yt-users July 2013

yt-users@python.org

27 participants
31 discussions

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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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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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

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Turn data serialization off by default
by Nathan Goldbaum 30 Jul '13

30 Jul '13

Hi all, I've just issued a PR that will hopefully fix a whole class of buggy behavior that both new and experienced yt users commonly run into. Specifically, I'd like it if we could turn off data serialization by default. This changes a long-lived default value in yt's configuration, so I wanted to bring this change to the attention of both the yt user and developer community. What is data serialization? Currently, yt will save the result of certain expensive calculations, including projections, the structure of the grid hierarchy, and the list of fields present in the data. While this does have the beneficial effect of saving time when a user needs to repetitively calculate these quantities on the same dataset, it has a number of features which lead to buggy, annoying behavior. Specifically, If I am developing my simulation code or repeatedly restarting my code, searching for a way to grind past a code crash, I will quite often regenerate the same simulation output file over and over, changing a line of code or switching out the value of a parameter each time. If yt's data serialization is turned on, it's likely that yt's visualizations will correspond to old versions of the data file. Since only certain operations are serialized, it's also possible for yt to get into an inconsistent state - one operation will show the current data file, while another operation will show an old version. It's possible to fix a bug in your code, but because yt is still loading the old data, you won't be able to tell that your bug is fixed until you realize that you have .yt and .harrays files littering your filesystem. I've personally wasted a lot of time due to yt's serialization 'feature' and denizens of our IRC channel and mailing list can attest to how often new users run into this behavior as well. My pull request only turns off serlialization by default, it doesn't disable the capability completely. Once the pull request is merged in, you can turn on serialization either by adding an entry to your config file: $ cat ~/.yt/config [yt] serialize = True Or on a per-script basis: from yt.config import ytcfg ytcfg['yt', 'serialize'] = 'True' from yt.mods import * The pull request is here: https://bitbucket.org/yt_analysis/yt/pull-request/558 I know several of you are big fans of this feature, so if you object to this change please leave a comment on the pull request so we can figure out a way forward. -Nathan

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Cluster Compile Issue
by Chenchong Zhu 28 Jul '13

28 Jul '13

Hello yt-users, I'm currently attempting to build yt on Scinet GPC cluster, where the Python module can only be loaded alongside Intel and gcc combined. Compiling with Intel modules leads to mercurial compile error. I've attempted to build yt with only the gcc module active, and have achieved a successful build (though ), and yt sources without any errors. Attempting to run ipython or yt serve, however, gives me this error: ImportError: libimf.so: cannot open shared object file: No such file or directory Is there a workaround to this issue? Assistance would be greatly appreciated! Best, Charles

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What are the "x", "y" and "z" fields in a disk?
by José Utreras 27 Jul '13

27 Jul '13

After defining a disk my_disk=pf.h.disk(sc, [0,0,1], 450.0*pc, 30.0*pc) I asked for the minimum and maximum values of these fields xmin= my_disk["x"].min() xmax= my_disk["x"].max() ymin= my_disk["y"].min() ymax= my_disk["y"].max() zmin=my_disk["z"].min() zmax=my_disk["z"].max() print xmin,xmax,ymin,ymax,zmin,zmax and got 0.00390625 0.99609375 0.00390625 0.99609375 0.00390625 0.99609375 xmin+xmax=ymin+ymax=zmin+zmax=1 So I really don't know what actually are these fields

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Finding the indices of a cell's neighbors
by Morgan Presley 26 Jul '13

26 Jul '13

Hello all, I'm trying to access the density for a cell and its six neighbors (in the x,y,z directions), but I can't figure out how I can get the information for the neighboring cells. The problem is that dd[ 'NumberDensity' ] is a one-dimensional array, and I don't know the original 3d shape of the data, so I can't reshape the array into three dimensions. Is there a way to get the indices of a cell's neighbors? Thanks for any help! Morgan

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Off-Axis Slices
by Munier Azzam Salem 26 Jul '13

26 Jul '13

Hey Guys, Quick question on off-axis slices: is the normal vector pointed into the page as you look at the slice, or out of the page? thanks! Munier -- Munier A. Salem // 845.489.6450

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error in installing yt-3.0a2
by Keita Todoroki 24 Jul '13

24 Jul '13

Hi, I'm getting this error during the installation and I'm not sure exactly why. Could you take a look at this? I just downloaded the 3.0a2 package publicly available on Bitbucket to try visualizing my SPH snaps. Any help would be greatly appreciated. Best, Keita 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, const void **rootp, ^ ------------------------------------------------------------ yt/geometry/oct_container.pxd:81:29: Expected ')', found '*' error: 2 errors while compiling 'yt/geometry/oct_container.pyx' with Cython

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yt-users July 2013