[yt-users] cylindrical coordinates

Fri May 9 09:04:43 PDT 2014

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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>>> yt-users at lists.spacepope.org
>>> 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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