Mailman 3 April 2020 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman 14 Aug '22

14 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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comoving scale annotation?
by Salome Mtchedlidze 05 Dec '20

05 Dec '20

Hello again, I am using yt slices and projections with scale annotation. I have my plots in comoving units ("Mpccm/h") but whenever I want to use the same units for annotation: slc.annotate_scale(corner='lower_right', coeff=10, units='Mpccm/h'), yt does not recognize these units. Am I missing something or only the physical scale annotation is possible ? Thanks, Salome

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Question about Projection Plot Color Coding
by sflarkin＠ucsc.edu 12 Jul '20

12 Jul '20

Hello All, I have a question about the Projection plot function in yt. I have a script that plots the smallest mass darkmatter particles of a simulation in all 3 of the 2-d coordinate projections, and overplots the halos found by a halo finder. This script works, and currently plots the colorbar based on the mass in a given 2-d bin as done in some of the basic yt plots included in the website. I am wondering if it is possible to have the color scheme of the particles be based on the squared mass or squared density of the particles in any given 2-d bin, so that the higher density regions are highlighted compared to the background lower density regions. I have included the plotting part of my script below, in case it is helpful. I hope everyone is having a great New Year! ds = yt.load(VELA_snaps[position[0]]) domain_width = float(ds.domain_width.in_units('Mpc/h')[0]) ad = ds.all_data() masses = yt.np.unique(ad[('darkmatter', 'particle_mass')]) #filter out the darkmatter0 particles def mass_filter(pfilter, data): filter = data[(pfilter.filtered_type, 'particle_mass')] == masses[0] return filter yt.add_particle_filter('darkmatter0', function=mass_filter, filtered_type='darkmatter', requires=['particle_mass']) ds.add_particle_filter('darkmatter0') scale = float(ds.scale_factor) fig = plt.figure() grid = AxesGrid(fig, (0.075,0.075,10,5), nrows_ncols = (3, 1), axes_pad = 1.0, label_mode = "L", share_all = False, cbar_location="right", cbar_mode="each", cbar_size="3%", cbar_pad="0%") zoom = 10 x0 = float(consistent.halo_data_sorted[index][0][17]) * scale / domain_width y0 = float(consistent.halo_data_sorted[index][0][18]) * scale / domain_width z0 = float(consistent.halo_data_sorted[index][0][19]) * scale / domain_width center = [x0, y0, z0] a = yt.ParticlePlot(ds, ('darkmatter0', 'particle_position_x'), ('darkmatter0', 'particle_position_y'),\ ('darkmatter0', 'particle_mass'), center=center) a.set_unit(('darkmatter0','particle_mass'), 'Msun') a.zoom(zoom) b = yt.ParticlePlot(ds, ('darkmatter0', 'particle_position_y'), ('darkmatter0', 'particle_position_z'),\ ('darkmatter0', 'particle_mass'), center=center) b.set_unit(('darkmatter0','particle_mass'), 'Msun') b.zoom(zoom) c = yt.ParticlePlot(ds, ('darkmatter0', 'particle_position_z'), ('darkmatter0', 'particle_position_x'),\ ('darkmatter0', 'particle_mass'), center=center) c.set_unit(('darkmatter0','particle_mass'), 'Msun') c.zoom(zoom) for halos in consistent.halo_data_sorted[index]: x = float(halos[17]) * scale / domain_width y = float(halos[18]) * scale / domain_width z = float(halos[19]) * scale / domain_width r = float(halos[11]) * scale / .7 center = [x, y, z] a.annotate_sphere(center, radius=(r, 'kpc'), circle_args={'color':'red'}) b.annotate_sphere(center, radius=(r, 'kpc'), circle_args={'color':'red'}) c.annotate_sphere(center, radius=(r, 'kpc'), circle_args={'color':'red'}) index = 0 for letter in [a,b,c]: plot = letter.plots[('darkmatter0', 'particle_mass')] plot.figure = fig plot.axes = grid[index].axes plot.cax = grid.cbar_axes[index] letter._setup_plots() index = index + 1 plt.savefig('{}/CatalogProjectionYT_VELA{}_Scale{}.png'.format(out_dir, VELA_number, str(scale)[2:5]), bbox_inches='tight') plt.close()

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Geometric Objects with periodic behavior
by Michael Jennings 01 May '20

01 May '20

Hello all, The documentation for the YTRegion class states "If the selected region extends past the edges of the domain, no data will be found there, though the object’s left_edge or right_edge are not modified.” Is there an easy way to change this to exhibit periodic behavior? For example: if the specified right_edge extended past the edges of the domain, data will be selected as continuing from the left of the domain. My ultimate goal is to create a square region centered on argmax(“density”) and calculate summed quantities in the region while successively increasing the size of the box assuming periodic boundaries. Does anyone have any insight?

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Plot a slice combining data from two datasets
by Ricardo Y 30 Apr '20

30 Apr '20

Hi all, I want a slice plot of pressure(x, y, z = 0, t) - pressure(x, y, z = 0, t = 0). I tried using a derived field as follows: ---- # Load the initial dataset ds0 = yt.load('my t=0 dataset') p0 = initialPressure = ds0.all_data()['pressure'] # Define the derived field def _perturbationPressure(field, data): return data['pressure'] - initialPressure # Add the derived field yt.add_field(('gas', 'perturbationPressure'), function=_perturbationPressure, units = "auto", dimensions = yt.units.dimensions.pressure) # Load the dataset of interest ds = yt.load('my dataset') yt.SlicePlot(ds, 'z', 'perturbationPressure') ---- The error: > ValueError: operands could not be broadcast together with shapes > (16,16,16) (134217728,) > I noticed the "data" in the definition of the derived field is a FieldDetector, so I'm not sure how I should define the derived field to plot the pressure difference (if using a derived field is the right approach at all!). The dataset I'm trying to plot is from FLASH, and I'm running yt 3.6.0. Thanks!

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Question about Yt Profiles
by sflarkin＠ucsc.edu 30 Apr '20

30 Apr '20

Hello All, I am trying to calculate the Mvir/Rvir based on the Bryan Norman definition using yt. I currently have a catalog of halos generated by running rockstar on the darkmatter particles of an ART simulation, and am trying to use the same centers to recalculate these values including the stellar and gas contents of each object. From looking into some of the yt processes, I thought that the profile function would be a perfect tool, but it seems like there is a bit of a problem with particle grids vs mesh grids that I am not sure if there is a way around. My goal was to use the yt.create_profile function to create a radial profile of the different masses using the following script: import yt from yt import YTQuantity largest_halo = consistent.halo_data_sorted[30][0] ds = yt.load('/Users/user1/documents/GEN6/VELA07_snap/10MpcBox_csf512_a0.400.d') x = ds.quan(float(largest_halo[17]), 'Mpccm/h') y = ds.quan(float(largest_halo[18]), 'Mpccm/h') z = ds.quan(float(largest_halo[19]), 'Mpccm/h') rvir = ds.quan(float(largest_halo[11]), 'kpccm/h') center = [x, y, z] sp = ds.sphere(center, (float(rvir.in_units('kpc'))*2, 'kpc')) rp = yt.create_profile(sp, 'radius', [('gas', 'density')], n_bins=4, accumulation = True, units = {'radius': 'kpc', 'density': 'Msun/kpc**3'}) rp1 = yt.create_profile(sp, 'radius', [('all', 'particle_mass')], n_bins=4, accumulation = True, units = {'radius': 'kpc'}, weight_field='particle_mass') This works perfectly for the gas, but I get the following error for the profile calculating the particle masses: YTIllDefinedProfile: Cannot create a profile object that mixes particle and mesh fields. Received the following bin_fields: ('index', 'radius'), particle_type = False Profile fields: ('all', 'particle_mass'), particle_type = True And weight field: ('all', 'particle_mass'), particle_type = True I am wondering if there is another radial-like field/it is possible to create such a field to make this profile properly match the particle_type? If not, are there any other yt functions that would simplify such an Mvir/Rvir calculation. I know it is possible to do this with a ds.sphere script call that varies the size of the region until the proper ratio is found, but I imagine that would not be a super efficient method, and it also might be interesting to see the density profile of each halo object outside of calculating its Mvir/Rvir. Thank you for your time!

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Cloud computing position for multi-messenger astrophysics (Michigan State University)
by OShea, Brian 28 Apr '20

28 Apr '20

Dear Colleagues, Michigan State University’s Institute for Cyber-Enabled Research and IceCube research group are searching for somebody who is interested in developing cloud computing tools relating to multi-messenger astrophysics, with a deadline of May 7th, 2020. The attached job ad summarizes the position and qualifications. Please note that we encourage all applicants that are interested in cloud computing and software development for multi-messenger astrophysics to apply, even if they don’t meet all of the listed qualifications. Please forward this on to potentially interested applicants, who are encouraged to contact me at oshea(a)msu.edu if they have any questions. Thank you! Regards, Brian ------------- Brian W. O’Shea Michigan State University http://www.pa.msu.edu/~osheabr Professor, Department of Computational Mathematics, Science and Engineering Department of Physics and Astronomy National Superconducting Cyclotron Laboratory Director, Institute for Cyber-Enabled Research http://icer.msu.edu/ -------------

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Velocity ProjectionPlot with yt-4.0
by Daniel DeFelippis 24 Apr '20

24 Apr '20

Hello, I'm trying to create a projection plot of velocity (e.g. velocity_x) for a halo from IllustrisTNG ('cutout_478037.hdf5' below). I'm using the demeshened version of yt (yt-4.0). When I try to do this it fails with the following error message. This only seems to occur when I try to make a projection of a quantity with positive and negative values. If I instead use 'density' or 'temperature' for example, it works fine. Any suggestions? Thank you, Daniel ds = yt.load('cutout_478037.hdf5') yt.ProjectionPlot(ds,'x',('gas','velocity_x'),width=(400,'kpc')) --------------------------------------------------------------------------- TypeError Traceback (most recent call last) ~/anaconda3/lib/python3.6/site-packages/numpy/core/function_base.py in linspace(start, stop, num, endpoint, retstep, dtype, axis) 116 try: --> 117 num = operator.index(num) 118 except TypeError: TypeError: 'numpy.float64' object cannot be interpreted as an integer During handling of the above exception, another exception occurred: TypeError Traceback (most recent call last) <ipython-input-21-7770240b54f8> in <module> 1 ds = yt.load('cutout_478037.hdf5') ----> 2 yt.ProjectionPlot(ds,'x',('gas','velocity_x'),width=(400,'kpc')) 3 #slc.save('testplot.pdf') 4 #slc.set_zlim(('gas','radial_velocity'),-200,200) 5 #slc.annotate_title(title) ~/yt/yt/visualization/plot_window.py in __init__(self, ds, axis, fields, center, width, axes_unit, weight_field, max_level, origin, right_handed, fontsize, field_parameters, data_source, method, proj_style, window_size, buff_size, aspect) 1609 PWViewerMPL.__init__(self, proj, bounds, fields=fields, origin=origin, 1610 right_handed=right_handed, fontsize=fontsize, window_size=window_size, -> 1611 aspect=aspect, buff_size=buff_size) 1612 if axes_unit is None: 1613 axes_unit = get_axes_unit(width, ds) ~/yt/yt/visualization/plot_window.py in __init__(self, *args, **kwargs) 780 self._plot_type = kwargs.pop("plot_type") 781 self._splat_color = kwargs.pop("splat_color", None) --> 782 PlotWindow.__init__(self, *args, **kwargs) 783 784 def _setup_origin(self): ~/yt/yt/visualization/plot_window.py in __init__(self, data_source, bounds, buff_size, antialias, periodic, origin, oblique, right_handed, window_size, fields, fontsize, aspect, setup) 215 self._field_transform[field] = linear_transform 216 self.setup_callbacks() --> 217 self._setup_plots() 218 219 def __iter__(self): ~/yt/yt/visualization/plot_window.py in _setup_plots(self) 1066 else: # symlog_transform 1067 flinthresh = 10**np.floor( np.log10( self.plots[f].cb.norm.linthresh ) ) -> 1068 mticks = self.plots[f].image.norm( get_symlog_minorticks(flinthresh, vmin, vmax) ) 1069 self.plots[f].cax.yaxis.set_ticks(mticks, minor=True) 1070 else: ~/yt/yt/visualization/plot_container.py in get_symlog_minorticks(linthresh, vmin, vmax) 129 return np.hstack((-get_log_minorticks(linthresh,-vmin)[::-1], 0) ) 130 else: --> 131 return np.hstack((-get_log_minorticks(linthresh,-vmin)[::-1], 0, 132 get_log_minorticks(linthresh, vmax))) 133 ~/yt/yt/visualization/plot_container.py in get_log_minorticks(vmin, vmax) 105 expA += 1 106 else: --> 107 lmticks = np.hstack( (lmticks, np.linspace(cofA, cofB, cofB-cofA+1)*10**expA) ) 108 expA += 1 109 return np.array(lmticks) <__array_function__ internals> in linspace(*args, **kwargs) ~/anaconda3/lib/python3.6/site-packages/numpy/core/function_base.py in linspace(start, stop, num, endpoint, retstep, dtype, axis) 119 raise TypeError( 120 "object of type {} cannot be safely interpreted as an integer." --> 121 .format(type(num))) 122 123 if num < 0: TypeError: object of type <class 'numpy.float64'> cannot be safely interpreted as an integer.

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Error loading active particles
by Muhammad Latif 13 Apr '20

13 Apr '20

Hi all, I am trying to read enzo dataset with active particles and getting the following error. There are active particles as indicated by print statement prior to datadump but yt immediately raises this error after loading it. Any help in this regard will be appreciated. yt : [INFO ] 2020-04-13 19:39:50,444 Parameters: current_time = 12.774511689726 yt : [INFO ] 2020-04-13 19:39:50,444 Parameters: domain_dimensions = [256 256 256] yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: domain_left_edge = [0. 0. 0.] yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: domain_right_edge = [1. 1. 1.] yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: cosmological_simulation = 1 yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: current_redshift = 23.138771212879 yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: omega_lambda = 0.6911 yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: omega_matter = 0.3089 yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: hubble_constant = 0.6774 Parsing Hierarchy : 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1771/1771 [00:00<00:00, 4770.60it/s] yt : [INFO ] 2020-04-13 19:39:50,937 Gathering a field list (this may take a moment.) Traceback (most recent call last): File "ytdiv.py", line 20, in <module> print(ds.derived_field_list) File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py", line 216, in ireq self.index File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py", line 509, in index self, dataset_type=self.dataset_type) File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/frontends/enzo/data_structures.py", line 195, in __init__ GridIndex.__init__(self, ds, dataset_type) File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/geometry/geometry_handler.py", line 58, in __init__ self._detect_output_fields() File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/frontends/enzo/data_structures.py", line 429, in _detect_output_fields ap_fields = self._detect_active_particle_fields() File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/frontends/enzo/data_structures.py", line 388, in _detect_active_particle_fields node = handle["/Grid%08i/Particles/" % g.id] File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/h5py/_hl/group.py", line 262, in __getitem__ oid = h5o.open(self.id, self._e(name), lapl=self._lapl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5o.pyx", line 190, in h5py.h5o.open KeyError: "Unable to open object (object 'Particles' doesn't exist)" Best wishes, Latif

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