<div dir="ltr">Hi Nathan, <div><br></div><div>I tried using the tipsy dataset from yt public data and I get the same error using version 3.1-dev.</div><div><br></div><div>I just installed the newest version (3.3-dev) and it works fine for both datasets, seems like the bug was corrected in the newer version.</div><div><br></div><div>Now I'm having problems with the smoothed_covering_grid, here is the code:</div><div>#######################################################################</div><div><div>ds = yt.load( dataDir + dataFile, parameter_file= dataDir + paramFile )</div><div>ad = ds.all_data()</div><div>left = ad.left_edge</div><div><br></div><div>level = 5</div><div>data = ds.covering_grid(level=level, left_edge=left,</div><div> dims=ds.domain_dimensions * 2**level)</div><div>dataSmoth = ds.smoothed_covering_grid(level=level, left_edge=left,</div><div> dims=ds.domain_dimensions * 2**level)</div><div><br></div><div>gasDens = dataSmoth[('deposit', 'Gas_smoothed_density')].v</div></div><div>#######################################################################</div><div><br></div><div>And with both my dataset and the public tipsy dataset I get this error:</div><div><div><br></div><div>In [38]: run volume_dm_simple.py</div><div>---------------------------------------------------------------------------</div><div>TypeError Traceback (most recent call last)</div><div>/home/bruno/Desktop/Dropbox/Developer/parallax/gas_images/volume_dm_simple.py in <module>()</div><div> 16 dims=ds.domain_dimensions * 2**level)</div><div> 17 </div><div>---> 18 gasDens = dataSmoth[('deposit', 'Gas_smoothed_density')].v</div><div><br></div><div>/home/bruno/apps/yt_3.3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key)</div><div> 266 return self.field_data[f]</div><div> 267 else:</div><div>--> 268 self.get_data(f)</div><div> 269 # fi.units is the unit expression string. We depend on the registry</div><div> 270 # hanging off the dataset to define this unit object.</div><div><br></div><div>/home/bruno/apps/yt_3.3/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.pyc in get_data(self, fields)</div><div> 611 if len(fields_to_get) == 0: return</div><div> 612 fill, gen, part, alias = self._split_fields(fields_to_get)</div><div>--> 613 if len(part) > 0: self._fill_particles(part)</div><div> 614 if len(fill) > 0: self._fill_fields(fill)</div><div> 615 for a, f in sorted(alias.items()):</div><div><br></div><div>/home/bruno/apps/yt_3.3/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.pyc in _fill_particles(self, part)</div><div> 641 def _fill_particles(self, part):</div><div> 642 for p in part:</div><div>--> 643 self[p] = self._data_source[p]</div><div> 644 </div><div> 645 def _fill_fields(self, fields):</div><div><br></div><div>TypeError: 'NoneType' object has no attribute '__getitem__'</div></div><div>########################################################################</div><div><br></div><div>Thanks for the help.</div><div>Bruno</div></div><div class="gmail_extra"><br><div class="gmail_quote">2015-12-14 10:33 GMT-06:00 Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Bruno,<div><br></div><div>Can you reproduce this using one of the test tipsy datasets we have on <a href="http://yt-project.org/data" target="_blank">yt-project.org/data</a>? The "agora_1e11.00400" dataset might be a good place to start.</div><div><br></div><div>If you can reproduce it using a public test dataset, you should create an issue to track this here, including your reproduction script:</div><div><br></div><div><a href="https://bitbucket.org/yt_analysis/yt/issues/new" target="_blank">https://bitbucket.org/yt_analysis/yt/issues/new</a><br></div><div><br></div><div>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.</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>-Nathan</div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Dec 11, 2015 at 10:45 PM, Bruno Villasenor <span dir="ltr"><<a href="mailto:br1villasen@gmail.com" target="_blank">br1villasen@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Matthew,<div><br></div><div>Here it goes:<br><div><br></div><div><div>---------------------------------------------------------------------------</div><div>ValueError Traceback (most recent call last)</div><div>/home/bruno/Desktop/Dropbox/Developer/parallax/gas_images/volume_dm.py in <module>()</div><div> 38 dims=ds.domain_dimensions * 2**level)</div><div> 39 </div><div>---> 40 dmDens = data[('deposit','DarkMatter_density')]</div><div> 41 </div><div> 42 </div><div><br></div><div>/home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key)</div><div> 238 return self.field_data[f]</div><div> 239 else:</div><div>--> 240 self.get_data(f)</div><div> 241 # fi.units is the unit expression string. We depend on the registry</div><div> 242 # hanging off the dataset to define this unit object.</div><div><br></div><div>/home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.pyc in get_data(self, fields)</div><div> 507 fill, gen, part = self._split_fields(fields_to_get)</div><div> 508 if len(part) > 0: self._fill_particles(part)</div><div>--> 509 if len(fill) > 0: self._fill_fields(fill)</div><div> 510 if len(gen) > 0: self._generate_fields(gen)</div><div> 511 </div><div><br></div><div>/home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.pyc in _fill_fields(self, fields)</div><div> 539 domain_dims = self.ds.domain_dimensions.astype("int64") \</div><div> 540 * self.ds.relative_refinement(0, self.level)</div><div>--> 541 for chunk in self._data_source.chunks(fields, "io"):</div><div> 542 input_fields = [chunk[field] for field in fields]</div><div> 543 # NOTE: This usage of "refine_by" is actually *okay*, because it's</div><div><br></div><div>/home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in chunks(self, fields, chunking_style, **kwargs)</div><div> 564 for chunk in self.index._chunk(self, chunking_style, **kwargs):</div><div> 565 with self._chunked_read(chunk):</div><div>--> 566 self.get_data(fields)</div><div> 567 # NOTE: we yield before releasing the context</div><div> 568 yield self</div><div><br></div><div>/home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields)</div><div> 670 </div><div> 671 fields_to_generate += gen_fluids + gen_particles</div><div>--> 672 self._generate_fields(fields_to_generate)</div><div> 673 for field in self.field_data.keys():</div><div> 674 if field not in ofields:</div><div><br></div><div>/home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _generate_fields(self, fields_to_generate)</div><div> 690 fi = self.ds._get_field_info(*field)</div><div> 691 try:</div><div>--> 692 fd = self._generate_field(field)</div><div> 693 if type(fd) == np.ndarray:</div><div> 694 fd = self.ds.arr(fd, fi.units)</div><div><br></div><div>/home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _generate_field(self, field)</div><div> 275 tr = self._generate_particle_field(field)</div><div> 276 else:</div><div>--> 277 tr = self._generate_fluid_field(field)</div><div> 278 if tr is None:</div><div> 279 raise YTCouldNotGenerateField(field, self.ds)</div><div><br></div><div>/home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _generate_fluid_field(self, field)</div><div> 293 finfo.check_available(gen_obj)</div><div> 294 except NeedsGridType as ngt_exception:</div><div>--> 295 rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones)</div><div> 296 else:</div><div> 297 rv = finfo(gen_obj)</div><div><br></div><div>/home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _generate_spatial_fluid(self, field, ngz)</div><div> 309 o = self._current_chunk.objs[0]</div><div> 310 with o._activate_cache():</div><div>--> 311 ind += o.select(self.selector, self[field], rv, ind)</div><div> 312 else:</div><div> 313 chunks = self.index._chunk(self, "spatial", ngz = ngz)</div><div><br></div><div>/home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key)</div><div> 238 return self.field_data[f]</div><div> 239 else:</div><div>--> 240 self.get_data(f)</div><div> 241 # fi.units is the unit expression string. We depend on the registry</div><div> 242 # hanging off the dataset to define this unit object.</div><div><br></div><div>/home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields)</div><div> 670 </div><div> 671 fields_to_generate += gen_fluids + gen_particles</div><div>--> 672 self._generate_fields(fields_to_generate)</div><div> 673 for field in self.field_data.keys():</div><div> 674 if field not in ofields:</div><div><br></div><div>/home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _generate_fields(self, fields_to_generate)</div><div> 690 fi = self.ds._get_field_info(*field)</div><div> 691 try:</div><div>--> 692 fd = self._generate_field(field)</div><div> 693 if type(fd) == np.ndarray:</div><div> 694 fd = self.ds.arr(fd, fi.units)</div><div><br></div><div>/home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _generate_field(self, field)</div><div> 275 tr = self._generate_particle_field(field)</div><div> 276 else:</div><div>--> 277 tr = self._generate_fluid_field(field)</div><div> 278 if tr is None:</div><div> 279 raise YTCouldNotGenerateField(field, self.ds)</div><div><br></div><div>/home/bruno/apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _generate_fluid_field(self, field)</div><div> 295 rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones)</div><div> 296 else:</div><div>--> 297 rv = finfo(gen_obj)</div><div> 298 return rv</div><div> 299 </div><div><br></div><div>/home/bruno/apps/yt-x86_64/src/yt-hg/yt/fields/derived_field.pyc in __call__(self, data)</div><div> 182 "for %s" % (<a href="http://self.name" target="_blank">self.name</a>,))</div><div> 183 with self.unit_registry(data):</div><div>--> 184 dd = self._function(self, data)</div><div> 185 for field_name in data.keys():</div><div> 186 if field_name not in original_fields:</div><div><br></div><div>/home/bruno/apps/yt-x86_64/src/yt-hg/yt/fields/particle_fields.pyc in particle_density(field, data)</div><div> 104 d = data.deposit(pos, [data[ptype, mass_name]], method = "sum")</div><div> 105 d = data.ds.arr(d, "code_mass")</div><div>--> 106 d /= data["index", "cell_volume"]</div><div> 107 return d</div><div> 108 </div><div><br></div><div>/home/bruno/apps/yt-x86_64/src/yt-hg/yt/units/yt_array.pyc in __idiv__(self, other)</div><div> 747 """ See __div__. """</div><div> 748 oth = sanitize_units_mul(self, other)</div><div>--> 749 np.divide(self, oth, out=self)</div><div> 750 return self</div><div> 751 </div><span><div><br></div><div>ValueError: operands could not be broadcast together with shapes (2,2,2,8) (2,2,2,0) (2,2,2,8)</div></span></div></div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">2015-12-11 22:27 GMT-06:00 Matthew Turk <span dir="ltr"><<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Bruno,<br>
<br>
That's an odd one -- can you supply the rest of the traceback?<br>
<div><div><br>
On Fri, Dec 11, 2015 at 10:16 PM, Bruno Villasenor<br>
<<a href="mailto:br1villasen@gmail.com" target="_blank">br1villasen@gmail.com</a>> wrote:<br>
> Hello yt-users,<br>
><br>
> I'm trying to get data from a TIPSY file to a fixed resolution array,<br>
> The simplest version of my code is below:<br>
><br>
> #####################################################<br>
> ds = yt.load( dataDir + dataFile,<br>
> parameter_file= dataDir + paramFile )<br>
><br>
> ad = ds.all_data()<br>
> left = ad.left_edge<br>
><br>
> level = 1<br>
> data = ds.covering_grid(level=level, left_edge=left,<br>
> dims=ds.domain_dimensions * 2**level)<br>
><br>
> dmDens = data[('deposit','DarkMatter_density')]<br>
> ####################################################<br>
><br>
> I'm getting this error:<br>
> ValueError: operands could not be broadcast together with shapes (2,2,2,8)<br>
> (2,2,2,0) (2,2,2,8)<br>
><br>
> Any ideas?<br>
><br>
> YT_version: 3.1-dev<br>
><br>
> Thanks in advance.<br>
> Bruno<br>
><br>
><br>
><br>
><br>
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