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

18 Aug 2016

      On Thu, Aug 18, 2016 at 2:03 PM, Sushilkumar 
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, 
wrote:
...
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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 
To: Discussion of the yt analysis package

Subject: [yt-users] Streamplot error
Message-ID:

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, 
wrote:
...
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Today's Topics:
1. Re: conda install (John Regan)
----------------------------------------------------------------------
Message: 1
Date: Tue, 16 Aug 2016 15:34:48 +0100
From: John Regan 
To: Discussion of the yt analysis package

Subject: Re: [yt-users] conda install
Message-ID:

Content-Type: text/plain; charset="utf-8"
perfect - thanks Nathan!
On Mon, Aug 15, 2016 at 5:20 PM, Nathan Goldbaum 
wrote:
...
On Mon, Aug 15, 2016 at 11:18 AM, John Regan <
johnanthonyregan@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
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*SK2*
*"**Claiming that something can move faster than light is a good
conversation-stopper in physics. People edge away from you in cocktail
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Message: 2
Date: Thu, 18 Aug 2016 13:10:08 -0500
From: Nathan Goldbaum 
To: Discussion of the yt analysis package

Subject: Re: [yt-users] Streamplot error
Message-ID:

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 
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, 
wrote:
...
Send yt-users mailing list submissions to
        yt-users@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
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You can reach the person managing the list at
        yt-users-owner@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 
To: Discussion of the yt analysis package

Subject: Re: [yt-users] conda install
Message-ID:

Content-Type: text/plain; charset="utf-8"
perfect - thanks Nathan!
On Mon, Aug 15, 2016 at 5:20 PM, Nathan Goldbaum <
nathan12343@gmail.com>
wrote:
...
On Mon, Aug 15, 2016 at 11:18 AM, John Regan <
johnanthonyregan@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@lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________
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*****************************************
--
*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.**"*
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*****************************************
--
*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.**"*
_______________________________________________
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