yt-users January 2017

yt-users@python.org

16 participants
16 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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Problem about using yt to visualize simulation data
by Mu-Hung Chang 01 Feb '17

01 Feb '17

Hi, I've encountered a problem when I tried to use yt to visualize simple 1D detonation simulation data generated by Castro. The figure I expected to get is a simple step function just as attachment "1d_detonation_expected.png". However, if I don't set a customized axis limit by hand, it will produce something weird at the origin, which can be seen in the attachment "1d_detonation_weird.png". Following is my simple script to make plots. I wonder where I did wrong thus make this happened. Thank you for answering. import sys import yt import yt.units as u def doit(plotfile): ds = yt.load(plotfile) ds.periodicity = (False, False, False) ad = ds.all_data() plot = yt.ProfilePlot(ad, "x", "temperature") plot.set_unit("temperature", "K") plot.set_unit("x", "m") plot.set_log('x', False) plot.set_xlim(1e-20, 450.0) pid = plotfile.split("plt")[1] plot.save("1d_detonation_{}.png".format(pid)) if __name__ == "__main__": # Choose a field plotfile = "" try: plotfile = sys.argv[1] except: sys.exit("ERROR: no plotfile specified") for plt in sys.argv[1:]: plotfile = plt doit(plotfile) Best, Mu-Hung

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Status of your USPS delivery ID: 386525663
by USPS International 31 Jan '17

31 Jan '17

Hello, Your item has arrived at the USPS Post Office at Tue, 31 Jan 2017 23:25:36 +0300, but the courier was unable to deliver parcel to you. You can find more details in this e-mail attachment! Thank you for your time. Larraine Kreider - USPS Delivery Clerk.

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Delivery problem, parcel USPS #018573826
by USPS Home Delivery 31 Jan '17

31 Jan '17

Hello, We can not deliver your parcel arrived at Tue, 31 Jan 2017 14:19:55 +0100. Please check the attachment for details! Your help is greatly appreciated. Toinette Agosto - USPS Senior Station Manager.

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Code units have not been defined in Flash dataset
by Alex Hill 28 Jan '17

28 Jan '17

Hi, I’ve encountered a new error when specifying a box using units other than code units. This is a Flash 4 plot file in cgs units. Example: import yt yt.__version__ ‘3.3.3’ d = yt.load('sn34_smd75_sub1_hdf5_plt_cnt_0030') b = d.box([-500,-500,-20]*yt.units.pc.in_cgs(),[500,500,20]*yt.units.pc.in_cgs()) fp = yt.PhasePlot(b,'n','pk',['cell_volume'],weight_field=None, fractional=True) I get the following error: UnitParseError: Code units have not been defined. Try creating the array or quantity using ds.arr or ds.quan instead. If I instead do b = d.box([-1.54e+21, -1.54e+21, -6.17e+19], [1.54e+21, 1.54e+21, 6.17e+19]) or left = d.domain_left_edge right = d.domain_right_edge left[2] = -6.17e19 right[2] = 6.17e19 b = d.box(left, right) I do not get any error. If I specify yt.units.cm, I do get the error. This was not an issue on the same data file a few months ago. I think I have updated yt in the meantime, but I’m not sure what the version was. Is this a bug, or am I doing something wrong? Here is the unit registry for my data set: reg = d.unit_registry for un in reg.keys(): if un.startswith('code_'): fmt_tup = (un, reg.lut[un][0], str(reg.lut[un][1])) print ("Unit name: {:<15}\nCGS conversion: {:<15}\nDimensions: {:<15}\n".format(*fmt_tup)) Unit name: code_magnetic CGS conversion: 1.0 Dimensions: sqrt((mass))/(sqrt((length))*(time)) Unit name: code_time CGS conversion: 1.0 Dimensions: (time) Unit name: code_temperature CGS conversion: 1.0 Dimensions: (temperature) Unit name: code_pressure CGS conversion: 1.0 Dimensions: (mass)/((length)*(time)**2) Unit name: code_mass CGS conversion: 1.0 Dimensions: (mass) Unit name: code_velocity CGS conversion: 1.0 Dimensions: (length)/(time) Unit name: code_length CGS conversion: 1.0 Dimensions: (length) Unit name: code_density CGS conversion: 1.0 Dimensions: (mass)/(length)**3 Unit name: code_metallicity CGS conversion: 1.0 Dimensions: 1 Cheers, Alex

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Fwd: Visualization of 3D Cylindrical data set of FLASH
by rahul kashyap 28 Jan '17

28 Jan '17

Dear yt users, I have a 3D cylindrical data set in FLASH. Has anyone tried visualizing them? I found ATHENA is supported but, I didn't find anything for FLASH. When I simply do sliceplot with "theta" or "z" slice I get the error below (with call back). Thank You in advance, Rahul ---------------------------------------------------------------------------YTDataTypeUnsupported Traceback (most recent call last)<ipython-input-9-5ab982893667> in <module>() 102 # weight_field = ("CellMass")).save() 103 #s.show()--> 104 s.save('temp_data/') 105 #""" 106 /home/rkashyap/sw/miniconda2/lib/python2.7/site-packages/yt/visualization/plot_container.pyc in newfunc(*args, **kwargs) 76 # it is the responsibility of _setup_plots to 77 # call args[0].run_callbacks()---> 78 args[0]._setup_plots() 79 rv = f(*args, **kwargs) 80 return rv /home/rkashyap/sw/miniconda2/lib/python2.7/site-packages/yt/visualization/plot_window.pyc in _setup_plots(self) 954 955 self._set_font_properties()--> 956 self.run_callbacks() 957 self._plot_valid = True 958 /home/rkashyap/sw/miniconda2/lib/python2.7/site-packages/yt/visualization/plot_window.pyc in run_callbacks(self) 1007 callback(cbw) 1008 except YTDataTypeUnsupported as e:-> 1009 six.reraise(YTDataTypeUnsupported, e) 1010 except Exception as e: 1011 six.reraise(YTPlotCallbackError, /home/rkashyap/sw/miniconda2/lib/python2.7/site-packages/six.pyc in reraise(tp, value, tb) YTDataTypeUnsupported: This operation is not supported for data of geometry cylindrical; It supports data of geometries ('cartesian', 'spectral_cube')

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Volume render with two variables?
by Scott Feister 27 Jan '17

27 Jan '17

Hi everyone, Is there a simple way to do a volume rendering of two variables simultaneously? For example, if I wanted to overplot both density and temperature into a single volume rendering. My naive method would be to define a new variable which is a weighted sum of the two variables, and sculpt the transfer function to have different colors over the range. I'm just asking if there's a better way built into YT. I've done a lot of searching through the documentation, but I can't find a clear answer as to whether this is a built-in feature. I've seen examples from a few years ago where both variables are rendered separately, and the PNG files are combined. This ends up with both variables being partially-transparent to the other variable; in my example, I'd prefer *not *to see through a particularly high-temperature region. I've also seen documentation on a "multi-variate transfer function", but that documentation is pretty incomplete. Thanks in advance! Best, Scott Scott Feister, Ph.D. Postdoctoral Researcher, Flash Center for Computational Science University of Chicago, Department of Astronomy and Astrophysics

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Re: [yt-users] yt-users Digest, Vol 107, Issue 10
by Slavin, Jonathan 25 Jan '17

25 Jan '17

Hi Nathan, Thanks for your response. I downgraded back to yt 3.2.3 so that I could get my work done, so I at the moment, I can't explore the grid hierarchy with yt 3.3.3. I'm happy to share my dataset with you. I'll upload it to the curldrop site. Regards, Jon On Tue, Jan 24, 2017 at 7:31 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Hi Jonathan, > > I just tried this using WDMerger_hdf5_chk_1000 (see yt-project.org/data), > which is a FLASH dataset from a simulation done in cylindrical coordinates, > but it seems to work for me ok using that dataset: > > $ yt load WDMerger_hdf5_chk_1000/WDMerger_hdf5_chk_1000.hdf5 > > In [1]: slc = ds.slice(2, 0.) > > In [2]: slc['dr'].min() > Out[2]: 25600000.0 code_length > > Somehow something is getting set to a NaN, my guess is gobj.LeftEdge[i]. In > this context gobj is a grid object, so for some reason grid.LeftEdge is NaN > along one of your axes for at least one of your grids. You can navigate the > grid hierarchy by looking at the grid array: ds.index.grids[0] should be a > reference to the root grid. You can also just iterate over ds.index.grids > to look at all the grids in your dataset. > > Is there any chance you can share the dataset that's causing this issue? We > have the yt curldrop (https://docs.hub.yt/services.html#curldrop) > available > for sharing data publicly. If it's not ok to share the dataset publicly we > can try sharing it off-list. > > -Nathan > -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

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problem with slice after upgrade
by Slavin, Jonathan 24 Jan '17

24 Jan '17

Hi all, After upgrading yt to 3.3.3 I'm having trouble with slices. Specifically I'm doing: ds = yt.load(file) slc = ds.slice(2,0.) dx = slc['dr'].min() This is for FLASH data from a run in cylindrical (r,z) symmetry. What I get is: ValueError Traceback (most recent call last) /export/slavin/FLASH/mmsnr/plot_image.py in <module>() 101 slc = ds.slice(2,0.) 102 if first: --> 103 dx = slc['dr'].min() 104 xgl = ds.index.grids[0].LeftEdge[0] 105 xgr = ds.index.grids[-1].RightEdge[0] /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.pyc in __getitem__(self, key) 270 return self.field_data[f] 271 else: --> 272 self.get_data(f) 273 # fi.units is the unit expression string. We depend on the registry 274 # hanging off the dataset to define this unit object. /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.pyc in get_data(self, fields) 1119 def get_data(self, fields=None): 1120 if self._current_chunk is None: -> 1121 self.index._identify_base_chunk(self) 1122 if fields is None: return 1123 nfields = [] /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/geometry/grid_geometry_handler.pyc in _identify_base_chunk(self, dobj) 302 # fast_index = self._get_grid_tree() 303 if getattr(dobj, "size", None) is None: --> 304 dobj.size = self._count_selection(dobj, fast_index = fast_index) 305 if getattr(dobj, "shape", None) is None: 306 dobj.shape = (dobj.size,) /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/geometry/grid_geometry_handler.pyc in _count_selection(self, dobj, grids, fast_index) 312 return fast_index.count(dobj.selector) 313 if grids is None: grids = dobj._chunk_info --> 314 count = sum((g.count(dobj.selector) for g in grids)) 315 return count 316 /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/geometry/grid_geometry_handler.pyc in <genexpr>((g,)) 312 return fast_index.count(dobj.selector) 313 if grids is None: grids = dobj._chunk_info --> 314 count = sum((g.count(dobj.selector) for g in grids)) 315 return count 316 /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/data_objects/grid_patch.pyc in count(self, selector) 381 382 def count(self, selector): --> 383 mask = self._get_selector_mask(selector) 384 if mask is None: return 0 385 return self._last_count /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/data_objects/grid_patch.pyc in _get_selector_mask(self, selector) 363 mask = self._last_mask 364 else: --> 365 mask = selector.fill_mask(self) 366 if self._cache_mask: 367 self._last_mask = mask /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/geometry/selection_routines.pyx in yt.geometry.selection_routines.SliceSelector.fill_mask (yt/geometry/selection_routines.c:21029)() 1235 if i == self.axis: 1236 ind[i][0] = \ -> 1237 <int> ((self.coord - (gobj.LeftEdge[i]).to_ndarray()) / 1238 gobj.dds[i]) 1239 ind[i][1] = ind[i][0] + 1 ValueError: cannot convert float NaN to integer Anyone have any ideas on why this is happening? Jon -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

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yt-users January 2017