[yt-users] profile plots combining different datasets
ｔyuta
y0u1t1a5.t at gmail.com
Fri Nov 3 15:53:57 PDT 2017
I tried on "Isolatedgalaxy" data. I made all the outputs to comments.
https://gist.github.com/Yuta-Tarumi/69ed0428db92553cd4f8ef9392429036#file-phase-plots-summing-up
2017-11-03 18:29 GMT-04:00 Nathan Goldbaum <nathan12343 at gmail.com>:
> So the error is coming from inside yt. Somehow yt is creating an array
> with shape (128) and trying to fill it with values from an array with shape
> (128, 128), causing numpy to complain. Unfortunately I'm still not sure
> what the underlying issue is just from looking at your code and the
> traceback. It's possible it's a yt bug, it's also possible that it's an
> issue in your notebook.
>
> Is there any chance you can make a script I can run that triggers the
> issue? That will make it much easier to understand what's going wrong. You
> could also just share your full notebook.
>
> If you can, please make use of a dataset from yt-project.org/data in your
> script. If that's not possible, you can also upload a dataset to the yt
> curldrop using the "yt upload" command line tool:
>
> $ yt upload /path/to/dataset.tar.gz
>
> and then include the link to the dataset that yt upload will print out
> once it's finished uploading the data.
>
> -Nathan
>
> On Fri, Nov 3, 2017 at 5:15 PM, ｔyuta <y0u1t1a5.t at gmail.com> wrote:
>
>> Dear Nathan,
>>
>> Sorry for the incompleteness.
>> This is the error message from jupyter notebook:
>>
>> ValueErrorTraceback (most recent call last)<ipython-input-63-383c90a16917> in <module>() 11 fields=["cell_mass"], 12 weight_field=None,---> 13 extrema=dict(density=(1e-30, 1e-20), temperature=(1e1, 1e8)) 14 ) 15
>> /home/ytarumi/.local/yt/yt/data_objects/profiles.pyc in create_profile(data_source, bin_fields, fields, n_bins, extrema, logs, units, weight_field, accumulation, fractional, deposition) 1093 setattr(obj, "fractional", fractional) 1094 if fields is not None:-> 1095 obj.add_fields([field for field in fields]) 1096 for field in fields: 1097 if fractional:
>> /home/ytarumi/.local/yt/yt/data_objects/profiles.pyc in add_fields(self, fields) 125 citer = self.data_source.chunks([], "io") 126 for chunk in parallel_objects(citer):--> 127 self._bin_chunk(chunk, fields, temp_storage) 128 self._finalize_storage(fields, temp_storage) 129
>> /home/ytarumi/.local/yt/yt/data_objects/profiles.pyc in _bin_chunk(self, chunk, fields, storage) 565 566 def _bin_chunk(self, chunk, fields, storage):--> 567 rv = self._get_data(chunk, fields) 568 if rv is None: return 569 fdata, wdata, (bf_x, bf_y) = rv
>> /home/ytarumi/.local/yt/yt/data_objects/profiles.pyc in _get_data(self, chunk, fields) 253 for i, field in enumerate(fields): 254 units = chunk.ds.field_info[field].output_units--> 255 arr[:,i] = chunk[field][filter].in_units(units) 256 if self.weight_field is not None: 257 units = chunk.ds.field_info[self.weight_field].output_units
>> ValueError: could not broadcast input array from shape (128,128) into shape (128)
>>
>>
>> 2017-11-03 17:08 GMT-04:00 Nathan Goldbaum <nathan12343 at gmail.com>:
>>
>>> Can you share the full traceback along with the error message you're
>>> seeing? You can use gist.github.com to avoid cluttering your e-mail.
>>>
>>> On Fri, Nov 3, 2017 at 3:54 PM, ｔyuta <y0u1t1a5.t at gmail.com> wrote:
>>>
>>>> Dear yt-users,
>>>>
>>>> Hi, I want to ask you about phase plot. Some days ago, I asked how to
>>>> sum up different datasets to make one profile plot, and it worked fine.
>>>> This time, I tried to do the same thing in phase plot, but it did not work
>>>> fine. Could you help me find out what the problem is?
>>>>
>>>> (inside for loop):
>>>> profile_medium = yt.create_profile(
>>>> data_source=medium_region,
>>>> bin_fields=["density", "temperature"],
>>>> fields=["cell_mass"],
>>>> n_bins=[128, 128],
>>>> units=dict(),
>>>> logs=dict(),
>>>> weight_field=None,
>>>> extrema=dict(density=(1e-30, 1e-20), temperature=(1e1,
>>>> 1e8))
>>>> )
>>>> plot_med = yt.ProfilePlot.from_profiles(profile_medium)
>>>> profile_med = plot_med.profiles[0]
>>>> profiles_sum_med = profiles_sum_med + profile_med["cell_mass"]
>>>>
>>>>
>>>> my_data_med = {"density": profile_med.x,
>>>> "temperature": profile_med.y,
>>>> "cell_mass": profiles_sum_med}
>>>> fake_ds_med = {"current_time": yt.YTQuantity(10, "Myr")}
>>>> yt.save_as_dataset(fake_ds_med, "phaseplots_med_all.h5", my_data_med)
>>>>
>>>> ds = yt.load("phaseplots_med_all.h5")
>>>> ad = ds.data
>>>>
>>>> profile = yt.create_profile(ad,
>>>> ["density", "temperature"],
>>>> n_bins=[128, 128],
>>>> fields=["cell_mass"],
>>>> weight_field=None,
>>>> extrema=dict(density=(1e-30, 1e-20),
>>>> temperature=(1e1, 1e8))
>>>> )
>>>>
>>>> and I got this error:
>>>>
>>>> could not broadcast input array from shape (128,128) into shape (128)
>>>>
>>>>
>>>> Sincerely,
>>>> Y.T.
>>>>
>>>> 2017-10-26 16:15 GMT-04:00 ｔyuta <y0u1t1a5.t at gmail.com>:
>>>>
>>>>> Hi Suoqing Ji,
>>>>>
>>>>> Thanks! I'll try that.
>>>>>
>>>>> 2017-10-26 15:59 GMT-04:00 Suoqing Ji <suoqing at physics.ucsb.edu>:
>>>>>
>>>>>> Hi t yuta,
>>>>>>
>>>>>> What you can do is to get the data as numpy array directly from the
>>>>>> profiles you’ve generated, and sum them up by yourself. You can follow the
>>>>>> last example at: http://yt-project.org/docs
>>>>>> /dev/visualizing/plots.html#d-profile-plots
>>>>>>
>>>>>> For each dataset, you can have one profile:
>>>>>> profile = plot.profiles[0]
>>>>>>
>>>>>> Then you can sum up profile[‘cell_mass'] over different datasets, and
>>>>>> plot it against profile.x
>>>>>>
>>>>>> Best wishes,
>>>>>> —
>>>>>> Suoqing Ji
>>>>>> Ph.D Candidate
>>>>>> Department of Physics
>>>>>> University of California, Santa Barbara
>>>>>> http://physics.ucsb.edu/~suoqing
>>>>>>
>>>>>> On Oct 26, 2017, 12:51 PM -0700, ｔyuta <y0u1t1a5.t at gmail.com>, wrote:
>>>>>>
>>>>>> Dear yt-users,
>>>>>>
>>>>>> Hi, I want to ask you about profile plot. I'm analyzing Enzo data,
>>>>>> and I'm trying to plot metallicity-cellmass of different 12 datasets into
>>>>>> one curve. I can plot 12 curves on one image, but that's not what I want.
>>>>>> Does anyone know some good way, or links to documentation?
>>>>>> I've attached the 12-curve plot. I want to sum up all the curves to
>>>>>> get one curve.
>>>>>>
>>>>>> Thanks,
>>>>>> Y.T.[image: 埋め込み画像 2]
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>>>>>
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