[yt-users] profile plots combining different datasets
ｔyuta
y0u1t1a5.t at gmail.com
Fri Nov 3 15:15:55 PDT 2017
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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