[yt-users] 2 ProfilePlot problems
Stephanie Tonnesen
stonnes at gmail.com
Tue Nov 7 19:10:58 PST 2017
Hi Nathan!
Okay, so the linewidth problem is just a small edit: instead of
lw = ['2']
it needs to be set as
lw = [2]
--not sure why that changed, but not a big deal. I can't remember or find
if the first version is in the docs or if I got it some other way.
I have submitted the other issue as a bug report with the working and
failing scripts attached!
Thanks! Best,
Stephanie
--
Dr. Stephanie Tonnesen
Associate Research Scientist
CCA, Flatiron Institute
New York, NY
stonnes at gmail.com
On Mon, Nov 6, 2017 at 5:17 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:
> These both sound like bugs. Can you please open two issues on github so we
> don't lose track? Please also use datasets from yt-project.org/data or
> include links to outputs so we can reproduce the issues locally.
>
> -Nathan
>
> On Mon, Nov 6, 2017 at 3:59 PM, Stephanie Tonnesen <stonnes at gmail.com>
> wrote:
>
>> Hi yt-users!
>>
>> I have two ProfilePlot issues. I have updated to yt version 3.5 dev0 to
>> try and get the standard_error on a ProfilePlot, but now am running into
>> other problems. Basically, I am trying to get the same result two ways,
>> and have run into two problems.
>>
>> 1) The linewidth call no longer works. This code worked in my old yt
>> version, but now gives me an error unless I take out the linewidth command:
>>
>> profiles = []
>> labels = []
>> plot_specs = []
>> linest = ['-','--','-.','-','--']
>> cols = ['red','red','red','green','green']
>> lws = ['2','2','2','2','2']
>>
>> i =0
>> while i < len(loop):
>> ds = yt.load("/mnt/ceph/users/stonnesen/data1/"+loopfile[i]+"/DD"
>> +loop[i]+"/"+loopfile[i]+loop[i])
>> disk = ds.disk([0.5,0.5,0.5],[0,0,-1.0],(40,"kpc"),(2,"kpc"))
>>
>>
>> profiles.append(yt.create_profile(
>> data_source=disk,
>> bin_fields=["radius"],
>> fields=["density"],
>> n_bins=52,
>> units=dict(radius="kpc",
>> density="g/cm**3"),
>> logs=dict(radius=False),
>> weight_field='ones',
>> extrema=dict(radius=(0,40)),
>> ))
>> labels.append("%s" % looptext[i])
>> plot_specs.append(dict(linestyle=linest[i],linewidth=lws[i],
>> color=cols[i]))
>>
>>
>> i = i+1
>>
>> plot = yt.ProfilePlot.from_profiles(profiles,labels=labels,plot_spe
>> cs=plot_specs)
>> plot.set_ylim('density',1e-27,1e-22)
>> plot.save()
>>
>> I get this error:
>> yt : [INFO ] 2017-11-06 16:44:12,585 Gathering a field list (this may
>> take a moment.)
>> Traceback (most recent call last):
>> File "yt_diskprofile_oplotdiffruns.py", line 61, in <module>
>> plot = yt.ProfilePlot.from_profiles(profiles,labels=labels,plot_spe
>> cs=plot_specs)
>> File "/mnt/home/stonnesen/yt-conda/yt/yt/visualization/profile_plotter.py",
>> line 443, in from_profiles
>> return cls._initialize_instance(obj, profiles, labels, plot_specs,
>> y_log)
>> File "/mnt/home/stonnesen/yt-conda/yt/yt/visualization/profile_plotter.py",
>> line 393, in _initialize_instance
>> obj._setup_plots()
>> File "/mnt/home/stonnesen/yt-conda/yt/yt/visualization/profile_plotter.py",
>> line 355, in _setup_plots
>> label=self.label[i], **self.plot_spec[i])
>> File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/__init__.py",
>> line 1710, in inner
>> return func(ax, *args, **kwargs)
>> File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/axes/_axes.py",
>> line 1437, in plot
>> for line in self._get_lines(*args, **kwargs):
>> File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/axes/_base.py",
>> line 404, in _grab_next_args
>> for seg in self._plot_args(this, kwargs):
>> File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/axes/_base.py",
>> line 394, in _plot_args
>> seg = func(x[:, j % ncx], y[:, j % ncy], kw, kwargs)
>> File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/axes/_base.py",
>> line 301, in _makeline
>> seg = mlines.Line2D(x, y, **kw)
>> File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/lines.py",
>> line 396, in __init__
>> self.set_linestyle(linestyle)
>> File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/lines.py",
>> line 1115, in set_linestyle
>> self._us_dashOffset, self._us_dashSeq, self._linewidth)
>> File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/lines.py",
>> line 69, in _scale_dashes
>> scaled_offset = offset * lw
>> TypeError: can't multiply sequence by non-int of type 'float'
>>
>>
>> 2) the plot copying the cookbook example (http://yt-project.org/doc/coo
>> kbook/simple_plots.html?highlight=profileplot%20standard%20deviation) is
>> giving me 0s and nans instead of the correct values:
>>
>> profiles = []
>> labels = []
>> plot_specs = []
>> linest = ['-','--','-.','-','--']
>> cols = ['red','red','red','green','green']
>> lw = ['2','2','2','2','2']
>>
>> i =0
>> while i < len(loop):
>> ds = yt.load("/mnt/ceph/users/stonnesen/data1/"+loopfile[i]+"/DD"
>> +loop[i]+"/"+loopfile[i]+loop[i])
>> disk = ds.disk([0.5,0.5,0.5],[0,0,-1.0],(40,"kpc"),(2,"kpc"))
>>
>> prof = yt.create_profile(disk,'radius',('gas','density'),
>> units={'radius':'kpc'}, extrema={'radius':((0.0,'kpc')
>> ,(40.0,'kpc'))},weight_field='ones')
>>
>> radius = prof.x
>> mean = prof['gas','density']
>> std = prof.standard_deviation['gas','density']
>> plt.semilogy(radius,mean,color=cols[i])#,linewidth=lw[i],
>> linestyle=linest[i])
>> print (mean)
>> print (radius)
>>
>> labels.append("%s" % looptext[i])
>> i = i+1
>>
>> plt.ylim(1e-27,1e-21)
>> plt.xlabel('r (kpc)')
>> plt.ylabel(r'density')
>> plt.legend()
>> plt.savefig('density_profiles_gasmassmatch.png')
>> plt.clf()
>>
>> The mean values are all zero, and the radius values are all nan. The code
>> will finish (unless I use the linewidth command), but of course the plots
>> have nothing on them!!
>>
>> Any ideas for these issues? I would be happy to send my full scripts or
>> output files.
>>
>> Thanks!
>> Stephanie
>>
>> --
>> Dr. Stephanie Tonnesen
>> Associate Research Scientist
>> CCA, Flatiron Institute
>> New York, NY
>>
>> stonnes at gmail.com
>>
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>>
>
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