Mailman 3 October 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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Sinkparticles in the Volumerendering
by Christian Karch 30 Oct '12

30 Oct '12

Hi everyone, is there a simple way to annotate sinkparticles (x, y, z) in the rendering? I thought about to define spheres and combine the regions with boolean "or", but I have no idea to show density (or another field) and accent the sinkparticles. I hope you can help me with this issue. regards Christian

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Mountain Lion install issue
by aaron.t.lee 25 Oct '12

25 Oct '12

Hey all, Potentially low level question. I noticed my local version of YT didn't seem to work anymore after upgrading to Mountain Lion, so I tried reinstalling, following the website instructions. I first received some compile errors, but the install script had a suggestion that fixed that issue. However, I now get the following error when running 'bash install_script.sh' : Installing BZLIB Installing ZLIB Installing PNG Installing FreeType2 Installing HDF5 ******************************************** FAILURE REPORT: ******************************************** _test_attr_bug4 in tattr.o _test_attr_bug1 in tattr.o _test_attr_bug3 in tattr.o _test_attr_dense_verify in tattr.o _test_attr_dense_dup_ids in tattr.o ... ld: symbol(s) not found for architecture x86_64 collect2: ld returned 1 exit status make[1]: *** [testhdf5] Error 1 make: *** [install-recursive] Error 1 ******************************************** ******************************************** Failure. Check /Users/AaronLee/yt-x86_64/yt_install.log. The last 10 lines are above. Am I doing something incorrect, or is there is quick fix for this? Thanks, Aaron

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camera and boolean object
by M Ryan Joung 24 Oct '12

24 Oct '12

Hi, I have a question about volume rendering. I'd like to run camera.allsky_projection on a data object with a particular shape, in this case a sphere with a cylindrical hole in the center. I was able to define such an object using the boolean operator "NOT". But feeding it to camera.allsky_projection leads to an error, with the traceback below. -------- Traceback (most recent call last): File "sky_maps.py", line 70, in <module> inner_radius = rr, rotation = rotation) File "/Users/mkjoung/work/yt/yt-i386/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 1526, in allsky_projection dx = min(g.dds.min() for g in pf.h.find_point(center)[0]) AttributeError: 'AMRBooleanRegion' object has no attribute 'h' -------- (allsky_projection runs successfully when I input 'pf' as an argument.) Is there a workaround so that allsky_projection will accept the boolean object as pf-like? Thanks, -Ryan

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Particle Angular momentum Profiles
by Jun-Hwan Choi 23 Oct '12

23 Oct '12

Hi I try to calculate the dark matter angular momentum profile using following routine: ##################################### import matplotlib.pyplot as plt import pylab as pl def _RadiuspcXY(field, data): center = data.get_field_parameter("center") DW = data.pf.domain_right_edge - data.pf.domain_left_edge radius = na.zeros(data["x"].shape, dtype='float64') for i, ax in enumerate('xy'): r = na.abs(data[ax] - center[i]) radius += na.minimum(r, na.abs(DW[i]-r))**2.0 na.sqrt(radius, radius) return radius def _ConvertRadius(data): return data.convert("pc") add_field("RadiuspcXY", function=_RadiuspcXY, validators=[ValidateParameter("center")], convert_function = _ConvertRadius, units=r"\rm{pc}", display_name="RadiusXY") Nbin = 75 rdisk = 2000 hdisk = 10 pf = load("DD0046/DD0046") rmin = 2.0*pf.h.get_smallest_dx()*pf.units['pc']] center = pf.h.find_max("Density")[1] disk = pf.h.disk(center, [0,0,1], rdisk/pf.units['pc'], hdisk/pf.units['pc'] ) profile = BinnedProfile1D(disk, Nbin, "Radiuspc", max(rmin), rdisk, log_space=True, lazy_reader=True, end_collect=False) profile.add_fields('ParticleSpecificAngularMomentumZ') plt.plot(profile['RadiuspcXY'], profile['ParticleSpecificAngularMomentumZ']) And I got the following error message: yt : [INFO ] 2012-10-23 11:16:00,124 Parameters: current_time = 4.600008999 yt : [INFO ] 2012-10-23 11:16:00,124 Parameters: domain_dimensions = [64 64 64] yt : [INFO ] 2012-10-23 11:16:00,125 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2012-10-23 11:16:00,125 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2012-10-23 11:16:00,126 Parameters: cosmological_simulation = 0.0 yt : [INFO ] 2012-10-23 11:16:00,138 Getting the binary hierarchy yt : [INFO ] 2012-10-23 11:16:00,168 Finished with binary hierarchy reading yt : [INFO ] 2012-10-23 11:16:00,623 Max Value is 1.55814e-16 at 0.5001935958862305 0.4999227523803749 0.4994192123413048 in grid EnzoGrid_1396 at level 13 (5, 3, 3) Traceback (most recent call last): File "JprofDM.py", line 51, in <module> profile.add_fields('ParticleSpecificAngularMomentumZ') File "/home/jhchoi/common/lib/python2.7/site-packages/yt-2.4-py2.7-linux-x86_64.egg/yt/data_objects/profiles.py", line 168, in add_fields self._lazy_add_fields(fields, weight, accumulation) File "/home/jhchoi/common/lib/python2.7/site-packages/yt-2.4-py2.7-linux-x86_64.egg/yt/data_objects/profiles.py", line 108, in _lazy_add_fields args=args, check_cut=True) File "/home/jhchoi/common/lib/python2.7/site-packages/yt-2.4-py2.7-linux-x86_64.egg/yt/data_objects/profiles.py", line 55, in save_state tr = func(*args, **kwargs) File "/home/jhchoi/common/lib/python2.7/site-packages/yt-2.4-py2.7-linux-x86_64.egg/yt/data_objects/profiles.py", line 275, in _bin_field source_data = source_data[mi] ValueError: too many boolean indices What can be the problem? I compute the gas Angular momentum by simply change ParticleSpecificAngularMomentumZ to SpecificAngularMomentumZ, it works. As a result, I suspect the way to handle the particles. Thanks in advance, Junhwan -- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

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Re: [yt-users] FLASH 2D color bar setting
by Ryan Sacks 22 Oct '12

22 Oct '12

Thank you for the explanation Nathan. I have a better feeling about this now. Also thanks to Ji Souqing for his help too, everything is working now due to your suggestions. Cheers, Ryan On 10/22/12, Nathan Goldbaum wrote: > > > > Hi Ryan, > > > I think the confusion may be that the SlicePlot object is a yt class and is not the same thing as a matplotlib plot. > > > > > I have attempted to add the line: > > p.set_zlim(zmin,zmax) > > into the script above and below the p.set_window command but it returns the error "set_zlim() takes exactly 4 arguments (3 given)". I have tried adding in other arguments to nticks, ticks and minmaxticks but to no avail. Thanks in advance to any advice. > > > > > You need to tell set_zlim which field you'd like to set the colorbar limits for: > > > p.set_zlim('tele',zmin, zmax). > > > The reason we've set things up this way is to allow a single plot window to display multiple fields. To do so, you would create the SlicePlot like this: > > > p = SlicePlot(pf,2,['tele','dens','velx'],origin='left-domain') > > > > > I have tried adding in other arguments to nticks, ticks and minmaxticks but to no avail. > > > > > > I'm not totally sure what you mean here, but maybe this cookbook recipe in the docs will be helpful: > > > http://yt-project.org/docs/2.4/cookbook/simple_plots.html?highlight=furlong… > > > One can directly access the underlying matplotlib figure object by doing something like (using the syntax in your script): > > > fig = p.plots['tele'].figure > > > From there it's possible to arbitrarily customize the plot. > > > This is of course a lot of overhead to customize your plot using SlicePlot. It may be easier in the long run to manually set up your own plots using FixedResolutionBuffer: > > > http://yt-project.org/docs/2.4/visualizing/manual_plotting.html > > > Lastly, for your script there is no need to import matplotlib and numpy, yt does that internally. If you're using matplotlib and numpy elsewhere in the script, you'll still need to import it yourself. > > > Cheers, > > > Nathan > > > On Oct 22, 2012, at 11:30 AM, Ryan Sacks wrote: > > > > Hello All, > > > > I am currently using YT to plot the results from 2D cylindrical FLASH simulations. I am trying to figure out how to set the pseudocolor bar in the Slice plots I am making so that they are consistent through multiple graphs and not automatically set by the data that is loaded in. Any advice that someone could offer as to what commands I should use would be greatly appreciated. The script I am using is below: > > > > from yt.mods import * > > import matplotlib.pyplot as plt > > import numpy as np > > > > str_list = ["../life_hdf5_chk_0001", > > "../life_hdf5_chk_0002", > > "../life_hdf5_chk_0003", > > "../life_hdf5_chk_0004", > > "../life_hdf5_chk_0005", ] > > > > for s in str_list: > > pf = load(s) > > p = SlicePlot(pf, 2,'tele',origin='left-domain') > > p.set_window((0.0, 250.0, 0.0, 250.0)) > > p.save() > > > > I have attempted to add the line: > > p.set_zlim(zmin,zmax) > > into the script above and below the p.set_window command but it returns the error "set_zlim() takes exactly 4 arguments (3 given)". I have tried adding in other arguments to nticks, ticks and minmaxticks but to no avail. Thanks in advance to any advice. > > -- > > Cheers, > > Ryan Sacks > > > > -- > > Ryan F. Sacks > > University of Wisconsin-Madison > > Nuclear Engineering and Engineering Physics > > rsacks(a)wisc.edu <rsacks(a)wisc.edu> > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > >

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FLASH 2D color bar setting
by Ryan Sacks 22 Oct '12

22 Oct '12

Hello All, I am currently using YT to plot the results from 2D cylindrical FLASH simulations. I am trying to figure out how to set the pseudocolor bar in the Slice plots I am making so that they are consistent through multiple graphs and not automatically set by the data that is loaded in. Any advice that someone could offer as to what commands I should use would be greatly appreciated. The script I am using is below: from yt.mods import * import matplotlib.pyplot as plt import numpy as np str_list = ["../life_hdf5_chk_0001", "../life_hdf5_chk_0002", "../life_hdf5_chk_0003", "../life_hdf5_chk_0004", "../life_hdf5_chk_0005", ] for s in str_list: pf = load(s) p = SlicePlot(pf, 2,'tele',origin='left-domain') p.set_window((0.0, 250.0, 0.0, 250.0)) p.save() I have attempted to add the line: p.set_zlim(zmin,zmax) into the script above and below the p.set_window command but it returns the error "set_zlim() takes exactly 4 arguments (3 given)". I have tried adding in other arguments to nticks, ticks and minmaxticks but to no avail. Thanks in advance to any advice. -- Cheers, Ryan Sacks -- Ryan F. Sacks University of Wisconsin-Madison Nuclear Engineering and Engineering Physics rsacks(a)wisc.edu

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possible error with spherical coordinate transforms
by M Ryan Joung 18 Oct '12

18 Oct '12

Hello, I am trying to produce an all-sky map projection of a field. Maybe I did something wrong here, but even after the fix described in https://bitbucket.org/yt_analysis/yt/issue/451/radialvelocity-now-seems-to-… (which sets 'normal' to [0,0,1]), there seems to be an array dimension mismatch between Jy and theta, phi, as you can see below. Can anyone help me with this problem? I attach a logfile (output with --detail) with this error. Thank you, -Ryan The part of the script where the error occurs: ----------------------------- [snipped] for _fields in grouper(3, field_names): f = h5py.File("hi_maps.h5", "a") fields = [fn for fn in _fields if fn not in f["/"]] allsky = camera.allsky_projection(pf, c, 300.0/pf['kpc'], NP, fields, inner_radius = rr, rotation = rotation) <-- line 60 [snipped] ----------------------------- ----------------------------- Traceback (most recent call last): File "sky_maps.py", line 60, in <module> inner_radius = rr, rotation = rotation) File "/Users/mkjoung/work/yt/yt-i386/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 1536, in allsky_projection for field in fields] File "/Users/mkjoung/work/yt/yt-i386/src/yt-hg/yt/data_objects/grid_patch.py", line 157, in __getitem__ self.get_data(key) File "/Users/mkjoung/work/yt/yt-i386/src/yt-hg/yt/data_objects/grid_patch.py", line 200, in get_data self._generate_field(field) File "/Users/mkjoung/work/yt/yt-i386/src/yt-hg/yt/data_objects/grid_patch.py", line 145, in _generate_field self[field] = self.pf.field_info[field](self) File "/Users/mkjoung/work/yt/yt-i386/src/yt-hg/yt/data_objects/field_info_container.py", line 316, in __call__ dd = self._function(self, data) File "sky_maps.py", line 50, in VelocityTransmittedHI (((vel * 1e5) < data["RadialVelocity"]) File "/Users/mkjoung/work/yt/yt-i386/src/yt-hg/yt/data_objects/grid_patch.py", line 157, in __getitem__ self.get_data(key) File "/Users/mkjoung/work/yt/yt-i386/src/yt-hg/yt/data_objects/grid_patch.py", line 200, in get_data self._generate_field(field) File "/Users/mkjoung/work/yt/yt-i386/src/yt-hg/yt/data_objects/grid_patch.py", line 145, in _generate_field self[field] = self.pf.field_info[field](self) File "/Users/mkjoung/work/yt/yt-i386/src/yt-hg/yt/data_objects/field_info_container.py", line 316, in __call__ dd = self._function(self, data) File "/Users/mkjoung/work/yt/yt-i386/src/yt-hg/yt/data_objects/universal_fields.py", line 885, in _RadialVelocity return get_sph_r_component(velocities, theta, phi, normal) File "/Users/mkjoung/work/yt/yt-i386/src/yt-hg/yt/utilities/math_utils.py", line 797, in get_sph_r_component Jy*np.sin(theta)*np.sin(phi) + \ ValueError: operands could not be broadcast together with shapes (128,128,128,3) (128,384,128) -----------------------------

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yt installation on mac
by Ricardo Fernandez 18 Oct '12

18 Oct '12

Hello everyone I tried installing yt on my mac (os X 10.6.8) today and I had a failure. The last lines in the log file are: gcc-4.2 -bundle -undefined dynamic_lookup -L/Applications/yt-i386/lib/ -L/Applications/yt-i386/lib64/ -L/Applications/yt-i386/lib/ -L/Applications/yt-i386/lib64/ -L/Applications/yt-i386/lib/ -L/Applications/yt-i386/lib64/ -L/Applications/yt-i386/lib/ -L/Applications/yt-i386/lib64/ -arch x86_64 build/temp.macosx-10.4-x86_64-2.7/fKDpymodule.o build/temp.macosx-10.4-x86_64-2.7/Forthon.o build/temp.macosx-10.4-x86_64-2.7/fKD.o build/temp.macosx-10.4-x86_64-2.7/fKD_p.o build/temp.macosx-10.4-x86_64-2.7/fKD_source.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2 -lgfortran -o ./fKDpy.so -flat_namespace ld: warning: directory '/Applications/yt-i386/lib64/' following -L not found ld: warning: directory '/Applications/yt-i386/lib64/' following -L not found ld: warning: directory '/Applications/yt-i386/lib64/' following -L not found ld: warning: directory '/Applications/yt-i386/lib64/' following -L not found Cython is a build-time requirement for the source tree of yt. Please either install yt from a provided, release tarball, or install Cython (version 0.16 or higher). You may be able to accomplish this by typing: pip install -U Cython I have cython 0.17 installed on my machine but I'm not sure why it does not recognize it. Any suggestions? Best Ricardo

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