Mailman 3 August 2016 - 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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Registration open for the Learn yt Workshop: Oct 10-12, 2016
by Nathan Goldbaum 20 Sep '16

20 Sep '16

Hi all, Registration is now open for the Learn yt Workshop at the University of Illinois Urbana-Champaign, October 10-12, 2016. This workshop will introduce attendees to the yt project (yt-project.org), a python toolkit for the analysis and visualization of volumetric data. We have create a website for the workshop with more information: http://yt-project.org/workshop2016/ In addition, if you wold like to register for the workshop, please fill out this online form: https://goo.gl/forms/c6oIzNQywU1YWgOe2 The workshop will cover basic usage of yt, including the yt data model, yt's field system, low-level data inspection, basic visualization workflows, and data analysis and reduction tasks. We will also cover more advanced usages like generating simulated observations, halo finding and halo analysis, volume rendering, advanced 3D visualizations, and advanced data analysis and reduction tasks. Finally, we will cover how to modify and extend yt, as well as the development and contribution process. In addition, there will be time set aside for exploring data you bring to the workshop, along with opportunities to work directly with yt developers to load and explore your data. The workshop will take place at the National Center for Supercomputing Applications building on the north end of the UIUC campus. The NCSA building is about a block away from the conference hotel and is next door to a parking structure that offers metered all-day parking. There are a number of food trucks nearby, a university-run cafeteria about 2 blocks away, and a university business district with many good lunch restaurants about a half a mile away. We are planning to offer funding for hotel and travel for those requesting support. If you request funding, you will be notified of available funds by September 15. Travel awards will be made in the form of arranged lodging and airfare, with reservations being made by the conference organizers. We hope to see you there. On behalf of the organizing committee, Matt Turk Nathan Goldbaum Jill Naiman John ZuHone Kandace Turner

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profile object / data container question
by Molly Peeples 31 Aug '16

31 Aug '16

Hi folks, I’m trying to construct and save a 2d profile container to make a phase plot. Here’s what I have: nhT_prof_new = yt.create_profile(sph, [('gas', 'H_number_density'),('gas','temperature')], fields='cell_mass', extrema=extrema,fractional=True, n_bins=6) nhT_prof_new.save_as_dataset() prof_ds = yt.load("snap_047_z000p000_Profile2D.h5") (just using a small number of bins for now to play with…) In [115]: prof_ds.data["temperature"] ...: prof_ds.data["H_number_density"] ...: prof_ds.data["cell_mass"] ...: Out[115]: YTArray([[ 0.01685665, 0.0405085 , 0.03575519, 0.03091732, 0.02552936, 0.0230379 ], [ 0.03770747, 0.05441198, 0.04859202, 0.03285325, 0.02385346, 0.04674817], [ 0.03022001, 0.05150457, 0.03591368, 0.01974481, 0.01052408, 0.00331175], [ 0.04278126, 0.01889035, 0.0177686 , 0.01644028, 0.01598129, 0.00578262], [ 0.05010083, 0.06573628, 0.04247398, 0.03914208, 0. , 0. ], [ 0. , 0.11691224, 0. , 0. , 0. , 0. ]]) dimensionless but when I try to create a PhasePlot: In [116]: p = yt.PhasePlot(prof_ds.data, "H_number_density", "temperature","cell_mass",weight_field=None) ...: --------------------------------------------------------------------------- KeyError Traceback (most recent call last) <ipython-input-116-37b81d75b563> in <module>() ----> 1 p = yt.PhasePlot(prof_ds.data, "H_number_density", "temperature","cell_mass",weight_field=None) /Users/molly/anaconda2/envs/astroconda/lib/python2.7/site-packages/yt/visualization/profile_plotter.pyc in __init__(self, data_source, x_field, y_field, z_fields, weight_field, x_bins, y_bins, accumulation, fractional, fontsize, figure_size) 756 757 type(self)._initialize_instance(self, data_source, profile, fontsize, --> 758 figure_size) 759 760 @classmethod /Users/molly/anaconda2/envs/astroconda/lib/python2.7/site-packages/yt/visualization/profile_plotter.pyc in _initialize_instance(cls, obj, data_source, profile, fontsize, figure_size) 773 obj.profile = profile 774 super(PhasePlot, obj).__init__(data_source, figure_size, fontsize) --> 775 obj._setup_plots() 776 obj._initfinished = True 777 return obj /Users/molly/anaconda2/envs/astroconda/lib/python2.7/site-packages/yt/visualization/profile_plotter.pyc in _setup_plots(self) 854 cax = self.plots[f].cax 855 --> 856 x_scale, y_scale, z_scale = self._get_field_log(f, self.profile) 857 x_title, y_title, z_title = self._get_field_title(f, self.profile) 858 /Users/molly/anaconda2/envs/astroconda/lib/python2.7/site-packages/yt/visualization/profile_plotter.pyc in _get_field_log(self, field_z, profile) 813 814 def _get_field_log(self, field_z, profile): --> 815 zfi = profile.field_info[field_z] 816 if self.x_log is None: 817 x_log = profile.x_log KeyError: ('data', 'cell_mass') Suggestions? —Molly

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phase plot background color
by Molly Peeples 31 Aug '16

31 Aug '16

Hi all, Another phase plot question: is there a way to get the background to be white instead of this weird purpley color? FWIW, the colormap goes down to a very pale grey, not white. [cid:3A7656EE-7769-4312-843B-2CD6051619ED] Thanks, —Molly

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And Google Summer of Code has ended this year!!!
by DVD PS 30 Aug '16

30 Aug '16

This year has been an amazing one! This year was the first one in which we've participated as an independent organisation covering many of the astronomy open source efforts under the Open Astronomy umbrella organisation. http://openastronomy.org/members/ Under the Open Astronomy organisation we have been accepted by Google directly, while in previous years the different organisations had participated under the Python Software Foundation or NumFocus. This is great because it gives us a higher visibility for students and in the open source communities, and in addition other important advantages: we get some compensation from Google and two of us will represent the organisation in the Google Summer of Code mentor summit happening at the end of October. We got 8 slots from Google, of which 5 went to Astropy and 3 to SunPy. Sadly the other sub-organisations (yt, chiantipy, juliaAstro, ...) didn't get any qualified student applicants this time but surely it will change in the future. From these 8 slots, 7 of them passed the mid-term and all the 7 passed the final evaluation. The students, their projects and the mentors are the following: For the Astropy project: Micky Costa: Astropy: Bridge Sherpa and astropy fitting <http://myopensauceadventure.blogspot.co.uk/2016/08/dessert.html> (Tom Aldcroft, Omar Laurino, and Moritz Guenther) Olga Vorokh: Image processing and source detection in Gammapy <https://github.com/search?p=1&q=author%3AOlgaVorokh+created%3A%222016-02-10…> (Johannes King and Christoph Deil) Zé Vinícius: Implement PSF photometry for fitting several overlapping objects at once <http://mirca.github.io/gsoc-astropy-final/> (Moritz Guenter, Brigitta Sipocz, and Erik Tollerud) Karl Vyhmeister: Scheduling capabilities for Astroplan <http://kvyhastroplan.blogspot.com/2016/08/cleaning-up-and-documenting.html?> (Brett Morris and Erik Tollerud) For SunPy: Tessa Wilkinson: Implementing AIA response function in Sunpy <http://tdwilkinson.blogspot.co.uk/2016/08/aia-response-summary-this-is-my-f…> (Drew Leonard and Will Barnes) Punyaslok Pattnaik: Improvements to the SunPy Database <https://punyaslokpattnaik.wordpress.com/2016/08/22/its-already-time/> (Stuart Mumford and Simon Liedtke) Sudarshan Konge: Real Time Data Access and Visualisation tools <https://sudonymousblog.wordpress.com/2016/08/19/gsoc-summary-post/> (David Perez-Suarez and Jack Ireland) You can still see all their trip that brought them till the end reading their blogs, available at: http://openastronomy.org/Universe_OA/ If you would like to give us suggestions on how to improve the program (to us as an umbrella, or to Google itself) or you want to get more involved either as a mentor or as a sub-organisation, do not hesitate to contact us. There's a lot that we can do better in the coming years!! Thanks for all the summer! David Perez-Suarez, Tom Aldcroft, Erik Tollerud, Stuart Mumford

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enzo embedded parallel yt problem with gradient field
by Bodo Schwabe 30 Aug '16

30 Aug '16

*Hi all,** ** **I currently try to run enzo with embedded parallelized python/yt with the following user_script.py :* /import yt// // //from yt.frontends.enzo.api import EnzoDatasetInMemory// // //from yt.fields.field_plugin_registry import \// // register_field_plugin// //from yt.fields.fluid_fields import \// // setup_gradient_fields// // //@register_field_plugin// //def setup_my_fields(registry, ftype="enzo", slice_info=None):// // setup_gradient_fields(registry, ('enzo','AxImaginary'), '', slice_info)// // //yt.enable_parallelism()// // //def main():// // // ds = EnzoDatasetInMemory()// // ds.index// // dd = ds.all_data()// // print dd.quantities.total_quantity('AxImaginary_gradient_z')/ *It works fine on a single processor (mpirun -n 1 ...) but gives my the following error message for multiple processors:* /Global Dir set to .// //ENZO_layout 1 x 1 x 2// //Successfully read in parameter file Bosonstar.enzo.// //INITIALIZATION TIME = 3.75330448e-02// //yt : [INFO ] 2016-08-30 15:02:40,868 Global parallel computation enabled: 0 / 2// //yt : [INFO ] 2016-08-30 15:02:40,868 Global parallel computation enabled: 1 / 2// //Continuation Flag = 1// //TopGrid dt = 2.000000e-05 time = 0 cycle = 0// //P000 yt : [INFO ] 2016-08-30 15:02:41,001 Parameters: current_time = 2e-05// //P000 yt : [INFO ] 2016-08-30 15:02:41,001 Parameters: domain_dimensions = [32 32 32]// //P000 yt : [INFO ] 2016-08-30 15:02:41,002 Parameters: domain_left_edge = [-0.256 -0.256 -0.256]// //P000 yt : [INFO ] 2016-08-30 15:02:41,002 Parameters: domain_right_edge = [ 0.256 0.256 0.256]// //P000 yt : [INFO ] 2016-08-30 15:02:41,003 Parameters: cosmological_simulation = 0.0// //P000 yt : [INFO ] 2016-08-30 15:02:41,005 Gathering a field list (this may take a moment.)// // File "<string>", line 1, in <module>// // File "./user_script.py", line 21, in main// // print dd.quantities.total_quantity('AxImaginary_gradient_z')// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/derived_quantities.py", line 176, in __call__// // rv = super(TotalQuantity, self).__call__(fields)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/derived_quantities.py", line 67, in __call__// // sto.result = self.process_chunk(ds, *args, **kwargs)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/derived_quantities.py", line 182, in process_chunk// // for field in fields]// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 279, in __getitem__// // File "<string>", line 1, in <module>// // File "./user_script.py", line 21, in main// // print dd.quantities.total_quantity('AxImaginary_gradient_z')// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/derived_quantities.py", line 176, in __call__// // self.get_data(f)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 1291, in get_data// // self._generate_fields(fields_to_generate)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 1311, in _generate_fields// // fd = self._generate_field(field)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 316, in _generate_field// // tr = self._generate_fluid_field(field)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 334, in _generate_fluid_field// // rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 364, in _generate_spatial_fluid// // gz[field][ngz:-ngz, ngz:-ngz, ngz:-ngz],// // rv = super(TotalQuantity, self).__call__(fields)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/derived_quantities.py", line 67, in __call__// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 279, in __getitem__// // sto.result = self.process_chunk(ds, *args, **kwargs)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/derived_quantities.py", line 182, in process_chunk// // for field in fields]// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 279, in __getitem__// // self.get_data(f)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/construction_data_containers.py", line 628, in get_data// // self.get_data(f)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 1291, in get_data// // self._generate_fields(fields_to_generate)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 1311, in _generate_fields// // fd = self._generate_field(field)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 316, in _generate_field// // tr = self._generate_fluid_field(field)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 334, in _generate_fluid_field// // rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 364, in _generate_spatial_fluid// // if len(fill) > 0: self._fill_fields(fill)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/construction_data_containers.py", line 947, in _fill_fields// // gz[field][ngz:-ngz, ngz:-ngz, ngz:-ngz],// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 279, in __getitem__// // for chunk in ls.data_source.chunks(fields, "io"):// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 1190, in chunks// // self.get_data(f)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/construction_data_containers.py", line 628, in get_data// // self.get_data(fields)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 1279, in get_data// // fluids, self, self._current_chunk)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/geometry/geometry_handler.py", line 245, in _read_fluid_fields// // chunk_size)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/frontends/enzo/io.py", line 380, in _read_fluid_selection// // if len(fill) > 0: self._fill_fields(fill)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/construction_data_containers.py", line 947, in _fill_fields// // for chunk in ls.data_source.chunks(fields, "io"):// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 1190, in chunks// // self.get_data(fields)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/data_objects/data_containers.py", line 1279, in get_data// // fluids, self, self._current_chunk)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/geometry/geometry_handler.py", line 245, in _read_fluid_fields// // data_view = self.grids_in_memory[g.id][fname][self.my_slice].swapaxes(0,2)// //P001 yt : [ERROR ] 2016-08-30 15:02:41,783 KeyError: 1// // chunk_size)// // File "/gfs2/work/nipbschw/yt-shared-smp/src/yt-hg/yt/frontends/enzo/io.py", line 380, in _read_fluid_selection// // data_view = self.grids_in_memory[g.id][fname][self.my_slice].swapaxes(0,2)// //P000 yt : [ERROR ] 2016-08-30 15:02:41,784 KeyError: 2// //[hsmp16:59147] 1 more process has sent help message help-mpi-btl-openib.txt / default subnet prefix// //[hsmp16:59147] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages// //[hsmp16:59147] 1 more process has sent help message help-mpi-runtime.txt / mpi_init:warn-fork// //[hsmp16:59147] 1 more process has sent help message help-mpi-api.txt / mpi-abort /*Thank you very much for any helpful suggestions,** **Bodo*/ /

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volume rendering annotation error for a derived field
by tazkera haque 28 Aug '16

28 Aug '16

Hi yt people, I just updated to yt 3.3.1 to use all the new features of volume rendering. I am trying to render ejected density which is a derived field and draw the coordinate triads, domain boundary along with labels showing the log range of ejected density. my code is attached. While my code worked fine with default field 'density', the following figure was produced for 'density', but I am getting error when the source field is set to 'ejected_density'. Also the 'density' figure still does not show either the coordinate triads or the domain boundary. I would appreciate your help to fix the error and thanks in advance. *Traceback (most recent call last):* * File "volume_render_test.py", line 117, in <module>* * text_annotate=[[(.1, 1.05), text_string]])* * File "/work/03858/thaque56/sw/yt-new-3.3/yt-conda/lib/python2.7/site-packages/yt/visualization/volume_rendering/scene.py", line 395, in save_annotated* * label = rs.data_source.ds._get_field_info(rs.field).get_label()* * File "/work/03858/thaque56/sw/yt-new-3.3/yt-conda/lib/python2.7/site-packages/yt/fields/derived_field.py", line 225, in get_label* * units = Unit(self.units, registry=self.ds.unit_registry)* *AttributeError: 'NoneType' object has no attribute 'unit_registry'* *Thanks* *Tazkera*

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yt 3.3.1 not working with yt 3.1 python scripts
by tazkera haque 26 Aug '16

26 Aug '16

Hi Nathan, I have just updated yt 3.3 and now I have this weird issue with the scripts , I am uploading my script for sliceplots, which should just analyse the super3d_hdf5_plt_cnt files but I have got issues which also pulls up the super3d_hdf5_part files which are also located in the same path and produces the error. *yt : [INFO ] 2016-08-26 13:23:36,817 Particle file found: super3d_hdf5_part_0000* *yt : [INFO ] 2016-08-26 13:23:36,840 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name* *yt : [INFO ] 2016-08-26 13:23:36,862 Parameters: current_time = 0.0* *yt : [INFO ] 2016-08-26 13:23:36,862 Parameters: domain_dimensions = [128 128 128]* *yt : [INFO ] 2016-08-26 13:23:36,863 Parameters: domain_left_edge = [ -2.80000000e+10 -2.80000000e+10 -2.80000000e+10]* *yt : [INFO ] 2016-08-26 13:23:36,863 Parameters: domain_right_edge = [ 2.80000000e+10 2.80000000e+10 2.80000000e+10]* *yt : [INFO ] 2016-08-26 13:23:36,864 Parameters: cosmological_simulation = 0.0* *yt : [INFO ] 2016-08-26 13:23:38,500 xlim = -28000000000.000000 28000000000.000000* *yt : [INFO ] 2016-08-26 13:23:38,500 ylim = -28000000000.000000 28000000000.000000* *yt : [INFO ] 2016-08-26 13:23:38,501 xlim = -28000000000.000000 28000000000.000000* *yt : [INFO ] 2016-08-26 13:23:38,501 ylim = -28000000000.000000 28000000000.000000* *yt : [INFO ] 2016-08-26 13:23:38,502 Making a fixed resolution buffer of (('flash', 'temp')) 800 by 800* *yt : [INFO ] 2016-08-26 13:23:39,016 Making a fixed resolution buffer of (('flash', 'temp')) 800 by 800* *yt : [INFO ] 2016-08-26 13:23:39,252 Saving plot Slice_z_temp/super3d_hdf5_plt_cnt_0000_Slice_z_temp.png* *yt : [INFO ] 2016-08-26 13:23:39,885 Particle file found: super3d_hdf5_part_0001* *Traceback (most recent call last):* * File "allSlices.py", line 115, in <module>* * ds=yt.load(filename)* * File "/work/03858/thaque56/sw/yt-new-3.3/yt-conda/lib/python2.7/site-packages/yt/convenience.py", line 86, in load* * return candidates[0](*args, **kwargs)* * File "/work/03858/thaque56/sw/yt-new-3.3/yt-conda/lib/python2.7/site-packages/yt/frontends/flash/data_structures.py", line 215, in __init__* * raise IOError('%s and %s are not at the same time.' % (self.particle_filename, filename))* *IOError: /work/03858/thaque56/runs/run_176/super3d_hdf5_part_0001 and /work/03858/thaque56/runs/run_176/super3d_hdf5_plt_cnt_0001 are not at the same time.* *[c558-502.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI process (rank: 0, pid: 13788) exited with status 1* *TACC: MPI job exited with code: 1* Please take a look at the error and let me know how to avoid the particle files in this circumstance. Best Tazkera

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