of time and you do not need to upgrade. = yt 3.0?! = yt 3.0 represents a new direction forward for yt: getting rid of all the underlying assumptions that data needs to be sectioned off into nice little grid patches. This includes supporting Octree codes natively (NMSU-ART and RAMSES), eventual support for SPH codes, and even opaque data structures where the data is extremely large (ARTIO). We're even planning support for natively handling cylindrical and spherical coordinates. More: http://blog.yt-project.org/post/WhatsUpWith30.html However, this *is* an alpha release. Not all of the existing codes have been ported to 3.0. Additionally, this release benefits from the technical and non-technical contributions from many new people. yt is developed in the context of a community of contributors, and with the push toward a new architecture, we aim to expand that community considerably. In particular, this release has considerably benefited from contributions from many new individuals. = Getting It! = To try out yt 3.0, you can now pull from the main yt repository, update to the yt-3.0 branch, and rebuild your extensions. Or, if you would like to create a new, safely sectioned off environment, simply re-run the normal "development" install script after changing the variable BRANCH to "yt-3.0". If you would like to try out yt 3.0 and are having trouble, please write to the yt-users mailing list for assistance. The yt 3.0 install script may also work, which can be obtained by executing these commands: wget http://hg.yt-project.org/yt/raw/yt-3.0/doc/install_script.sh bash install_script.sh = What's New? = A demo notebook demonstrating much new functionality, and including the full release notes, can be found here: http://hub.yt-project.org/nb/88u14f The bullet-pointed release notes can be found at the end of this email, as well. The main improvements include *considerable* memory usage reduction, ARTIO spatial data indexing support, better particle support, an overhaul of the selection methods for data objects, and a mechanism for on-the-fly definitions of particle types based on boolean filters. Additionally, this release was used in the production of the AGORA project flagship paper. The analysis script used there can be seen at this short URL: http://goo.gl/SwY9Uv and the paper can be found here: http://arxiv.org/abs/1308.2669 = Reporting Problems = If you test out yt 3.0 we want to hear if it DID or DID NOT work! Feedback is crucial at this time. yt-users and yt-dev are both good forums for discussion, asking questions, and reporting problems. Lots of things have changed on the backend, but we have attempted to minimize the user-facing changes. To report a bug please go here: https://bitbucket.org/yt_analysis/yt/issues/new Note that you will not receive updates if you are not logged in when you create the bug. = What's Next? = The next alpha release (3.0a4) will be released sometime this fall, but development can be monitored either at http://bitbucket.org/yt_analysis/yt-3.0 or in the main yt repository under the named branch "yt-3.0". We hope to focus on generalizing Octree support further, adding better non-Cartesian support, and supporting generic smoothing kernel definitions. If you'd like to participate in yt development, please stop by #yt on irc.freenode.net ( http://yt-project.org/irc.html ) or yt-dev ( http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org ), or submit a pull request on BitBucket. Thanks very much, Matt, on behalf of the yt development team Changelog: (Including 434 changesets from 7 contributors since 3.0a2) * Fixes for volume rendering and porting of the Cython kD-tree. VR now works for octree codes, albeit slowly. * Major reorganization and simplification of selector code, including generic periodicity * ARTIO now has spatial data support * Major bug fix for FLASH IO. FLASH works again, following a regression in 3.0a2. * Merged with mainline yt development, bringing developments from yt 2.5.3 and 2.5.4 into 3.0. * OWLS (Gadget-HDF5) data now updated to match functionality of other Gadget datasets. * Creationg of "arbitrary_grid" data selector for flexible particle deposition operations. This enables creation of a grid of arbitrary dimensions that can have particles smoothed or deposited within them. * Conversion of all CIC operations to particle deposition operations. This results in much more flexible particle type selection and speed improvements. * Refactoring of particle fields to enable simpler creation and collection of particle fields. Particle fields defined for Eulerian codes and Lagrangian codes are now interchangeable. * New, currently unused parallel ring iteration. To be explored in the future for smoothing kernels. * Many improvements for NMSU-ART * Fixed a crazy QuadTree deposition bug for projections that showed up when projecting octree particle deposition results through a restricted data object. * Fixed a crazy off-by-one bug for binary Gadget IO. * Enormous Octree diet. * Oct leaf nodes now cost 256 bits each, which may eventually be reduced to 192 bits. Previous versions were considerably larger. * Octree traversal is strictly recursive, enabling distributed-memory octrees to be implemented. * RAMSES octrees are created by-domain instead of globally. This will enable better parallelism in the future and faster ghost zone generation when that is implemented. * Particle octree are now constructed via Z-curve generation. This is considerably faster (10-20x) as well as much more memory conservative. This was designed to utilize parallel octree construction in the future. * Particle octrees are now indexed by coarse base-level indexing of domain regions. This enables unsorted particle files to be indexed for IO as well as spatial selection without mandating that leaf nodes are fully-contained within a single file. Reduction in total oct leaf count of ~8x for multi-file particle datasets. * YTDataContainer no longer requires .shape and .size * Only requested fields are plotted, not translated fields * Reduce memory usage of spatially-chunked fields for patch datasets * Added arbitrary particle loader, load_particles. * Units fix for RAMSES boxlen!=1.0 datasets * Particle filtering for dynamically-created particle types, similar to derived fields * Improve type consistency in TotalQuantity and other derived quantities. * Fixed major error with ghost zone generation and uninitialized values * Some resiliency for particle datasets that do not specify a domain * Bugfix for 1- and 2-D Enzo datasets * Improvements to the Tipsy frontend, including auto-detecting parameter files * Enable specification of n_ref when creating particle dataset * Enable particle deposition to back-act on particle fields * Major fix for octree particle counting, resulting in smaller meshes * Enable "source" specification for volume rendering * Enable initial volume rendering of octree datasets * Fixed error with RAMSES C/F ordering of data * Many fixes related to field dependency calculation * FLASH cylindrical & polar pixelization fix

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questions on projection
by Semyeong Oh 21 Aug '13

21 Aug '13

Hi all, I'm new to yt. I have questions about making projections of certain region, and inspecting the data returned. I made a cube as follows: import pylab as pl center = [0.5, 0.5, 0.5] halfwidth = 0.005 cube = pf.h.region(center, center-pl.ones(3)*halfwidth, center+pl.ones(3)*halfwidth, ['Density']) print min(cube['x']), max(cube['x']) 0.494873046875 0.505126953125 When I print cube['x'].shape, I get (10728,). I tried to make a projection of this cube along z-axis as follows: proj2 = pf.h.proj(2, 'Density', center=center, source=cube) But I could not understand what is returned. print min(proj2['p x']), max(proj2['py']), proj2['px'].shape 0.00390625 0.99609375 (19648,) print proj2['Density'] [ 0. 0. 0. ..., 0. 0. 0.] My questions are: 1. What exactly is returned in proj2? Why does it span from 0. to 1. when I specified source=cube? 2. I also tried 'data_source=cube' instead of 'source=cube'. It did not raise any error, and returned something different: array of same shape, but with different data values. Is this keyword also used for projection object? Is there a consistent difference between the two keywords in yt? 3. I could not find documentation on some fields like 'px', 'py' that seem to be generated for certain data containers (e.g., 't' for ray objects). Is there an exhaustive list of such fields in the documentation? Thanks in advance. Semyeong

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segmentation fault while extract_obj
by Lucky Puspitarini 20 Aug '13

20 Aug '13

Hello all, My name is Luki. I'm new in yt. I have a problem in extracting object from yt. I want to have the surface object in .obj or .ply file so then i can transform it to .u3d for 3d pdf I have a data cube that i build this way. from yt.mods import * from numpy import * myfile=loadtxt("3ddata_300_lowerres.txt") dens=myfile[:,3] densitycube=dens.reshape(61,61,61) mydata=dict(Density=densitycube) bbox=np.array([[-300,300],[-300,300],[-300,300]]) pf=load_uniform_grid(mydata,densitycube.shape,3.08e18,bbox=bbox) Then, I would like to have a surface of certain value in my data and extract it to .obj files sp = pf.h.sphere("center", (250, "pc")) trans = 1.0 distf = 3.08e18 surf = pf.h.surface(sp, "Density", 0.0006) surf.export_obj("myism.obj", transparency=trans, dist_fac = distf) But i have a problem with segmentation fault. Segmentation fault: 11 I'll also try export_ply but i have the same problem :( sp = pf.h.sphere("center", (250, "pc")) surf = pf.h.surface(sp, "Density", 0.0006) bounds = [(sp.center[i] - 125.0/pf['pc'],sp.center[i] + 125.0/pf['pc']) for i in range(3)] surf.export_ply("myism.ply",bounds=bounds) Can you help me? Thankyou in advance Best regards, luki

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How to address yt issues
by Nathan Goldbaum 20 Aug '13

20 Aug '13

Hi all, This past week I prepared some slides on how to deal with and report issues that may come up in daily use of yt. The slides are available here: http://ngoldbaum.net/for_agora/get_help.pdf The slides were based on a talk Cameron gave at the first yt workshop at the FLASH center in January 2012 but I went ahead and updated them to reflect current best practices. If you have a minute, please take a look. Cheers, Nathan PS: The slides for the yt-3.0 demo I gave are also available: http://ngoldbaum.net/for_agora/Agora_ytdemo.slides.html

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Trouble plotting 1D scatter data from 3D Athena vtk data.
by Timothy Waters 20 Aug '13

20 Aug '13

Hi, Here is the data and simple script to make a scatter or profile plot of my simulation output, https://www.dropbox.com/sh/ibpda938ltsxl0j/2AA2FYDUH8#/ This is a spherically symmetric (cartesian [-0.5,0.5]^3, 32cells^3) hydro simulation with initial conditions density = 1.0 if radius <= 1/3; density falls off as 1/r^2 if r > 1/3; velocity is everywhere 0 The output with these ICs is WP12.0000.vtk. When I run my script the first time using iyt I get the first image with the expected ICs. Running it again gives the second image and I don't know why. I'm hoping those other points don't actually exist in my data. Maybe I am just missing something simple? The evolved data, WP12.0030.vtk, is provided as well. Running this data 'cleans the slate' so that I can then go back to see the problem with my initial conditions again. Of course, the problem shows up in this data too. Thanks in advance! Tim

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Cylindrical and Polar Slicing (FLASH)
by Morgan MacLeod 20 Aug '13

20 Aug '13

Dear yt gurus, I've enjoyed using yt for a number of FLASH problems in cartesian geometry. Right now I'm just starting on a setup in FLASH 2D polar (eventually also in 3D cylindrical) geometries. These are ordered 2D polar: r, theta 3D cylindrical: r, theta, z I was intrigued when I noticed this image on the yt-blog ( http://blog.yt-project.org/post/WhatsUpWith30.html) -- which is almost exactly what I would like to do. [image: http://blog.yt-project.org/attachments/cylindrical_pixelizer.png] I have updated to yt-3.0, and tried the simplest "Sliceplot" of the data: fn = "const_rho_g_atm_hdf5_plt_cnt_0013" pf = load(fn) fig = SlicePlot(pf, 2,'dens').save("myfig.png") This reads loads the 2D polar plot file correctly, but renders the result in a cartesian sense. Does anyone have advice/recipes for how to proceed with Slices rendered "cylindrically"? I understand that this feature set is not yet fully developed but I was curious if there was a solution (or parts of a solution) floating around out there. Thanks so much, Morgan MacLeod ------------------------------------------------- Graduate Student Astronomy & Astrophysics UC Santa Cruz

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Re: [yt-users] Cylindrical and Polar Slicing (FLASH)
by Mark Subbarao 19 Aug '13

19 Aug '13

I'll be away till August 19th, with semi-limited connectivity. Will respond when I can. Visit our website: http://www.adlerplanetarium.org

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Re: [yt-users] Cylindrical and Polar Slicing (FLASH)
by Mark Subbarao 16 Aug '13

16 Aug '13

I'll be away till August 19th, with semi-limited connectivity. Will respond when I can. Visit our website: http://www.adlerplanetarium.org

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Re: [yt-users] Cylindrical and Polar Slicing (FLASH)
by Mark Subbarao 16 Aug '13

16 Aug '13

I'll be away till August 19th, with semi-limited connectivity. Will respond when I can. Visit our website: http://www.adlerplanetarium.org

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Field Cuts in Off-Axis Projections
by Munier Azzam Salem 14 Aug '13

14 Aug '13

Hey guys, I've been trying to make slices of density only looking at cooler gas (i.e. with a cut in Temperature). I've found a nice way to do this for simple projections. But my strategy breaks for Off-Axis projections. Specifically, this works fine: * * *field_parameters={'field_cuts':["grid['Temperature'] < 1e6 "]})* *cold_proj = ProjectionPlot(pf,0,'Density',field_parameters=field_parameters)* * * but this does not: *cold_proj = OffAxisProjectionPlot(pf,axis,'Density',north_vector=north,* * field_parameters= field_parameters)* sensibly enough, since field_parameters is not a keyword argument for off axis projections. Is there a decent workaround for this? Or would this be simple to add into yt's functionality? I've looked briefly into the source<http://yt-project.org/doc/_modules/yt/visualization/plot_window.html#OffAxi…>and it doesn't seem obvious how to slip this in. thanks! Munier -- Munier A. Salem // 845.489.6450

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convering_grid question
by barbara ramirez 14 Aug '13

14 Aug '13

Hello Everyone! So, I have a question about how does covering grid actually works. I have a Flash simulation output of a 28*28 Mpc box containing a cluster. I am trying to simulate the spectra from a region of size (0.08 Mpc x, 0.08 Mpc y, 28 Mpc z) around the centre, (I will assume z is my line of sight) so I use this line to define the region: #The shape of my region cube = pf.h.covering_grid(level_max, left_edge=newlep, right_edge=newrep,dims=[6, 6, 128]) where level = 5 (max level of refinement for my Flash data), "newlep" is centre coordinates (Mpc) minus 0.08 Mpc and newrep is centre coordinates plus 0.08 Mpc, and then into percentage units. I put them into an array of dimensions [6,6,128] because I want 36 spectra (one for each pixel of the ccd) so I will fix an (x,y) position and write an XSPEC file for all z elements. (I need basically temperature and density of all the elements). My question is: how does covering grid makes a single field value (temperature, for example) inside the (x,y,z) position? because I am arbitrarily saying to divide the region into 6 pixel, but the data file might have many simulation pixels inside , so how are the field values calculated? is it just an average? or are just certain points taken into consideration? Thanks for any hints/tips/help! Barbara Ramirez University of Innsbruck, Austria

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Re: [yt-users] problem with covering_grid for Nyx data sets (Wolfram Schmidt), yt-users Digest, Vol 66, Issue 17
by Wolfram Schmidt 14 Aug '13

14 Aug '13

Hi Nathan, thanks a lot for your suggestions! I updated yt to the current development version, which didn't fix the problem. So I tried what you suggested: On 08/06/2013 07:52 PM, yt-users-request(a)lists.spacepope.org wrote: > and then try your script again. If the issue isn't fixed by updating, I > would then try applying the following diff to the nyx frontend: > > diff -r f936432ed45d yt/frontends/nyx/data_structures.py > --- a/yt/frontends/nyx/data_structures.py Tue Jul 30 10:08:24 2013 > -0700 > +++ b/yt/frontends/nyx/data_structures.py Tue Aug 06 08:10:25 2013 > -0700 > @@ -611,7 +611,7 @@ > # aliases we need > self.parameters["TopGridRank"] = > len(self.parameters["TopGridDimensions"] > self.dimensionality = self.parameters["TopGridRank"] > - self.domain_dimensions = self.parameters["TopGridDimensions"] > + self.domain_dimensions = > np.array(self.parameters["TopGridDimensions"]) > self.refine_by = self.parameters.get("RefineBy", 2) # 2 is silent > defaul > > # Nyx is always cosmological. > I replaced the definition of self.domain_dimensions with the np.array thing. Now, the script actually reads in the data, but then another problem is encountered when an FFT is applied to the data: Searching grids for values 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:03:04 yt : [ERROR ] 2013-08-07 11:56:48,958 Covering problem: 16777216 cells are uncovered Traceback (most recent call last): File "/usr/users/wschmid2/scripts/spect_sb.py", line 72, in <module> velx_hat = na.fft.fftn( cg['xmom']/cg['density'] )/cg['xmom'].size File "/home/uni05/wschmid2/yt-i686/src/yt-hg/yt/data_objects/data_containers.py", line 332, in __getitem__ self.get_data(key) File "/home/uni05/wschmid2/yt-i686/src/yt-hg/yt/data_objects/data_containers.py", line 3776, in get_data raise KeyError(n_bad) KeyError: 16777216 The line with the fft actually used to work and it still works just fine if I use an old yt version (which, fortunately, I was able to dig out). Do you understand what is the problem here? Cheers, Wolfram

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Re: [yt-users] convering_grid question
by Mark Subbarao 14 Aug '13

14 Aug '13

I'll be away till August 19th, with semi-limited connectivity. Will respond when I can. Visit our website: http://www.adlerplanetarium.org

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line annotations, center and zooming
by David Collins 12 Aug '13

12 Aug '13

Hi, everybody-- I'm having trouble getting plot_window coordinages and annotate_image_line coordinates to agree. I have a small region that I'm trying to annotate with lines, and zoom in on. I'm having trouble getting my coordinates working together. If I do proj = oober.pf.h.proj(ax,'Density',source=source) pw = proj.to_pw(center=proj_center,origin='domain' ) pw.zoom( 1/size) I have the object centered on the plot and zoomed appropriately. If I do proj = oober.pf.h.proj(ax,'Density',source=source) pw = proj.to_pw() pw.annotate_image_line(p1, p2, data_coords=True) the lines show up in the position I expect relative to my object. However, if I include both the re-centering in to_pw and the call to annotate_image_line, the line doesn't show up where I want relative to the object. If I skip the data_coords or origin argument it doesn't seem to help. I've dug around the docs and source but haven't sorted how to make the plot window coordinages and annotate_image_line coordinates agree. Thanks! d. -- -- Sent from a computer.

2 4

Re: [yt-users] line annotations, center and zooming
by Mark Subbarao 12 Aug '13

12 Aug '13

I'll be away till August 19th, with semi-limited connectivity. Will respond when I can. Visit our website: http://www.adlerplanetarium.org

1 0

In temperature plot unable to plot in normal scale
by Reju Sam John 10 Aug '13

10 Aug '13

Dear All, I am trying to plot a multi plot of temperatures at different red-shifts with following script. from yt.mods import * # set up our namespace import matplotlib.colorbar as cb fig, axes, colorbars = get_multi_plot( 3, 1, colorbar='vertical', bw = 4) file1="/app/run/csarkar/surajit/simulation_shock/simulation5/RD00" file2="/RedshiftOutput00" list = [11,13,22] m=0 #for kk in range(20,37): for kk in list: fn_i=str(kk) fn=file1+fn_i+file2+fn_i # parameter file to load print fn pf = load(fn) # load data pc = PlotCollection(pf, center=[0.5,0.5,0.5]) # defaults to center at most dense point#dd = pf.h.all_data() p = pc.add_slice("Temperature", 1, figure = fig, axes = axes[0][m], use_colorbar=False) p.set_log_field(False) p.set_zlim(1e4,5e7) #p.set_cmap("jet")# a different colormap p.modify["contour"]("Density", ncont=9, plot_args = {'colors':'w'},clim=(5e-30,5e-25)) #p.modify["contour"]("Temperature", ncont=10, plot_args = {'colors':'k'},clim=(3e7,1e8)) pc.set_width(15, 'mpc') # change width of all plots in pc m=m+1 #pc.save("%s_p.png" % pf) # save all plots for p, cax in zip(pc.plots, colorbars): cbar = cb.Colorbar(cax, p.image, orientation='vertical') p.colorbar = cbar p._autoset_label() fig.savefig("Temperature_at_rd00_11,13,22" % pf) The problem is that I am getting the temperature in log scale, even-though I used p.set_log_field(False) in my script. Please suggest me how to get-rid of this problem. -- Reju Sam John

2 5

Re: [yt-users] yt-3.0 error on update, now yt doesn't work (Kyle Stewart)
by Kyle Stewart 09 Aug '13

09 Aug '13

Ah, that was the problem. After updating all, including updating Cython, it works fine. Thanks! -Kyle -- Kyle Stewart, Ph.D. Assistant Professor of Physics Department of Natural and Mathematical Sciences California Baptist University 8432 Magnolia Avenue Riverside, CA 92504 On 8/9/13 10:55 AM, "yt-users-request(a)lists.spacepope.org" <yt-users-request(a)lists.spacepope.org> wrote: >Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > >To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > >You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of yt-users digest..." > > >Today's Topics: > > 1. yt-3.0 error on update, now yt doesn't work (Kyle Stewart) > 2. Re: yt-3.0 error on update, now yt doesn't work (Kacper Kowalik) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Fri, 9 Aug 2013 16:06:26 +0000 >From: Kyle Stewart <kstewart(a)calbaptist.edu> >To: "yt-users(a)lists.spacepope.org" <yt-users(a)lists.spacepope.org> >Subject: [yt-users] yt-3.0 error on update, now yt doesn't work >Message-ID: <CE2A61BA.2EB2%kstewart(a)calbaptist.edu> >Content-Type: text/plain; charset="us-ascii" > >After updating yt (3.0) to the latest version with a simple "yt update" >command, I got the following error in the update log: > >Error compiling Cython file: >------------------------------------------------------------ >... > cdef void *tree_root > cdef int num_root > cdef int max_root > >cdef extern from "search.h" nogil: > void *tsearch(const void *key, void **rootp, > ^ >------------------------------------------------------------ > >yt/geometry/oct_container.pxd:81:29: Expected ')', found '*' > >error: 2 errors while compiling 'yt/geometry/oct_container.pyx' with >Cython > > > >Now yt won't work at all. If I try to call it I get the error: >"ImportError: No module named particle_oct_container" > >Does anyone know what's going on here? >Thanks! > >-Kyle > >-- >Kyle Stewart, Ph.D. >Assistant Professor of Physics >Department of Natural and Mathematical Sciences >California Baptist University >8432 Magnolia Avenue >Riverside, CA 92504 > >

1 0

yt-3.0 error on update, now yt doesn't work
by Kyle Stewart 09 Aug '13

09 Aug '13

After updating yt (3.0) to the latest version with a simple "yt update" command, I got the following error in the update log: Error compiling Cython file: ------------------------------------------------------------ ... cdef void *tree_root cdef int num_root cdef int max_root cdef extern from "search.h" nogil: void *tsearch(const void *key, void **rootp, ^ ------------------------------------------------------------ yt/geometry/oct_container.pxd:81:29: Expected ')', found '*' error: 2 errors while compiling 'yt/geometry/oct_container.pyx' with Cython Now yt won't work at all. If I try to call it I get the error: "ImportError: No module named particle_oct_container" Does anyone know what's going on here? Thanks! -Kyle -- Kyle Stewart, Ph.D. Assistant Professor of Physics Department of Natural and Mathematical Sciences California Baptist University 8432 Magnolia Avenue Riverside, CA 92504

2 1

Problem with multi plot
by Reju Sam John 07 Aug '13

07 Aug '13

Dear all, I am trying to create a muti plot of density's at different red-shift with the following code. from yt.mods import * import matplotlib.colorbar as cb fig, axes, colorbars = get_multi_plot( 3, 3, colorbar='vertical', bw = 3) file1="/app/run/csarkar/surajit/simulation_shock/simulation5/RD00" file2="/RedshiftOutput00" L = [11,15,18,20,22,25,30,35,40] #for i in range (0, 8): for kk in L: fn_i=str(kk) fn=file1+fn_i+file2+fn_i print fn pf = load(fn) pc = PlotCollection(pf, center=[0.5, 0.5, 0.5]) for i in range (0,3): for j in range (0, 3): p = pc.add_slice("Density", 2, axes = axes[i][j],figure = fig, use_colorbar=False) p.set_log_field(True) p.set_zlim(1e-31,5e-26) p.set_cmap("jet") p.modify["contour"]("Density", ncont=10, plot_args = {'colors':'w'},clim=(2e-28,2e-26)) p.modify["contour"]("Temperature", ncont=10, plot_args = {'colors':'k'},clim=(3e7,1e8)) #pc.set_width(3.0, 'mpc') #break # i = i+1 for p, cax in zip(pc.plots, colorbars): cbar = cb.Colorbar(cax, p.image, orientation='vertical') p.colorbar = cbar p._autoset_label() fig.savefig("multi_plot_3_3" % pf) But I am getting a wrong result. It is printing same figure in all panels. I think my logic(algorithm) is wrong. We have to reverse first two for loop. But that also making problem. Please help me. And also if I include the following line in the code. (in my code I commented it out) pc.set_width(3.0, 'mpc') it is showing following error. *Traceback (most recent call last):* * File "multi_plot_loop.py", line 24, in <module>* * pc.set_width(3.0, 'mpc') * * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py", line 292, in set_width* * plot.set_width(width, unit)* * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 458, in set_width* * self._refresh_display_width()* * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 476, in _refresh_display_width* * self._redraw_image()* * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 423, in _redraw_image* * self._run_callbacks()* * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 263, in _run_callbacks* * cb(self)* * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", line 312, in __call__* * self.ncont = np.linspace(self.clim[0], self.clim[1], self.ncont)* * File "/data1/pdf/csurajit/yt-x86_64/lib/python2.7/site-packages/numpy/core/function_base.py", line 74, in linspace* * num = int(num)* *TypeError: only length-1 arrays can be converted to Python scalars* Please suggest me the most efficient way to achieve my goal (create a muti plot of density's at different red-shift). -- Reju Sam John

2 5

problem with covering_grid for Nyx data sets
by Wolfram Schmidt 06 Aug '13

06 Aug '13

Hi, I have got problem that concerns Nyx users and/or yt developers. I want to read the root-grid level from AMR data sets with the following piece of code: num_ghost_zones=2 left=na.amin(pf.h.grid_left_edge,axis=0) right=na.amax(pf.h.grid_right_edge,axis=0) resolution = (right-left)/pf.h.grids[0]['dx']+2*num_ghost_zones cg = pf.h.covering_grid(0,left,resolution,num_ghost_zones=num_ghost_zones) This works for Enzo data sets, but it fails for Nyx data sets. The error message is Traceback (most recent call last): File "/home/h/nipiagws/scripts/spect_sb.py", line 52, in <module> cg = pf.h.covering_grid(0,left,resolution,num_ghost_zones=num_ghost_zones) File "/home/h/nipschul/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 3727, in __init__ self.dds = self.pf.domain_width/rdx.astype("float64") AttributeError: 'list' object has no attribute 'astype' The script used to work also for Nyx data sets, with an older version of yt (about a year ago). How can this be fixed? Thanks a lot, Wolfram

2 1

Making slices of Athena SMR data
by Eve Lee 06 Aug '13

06 Aug '13

Hello, I'm trying to make a slice plot of Athena MPI SMR data using TimeSeriesData, and I find that the code only make slices out of the base level and blanks out deeper level regions. Following is how I read in the Athena vtk files: ts = TimeSeriesData.from_filenames('id0/kh*.vtk', parallel=True) my_storage={} for sto,pf in ts.piter(storage=my_storage): slc = SlicePlot(pf, 'z', 'Density') slc.set_zlim('Density', 0.0, 3.0) num = (pf.h.hierarchy_filename).split('.')[1] slc.save('./slice/'+num) all my vtk files are in id0, ..., idn where n=number of processors I used, and I'm only using 1 more level of refinement. Thanks in advance! Best Regards, Eve

3 15

Problem with Rockstar in yt
by Brian O'Shea 05 Aug '13

05 Aug '13

Dear yt-users, I'm trying to use the Rockstar halo finder within yt, and am encountering some odd problems. I'm using the main development tree ( https://bitbucket.org/yt_analysis/yt) with changeset f936432ed45d, and attempting to use Rockstar to find halos on a small server running Ubuntu 12.04. When I call this script: ---- file test_rockstar.py ---- from yt.mods import * from yt.analysis_modules.halo_finding.rockstar.api import RockstarHaloFinder pf = load("DD0057/data0057") rh = RockstarHaloFinder(pf) --- using the command line sequence "mpirun -np 2 python ./test_rockstar.py --parallel", I seem to be getting a seg fault (as can be seen at http://paste.yt-project.org/show/3745/). However, if I use a single processor (with "mpirun -np 1 python ./test_rockstar.py --parallel"), I get a very different error: Traceback (most recent call last): File "./test_rockstar.py", line 6, in <module> rh = RockstarHaloFinder(pf) File "/data/bwoshea/galparttest/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 230, in __init__ self.pool, self.workgroup = self.runner.setup_pool() File "/data/bwoshea/galparttest/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 112, in setup_pool (self.num_writers, "writers") ] File "/data/bwoshea/galparttest/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 335, in from_sizes pool.add_workgroup(size, name = name) File "/data/bwoshea/galparttest/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 303, in add_workgroup group = self.comm.comm.Get_group().Incl(ranks) AttributeError: 'NoneType' object has no attribute 'Get_group' I'm puzzled about the error, since I can use other parallel yt scripts without any problems (a 4-processor script making projections works just fine). This machine doesn't have infiniband (as warned about at http://yt-project.org/doc/analysis_modules/running_halofinder.html#rockstar…), and both FOF and Hop find several hundred halos with my dataset. I'd just use another halo finder, but I'm trying to do something that requires Rockstar to be run inline with Enzo, so I'm stuck with it... Does anybody have any idea what might be going on? Thanks! Brian

3 6

MultiVariate volume rendering difficulties
by Noel Scudder 05 Aug '13

05 Aug '13

Hi all, I'm attempting to visualize multiple variables in the same volume rendering. For instance, I'd like to show some density surfaces of a star and then get temperature overlayed to show hotspots. I found the MultiVariateTransferFunction, but it is unfortunately not particularly well documented yet, and I'm being repeatedly thwarted. I'm not sure if I've set it up correctly, or how to go from the transfer function to an image. Here's my current script, using just one variable for now: #---------------------------------- from yt.mods import * pf = load('plt00100') #<some constants> pf.h pf.field_info['density'].take_log=True mv = MultiVariateTransferFunction() tf = TransferFunction((mi-1, ma+1), nbins=1.0e6) tf.add_gaussian(np.log10(9.0e5), 0.01, 1.0) mv.add_field_table(tf, 0) mv.link_channels(0, [0,1,2,3]) c = [5.0e9, 5.0e9, 5.0e9] L = [0.15, 1.0, 0.40] W = wi*0.7 Nvec = 1024 cam = pf.h.camera(c, L, W, (Nvec,Nvec), transfer_function = mv, fields=['density'], pf=pf, no_ghost=True) im = cam.snapshot(num_threads=4) im.write_png('plt00100.png' ) #---------------------------------- I checked to make sure density is indeed my 0-index field. I get the following error after ray casting: Traceback (most recent call last): File "<stdin>", line 1, in <module> File "multivol.py", line 153, in <module> im = cam.snapshot(num_threads=4) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 742, in snapshot image, sampler), File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 632, in _render image = self.finalize_image(image) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 611, in finalize_image if self.transfer_function.grey_opacity is False: AttributeError: 'MultiVariateTransferFunction' object has no attribute 'grey_opacity' Can I not use snapshot in this case, or is something else the matter entirely? Thanks, Noel Scudder

5 8

how to fix a constant density scale to all out figures?
by Reju Sam John 05 Aug '13

05 Aug '13

Dear all, I am trying to visualize the density slices of my simulation output at different red-shift. But the output files (RedshiftOutput0010_Slice_z_Density.png to RedshiftOutput0058_Slice_z_Density.png) are density color coded differently. My problem is how to make the density color code scale common for all. -- Reju Sam John

3 4

Re: [yt-users] Error with annotate_marker: Unknown property
by Chao Shi 02 Aug '13

02 Aug '13

On Thu, Aug 1, 2013 at 10:49 PM, <yt-users-request(a)lists.spacepope.org>wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. Re: Error with annotate_marker: Unknown property (Nathan Goldbaum) > 2. ANN: matplotlib 1.3.0 released (Nathan Goldbaum) > 3. Re: MultiVariate volume rendering difficulties (Cameron Hummels) > > > ---------------------------------------------------------------------- > Hi Nathan, Thanks. That's very informative. Would you mind tell me how you found that? I also tried to search for the allowed keywords for that callback but didn't find any useful information. Just in case next time I run into such kind of problems. Thank you very much. Chao > Message: 1 > Date: Thu, 1 Aug 2013 16:35:55 -0700 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Error with annotate_marker: Unknown property > Message-ID: > <CAJXewO= > bQbfRxAFjwR-2Q3Wsb5ZvGJPxwtRsk_Kfqc0zVa1cCg(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Chao, > > For that callback, you're only allowed to specify keyword arguments > accepted by matplotlib.axes.Axes.scatter: > http://matplotlib.org/api/axes_api.html#matplotlib.axes.Axes.scatter > > or Collection properties: > > http://matplotlib.org/api/collections_api.html#matplotlib.collections.Colle… > > I'd have to look closer to figure out which keyword corresponds to what > you're looking for, but hopefully that leaves you enough information to > figure out how to do what you're trying to do. > > -Nathan > > > On Thu, Aug 1, 2013 at 3:53 PM, Chao Shi <shichao116(a)gmail.com> wrote: > > > Hi all, > > > > I'm trying to mark some positions with circle on slice and projection > > plot. But it can't recognize arguments used for specifying the property > of > > the marker. For example: > > > > > > >>> p = SlicePlot(pf,'x','Density') > > > > >>> p.annotate_marker([0.5]*3,marker='o', plot_args={'color': 'red', > > 'mew': 5}) > > > > Traceback (most recent call last): > > File "<stdin>", line 1, in <module> > > File > "/home/cshi31/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", > > line 100, in newfunc > > args[0]._setup_plots() > > File > "/home/cshi31/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", > > line 886, in _setup_plots > > self.run_callbacks(f) > > File > "/home/cshi31/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", > > line 896, in run_callbacks > > callback(cbw) > > File > > > "/home/cshi31/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", > > line 777, in __call__ > > plot._axes.scatter(x,y, marker = self.marker, **self.plot_args) > > File > > "/home/cshi31/yt-x86_64/lib/python2.7/site-packages/matplotlib/axes.py", > > line 6123, in scatter > > collection.update(kwargs) > > File > > > "/home/cshi31/yt-x86_64/lib/python2.7/site-packages/matplotlib/artist.py", > > line 670, in update > > raise AttributeError('Unknown property %s' % k) > > AttributeError: Unknown property mew > > > > mew is an alias for markeredgewidth. I also tried with 'markeredgewidth' > > but it gave the same error. > > > > Besides, 'mec', 'ms' also can't be recognized. Only 'color' works. > > > > Does anyone have a clue about this? > > > > Thanks very much. > > > > Chao > > > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 2 > Date: Thu, 1 Aug 2013 18:24:41 -0700 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: [yt-users] ANN: matplotlib 1.3.0 released > Message-ID: > < > CAJXewOkcnia2Y6gkO6QN9a2K-+Xr7_FGTGKLUySFQDjarbnf_w(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > > Please see the matplotlib mailing list archives for the release notes and > official announcement e-mail: > > http://matplotlib.1069221.n5.nabble.com/ANN-matplotlib-1-3-0-released-td416… > > This big new feature for this version is the WebAGG backend, which is a new > plotting interface specially made for the IPython notebook. It also > includes a convenience function that alters the plotting settings to > generate xkcd-style plots. > > There may be some incompatibilities with yt - if anyone notices any issues > please report it on the issue tracker. > > Cheers, > > Nathan > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 3 > Date: Thu, 1 Aug 2013 19:39:02 -0700 > From: Cameron Hummels <chummels(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] MultiVariate volume rendering difficulties > Message-ID: > < > CACyTu7ERKuNSgCY3HMQGPXL3UPhRspyUG_r3V8L1-rzxTaPNeQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > I agree with Stella's solution, as that's what I've done in the past. > Obviously you can get some blending between the two CTFs, but that's the > point right? > > Cameron > > > On Thu, Aug 1, 2013 at 2:31 PM, Nathan Goldbaum <nathan12343(a)gmail.com > >wrote: > > > Wow Noel, keep up the awesome work! > > > > I'm sure this will be helpful for Sam when he looks at this stuff next > > week. > > > > > > On Thu, Aug 1, 2013 at 1:53 PM, Noel Scudder < > noel.scudder(a)stonybrook.edu>wrote: > > > >> Hi all, > >> > >> Over the past few days I've been investigating the > >> MultiVariateTransferFunction and receiving feedback from Matt. Since it > >> needs some updating and the documentation is so vague, I thought I'd > try to > >> outline the basic flow and idea of an MVTF (thanks to Matt for his > >> outline), address a couple problems that have been noticed, and give an > >> example script with images. Please feel free to correct my mistakes, ask > >> questions, and add your own knowledge! > >> > >> The code for the MVTF is > >> in yt/visualization/volume_rendering/transfer_functions.py . It's also > >> useful to check out the Planck and Color Transfer Functions in the same > >> file. > >> > >> With a CTF, you are limited to one field, which is linked identically to > >> each of the RGB color channels and an alpha channel. However, an MVTF > >> allows you to set up different fields that control each channel and each > >> channel's opacity through the use of standard Transfer Functions. For > >> instance, I could link the red color channel and the red alpha channel > to > >> Density, the blue and blue alpha channels to Temperature, and the green > and > >> green alpha channels to Kinetic Energy. > >> It is important to note that only *one* field (and associated transfer > >> function) may be linked to any channel. This limits the number of > variables > >> one can conceivably include to three. > >> > >> When an MVTF is created, it sets up a few variables: > >> > >> n_field_tables > >> tables > >> field_ids > >> weight_field_ids > >> field_table_ids > >> weight_table_ids > >> grad_field > >> light_source_v > >> > >> The important ones here are tables, field_ids, weight_field_ids, > >> field_table_ids, and weight_table_ids. > >> After creating your MVTF, the first thing you must do is create a > >> TransferFunction, which has some range and number of bins. This can > then be > >> added as a "table" to your MVTF using add_field_table, which accepts the > >> table, the field_id used for interpolating on the x-axis of this table, > a > >> weight_field_id, and/or a weight_table id. > >> The field_id is *not* the field index you get from pf.h.field_indexes . > >> Here, the field_id actually specifies the index of a certain field in > the > >> field list you supply to the camera object. For instance, if I gave the > >> camera > >> > >> fields=['density', 'Temp'] > >> > >> I would have previously called add_field_table using a field_id of 0 for > >> the TransferFunctions I wanted for density, and using a field_id of 1 > for > >> the TransferFunctions I wanted for temperature. > >> The same specification with the field_id goes for weight_field_id, which > >> is used if the field itself should be a weighting factor for the > >> emission/absorption (although this does not do scaling, so you will > likely > >> need to supply a pre-scaled field). > >> By supplying a weight_table_id, you are taking the results of > >> interpolation along the x-axis to get a y value from *another* field > table > >> and using that as a weight. > >> > >> *Apparently density is typically logged by default. If you want to use > it > >> as a weight, you probably want it un-logged. > >> > >> At this point you have added all of your field tables. The second step > is > >> to link the field tables to the channels you want. Right now, all you > have > >> is a set of "tables," TransferFunctions that describe how to get a value > >> out as a combination of: > >> > >> 1) The y-value interpolated along the x-axis defined by the table > >> 2) The weighting from a given field > >> 3) The weighting from a given field_table (i.e., if you had some scaling > >> that was a function of temperature) > >> > >> On its own, a table will do nothing--you must link it to a channel. > These > >> are, in order, RGB and aR, aG, aB. You use the link_channels function > for > >> this purpose, for instance linking table 0 to channel 0 (R). When > linking > >> channels, there are a couple things to keep in mind. The two arguments > you > >> supply are the table_id and the channel, both *integers *(seems like a > >> common theme for MVTF stuff :-) ). The channel can be integers 0-5, > >> assigned in the order above. The table_id is a bit more nebulous: a > >> table_id is assigned to a table when it is created, meaning that the > first > >> table you create using add_field_table will have a table_id of 0, the > next > >> will have a table_id of 1, and so on. Although you cannot link more than > >> one table to a channel, you can have more than one channel linked to a > >> single table--simply supply a list in place of an integer for the > channel > >> argument. > >> > >> Finally, don't leave your TransferFunctions empty! Add some gaussians, > >> keeping in mind the channel and field each TF uses. After that your MVTF > >> will be ready, and you can supply it to the camera object like any other > >> transfer function and take a snapshot. > >> > >> Here's a example script: http://pastebin.com/NC4pHPR7 > >> > >> Which creates this image: http://i.imgur.com/EKv943G.png > >> > >> The main problem I've been noticing is with the grey_opacity, which was > >> already discussed--apparently the MVTF was never updated after opaque > >> volume rendering was implemented. Although by default an MVTF doesn't > have > >> a grey_opacity attribute and yt will complain about this, you can > placate > >> the beast by supplying > >> > >> mv.grey_opacity=False > >> > >> anyway. If you set grey_opacity to True, however, odd things will > happen, > >> which I suspect is simply due to the MVTF not having been updated for > >> opaque rendering yet: http://i.imgur.com/rrOnbgy.png > >> I think that about sums up my two cents on the MVTF. > >> > >> > >> Finally, my original desire was to have two different > >> ColorTransferFunctions with two different fields rendered by one camera > at > >> once. In other words, simultaneously render two different colormaps > applied > >> to two different fields. Right now this isn't possible in yt (although > Matt > >> thinks it may be somewhat straightforward to implement), so I came up > with > >> a makeshift way, where I render one TF for the first field without a > >> background and the second TF for the second field *with* a background, > >> and then overlay them using ImageMagick: > >> > >> im.write_png('transparent_temp.png', background=None) > >> ... > >> im2.write_png('dens_and_background.png') > >> os.system('composite transparent_temp.png dens_and_background.png > >> multi.png') > >> > >> However, it's expensive, and it goes outside yt. Does anyone know if > >> there's a way to combine these images without leaving yt? > >> > >> Thanks for reading! > >> > >> -Noel > >> > >> > >> On Tue, Jul 30, 2013 at 1:03 PM, Sam Skillman <samskillman(a)gmail.com > >wrote: > >> > >>> Hi all, > >>> The multivariate tf could use both some updating and documentation. I'm > >>> offline for the next few days but if it hasn't been fixed by next week > I > >>> can take a look. > >>> > >>> Sam > >>> On Jul 30, 2013 8:40 AM, "Nathan Goldbaum" <nathan12343(a)gmail.com> > >>> wrote: > >>> > >>>> Hi Noel, > >>>> > >>>> I believe this is a bug that needs to be fixed. It seems > >>>> MultiVariateTransferFunction was never updated after opaque volume > >>>> rendering was added. > >>>> > >>>> Can you please open a new issue about this? > >>>> > >>>> Nathan > >>>> > >>>> On Tuesday, July 30, 2013, Noel Scudder wrote: > >>>> > >>>>> Hi all, > >>>>> > >>>>> I'm attempting to visualize multiple variables in the same volume > >>>>> rendering. For instance, I'd like to show some density surfaces of a > star > >>>>> and then get temperature overlayed to show hotspots. I found the > >>>>> MultiVariateTransferFunction, but it is unfortunately not > particularly well > >>>>> documented yet, and I'm being repeatedly thwarted. I'm not sure if > I've set > >>>>> it up correctly, or how to go from the transfer function to an image. > >>>>> Here's my current script, using just one variable for now: > >>>>> > >>>>> #---------------------------------- > >>>>> from yt.mods import * > >>>>> pf = load('plt00100') > >>>>> > >>>>> #<some constants> > >>>>> > >>>>> pf.h > >>>>> pf.field_info['density'].take_log=True > >>>>> > >>>>> mv = MultiVariateTransferFunction() > >>>>> > >>>>> tf = TransferFunction((mi-1, ma+1), nbins=1.0e6) > >>>>> tf.add_gaussian(np.log10(9.0e5), 0.01, 1.0) > >>>>> > >>>>> mv.add_field_table(tf, 0) > >>>>> mv.link_channels(0, [0,1,2,3]) > >>>>> > >>>>> c = [5.0e9, 5.0e9, 5.0e9] > >>>>> L = [0.15, 1.0, 0.40] > >>>>> W = wi*0.7 > >>>>> Nvec = 1024 > >>>>> > >>>>> cam = pf.h.camera(c, L, W, (Nvec,Nvec), transfer_function = mv, > >>>>> fields=['density'], pf=pf, > no_ghost=True) > >>>>> > >>>>> im = cam.snapshot(num_threads=4) > >>>>> > >>>>> im.write_png('plt00100.png' ) > >>>>> #---------------------------------- > >>>>> > >>>>> I checked to make sure density is indeed my 0-index field. I get the > >>>>> following error after ray casting: > >>>>> > >>>>> Traceback (most recent call last): > >>>>> File "<stdin>", line 1, in <module> > >>>>> File "multivol.py", line 153, in <module> > >>>>> im = cam.snapshot(num_threads=4) > >>>>> File > >>>>> > "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", > >>>>> line 742, in snapshot > >>>>> image, sampler), > >>>>> File > >>>>> > "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", > >>>>> line 632, in _render > >>>>> image = self.finalize_image(image) > >>>>> File > >>>>> > "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", > >>>>> line 611, in finalize_image > >>>>> if self.transfer_function.grey_opacity is False: > >>>>> AttributeError: 'MultiVariateTransferFunction' object has no > attribute > >>>>> 'grey_opacity' > >>>>> > >>>>> > >>>>> Can I not use snapshot in this case, or is something else the matter > >>>>> entirely? > >>>>> > >>>>> Thanks, > >>>>> Noel Scudder > >>>>> > >>>> > >>>> _______________________________________________ > >>>> yt-users mailing list > >>>> yt-users(a)lists.spacepope.org > >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >>>> > >>>> > >>> _______________________________________________ > >>> yt-users mailing list > >>> yt-users(a)lists.spacepope.org > >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >>> > >>> > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > > > -- > Cameron Hummels > Postdoctoral Researcher > Steward Observatory > University of Arizona > http://chummels.org > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > End of yt-users Digest, Vol 66, Issue 3 > *************************************** >

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ANN: matplotlib 1.3.0 released
by Nathan Goldbaum 02 Aug '13

02 Aug '13

Hi all, Please see the matplotlib mailing list archives for the release notes and official announcement e-mail: http://matplotlib.1069221.n5.nabble.com/ANN-matplotlib-1-3-0-released-td416… This big new feature for this version is the WebAGG backend, which is a new plotting interface specially made for the IPython notebook. It also includes a convenience function that alters the plotting settings to generate xkcd-style plots. There may be some incompatibilities with yt - if anyone notices any issues please report it on the issue tracker. Cheers, Nathan

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Error with annotate_marker: Unknown property
by Chao Shi 01 Aug '13

01 Aug '13

Hi all, I'm trying to mark some positions with circle on slice and projection plot. But it can't recognize arguments used for specifying the property of the marker. For example: >>> p = SlicePlot(pf,'x','Density') >>> p.annotate_marker([0.5]*3,marker='o', plot_args={'color': 'red', 'mew': 5}) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/cshi31/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 100, in newfunc args[0]._setup_plots() File "/home/cshi31/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 886, in _setup_plots self.run_callbacks(f) File "/home/cshi31/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 896, in run_callbacks callback(cbw) File "/home/cshi31/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", line 777, in __call__ plot._axes.scatter(x,y, marker = self.marker, **self.plot_args) File "/home/cshi31/yt-x86_64/lib/python2.7/site-packages/matplotlib/axes.py", line 6123, in scatter collection.update(kwargs) File "/home/cshi31/yt-x86_64/lib/python2.7/site-packages/matplotlib/artist.py", line 670, in update raise AttributeError('Unknown property %s' % k) AttributeError: Unknown property mew mew is an alias for markeredgewidth. I also tried with 'markeredgewidth' but it gave the same error. Besides, 'mec', 'ms' also can't be recognized. Only 'color' works. Does anyone have a clue about this? Thanks very much. Chao

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