[yt-users] yt-users Digest, Vol 102, Issue 25

Nathan Goldbaum nathan12343 at gmail.com
Thu Aug 18 12:05:17 PDT 2016 

On Thu, Aug 18, 2016 at 2:03 PM, Sushilkumar <sushil.sush19us at gmail.com>
wrote:

> Dear Nathan:
>
> I am still getting the same error and the changes.
>
> https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc
>

I guess you also need to cast X and Y to ndarray.

>
>
> /state/partition1/anaconda/lib/python2.7/site-packages/numpy/lib/nanfunctions.py:338:
> RuntimeWarning: All-NaN axis encountered
>   warnings.warn("All-NaN axis encountered", RuntimeWarning)
> /state/partition1/anaconda/lib/python2.7/site-packages/numpy/lib/nanfunctions.py:239:
> RuntimeWarning: All-NaN axis encountered
>   warnings.warn("All-NaN axis encountered", RuntimeWarning)
> yt : [WARNING  ] 2016-08-18 13:45:25,092 Plot image for field ('gas',
> 'cutting_plane_velocity_x') is filled with NaNs.
> yt : [WARNING  ] 2016-08-18 13:45:25,092 Switching to linear colorbar
> scaling.
> Traceback (most recent call last):
>   File "yt_frb_streamplot.py", line 66, in <module>
>     plt.streamplot(X, Y, np.array(U), np.array(V), density=2,color='blue')
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.py",
> line 3339, in streamplot
>     zorder=zorder)
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/axes/_axes.py",
> line 4204, in streamplot
>     zorder=zorder)
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/streamplot.py",
> line 74, in streamplot
>     grid = Grid(x, y)
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/streamplot.py",
> line 261, in __init__
>     assert np.allclose(x_row, x)
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/numpy/core/numeric.py",
> line 2372, in allclose
>     res = all(isclose(a, b, rtol=rtol, atol=atol, equal_nan=equal_nan))
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/numpy/core/numeric.py",
> line 2453, in isclose
>     return within_tol(x, y, atol, rtol)
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/numpy/core/numeric.py",
> line 2436, in within_tol
>     result = less_equal(abs(x-y), atol + rtol * abs(y))
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/units/yt_array.py",
> line 732, in __radd__
>     lo = sanitize_units_add(self, left_object, "addition")
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/units/yt_array.py",
> line 134, in sanitize_units_add
>     raise YTUnitOperationError(op_string, inp.units, dimensionless)
> yt.utilities.exceptions.YTUnitOperationError: The addition operator for
> YTArrays with units (km) and (1) is not well defined.
>
>
>
>
>
> On Thu, Aug 18, 2016 at 1:11 PM, <yt-users-request at lists.spacepope.org>
> wrote:
>
>> Send yt-users mailing list submissions to
>>         yt-users at lists.spacepope.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>>         http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> or, via email, send a message with subject or body 'help' to
>>         yt-users-request at lists.spacepope.org
>>
>> You can reach the person managing the list at
>>         yt-users-owner at lists.spacepope.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of yt-users digest..."
>>
>>
>> Today's Topics:
>>
>>    1. Streamplot error (Sushilkumar)
>>    2. Re: Streamplot error (Nathan Goldbaum)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 18 Aug 2016 13:03:05 -0500
>> From: Sushilkumar <sushil.sush19us at gmail.com>
>> To: Discussion of the yt analysis package
>>         <yt-users at lists.spacepope.org>
>> Subject: [yt-users] Streamplot error
>> Message-ID:
>>         <CAKARaKVO083ut=_zq1rWgbbuJu5qX0GG=2WORSuX99a5FxzY+Q at mail.gm
>> ail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Dear yt:
>>
>> I am getting the error as below while plotting streamplots. Could you let
>> me know what is causing this problem? drive link to my code
>> (yt_frb_streamplot.py) is also below.
>>
>> https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc
>>
>> Traceback (most recent call last):
>>   File "yt_frb_streamplot.py", line 67, in <module>
>>     plt.streamplot(X, Y, U, V, density=2,color='blue') # Here density
>> adjusts the density of streamlines
>>   File
>> "/state/partition1/anaconda/lib/python2.7/site-packages/matp
>> lotlib/pyplot.py",
>> line 3339, in streamplot
>>     zorder=zorder)
>>   File
>> "/state/partition1/anaconda/lib/python2.7/site-packages/matp
>> lotlib/axes/_axes.py",
>> line 4204, in streamplot
>>     zorder=zorder)
>>   File
>> "/state/partition1/anaconda/lib/python2.7/site-packages/matp
>> lotlib/streamplot.py",
>> line 74, in streamplot
>>     grid = Grid(x, y)
>>   File
>> "/state/partition1/anaconda/lib/python2.7/site-packages/matp
>> lotlib/streamplot.py",
>> line 261, in __init__
>>     assert np.allclose(x_row, x)
>>   File
>> "/state/partition1/anaconda/lib/python2.7/site-packages/nump
>> y/core/numeric.py",
>> line 2372, in allclose
>>     res = all(isclose(a, b, rtol=rtol, atol=atol, equal_nan=equal_nan))
>>   File
>> "/state/partition1/anaconda/lib/python2.7/site-packages/nump
>> y/core/numeric.py",
>> line 2453, in isclose
>>     return within_tol(x, y, atol, rtol)
>>   File
>> "/state/partition1/anaconda/lib/python2.7/site-packages/nump
>> y/core/numeric.py",
>> line 2436, in within_tol
>>     result = less_equal(abs(x-y), atol + rtol * abs(y))
>>   File
>> "/state/partition1/anaconda/lib/python2.7/site-packages/yt/u
>> nits/yt_array.py",
>> line 732, in __radd__
>>     lo = sanitize_units_add(self, left_object, "addition")
>>   File
>> "/state/partition1/anaconda/lib/python2.7/site-packages/yt/u
>> nits/yt_array.py",
>> line 134, in sanitize_units_add
>>     raise YTUnitOperationError(op_string, inp.units, dimensionless)
>> yt.utilities.exceptions.YTUnitOperationError: The addition operator for
>> YTArrays with units (km) and (1) is not well defined.
>>
>>
>>
>>
>>
>>
>> On Tue, Aug 16, 2016 at 1:00 PM, <yt-users-request at lists.spacepope.org>
>> wrote:
>>
>> > Send yt-users mailing list submissions to
>> >         yt-users at lists.spacepope.org
>> >
>> > To subscribe or unsubscribe via the World Wide Web, visit
>> >         http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> > or, via email, send a message with subject or body 'help' to
>> >         yt-users-request at lists.spacepope.org
>> >
>> > You can reach the person managing the list at
>> >         yt-users-owner at lists.spacepope.org
>> >
>> > When replying, please edit your Subject line so it is more specific
>> > than "Re: Contents of yt-users digest..."
>> >
>> >
>> > Today's Topics:
>> >
>> >    1. Re: conda install (John Regan)
>> >
>> >
>> > ----------------------------------------------------------------------
>> >
>> > Message: 1
>> > Date: Tue, 16 Aug 2016 15:34:48 +0100
>> > From: John Regan <johnanthonyregan at gmail.com>
>> > To: Discussion of the yt analysis package
>> >         <yt-users at lists.spacepope.org>
>> > Subject: Re: [yt-users] conda install
>> > Message-ID:
>> >         <CABzd+TFisnpj44UZ3NUQ4HnEHNAuS_iQR+LzM2YRU_a9DntX=Q at mail.g
>> mail.
>> > com>
>> > Content-Type: text/plain; charset="utf-8"
>> >
>> > perfect - thanks Nathan!
>> >
>> > On Mon, Aug 15, 2016 at 5:20 PM, Nathan Goldbaum <nathan12343 at gmail.com
>> >
>> > wrote:
>> >
>> > >
>> > >
>> > > On Mon, Aug 15, 2016 at 11:18 AM, John Regan <
>> johnanthonyregan at gmail.com
>> > >
>> > > wrote:
>> > >
>> > >> Hi All,
>> > >>
>> > >> Quick question on the conda install system.
>> > >>
>> > >> I'm sure this is very easy but when I update the source folder e.g.
>> > >> ~/ytfork/yt/analysis_modules/.....
>> > >> how do I then get that reflected in the yt-conda installation e.g. in
>> > >> ~/ytfork/doc/yt-conda/lib/.../analysis_modules?
>> > >>
>> > >> I could copy the "source" files directly into the "lib" directory but
>> > I'm
>> > >> guessing there is a better way?
>> > >>
>> > >
>> > > $ conda uninstall yt
>> > > $ pip uninstall yt
>> > > $ cd ~/ytfork/
>> > > $ python setup.py develop
>> > >
>> > > And now ~/ytfork/ will be the "active" installation.
>> > >
>> > >
>> > >>
>> > >>
>> > >> John
>> > >>
>> > >>
>> > >>
>> > >>
>> > >> _______________________________________________
>> > >> yt-users mailing list
>> > >> yt-users at lists.spacepope.org
>> > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> > >>
>> > >>
>> > >
>> > > _______________________________________________
>> > > yt-users mailing list
>> > > yt-users at lists.spacepope.org
>> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> > >
>> > >
>> > -------------- next part --------------
>> > An HTML attachment was scrubbed...
>> > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.
>> > org/attachments/20160816/30447b70/attachment.html>
>> >
>> > ------------------------------
>> >
>> > Subject: Digest Footer
>> >
>> > _______________________________________________
>> > yt-users mailing list
>> > yt-users at lists.spacepope.org
>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >
>> >
>> > ------------------------------
>> >
>> > End of yt-users Digest, Vol 102, Issue 22
>> > *****************************************
>> >
>>
>>
>>
>> --
>> *SK2*
>>
>> *"**Claiming that something can move faster than light is a good
>> conversation-stopper in physics. People edge away from you in cocktail
>> parties; friends never return phone calls. You just don?t mess with Albert
>> Einstein.**"*
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org
>> /attachments/20160818/bcca2029/attachment-0001.htm>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 18 Aug 2016 13:10:08 -0500
>> From: Nathan Goldbaum <nathan12343 at gmail.com>
>> To: Discussion of the yt analysis package
>>         <yt-users at lists.spacepope.org>
>> Subject: Re: [yt-users] Streamplot error
>> Message-ID:
>>         <CAJXewOmv8aTEMK_Ww0_g6d1AOVfoo4O0fBoqtwsmJudwcSu4pw at mail.gm
>> ail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> In your script, where you have:
>>
>> plt.streamplot(X, Y, U, V, density=2,color='blue')
>>
>> replace that with:
>>
>> plt.streamplot(X, Y, np.array(U), np.array(V), density=2,color='blue')
>>
>> U and V have units attached, but streamplot doesn't know about yt's unit
>> system, so you need to make sure they're plain old ndarrays (with no
>> units)
>> before passing them to matplotlib.
>>
>> On Thu, Aug 18, 2016 at 1:03 PM, Sushilkumar <sushil.sush19us at gmail.com>
>> wrote:
>>
>> > Dear yt:
>> >
>> > I am getting the error as below while plotting streamplots. Could you
>> let
>> > me know what is causing this problem? drive link to my code
>> > (yt_frb_streamplot.py) is also below.
>> >
>> > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc
>> >
>> > Traceback (most recent call last):
>> >   File "yt_frb_streamplot.py", line 67, in <module>
>> >     plt.streamplot(X, Y, U, V, density=2,color='blue') # Here density
>> > adjusts the density of streamlines
>> >   File "/state/partition1/anaconda/lib/python2.7/site-packages/matp
>> lotlib/pyplot.py",
>> > line 3339, in streamplot
>> >     zorder=zorder)
>> >   File "/state/partition1/anaconda/lib/python2.7/site-packages/matp
>> lotlib/axes/_axes.py",
>> > line 4204, in streamplot
>> >     zorder=zorder)
>> >   File "/state/partition1/anaconda/lib/python2.7/site-packages/matp
>> lotlib/streamplot.py",
>> > line 74, in streamplot
>> >     grid = Grid(x, y)
>> >   File "/state/partition1/anaconda/lib/python2.7/site-packages/matp
>> lotlib/streamplot.py",
>> > line 261, in __init__
>> >     assert np.allclose(x_row, x)
>> >   File "/state/partition1/anaconda/lib/python2.7/site-packages/nump
>> y/core/numeric.py",
>> > line 2372, in allclose
>> >     res = all(isclose(a, b, rtol=rtol, atol=atol, equal_nan=equal_nan))
>> >   File "/state/partition1/anaconda/lib/python2.7/site-packages/nump
>> y/core/numeric.py",
>> > line 2453, in isclose
>> >     return within_tol(x, y, atol, rtol)
>> >   File "/state/partition1/anaconda/lib/python2.7/site-packages/nump
>> y/core/numeric.py",
>> > line 2436, in within_tol
>> >     result = less_equal(abs(x-y), atol + rtol * abs(y))
>> >   File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/u
>> nits/yt_array.py",
>> > line 732, in __radd__
>> >     lo = sanitize_units_add(self, left_object, "addition")
>> >   File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/u
>> nits/yt_array.py",
>> > line 134, in sanitize_units_add
>> >     raise YTUnitOperationError(op_string, inp.units, dimensionless)
>> > yt.utilities.exceptions.YTUnitOperationError: The addition operator for
>> > YTArrays with units (km) and (1) is not well defined.
>> >
>> >
>> >
>> >
>> >
>> >
>> > On Tue, Aug 16, 2016 at 1:00 PM, <yt-users-request at lists.spacepope.org>
>> > wrote:
>> >
>> >> Send yt-users mailing list submissions to
>> >>         yt-users at lists.spacepope.org
>> >>
>> >> To subscribe or unsubscribe via the World Wide Web, visit
>> >>         http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >> or, via email, send a message with subject or body 'help' to
>> >>         yt-users-request at lists.spacepope.org
>> >>
>> >> You can reach the person managing the list at
>> >>         yt-users-owner at lists.spacepope.org
>> >>
>> >> When replying, please edit your Subject line so it is more specific
>> >> than "Re: Contents of yt-users digest..."
>> >>
>> >>
>> >> Today's Topics:
>> >>
>> >>    1. Re: conda install (John Regan)
>> >>
>> >>
>> >> ----------------------------------------------------------------------
>> >>
>> >> Message: 1
>> >> Date: Tue, 16 Aug 2016 15:34:48 +0100
>> >> From: John Regan <johnanthonyregan at gmail.com>
>> >> To: Discussion of the yt analysis package
>> >>         <yt-users at lists.spacepope.org>
>> >> Subject: Re: [yt-users] conda install
>> >> Message-ID:
>> >>         <CABzd+TFisnpj44UZ3NUQ4HnEHNAuS_iQR+LzM2YRU_a9DntX=Q at mail.
>> >> gmail.com>
>> >> Content-Type: text/plain; charset="utf-8"
>> >>
>> >> perfect - thanks Nathan!
>> >>
>> >> On Mon, Aug 15, 2016 at 5:20 PM, Nathan Goldbaum <
>> nathan12343 at gmail.com>
>> >> wrote:
>> >>
>> >> >
>> >> >
>> >> > On Mon, Aug 15, 2016 at 11:18 AM, John Regan <
>> >> johnanthonyregan at gmail.com>
>> >> > wrote:
>> >> >
>> >> >> Hi All,
>> >> >>
>> >> >> Quick question on the conda install system.
>> >> >>
>> >> >> I'm sure this is very easy but when I update the source folder e.g.
>> >> >> ~/ytfork/yt/analysis_modules/.....
>> >> >> how do I then get that reflected in the yt-conda installation e.g.
>> in
>> >> >> ~/ytfork/doc/yt-conda/lib/.../analysis_modules?
>> >> >>
>> >> >> I could copy the "source" files directly into the "lib" directory
>> but
>> >> I'm
>> >> >> guessing there is a better way?
>> >> >>
>> >> >
>> >> > $ conda uninstall yt
>> >> > $ pip uninstall yt
>> >> > $ cd ~/ytfork/
>> >> > $ python setup.py develop
>> >> >
>> >> > And now ~/ytfork/ will be the "active" installation.
>> >> >
>> >> >
>> >> >>
>> >> >>
>> >> >> John
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> _______________________________________________
>> >> >> yt-users mailing list
>> >> >> yt-users at lists.spacepope.org
>> >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >> >>
>> >> >>
>> >> >
>> >> > _______________________________________________
>> >> > yt-users mailing list
>> >> > yt-users at lists.spacepope.org
>> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >> >
>> >> >
>> >> -------------- next part --------------
>> >> An HTML attachment was scrubbed...
>> >> URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org
>> >> /attachments/20160816/30447b70/attachment.html>
>> >>
>> >> ------------------------------
>> >>
>> >> Subject: Digest Footer
>> >>
>> >> _______________________________________________
>> >> yt-users mailing list
>> >> yt-users at lists.spacepope.org
>> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >>
>> >>
>> >> ------------------------------
>> >>
>> >> End of yt-users Digest, Vol 102, Issue 22
>> >> *****************************************
>> >>
>> >
>> >
>> >
>> > --
>> > *SK2*
>> >
>> > *"**Claiming that something can move faster than light is a good
>> > conversation-stopper in physics. People edge away from you in cocktail
>> > parties; friends never return phone calls. You just don?t mess with
>> Albert
>> > Einstein.**"*
>> >
>> >
>> > _______________________________________________
>> > yt-users mailing list
>> > yt-users at lists.spacepope.org
>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >
>> >
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org
>> /attachments/20160818/8f733032/attachment.htm>
>>
>> ------------------------------
>>
>> Subject: Digest Footer
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>> ------------------------------
>>
>> End of yt-users Digest, Vol 102, Issue 25
>> *****************************************
>>
>
>
>
> --
> *SK2*
>
> *"**Claiming that something can move faster than light is a good
> conversation-stopper in physics. People edge away from you in cocktail
> parties; friends never return phone calls. You just don’t mess with Albert
> Einstein.**"*
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160818/e3c2c05b/attachment.html>

More information about the yt-users mailing list