Re: [Matplotlib-users] Options for speeding up matplotlib, spectrogram with log scale axis, etc.

2012-10-09 Thread Eric Firing
On 2012/10/09 4:46 PM, Mike Kaufman wrote:
> On 10/9/12 10:03 PM, Jody Klymak wrote:
>> Hi Eric,
>>
>>>The pcolormesh docstring notes that it is
>>> much faster than pcolor; the pcolor docstring probably should refer
>>> people to pcolormesh, since matlab users are likely to go straight to
>>> pcolor without realizing that they should be using pcolormesh.
>>
>> I'd agree with this.  pcolormesh is not even in the "See Also", and there is 
>> no warning about the effciency of pcolor.
>>
>> I'd even go so far as to suggest that pcolor be deprecated so new users are 
>> more likely to find pcolormesh.
>
> While we're on this subject, pcolorfast doesn't have a pyplot function
> and its documentation refers to pcolor rather than itself. Also pcolor
> and pcolormesh ought to See Also this (or is it still experimental?)

pcolorfast is a bit odd in that it uses one of three different 
mechanisms depending on its inputs, and it is not quite as flexible 
about input dimensions as pcolormesh, so the lack of a pyplot function 
for it is deliberate.

Thanks for pointing out the references to pcolor in the docstring--I 
don't know how that has passed apparently unnoticed so long!

Eric

>
> M
>
>
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Re: [Matplotlib-users] Options for speeding up matplotlib, spectrogram with log scale axis, etc.

2012-10-09 Thread Mike Kaufman
On 10/9/12 10:03 PM, Jody Klymak wrote:
> Hi Eric,
>
>>   The pcolormesh docstring notes that it is
>> much faster than pcolor; the pcolor docstring probably should refer
>> people to pcolormesh, since matlab users are likely to go straight to
>> pcolor without realizing that they should be using pcolormesh.
>
> I'd agree with this.  pcolormesh is not even in the "See Also", and there is 
> no warning about the effciency of pcolor.
>
> I'd even go so far as to suggest that pcolor be deprecated so new users are 
> more likely to find pcolormesh.

While we're on this subject, pcolorfast doesn't have a pyplot function 
and its documentation refers to pcolor rather than itself. Also pcolor 
and pcolormesh ought to See Also this (or is it still experimental?)

M


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Re: [Matplotlib-users] Corrupted percent signs in labels

2012-10-09 Thread Benjamin Root
On Tuesday, October 9, 2012, Nikolaus Rath wrote:

> Damon McDougall 
> >
> writes:
> > On Tue, Oct 9, 2012 at 10:56 PM, Damon McDougall
> > >
> wrote:
> >> On Tue, Oct 9, 2012 at 10:32 PM, Nikolaus Rath <
> nikolaus-bth8mxji...@public.gmane.org > wrote:
> >>> Hello,
> >>>
> >>> For some reason, my matplotlib isn't able to print percent signs ('%')
> >>> properly:
> >>>
> >>> [1] inspiron:~/tmp# cat mplbug.py
> >>>
> >>> import matplotlib
> >>> import matplotlib.pyplot as plt
> >>> import numpy as np
> >>>
> >>> print matplotlib.__version__
> >>> plt.plot(np.arange(10), np.arange(10)**2)
> >>> plt.xlabel('Percent [%]')
> >>> plt.savefig('mplbug.pdf')
> >>>
> >>> [0] inspiron:~/tmp# python mplbug.py
> >>> 1.1.1rc2
> >>>
> >>> I have attached the resulting PDF. For some reason, the slash in the
> >>> percent sign becomes a triangle that partially covers the upper left
> >>> circle.
> >>>
> >>> Known bug? Any workarounds that don't require upgrading (I'd like to
> >>> stick with the Debian package)?
> >>
> >> I'm using the AGG backend and saving to a png file without any
> >> problems, but I'm using the current git master branch. I'll try to see
> >> if I can recreate on 1.1.1rc2. Watch this space.
> >
> > No dice. I still can't recreate your problem on OS X 10.7.4 with
> > matplotlib version 1.1.1-rc2.
> >
> > What are your font/tex specifications in the matplotlib.rcParams
> dictionary?
>
> For me the problem occurs with PDF files, not PNG files. Or was that
> just a typo?
>
> Font specifications are all default.
>
> # python -c 'import matplotlib; import pprint;
> # pprint.pprint(matplotlib.rcParams)' | egrep 'tex'
>  'legend.handletextpad': 0.8,
>  'mathtext.bf': 'serif:bold',
>  'mathtext.cal': 'cursive',
>  'mathtext.default': 'it',
>  'mathtext.fallback_to_cm': True,
>  'mathtext.fontset': 'cm',
>  'mathtext.it': 'serif:italic',
>  'mathtext.rm': 'serif',
>  'mathtext.sf': 'sans\\-serif',
>  'mathtext.tt': 'monospace',
>  'text.antialiased': True,
>  'text.color': 'k',
>  'text.dvipnghack': None,
>  'text.hinting': True,
>  'text.latex.preamble': [''],
>  'text.latex.preview': False,
>  'text.latex.unicode': False,
>  'text.usetex': False,
>
> Best,
>
>-Nikolaus
>
>
I think I know why this is happening.  Iirc, we recently took on a patch to
allow string formatting for labels.  For most cases, it shouldn't effect
anybody, but if there is a lonely percent sign, I would imagine it could
cause issues.  As a test, try a double percent sign '%%'.  If that works,
the my theory might be right.

In addition, I think it is only in master, not v1.2.x.

Ben Root
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Re: [Matplotlib-users] Options for speeding up matplotlib, spectrogram with log scale axis, etc.

2012-10-09 Thread Jody Klymak
Hi Eric,

>  The pcolormesh docstring notes that it is 
> much faster than pcolor; the pcolor docstring probably should refer 
> people to pcolormesh, since matlab users are likely to go straight to 
> pcolor without realizing that they should be using pcolormesh.

I'd agree with this.  pcolormesh is not even in the "See Also", and there is no 
warning about the effciency of pcolor. 

I'd even go so far as to suggest that pcolor be deprecated so new users are 
more likely to find pcolormesh.  

Anyway, thanks for the pointer!

Cheers,   Jody

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http://web.uvic.ca/~jklymak/





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[Matplotlib-users] Pylab import error due to dateutil

2012-10-09 Thread Gökhan Sever
Hello,

With a fresh

git clone git://github.com/matplotlib/matplotlib.git
sudo python setupegg.py develop

Starting ipython --pylab I get this error:

.../matplotlib/lib/matplotlib/dates.py in ()
120 import matplotlib.ticker as ticker
121
--> 122 from dateutil.rrule import rrule, MO, TU, WE, TH, FR, SA, SU,
YEARLY, \
123  MONTHLY, WEEKLY, DAILY, HOURLY, MINUTELY, SECONDLY
124 from dateutil.relativedelta import relativedelta

ImportError: No module named dateutil.rrule


Installing dateutil 1.5 fixes this.

mpl install log shows the following:

OPTIONAL DATE/TIMEZONE DEPENDENCIES
  dateutil: matplotlib will provide
  pytz: matplotlib will provide

Will dateutil be shipped with mpl or this line needs to be updated?

Thanks.


-- 
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Re: [Matplotlib-users] Corrupted percent signs in labels

2012-10-09 Thread Nikolaus Rath
Damon McDougall  
writes:
> On Tue, Oct 9, 2012 at 10:56 PM, Damon McDougall
>  wrote:
>> On Tue, Oct 9, 2012 at 10:32 PM, Nikolaus Rath 
>>  wrote:
>>> Hello,
>>>
>>> For some reason, my matplotlib isn't able to print percent signs ('%')
>>> properly:
>>>
>>> [1] inspiron:~/tmp# cat mplbug.py
>>>
>>> import matplotlib
>>> import matplotlib.pyplot as plt
>>> import numpy as np
>>>
>>> print matplotlib.__version__
>>> plt.plot(np.arange(10), np.arange(10)**2)
>>> plt.xlabel('Percent [%]')
>>> plt.savefig('mplbug.pdf')
>>>
>>> [0] inspiron:~/tmp# python mplbug.py
>>> 1.1.1rc2
>>>
>>> I have attached the resulting PDF. For some reason, the slash in the
>>> percent sign becomes a triangle that partially covers the upper left
>>> circle.
>>>
>>> Known bug? Any workarounds that don't require upgrading (I'd like to
>>> stick with the Debian package)?
>>
>> I'm using the AGG backend and saving to a png file without any
>> problems, but I'm using the current git master branch. I'll try to see
>> if I can recreate on 1.1.1rc2. Watch this space.
>
> No dice. I still can't recreate your problem on OS X 10.7.4 with
> matplotlib version 1.1.1-rc2.
>
> What are your font/tex specifications in the matplotlib.rcParams dictionary?

For me the problem occurs with PDF files, not PNG files. Or was that
just a typo?

Font specifications are all default. 

# python -c 'import matplotlib; import pprint;
# pprint.pprint(matplotlib.rcParams)' | egrep 'tex'
 'legend.handletextpad': 0.8,
 'mathtext.bf': 'serif:bold',
 'mathtext.cal': 'cursive',
 'mathtext.default': 'it',
 'mathtext.fallback_to_cm': True,
 'mathtext.fontset': 'cm',
 'mathtext.it': 'serif:italic',
 'mathtext.rm': 'serif',
 'mathtext.sf': 'sans\\-serif',
 'mathtext.tt': 'monospace',
 'text.antialiased': True,
 'text.color': 'k',
 'text.dvipnghack': None,
 'text.hinting': True,
 'text.latex.preamble': [''],
 'text.latex.preview': False,
 'text.latex.unicode': False,
 'text.usetex': False,

Best,

   -Nikolaus

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Re: [Matplotlib-users] Corrupted percent signs in labels

2012-10-09 Thread Damon McDougall
On Tue, Oct 9, 2012 at 10:56 PM, Damon McDougall
 wrote:
> On Tue, Oct 9, 2012 at 10:32 PM, Nikolaus Rath  wrote:
>> Hello,
>>
>> For some reason, my matplotlib isn't able to print percent signs ('%')
>> properly:
>>
>> [1] inspiron:~/tmp# cat mplbug.py
>>
>> import matplotlib
>> import matplotlib.pyplot as plt
>> import numpy as np
>>
>> print matplotlib.__version__
>> plt.plot(np.arange(10), np.arange(10)**2)
>> plt.xlabel('Percent [%]')
>> plt.savefig('mplbug.pdf')
>>
>> [0] inspiron:~/tmp# python mplbug.py
>> 1.1.1rc2
>>
>> I have attached the resulting PDF. For some reason, the slash in the
>> percent sign becomes a triangle that partially covers the upper left
>> circle.
>>
>> Known bug? Any workarounds that don't require upgrading (I'd like to
>> stick with the Debian package)?
>>
>>
>> Thanks,
>>
>>-Nikolaus
>>
>> --
>>  »Time flies like an arrow, fruit flies like a Banana.«
>>
>>   PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6  02CF A9AD B7F8 AE4E 425C
>
> I'm using the AGG backend and saving to a png file without any
> problems, but I'm using the current git master branch. I'll try to see
> if I can recreate on 1.1.1rc2. Watch this space.

No dice. I still can't recreate your problem on OS X 10.7.4 with
matplotlib version 1.1.1-rc2.

What are your font/tex specifications in the matplotlib.rcParams dictionary?

-- 
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http://www.damon-is-a-geek.com
B2.39
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University of Warwick
Coventry
West Midlands
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United Kingdom

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Re: [Matplotlib-users] Corrupted percent signs in labels

2012-10-09 Thread Damon McDougall
On Tue, Oct 9, 2012 at 10:32 PM, Nikolaus Rath  wrote:
> Hello,
>
> For some reason, my matplotlib isn't able to print percent signs ('%')
> properly:
>
> [1] inspiron:~/tmp# cat mplbug.py
>
> import matplotlib
> import matplotlib.pyplot as plt
> import numpy as np
>
> print matplotlib.__version__
> plt.plot(np.arange(10), np.arange(10)**2)
> plt.xlabel('Percent [%]')
> plt.savefig('mplbug.pdf')
>
> [0] inspiron:~/tmp# python mplbug.py
> 1.1.1rc2
>
> I have attached the resulting PDF. For some reason, the slash in the
> percent sign becomes a triangle that partially covers the upper left
> circle.
>
> Known bug? Any workarounds that don't require upgrading (I'd like to
> stick with the Debian package)?
>
>
> Thanks,
>
>-Nikolaus
>
> --
>  »Time flies like an arrow, fruit flies like a Banana.«
>
>   PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6  02CF A9AD B7F8 AE4E 425C

I'm using the AGG backend and saving to a png file without any
problems, but I'm using the current git master branch. I'll try to see
if I can recreate on 1.1.1rc2. Watch this space.

-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

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Re: [Matplotlib-users] Corrupted percent signs in labels

2012-10-09 Thread Daπid
On Windows it works just fine. Just a wild guess, can you try to make
it a raw string?

plt.xlabel(r'Percent [%]')

On Tue, Oct 9, 2012 at 10:45 PM, Francesco Montesano
 wrote:
> Hi
>
> 2012/10/9 Nikolaus Rath 
>>
>> Hello,
>>
>> For some reason, my matplotlib isn't able to print percent signs ('%')
>> properly:
>>
>> [1] inspiron:~/tmp# cat mplbug.py
>>
>> import matplotlib
>> import matplotlib.pyplot as plt
>> import numpy as np
>>
>> print matplotlib.__version__
>> plt.plot(np.arange(10), np.arange(10)**2)
>> plt.xlabel('Percent [%]')
>> plt.savefig('mplbug.pdf')
>>
>> [0] inspiron:~/tmp# python mplbug.py
>> 1.1.1rc2
>>
>> I have attached the resulting PDF. For some reason, the slash in the
>> percent sign becomes a triangle that partially covers the upper left
>> circle.
>>
>> Known bug? Any workarounds that don't require upgrading (I'd like to
>> stick with the Debian package)?
>
>
> confirmed for pdf and eps figures. For jpg and png, as well as the
> matplotlib window with TkAgg the percentage looks fine.
> matplotlib version: 1.1.1 shipped with kubuntu 12.10
>
> Francesco
>
>>
>>
>>
>> Thanks,
>>
>>-Nikolaus
>>
>> --
>>  »Time flies like an arrow, fruit flies like a Banana.«
>>
>>   PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6  02CF A9AD B7F8 AE4E 425C
>>
>>
>> --
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>
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Re: [Matplotlib-users] Corrupted percent signs in labels

2012-10-09 Thread Francesco Montesano
Hi

2012/10/9 Nikolaus Rath 

> Hello,
>
> For some reason, my matplotlib isn't able to print percent signs ('%')
> properly:
>
> [1] inspiron:~/tmp# cat mplbug.py
>
> import matplotlib
> import matplotlib.pyplot as plt
> import numpy as np
>
> print matplotlib.__version__
> plt.plot(np.arange(10), np.arange(10)**2)
> plt.xlabel('Percent [%]')
> plt.savefig('mplbug.pdf')
>
> [0] inspiron:~/tmp# python mplbug.py
> 1.1.1rc2
>
> I have attached the resulting PDF. For some reason, the slash in the
> percent sign becomes a triangle that partially covers the upper left
> circle.
>
> Known bug? Any workarounds that don't require upgrading (I'd like to
> stick with the Debian package)?
>

confirmed for pdf and eps figures. For jpg and png, as well as the
matplotlib window with TkAgg the percentage looks fine.
matplotlib version: 1.1.1 shipped with kubuntu 12.10

Francesco


>
>
> Thanks,
>
>-Nikolaus
>
> --
>  »Time flies like an arrow, fruit flies like a Banana.«
>
>   PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6  02CF A9AD B7F8 AE4E 425C
>
>
> --
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[Matplotlib-users] Accessing WMS and ESRI REST services in Matplotlib

2012-10-09 Thread Rich Signell
Matplotlib folks,

Probably the two most common web map services are the OGC-standard WMS
service and ESRI's non-standard custom REST service.

I was looking for how to do WMS request in basemap and found
"testarcgisimage.py" which uses the "arcgisimage" method.

 It look like there was a "wmsimage" method in Basemap that was folded
into a "arcgisimage" method?

I think users might find that confusing (at least I did).  Should
these methods be different?

Also for the WMS request, we want to make sure that it's possible to
specify ELEVATION and TIME as parameters, since these are necessary to
require WMS from > 2D datasets (e.g. time series of remote sensing
data, 4D atmospheric and oceanic models, etc).

1. Example of  ArcGIS REST request:

http://server.arcgisonline.com/ArcGIS/rest/services/NatGeo_World_Map/MapServer/export?bbox=-1,0,-1,0&bboxSR=4326&imageSR=4326&size=600,800&dpi=96&format=png32&f=image

2. Example of OGC-compliant WMS request, here requesting from
temperature data from NAM at 2 m above ground (ELEVATION=2) and for a
specified time (TIME=2012-10-09T00%3A00%3A00.000Z).  Motherlode only
keeps data around for a week or so, so if the URL below stops working,
try a date that is more current.

http://motherlode.ucar.edu:8080/thredds/wms/fmrc/NCEP/NAM/CONUS_12km/NCEP-NAM-CONUS_12km-noaaport_best.ncd?LAYERS=Temperature_height_above_ground&ELEVATION=2&TIME=2012-10-09T00%3A00%3A00.000Z&TRANSPARENT=true&STYLES=boxfill%2Frainbow&CRS=EPSG%3A4326&COLORSCALERANGE=271.2%2C308&NUMCOLORBANDS=20&LOGSCALE=false&SERVICE=WMS&VERSION=1.3.0&REQUEST=GetMap&EXCEPTIONS=XML&FORMAT=image%2Fpng&BBOX=-118.82657218194,22.15128433311,-108.63100087893,32.34685563612&WIDTH=256&HEIGHT=256

Thanks,
Rich
-- 
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USGS, 384 Woods Hole Rd.
Woods Hole, MA 02543-1598

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[Matplotlib-users] Corrupted percent signs in labels

2012-10-09 Thread Nikolaus Rath
Hello,

For some reason, my matplotlib isn't able to print percent signs ('%')
properly:

[1] inspiron:~/tmp# cat mplbug.py 

import matplotlib
import matplotlib.pyplot as plt
import numpy as np

print matplotlib.__version__
plt.plot(np.arange(10), np.arange(10)**2)
plt.xlabel('Percent [%]')
plt.savefig('mplbug.pdf')

[0] inspiron:~/tmp# python mplbug.py 
1.1.1rc2

I have attached the resulting PDF. For some reason, the slash in the
percent sign becomes a triangle that partially covers the upper left
circle.

Known bug? Any workarounds that don't require upgrading (I'd like to
stick with the Debian package)?


Thanks,

   -Nikolaus

-- 
 »Time flies like an arrow, fruit flies like a Banana.«

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mplbug.pdf
Description: Adobe PDF document
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Re: [Matplotlib-users] trouble switching off smoothing in imshow()

2012-10-09 Thread Pierre Haessig
Hi,
Le 09/10/2012 16:37, Warren Weckesser a écrit :
>
> That's strange.  `imshow(img, interpolation='nearest')` works for me.
>

I'm not sure I understand well the subtle difference between 'nearest'
and 'none' interpolations, but I found in this commit
https://github.com/jkseppan/matplotlib/commit/6923c7f04fbafa23766250d710cc6b37373c816f
a PDF file (interp_nearest_vs_none.pdf) which compares the output of
imshow with these two different settings. It seems there is a difference
in where the boundaries of pixels are...

Maybe somebody familiar with this 'nearest' and 'none' topic could edit
the interpolation example ?
(http://matplotlib.org/examples/pylab_examples/image_interp.html)

Best,
Pierre



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Re: [Matplotlib-users] trouble switching off smoothing in imshow()

2012-10-09 Thread Warren Weckesser
On Tue, Oct 9, 2012 at 10:11 AM, Anand Sivaramakrishnan wrote:

>  I ask having trouble getting imshow to plot e.g. a detector image
> showing pixels as little rectangular or square uniform color blocks -
> imshow seems to want to interpolate or smooth the image.
> Using imshow("nearest") still produces a 'soft' image.
>


That's strange.  `imshow(img, interpolation='nearest')` works for me.

Warren



>
>  I have solved this problem earlier using figimage(), but that was a lot
> of work (I had to create a pixel-by-pixel array with all greyscale values
> set myself, and then I was working in pixel coordinates rather than my data
> coordinates).  Has anyone figured out how to get imshow to stop smoothing
> the image?  Using imshow(… interpolation='none'…) or imshow(…
> interpolation=None…) raise exceptions.
>
>  I found NonUniformImage too hard to figure out from the documentation.
>
>
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Re: [Matplotlib-users] trouble switching off smoothing in imshow()

2012-10-09 Thread Benjamin Root
On Tue, Oct 9, 2012 at 10:11 AM, Anand Sivaramakrishnan wrote:

>  I ask having trouble getting imshow to plot e.g. a detector image
> showing pixels as little rectangular or square uniform color blocks -
> imshow seems to want to interpolate or smooth the image.
> Using imshow("nearest") still produces a 'soft' image.
>
>  I have solved this problem earlier using figimage(), but that was a lot
> of work (I had to create a pixel-by-pixel array with all greyscale values
> set myself, and then I was working in pixel coordinates rather than my data
> coordinates).  Has anyone figured out how to get imshow to stop smoothing
> the image?  Using imshow(… interpolation='none'…) or imshow(…
> interpolation=None…) raise exceptions.
>
>  I found NonUniformImage too hard to figure out from the documentation.
>
>
If you are using mpl v1.1.x or greater, try interpolation='none'.  Note,
that is the string 'none', not the python None.

Ben Root
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[Matplotlib-users] trouble switching off smoothing in imshow()

2012-10-09 Thread Anand Sivaramakrishnan
I ask having trouble getting imshow to plot e.g. a detector image showing 
pixels as little rectangular or square uniform color blocks - imshow seems to 
want to interpolate or smooth the image.
Using imshow("nearest") still produces a 'soft' image.

I have solved this problem earlier using figimage(), but that was a lot of work 
(I had to create a pixel-by-pixel array with all greyscale values set myself, 
and then I was working in pixel coordinates rather than my data coordinates).  
Has anyone figured out how to get imshow to stop smoothing the image?  Using 
imshow(… interpolation='none'…) or imshow(… interpolation=None…) raise 
exceptions.

I found NonUniformImage too hard to figure out from the documentation.
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