Mailman 3 May 2013 - yt-users

Re: [yt-users] yt-users Digest, Vol 63, Issue 10
by Wolfram Schmidt 20 May '13

20 May '13

Hi Sam, thanks for your response. The most recent code version I used is e6227ef4338b (stable) Would you suggest to alterntively use the simple volume rendering script? Cheers, Wolfram On Fri, 17 May 2013, yt-users-request(a)lists.spacepope.org wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. Re: volume rendering of other fields than the density > (Sam Skillman) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 16 May 2013 14:08:53 -0600 > From: Sam Skillman <samskillman(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] volume rendering of other fields than the > density > Message-ID: > <CAB4=1s3vHjqFtEjH8EwGGBR71rw5LhQo=-Zp6F1ugRd9dwAy5A(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Wolfram, > > Sorry for the trouble -- the adaptive healpix rendering is fairly beta, as > noted in that example, and I fear it may have gotten left behind in some of > the recent developments. Could you let me know what version of yt you are > using? You can check this with: > > yt instinfo > > It should spit out something like (in addition to other things): > The current version of the code is: > > --- > 1158e48daef2 > --- > > Thanks, > Sam > >

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clump to field?
by david collins 17 May '13

17 May '13

Hi, all-- I have a clump that I've gotten with the clump finder. I'd like to paint those zones of that clump with a flag, so I can exclude that region from other analysis. I'm a little stuck on how to get this done-- I feel like it needs to involve clump.data._flush_data_to_grids and a cut_mask, but I'm a little stuck on how to define the field that I flush_to_grids. Specifically, how to get the cut_mask information to the field, and how to avoid clobbering the paint from one clump with another (or, from one grid with another) I'm trying to do something like: <code> for grid in clump.data._grids: cut_mask = clump.data._get_cut_mask(grid) def masked_region(field,data): cut_mask = data.get_field_parameter('cut_mask', None) try: base = data['masked_region'] except: base = na.zeros(data['Density'].shape) if cut_mask is not None: base = na.maximum(base,cut_mask) return base add_field('masked_region',function=masked_region,validators=[ValidateGridType()], not_in_all=True) grid.set_field_parameter('cut_mask',cut_mask) print grid, cut_mask.sum(), grid['masked_region'].sum() clump.data._flush_to_grids('masked_region',0) </code> but clump['masked_region'].sum() only returns the flagged zones in the first of the grids. I feel like this is something I've done before, but can't find any reference to it in my email or old scripts. Apologies if this has been answered elsewhere, or it's obvious and I'm being thick. Thanks! d.

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volume rendering of other fields than the density
by Wolfram Schmidt 17 May '13

17 May '13

Hi all, I used the example script from the Tutorial section of the Volume Rendering page: http://yt-project.org/doc/visualizing/volume_rendering.html#adaptive-healpi… It works fine for the density, but for any other field (e.g. temperature) the output is just blank. I don't see why I wouldn't work for other fields, as the script appears to be written for arbitrary fields. Changing level bounds, use_log, etc. doesn't help. Does anyone how to fix this? Cheers, Wolfram

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Arbitrary Angle Projections
by Haig, Christina 16 May '13

16 May '13

This is a question of capability / feature suggestion if it doesn't exist. I see that yt can make projection plots along the cartesian axes, and can also do a light-ray through a particular line of sight. My question is: Can yt make a projection plot along an arbitrary axis, specified by some rotation angle? Many Thanks, Christina Haig

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star particles count
by Latif 14 May '13

14 May '13

Hi all, I have star particles in enzo simulations. Counting the particles by creation time and type gave different results. Is it a problem with Yt or comes from simulation? Any ideas? star_particles = dd["creation_time"] > 0.0 print "Number of star particles by creation time", star_particles.sum() star_particles = dd["particle_type"] == 2 print "Number of star particles by type", star_particles.sum() Number of star particles by creation time 3818 Number of star particles by type 0 thanks in advance, Cheers Latif

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strange particle field behavior
by Britton Smith 10 May '13

10 May '13

Hi all, I am seeing something odd with a field called "IsStarParticle". This is an Enzo field defined in the following way: def _IsStarParticle(field, data): is_star = (data['creation_time'] > 0).astype('float64') return is_star When I do the following: print pf.h.grids[0]['IsStarParticle'] I get the expected field of 1s and 0s. When I do this: all_data = pf.h.all_data() print all_data['IsStarParticle'] I get the values that correspond to the creation_time field. It does not matter in what order I do this. Whenever I try to access the field from a geometric object, I get the actual creation time and not the field I expect. Whenever I access it from a grid object, I get the right thing. Does anyone know what's going on here? Britton

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plot with source region and field parameters
by david collins 09 May '13

09 May '13

Hi, Everybody-- I have a field that I have defined that uses a field_parameter, but I don't seem to be able to get it to work with a projection. >>> region AMRRegion (time0050): center=[ 0.5 0.03369141 0.68457031], left_edge=[ 0. 0.00195312 0.63378906], right_edge=[ 1. 0.06542969 0.73535156] def linewidth(field,data): avg_vx = data.get_field_parameter('avg_vx') return (data['x-velocity']-avg_vx)**2 add_field('linewidth',function=linewidth, validators=[ValidateParameter('avg_vx')]) avg_vx = 7 region.set_field_parameter('avg_vx',avg_vx) print region['linewidth'].min() print region.get_field_parameter('avg_vx') which yields expected output, 1.15751883639e-07 7 But trying to make a projection of that source gives the error below. Is it obvious what I'm doing wrong? I can plot 'Density' just fine. Thanks! >>> proj = oober.pf.h.proj(2,'linewidth',source=region) Initializing tree 0 / 4100% |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 Traceback (most recent call last): | ETA: --:--:-- File "<stdin>", line 1, in <module> File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/data_containers.py", line 1758, in __init__ self._refresh_data() File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/data_containers.py", line 318, in _refresh_data self.get_data() File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/data_containers.py", line 1859, in get_data self._add_level_to_tree(tree, level, fields) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/data_containers.py", line 1981, in _add_level_to_tree self._add_grid_to_tree(tree, grid, fields, zero_out, dls) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/data_containers.py", line 1925, in _add_grid_to_tree for fd in self._get_data_from_grid(grid, fields)] File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/data_containers.py", line 93, in save_state tr = func(self, grid, field, *args, **kwargs) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/data_containers.py", line 2003, in _get_data_from_grid return [grid[field] * bad_points for field in fields] File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/grid_patch.py", line 157, in __getitem__ self.get_data(key) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/grid_patch.py", line 200, in get_data self._generate_field(field) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/grid_patch.py", line 132, in _generate_field self.pf.field_info[field].check_available(self) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/field_info_container.py", line 364, in check_available validator(data) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/field_info_container.py", line 440, in __call__ raise NeedsParameter(doesnt_have) yt.data_objects.field_info_container.NeedsParameter: (['avg_vx'])

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TotalMass for ORION data
by Mark Krumholz 06 May '13

06 May '13

Hi All, I just updated to the latest version of yt, hoping that this would be fixed, but it seems not to be: the "TotalMass" function is broken for Orion data, and, from what I can tell, for any data set that doesn't contain dark matter particles. Here's what I get when I try to use it: In [1]: pf=load('data.0030.3d.hdf5') yt : [WARNING ] 2013-05-06 16:43:36,339 Setting 1.0 in code units to be 1.0 cm yt : [WARNING ] 2013-05-06 16:43:36,339 No time units. Setting 1.0 = 1 second. yt : [INFO ] 2013-05-06 16:43:36,340 Parameters: current_time = 6.78585436617e+13 yt : [INFO ] 2013-05-06 16:43:36,340 Parameters: domain_dimensions = [256 256 256] yt : [INFO ] 2013-05-06 16:43:36,341 Parameters: domain_left_edge = [ -1.68000000e+18 -1.68000000e+18 -1.68000000e+18] yt : [INFO ] 2013-05-06 16:43:36,341 Parameters: domain_right_edge = [ 1.68000000e+18 1.68000000e+18 1.68000000e+18] In [2]: dd=pf.h.all_data() ^[[Ayt : [INFO ] 2013-05-06 16:43:53,804 Adding unknown field gravitational-potential to list of fields In [3]: dd.quantities["TotalMass"]() --------------------------------------------------------------------------- KeyError Traceback (most recent call last) /home3/mkrumhol/yt-x86_64/src/yt-hg/scripts/iyt in <module>() ----> 1 dd.quantities["TotalMass"]() /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.pyc in __call__(self, *args, **kwargs) 90 self._data_source.pf.h.io) 91 if lazy_reader and not self.force_unlazy: ---> 92 return self._call_func_lazy(args, kwargs) 93 else: 94 return self._call_func_unlazy(args, kwargs) /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.pyc in _call_func_lazy(self, args, kwargs) 97 self.retvals = [ [] for i in range(self.n_ret)] 98 for gi,g in enumerate(self._get_grids()): ---> 99 rv = self.func(GridChildMaskWrapper(g, self._data_source), *args, **kwargs) 100 if not iterable(rv): rv = (rv,) 101 for i in range(self.n_ret): self.retvals[i].append(rv[i]) /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.pyc in _TotalMass(data) 152 """ 153 baryon_mass = data["CellMassMsun"].sum() --> 154 particle_mass = data["ParticleMassMsun"].sum() 155 return [baryon_mass + particle_mass] 156 def _combTotalMass(data, total_mass): /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.pyc in __getitem__(self, item) 58 def __getitem__(self, item): 59 if item not in self.local_cache: ---> 60 data = self.data_source._get_data_from_grid(self.grid, item) 61 self.local_cache[item] = data 62 return self.local_cache[item] /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 93 old_keys = grid.field_data.keys() 94 grid.field_parameters = self.field_parameters ---> 95 tr = func(self, grid, field, *args, **kwargs) 96 grid.field_parameters = old_params 97 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] ) /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 2643 return np.array([f[i,:][pointI] for i in range(3)]) 2644 else: -> 2645 tr = grid[field] 2646 if tr.size == 1: # dx, dy, dz, cellvolume 2647 tr = tr * np.ones(grid.ActiveDimensions, dtype='float64') /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in __getitem__(self, key) 155 """ 156 if key not in self.field_data: --> 157 self.get_data(key) 158 return self.field_data[key] 159 /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in get_data(self, field, convert) 198 else: raise 199 else: --> 200 self._generate_field(field) 201 return self.field_data[field] 202 /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in _generate_field(self, field) 145 self[field] = self.pf.field_info[field](self) 146 else: # Can't find the field, try as it might --> 147 raise exceptions.KeyError(field) 148 149 def has_key(self, key): KeyError: 'ParticleMassMsun' This isn't a huge deal, because I can use "TotalQuantity" on "Density" as a workaround, but I thought I would report it. -- Mark Krumholz krumholz(a)ucolick.org

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question about interpolation to a point
by Brian O'Shea 03 May '13

03 May '13

Hi folks, I have been looking around the yt docs in hopes of finding a routine that does a trilinear interpolation of a grid quantity to an arbitrary point in space. Does such a thing exist, and I simply can't come up with the right search string? Thanks! --Brian

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Release of yt-2.5.2
by Matthew Turk 01 May '13

01 May '13

Hi all, We're proud to release yt version 2.5.2. This is a scheduled point release that includes all bug fixes identified and fixed since the release of 2.5.1 on April 1. Changes and bug fixes include: * Upgrades to most of the dependencies in the install script * Speed improvements to ellipsoidal particle detection * Updates to FLASH fields * CASTRO frontend bug fixes * Fisheye camera bug fixes * ProjectionPlot now accepts a data_source keyword argument * Answer testing now includes plot window answer testing * Athena data serialization If you are using the stable branch of yt from an installation script, you can upgrade using "yt update" or "yt update --all" to upgrade your full dependency stack. If you are using the development branch, you may already have these fixes. A tarball of this release has been uploaded to the Python Package Index (PyPI), although due to user error (me) it includes the Cython sources instead of the C sources for the generated code. Oops. Thanks very much, Matt, on behalf of the yt development team

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