[yt-users] TIPSY to regular grid
Nathan Goldbaum
nathan12343 at gmail.com
Mon Dec 14 08:33:43 PST 2015
Hi Bruno,
Can you reproduce this using one of the test tipsy datasets we have on
yt-project.org/data? The "agora_1e11.00400" dataset might be a good place
to start.
If you can reproduce it using a public test dataset, you should create an
issue to track this here, including your reproduction script:
https://bitbucket.org/yt_analysis/yt/issues/new
If it doesn't trigger on anything but your data, we can try sharing your
dataset offline so that one of us can reproduce the issue on our local
machine.
-Nathan
On Fri, Dec 11, 2015 at 10:45 PM, Bruno Villasenor <br1villasen at gmail.com>
wrote:
> Hi Matthew,
>
> Here it goes:
>
> ---------------------------------------------------------------------------
> ValueError Traceback (most recent call last)
> /home/bruno/Desktop/Dropbox/Developer/parallax/gas_images/volume_dm.py in
> <module>()
> 38 dims=ds.domain_dimensions *
> 2**level)
> 39
> ---> 40 dmDens = data[('deposit','DarkMatter_density')]
> 41
> 42
>
> /home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in __getitem__(self, key)
> 238 return self.field_data[f]
> 239 else:
> --> 240 self.get_data(f)
> 241 # fi.units is the unit expression string. We depend on the
> registry
> 242 # hanging off the dataset to define this unit object.
>
> /home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.pyc
> in get_data(self, fields)
> 507 fill, gen, part = self._split_fields(fields_to_get)
> 508 if len(part) > 0: self._fill_particles(part)
> --> 509 if len(fill) > 0: self._fill_fields(fill)
> 510 if len(gen) > 0: self._generate_fields(gen)
> 511
>
> /home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.pyc
> in _fill_fields(self, fields)
> 539 domain_dims = self.ds.domain_dimensions.astype("int64") \
> 540 * self.ds.relative_refinement(0, self.level)
> --> 541 for chunk in self._data_source.chunks(fields, "io"):
> 542 input_fields = [chunk[field] for field in fields]
> 543 # NOTE: This usage of "refine_by" is actually *okay*,
> because it's
>
> /home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in chunks(self, fields, chunking_style, **kwargs)
> 564 for chunk in self.index._chunk(self, chunking_style,
> **kwargs):
> 565 with self._chunked_read(chunk):
> --> 566 self.get_data(fields)
> 567 # NOTE: we yield before releasing the context
> 568 yield self
>
> /home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in get_data(self, fields)
> 670
> 671 fields_to_generate += gen_fluids + gen_particles
> --> 672 self._generate_fields(fields_to_generate)
> 673 for field in self.field_data.keys():
> 674 if field not in ofields:
>
> /home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in _generate_fields(self, fields_to_generate)
> 690 fi = self.ds._get_field_info(*field)
> 691 try:
> --> 692 fd = self._generate_field(field)
> 693 if type(fd) == np.ndarray:
> 694 fd = self.ds.arr(fd, fi.units)
>
> /home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in _generate_field(self, field)
> 275 tr = self._generate_particle_field(field)
> 276 else:
> --> 277 tr = self._generate_fluid_field(field)
> 278 if tr is None:
> 279 raise YTCouldNotGenerateField(field, self.ds)
>
> /home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in _generate_fluid_field(self, field)
> 293 finfo.check_available(gen_obj)
> 294 except NeedsGridType as ngt_exception:
> --> 295 rv = self._generate_spatial_fluid(field,
> ngt_exception.ghost_zones)
> 296 else:
> 297 rv = finfo(gen_obj)
>
> /home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in _generate_spatial_fluid(self, field, ngz)
> 309 o = self._current_chunk.objs[0]
> 310 with o._activate_cache():
> --> 311 ind += o.select(self.selector,
> self[field], rv, ind)
> 312 else:
> 313 chunks = self.index._chunk(self, "spatial", ngz = ngz)
>
> /home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in __getitem__(self, key)
> 238 return self.field_data[f]
> 239 else:
> --> 240 self.get_data(f)
> 241 # fi.units is the unit expression string. We depend on the
> registry
> 242 # hanging off the dataset to define this unit object.
>
> /home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in get_data(self, fields)
> 670
> 671 fields_to_generate += gen_fluids + gen_particles
> --> 672 self._generate_fields(fields_to_generate)
> 673 for field in self.field_data.keys():
> 674 if field not in ofields:
>
> /home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in _generate_fields(self, fields_to_generate)
> 690 fi = self.ds._get_field_info(*field)
> 691 try:
> --> 692 fd = self._generate_field(field)
> 693 if type(fd) == np.ndarray:
> 694 fd = self.ds.arr(fd, fi.units)
>
> /home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in _generate_field(self, field)
> 275 tr = self._generate_particle_field(field)
> 276 else:
> --> 277 tr = self._generate_fluid_field(field)
> 278 if tr is None:
> 279 raise YTCouldNotGenerateField(field, self.ds)
>
> /home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in _generate_fluid_field(self, field)
> 295 rv = self._generate_spatial_fluid(field,
> ngt_exception.ghost_zones)
> 296 else:
> --> 297 rv = finfo(gen_obj)
> 298 return rv
> 299
>
> /home/bruno/apps/yt-x86_64/src/yt-hg/yt/fields/derived_field.pyc in
> __call__(self, data)
> 182 "for %s" % (self.name,))
> 183 with self.unit_registry(data):
> --> 184 dd = self._function(self, data)
> 185 for field_name in data.keys():
> 186 if field_name not in original_fields:
>
> /home/bruno/apps/yt-x86_64/src/yt-hg/yt/fields/particle_fields.pyc in
> particle_density(field, data)
> 104 d = data.deposit(pos, [data[ptype, mass_name]], method =
> "sum")
> 105 d = data.ds.arr(d, "code_mass")
> --> 106 d /= data["index", "cell_volume"]
> 107 return d
> 108
>
> /home/bruno/apps/yt-x86_64/src/yt-hg/yt/units/yt_array.pyc in
> __idiv__(self, other)
> 747 """ See __div__. """
> 748 oth = sanitize_units_mul(self, other)
> --> 749 np.divide(self, oth, out=self)
> 750 return self
> 751
>
> ValueError: operands could not be broadcast together with shapes (2,2,2,8)
> (2,2,2,0) (2,2,2,8)
>
> 2015-12-11 22:27 GMT-06:00 Matthew Turk <matthewturk at gmail.com>:
>
>> Hi Bruno,
>>
>> That's an odd one -- can you supply the rest of the traceback?
>>
>> On Fri, Dec 11, 2015 at 10:16 PM, Bruno Villasenor
>> <br1villasen at gmail.com> wrote:
>> > Hello yt-users,
>> >
>> > I'm trying to get data from a TIPSY file to a fixed resolution array,
>> > The simplest version of my code is below:
>> >
>> > #####################################################
>> > ds = yt.load( dataDir + dataFile,
>> > parameter_file= dataDir + paramFile )
>> >
>> > ad = ds.all_data()
>> > left = ad.left_edge
>> >
>> > level = 1
>> > data = ds.covering_grid(level=level, left_edge=left,
>> > dims=ds.domain_dimensions *
>> 2**level)
>> >
>> > dmDens = data[('deposit','DarkMatter_density')]
>> > ####################################################
>> >
>> > I'm getting this error:
>> > ValueError: operands could not be broadcast together with shapes
>> (2,2,2,8)
>> > (2,2,2,0) (2,2,2,8)
>> >
>> > Any ideas?
>> >
>> > YT_version: 3.1-dev
>> >
>> > Thanks in advance.
>> > Bruno
>> >
>> >
>> >
>> >
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