[yt-users] cylindrical coordinates
Τρίτσης Άρης- Ευάγγελος
tritsis at physics.uoc.gr
Fri May 9 10:11:21 PDT 2014
On 2014-05-09 19:04, Matthew Turk wrote:
> Hi Aris,
>
> Ah! I see the problem -- the off-axis slice plot probably isn't
> implemented. I'm sorry to say that might take a bit more work and
> won't be a readily added improvement; on-axis should work, however.
>
> -Matt
>
> On Fri, May 9, 2014 at 12:02 PM, Τρίτσης Άρης- Ευάγγελος
> <tritsis at physics.uoc.gr> wrote:
>> On 2014-05-09 18:43, Matthew Turk wrote:
>>>
>>> Hi Aris,
>>>
>>> On Fri, May 9, 2014 at 9:21 AM, Τρίτσης Άρης- Ευάγγελος
>>> <tritsis at physics.uoc.gr> wrote:
>>>>
>>>> Hi yt users!
>>>>
>>>> I am new to yt and would like to ask if anyone has come across
>>>> issues
>>>> similar to mine.
>>>> Is it possible to make slice,projection and 1D-profle plots in
>>>> cylindrical
>>>> coordinates in a Flash output file
>>>> in any orientation and if not does anyone know when such a feature
>>>> will
>>>> be
>>>> implemented to yt?
>>>> Secondly, when I try to update all dependencies I get the following
>>>> error:
>>>
>>>
>>> In terms of cylindrical coordinates, yt-3.0 ("bleeding edge" on the
>>> website) should fully support them. I'm not entirely sure I
>>> understand the question of orientation, though.
>>>
>>>>
>>>> /home/*/yt-x86_64/bin/python2.7: can't open file
>>>> '/distribute_setup.py':
>>>> [Errno 2] No such file or directory
>>>
>>>
>>> Ah, I think this might mean you are missing the libssl-dev
>>> dependencies? I'm not sure, though. Kacper?
>>>
>>> -Matt
>>>
>>>>
>>>> I would appreciate any help :)
>>>>
>>>> Aris
>>>> _______________________________________________
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>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
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>>
>>
>>
>> Hi Matt,
>>
>> I do use the bleeding edge version which I installed from the
>> installation
>> script. However, when I try to produce an off axis slice plot I get
>> the
>> following:
>>
>> YTCoordinateNotImplemented Traceback (most recent call
>> last)
>> <ipython-input-67-440c2559450b> in <module>()
>> ----> 1 cut=OffAxisSlicePlot(pf, L, 'density', width=(25, 'pc'),
>> north_vector=north_vector)
>>
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in
>> __init__(self, pf, normal, fields, center, width, axes_unit,
>> north_vector,
>> fontsize, field_parameters)
>> 1246 PWViewerMPL.__init__(self, cutting, bounds,
>> fields=fields,
>> 1247
>> origin='center-window',periodic=False,
>> -> 1248 oblique=True, fontsize=fontsize)
>> 1249 if axes_unit is None:
>> 1250 axes_unit = get_axes_unit(width, pf)
>>
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in
>> __init__(self, *args, **kwargs)
>> 675 if self._plot_type is None:
>> 676 self._plot_type = kwargs.pop("plot_type")
>> --> 677 PlotWindow.__init__(self, *args, **kwargs)
>> 678
>> 679 def _setup_origin(self):
>>
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in
>> __init__(self, data_source, bounds, buff_size, antialias, periodic,
>> origin,
>> oblique, window_size, fields, fontsize, aspect, setup)
>> 300 self.fields = fields
>> 301 super(PlotWindow, self).__init__(data_source,
>> window_size,
>> fontsize)
>> --> 302 self._set_window(bounds) # this automatically updates
>> the
>> data and plot
>> 303 self.origin = origin
>> 304 if self.data_source.center is not None and oblique ==
>> False:
>>
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/visualization/plot_container.pyc
>> in
>> newfunc(*args, **kwargs)
>> 29 args[0]._plot_valid = False
>> 30 if hasattr(args[0], '_recreate_frb'):
>> ---> 31 args[0]._recreate_frb()
>> 32 if args[0]._initfinished:
>> 33 args[0]._setup_plots()
>>
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in
>> _recreate_frb(self)
>> 349
>> periodic=self._periodic)
>> 350 if old_fields is None:
>> --> 351 self.frb._get_data_source_fields()
>> 352 else:
>> 353 for key, unit in zip(old_fields, old_units):
>>
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/visualization/fixed_resolution.pyc
>> in
>> _get_data_source_fields(self)
>> 140 for f in fields:
>> 141 if f not in exclude and f[0] not in
>> self.data_source.pf.particle_types:
>> --> 142 self[f]
>> 143
>> 144
>>
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/visualization/fixed_resolution.pyc
>> in
>> __getitem__(self, item)
>> 370 def __getitem__(self, item):
>> 371 if item in self.data: return self.data[item]
>> --> 372 indices = np.argsort(self.data_source['dx'])[::-1]
>> 373 bounds = []
>> 374 for b in self.bounds:
>>
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>> in
>> __getitem__(self, key)
>> 210 return self.field_data[f]
>> 211 else:
>> --> 212 self.get_data(f)
>> 213 # fi.units is the unit expression string. We depend on
>> the
>> registry
>> 214 # hanging off the dataset to define this unit object.
>>
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>> in
>> get_data(self, fields)
>> 619
>> 620 fields_to_generate += gen_fluids + gen_particles
>> --> 621 self._generate_fields(fields_to_generate)
>> 622
>> 623 def _generate_fields(self, fields_to_generate):
>>
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>> in
>> _generate_fields(self, fields_to_generate)
>> 636 fi = self.pf._get_field_info(*field)
>> 637 try:
>> --> 638 fd = self._generate_field(field)
>> 639 if type(fd) == np.ndarray:
>> 640 fd = self.pf.arr(fd, fi.units)
>>
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>> in
>> _generate_field(self, field)
>> 247 tr = self._generate_particle_field(field)
>> 248 else:
>> --> 249 tr = self._generate_fluid_field(field)
>> 250 if tr is None:
>> 251 raise YTCouldNotGenerateField(field, self.pf)
>>
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>> in
>> _generate_fluid_field(self, field)
>> 267 rv = self._generate_spatial_fluid(field,
>> ngt_exception.ghost_zones)
>> 268 else:
>> --> 269 rv = finfo(gen_obj)
>> 270 return rv
>> 271
>>
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/fields/derived_field.pyc in
>> __call__(self, data)
>> 176 "for %s" % (self.name,))
>> 177 with self.unit_registry(data):
>> --> 178 dd = self._function(self, data)
>> 179 for field_name in data.keys():
>> 180 if field_name not in original_fields:
>>
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/geometry/coordinate_handler.pyc
>> in
>> _unknown_coord(field, data)
>> 31
>> 32 def _unknown_coord(field, data):
>> ---> 33 raise YTCoordinateNotImplemented
>> 34
>> 35 def _get_coord_fields(axi, units = "code_length"):
>>
>> YTCoordinateNotImplemented: This coordinate is not implemented for
>> this
>> geometry type
>>
>>
>> Plus I checked and I have all libssl-dev dependencies. Thanks again.
>>
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> _______________________________________________
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Hi Matt,
Thanks a million for you immediate responses!! Since my main objective
is to produce column density plots
and then projection plots can you also tell me if such a feature is
implemented for cylindrical coordinates?
When I try to produce such plots with the ProjectionPlot and ProfilePlot
routines I get wrong results. I
have attached the plots I get from yt plus a dump from my model so you
can check it if you like. Again I would really
appreciate any help :).
Aris
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