Mailman 3 November 2014 - yt-users

Isocontours for two fields in volume rendering.
by Daniel Fenn Nov. 17, 2014

Nov. 17, 2014

Hi--I've got a question I'm hoping someone can help me with. I'm trying to do a volume rendering including 2 different fields whose scales differ by ~8 orders of magnitude. I'd like to be able to specify isocontours for specific values for each of the fields. I've been able to achieve this with just one field, but how can I do it for multiple fields? Thanks. Daniel

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create_profile in 3.0
by John Regan Nov. 17, 2014

Nov. 17, 2014

Hi All, I was wondering about the behaviour of create_profile in 3.0. If I do something like yt.create_profile(sphere, 'particle_radius', 'all_density') it will fail but yt.create_profile(sphere, 'radius', 'all_density') will succeed. And yt.create_profile(sphere, 'particle_radius', 'particle_mass', weight_field=None) will also be OK as long as I set the weight_field = None otherwise it fails. I'm able to plot enclosed dark matter profiles but when it comes to density profiles the above difficulties are proving troublesome :) Any tips would be appreciated! Simple script attached. John

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Error in simple volume rendering
by Daniel Fenn Nov. 16, 2014

Nov. 16, 2014

Hi, I'm trying to do the simple volume rendering from the cookbook. The data is FLASH HDF5 data, and I'm using version 3.0.2 of yt. The script I'm running is here: http://paste.yt-project.org/show/5183/ However, I'm getting the following error: http://paste.yt-project.org/show/5184/ I guess it has something to do with the AMR tree, but unfortunately I don't know a lot about the specifics of that. Could anyone offer any insight into this problem? Thanks, Daniel

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yt-3.0 : derived fields in python notebooks
by Elizabeth Tasker Nov. 14, 2014

Nov. 14, 2014

Hi, I'm hitting a problem with deriving a field within a python notebook with yt 3.0. I'm following: http://yt-project.org/docs/3.0/quickstart/derived_fields_and_profiles.html and have: @derived_field(name = "thermenergy", units = "g * cm**2/s**2") def _thermenergy(field, data): return data[("gas", "cell_mass")]*data[("gas", "thermal_energy")] but I get: TypeError Traceback (most recent call last) <ipython-input-30-55b30d60c209> in <module>() ----> 1 @derived_field(name = "thermenergy", units = "g * cm**2/s**2") 2 def _thermenergy(field, data): 3 return data[("gas", "cell_mass")]*data[("gas", "thermal_energy")] 4 5 yt.add_field("thermenergy", function=_thermenergy, units="gcm**2/s**2") TypeError: 'NoneType' object is not callable I don't get an error if I do: def _thermenergy(field, data): return data[("gas", "cell_mass")]*data[("gas", "thermal_energy")] yt.add_field("thermenergy", function=_thermenergy, units="gcm**2/s**2") but nor can I use the field: ds = yt.load("DD0002/sbcool_0002") dd = ds.all_data() dd["thermenergy"] YTFieldNotFound Traceback (most recent call last) <ipython-input-33-c293394ac99f> in <module>() 1 ds = yt.load("DD0002/sbcool_0002") 2 dd = ds.all_data() ----> 3 dd["thermenergy"] ... what did I do wrong? Elizabeth

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Exporting notebooks
by Elizabeth Tasker Nov. 14, 2014

Nov. 14, 2014

Hi, I’m getting a batch of errors (OK… 2) when using python notebooks with yt 3.0: (1) I’m trying to export my python notebook into something shareable (ideally a pdf document). However, when I click ‘Print Preview’ or ‘Download as—> html’ I get the error: No module named pygments.formatters tornado.access: [ERROR ] Is there something extra I need to add to the yt python install to get this working? This happens both on my linux workstation and my macbook when I try and run nbconvert. (2) when I try: ts = DatasetSeries([“DD0002/sbcool_0002”, “DD0010/sbcool_0010”]) I get the error NameError: name ‘DatasetSeries' is not defined is this something that slipped through being imported int yt 3? Elizabeth

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PHOX module memory error and Derived field
by Barbara Ramirez Nov. 11, 2014

Nov. 11, 2014

Hello! I have recently upgraded from v2.6 to v.3 of yt and I'm having some difficulties 1) I was trying to use the Phox module to generate an x-ray mock observation from a simulated galaxy cluster, however the code gives a memory error while generating "PhotonList"; when doing $top I can see the code taking up to 24Gb of memory. This happens if I select a spherical region bigger than 100 kpc. Simulation details: I have a 200 Mpc cosmological simulation made in Flash, the smallest resolution cells are 14Kpc. Ideally, I would like to generate a mock observation of at least 5mpc... is this simply not possible? Any ideas how to tackle this issue? 2) The syntax of the first projection PHOX example is a bit strange. shouldn't it be >ds.add_field instead?, Otherwise, we get NameError:name 'add_field' is not defined Thanks for any suggestions/help! Barbara L. Ramirez M. MSc. Institut für Astro- und Teilchenphysik University of Innsbruck

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adding a smoothed field
by Desika Narayanan Nov. 11, 2014

Nov. 11, 2014

Hey All, I'm trying to figure out how to add a new smoothed field to a data set. Specifically, I want to add a (particle) field, and then be able to access the smoothed mesh quantities (the same way I would access the mesh quantities of density as below, for example) ad = ds.all_data() ad["deposit","PartType0_smoothed_desnsity"] (in this case PartType0 is gas). I'm adding a field prior to loading the data set as described here: http://yt-project.org/doc/developing/creating_derived_fields.html#defining-… thanks, desika

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Mismatched array dimensions when trying to construct surface.triangles
by David Ketcheson Nov. 11, 2014

Nov. 11, 2014

I'm trying to plot isosurfaces from AMRClaw data. I've been able to successfully plot slices and projections. Here is the script I'm using for isosurfaces: https://gist.github.com/ketch/30d8bdf41422dc20bb95 (based on http://yt-project.org/doc/cookbook/complex_plots.html#plotting-isocontours) I get the following error: --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /Users/ketch/Downloads/plot_yt_amrclaw.py in <module>() 35 ad = ds.all_data() 36 surface = ds.h.surface(ad,"q",0.2) ---> 37 p3dc = Poly3DCollection(surface.triangles, linewidth=0)#, linewidth=0.1,alpha=0.9) 38 colors = yt.apply_colormap((surface["q"]), cmap_name="hot") 39 p3dc.set_facecolors(colors[0,:,:]/255.) /Users/ketch/anaconda/lib/python2.7/site-packages/yt/data_objects/construction_data_containers.pyc in triangles(self) 1021 def triangles(self): 1022 if self.vertices is None: -> 1023 self.get_data() 1024 vv = np.empty((self.vertices.shape[1]/3, 3, 3), dtype="float64") 1025 for i in range(3): /Users/ketch/anaconda/lib/python2.7/site-packages/yt/data_objects/construction_data_containers.pyc in get_data(self, fields, sample_type) 913 my_verts = self._extract_isocontours_from_grid( 914 block, self.surface_field, self.field_value, --> 915 mask, fields, sample_type) 916 if fields is not None: 917 my_verts, svals = my_verts /Users/ketch/anaconda/lib/python2.7/site-packages/yt/data_objects/construction_data_containers.pyc in _extract_isocontours_from_grid(self, grid, field, value, mask, sample_values, sample_type) 933 mask, sample_values = None, 934 sample_type = "face"): --> 935 vals = grid.get_vertex_centered_data(field, no_ghost = False) 936 if sample_values is not None: 937 svals = grid.get_vertex_centered_data(sample_values) /Users/ketch/anaconda/lib/python2.7/site-packages/yt/data_objects/grid_patch.py in get_vertex_centered_data(self, field, smoothed, no_ghost) 289 else: 290 cg = self.retrieve_ghost_zones(1, field, smoothed=smoothed) --> 291 np.add(new_field, cg[field][1: ,1: ,1: ], new_field) 292 np.add(new_field, cg[field][:-1,1: ,1: ], new_field) 293 np.add(new_field, cg[field][1: ,:-1,1: ], new_field) ValueError: operands could not be broadcast together with shapes (47,47,47) (48,48,48) (47,47,47) I get the same error if I just ask for surface.triangles. After a bit of hunting, I found that the whole thing works fine if I set smoothed=False in line 290. Any ideas as to why the array size comes out wrong?

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Re: [yt-users] yt-users Digest, Vol 81, Issue 30
by David Ketcheson Nov. 10, 2014

Nov. 10, 2014

On Mon, Nov 10, 2014 at 7:44 PM, <yt-users-request(a)lists.spacepope.org<mailto:yt-users-request@lists.spacepope.org>> wrote: for state in sorted(sol.states, key = lambda a: a.patch.level): That did indeed fix it; thanks! It looks like we (Clawpack) may adopt yt as our preferred package for 3d plotting. If so, we may write a frontend at some point. Thanks to all of you for creating yt. ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Error on loading generic AMR grid data and plotting a slice: AttributeError: 'StreamGrid' object has no attribute 'dds'
by David Ketcheson Nov. 10, 2014

Nov. 10, 2014

I have some AMR output data (from AMRClaw, for which there is not a yt front end) and I'm following instructions here: http://yt-project.org/docs/3.0/examining/loading_data.html#generic-amr-data My script is here: https://gist.github.com/30d8bdf41422dc20bb95 The yt.load_amr_grids() command seems to complete successfully. But when I try to generate a slice plot, I get the following: AttributeError Traceback (most recent call last) <ipython-input-30-384f3d2d8b79> in <module>() ----> 1 yt.SlicePlot(ds, 0, "density") /Users/ketch/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.pyc in SlicePlot(ds, normal, fields, axis, *args, **kwargs) 1840 del kwargs['north_vector'] 1841 -> 1842 return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs) /Users/ketch/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.pyc in __init__(self, ds, axis, fields, center, width, axes_unit, origin, fontsize, field_parameters, window_size, aspect) 1012 slc = ds.slice(axis, center[axis], 1013 field_parameters = field_parameters, center=center) -> 1014 slc.get_data(fields) 1015 PWViewerMPL.__init__(self, slc, bounds, origin=origin, 1016 fontsize=fontsize, fields=fields, /Users/ketch/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.pyc in get_data(self, fields) 600 def get_data(self, fields=None): 601 if self._current_chunk is None: --> 602 self.index._identify_base_chunk(self) 603 if fields is None: return 604 nfields = [] /Users/ketch/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.pyc in index(self) 127 if self._index is not None: 128 return self._index --> 129 self._index = self.ds.index 130 return self._index 131 /Users/ketch/anaconda/lib/python2.7/site-packages/yt/data_objects/static_output.pyc in index(self) 272 raise RuntimeError("You should not instantiate Dataset.") 273 self._instantiated_index = self._index_class( --> 274 self, dataset_type=self.dataset_type) 275 # Now we do things that we need an instantiated index for 276 # ...first off, we create our field_info now. /Users/ketch/anaconda/lib/python2.7/site-packages/yt/frontends/stream/data_structures.pyc in __init__(self, ds, dataset_type) 167 self.float_type = "float64" 168 self.directory = os.getcwd() --> 169 GridIndex.__init__(self, ds, dataset_type) 170 171 def _count_grids(self): /Users/ketch/anaconda/lib/python2.7/site-packages/yt/geometry/geometry_handler.pyc in __init__(self, ds, dataset_type) 55 56 mylog.debug("Setting up domain geometry.") ---> 57 self._setup_geometry() 58 59 mylog.debug("Initializing data grid data IO") /Users/ketch/anaconda/lib/python2.7/site-packages/yt/geometry/grid_geometry_handler.pyc in _setup_geometry(self) 56 57 mylog.debug("Constructing grid objects.") ---> 58 self._populate_grid_objects() 59 60 mylog.debug("Re-examining index") /Users/ketch/anaconda/lib/python2.7/site-packages/yt/frontends/stream/data_structures.pyc in _populate_grid_objects(self) 242 def _populate_grid_objects(self): 243 for g in self.grids: --> 244 g._setup_dx() 245 self.max_level = self.grid_levels.max() 246 /Users/ketch/anaconda/lib/python2.7/site-packages/yt/data_objects/grid_patch.pyc in _setup_dx(self) 136 id = self.id - self._id_offset 137 if self.Parent is not None: --> 138 self.dds = self.Parent.dds.ndarray_view() / self.ds.refine_by 139 else: 140 LE, RE = self.index.grid_left_edge[id,:], \ AttributeError: 'StreamGrid' object has no attribute 'dds' I would greatly appreciate any help.

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