[yt-users] Radial-averaged Profile error

[Nathan Goldbaum]

On Mon, Dec 14, 2015 at 8:08 PM, Junhwan Choi (최준환) <choi.junhwan at gmail.com>
wrote:

> Hi Nathan,
>
> Now, I change the previous script as follow:
> ======================
> import matplotlib as matplotlib
> matplotlib.use('Agg')
> import yt
> import yt.units as units
> import numpy as np
> import matplotlib.pyplot as plt
>
>
> def _radiuspc(field, data):
>     return data[('radius')].in_units('pc')
> yt.add_field('radiuspc', function=_radiuspc, units="pc")
>
> rmax = 1000
> Nbin = 50
> ds = yt.load("../DD0099/DD0099")
> ds.index
> ad= ds.all_data()
>
> center = ds.find_max("density")[1]
> my_sphere = ds.sphere("center", (rmax, "pc"))
>
> rmin = max([0.1,2.0*ds.index.get_smallest_dx().in_units('pc')])
> profile = yt.Profile1D(my_sphere, 'radiuspc', Nbin, x_min=rmin,
> x_max=rmax, x_log=True, weight_field='cell_volume')
> profile.add_fields(('gas','density'))
>
> plt.plot(np.log10(profile['radiuspc']), np.log10(profile['density']))
> plt.savefig('ProfGasDensity')
> =======================
> It changes BinnedProfile1D to Profile1D.
> And, now I get new error message.
> ……
> Traceback (most recent call last):
>   File "test_prof.py", line 30, in <module>
>     plt.plot(np.log10(profile['radiuspc']), np.log10(profile['density']))
>


Profile1D objects have a somewhat different API compared to the old
BinnedProfile1D objects.

In the line above, you should be doing something like
plt.plot(np.log10(profile.x), np.log10(profile['density']))



>   File "/home/jhchoi/common-anaconda/src/yt/yt/data_objects/profiles.py",
> line 930, in __getitem__
>     raise KeyError(field)
> KeyError: 'radiuspc'


> Do I need set radiuspc in add_fields, too?
> Or, may the different field_type between radiuspc and density cause a
> conflict?
> I tried couple different tests, but I cannot resolve it yet.
>
> Thank you for your help, again.
> Junhwan
>
>
>
>
>
> On Mon, Dec 14, 2015 at 5:08 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
> > Hi Junhwan,
> >
> > Which yt version is this? If it's yt-3 or newer, you should probably be
> > using Profile1D instead of BinnedProfile1D. The latter was deprecated and
> > will be removed in yt 3.3.
> >
> > On Mon, Dec 14, 2015 at 5:00 PM, Junhwan Choi (최준환) <
> choi.junhwan at gmail.com>
> > wrote:
> >>
> >> Dear yt users and developers,
> >>
> >> I get an error while I try to make a  radial-averaged  profile using yt.
> >> In order to compute the profile I wrote the following script:
> >> ===================================
> >> import matplotlib as matplotlib
> >> matplotlib.use('Agg')
> >> import yt
> >> import yt.units as units
> >> import numpy as np
> >> import matplotlib.pyplot as plt
> >>
> >> def _radiuspc(field, data):
> >>     return data[('radius')].in_units('pc')
> >> yt.add_field('radiuspc', function=_radiuspc, units="pc")
> >>
> >> rmax = 1000
> >> Nbin = 50
> >> ds = yt.load("../DD0099/DD0099")
> >> ds.index
> >> ad= ds.all_data()
> >>
> >> center = ds.find_max("density")[1]
> >> my_sphere = ds.sphere("center", (rmax, "pc"))
> >>
> >> rmin = max([0.1,2.0*ds.index.get_smallest_dx().in_units('pc')])
> >> profile = yt.BinnedProfile1D(my_sphere, Nbin, 'radius', rmin,
> >> rmax*units.pc, log_space=True, end_collect=False)
> >> profile.add_fields(('gas','density'), weight='cell_volume')
> >>
> >> plt.plot(na.log10(profile['radius']), na.log10(profile['density']))
> >> plt.savefig('ProfGasDensity')
> >> ===================================
> >>
> >> And, I get an following error to compute the density profile
> >> …….
> >> yt : [INFO     ] 2015-12-14 17:54:21,484 Max Value is 5.46111e-09 at
> >> 0.5093630427891190 0.4991425970893048 0.5065899804849306
> >> Traceback (most recent call last):
> >>   File "test_prof.py", line 26, in <module>
> >>     profile.add_fields(('gas','density'), weight='cell_volume')
> >>   File
> "/home/jhchoi/common-anaconda/src/yt/yt/data_objects/profiles.py",
> >> line 117, in add_fields
> >>     self["%s_std" % field] = np.sqrt(std_data[field])
> >> TypeError: not all arguments converted during string formatting
> >>
> >> Could anyone inform me how to resolve this error?
> >>
> >> Thank you in advance,
> >> Junhwan
> >> _______________________________________________
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> >
> >
> >
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