Re: [Matplotlib-users] segfault on OSX

2011-05-07 Thread Ondrej Certik
On Sat, May 7, 2011 at 3:34 PM, Ondrej Certik  wrote:
> Hi,
>
> I am using Matplotlib 1.0 precisely from this branch:
>
> https://github.com/matplotlib/matplotlib/tree/v1.0.x
>
> everything works on Linux, and on Mac, I am getting a segfault when I
> do "import pylab". Stacktrace is here:
>
> https://gist.github.com/960896
>
> I produced it by:
>
> gdb python
> (gdb) run
>>>> import pylab
>
> So it looks like TTF related. Here are some relevant links:
>
> https://github.com/qsnake/qsnake/issues/9
> http://trac.sagemath.org/sage_trac/ticket/7022
>
> I have tried to copy ontList.cache (from the Sage ticket 7022) in to
> ~/.qsnake/matplotlib/, but it still segfaults.
>
> Would anyone know what exactly the problem is, and how to fix it? I
> have numpy 1.6.0. Let me know which other debugging information is
> needed.

Min has solved it --- the problem was in using incorrect options to
build the package. Now we use the make.osx to set the environment
flags correctly and everything works now.

I have no idea what the problem was, but it's gone.

Ondrej

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[Matplotlib-users] segfault on OSX

2011-05-07 Thread Ondrej Certik
Hi,

I am using Matplotlib 1.0 precisely from this branch:

https://github.com/matplotlib/matplotlib/tree/v1.0.x

everything works on Linux, and on Mac, I am getting a segfault when I
do "import pylab". Stacktrace is here:

https://gist.github.com/960896

I produced it by:

gdb python
(gdb) run
>>> import pylab

So it looks like TTF related. Here are some relevant links:

https://github.com/qsnake/qsnake/issues/9
http://trac.sagemath.org/sage_trac/ticket/7022

I have tried to copy ontList.cache (from the Sage ticket 7022) in to
~/.qsnake/matplotlib/, but it still segfaults.

Would anyone know what exactly the problem is, and how to fix it? I
have numpy 1.6.0. Let me know which other debugging information is
needed.

Thanks,
Ondrej

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[Matplotlib-users] pcolor() to VTK

2009-07-08 Thread Ondrej Certik
Hi,

I just wanted to share a simple code that I wrote:

http://certik.github.com/visit_writer/

which uses Visit's VTK writer (written in C, wrapped in Python). I
wrote a pcolor() function, that works just like the one in matplotlib,
only it produces a vtk file (resp. data that you then pass to the vtk
writer). See the pictures and demos on the webpage above.

With this, it's very easy to write VTK files, no need to fiddle with
the ASCII format --- btw, the module can produces a binary VTK file
too, so it really saved me lots of troubles.

Ondrej

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Re: [Matplotlib-users] calling show() twice in a row

2009-07-07 Thread Ondrej Certik
Hi Matthias!

many thanks for the help, that was it. I will now remember to use
show() only once and use other techniques to create something like
show(), but that can be called multiple times.

Thanks,
Ondrej

On Tue, Jul 7, 2009 at 5:35 AM, Matthias Michler wrote:
> Hi Ondrej,
>
> I'm not sure where to find a good explanation of that, but let me give you
> some hints. It is intended to use show only once per program. Namely 'show'
> should be the last line in your script. If you want interactive plotting you
> may consider interactive mode (pyplot.ion-ioff) like in the example below.
>
> Furthermore for dynamic plotting all animation demos might be useful.
>
> Maybe you want to have also a look at
> http://matplotlib.sourceforge.net/users/shell.html .
>
> best regards Matthias
>
> 
> from pylab import *
>
> t = linspace(0.0, pi, 100)
> x = cos(t)
> y = sin(t)
>
> ion()  # turn on interactive mode
> figure(0)
> subplot(111, autoscale_on=False, xlim=(-1.2, 1.2), ylim=(-.2, 1.2))
>
> point = plot([x[0]], [y[0]], marker='o', mfc='r', ms=3)
>
> for j in arange(len(t)):
>    # reset x/y-data of point
>    setp(point[0], data=(x[j], y[j]))
>    draw() # redraw current figure
>
> ioff() # turn off interactive mode
> show()
> 
>
> On Monday 06 July 2009 08:13:37 Ondrej Certik wrote:
>> On Tue, Jun 30, 2009 at 12:09 PM, Ondrej Certik wrote:
>> > Hi,
>> >
>> > this must have been answered many times already, but I searched the
>> > archives, online docs, but couldn't find anything.
>> >
>> > If I do:
>> >
>> > $ python
>> > Python 2.6.2 (release26-maint, Apr 19 2009, 01:58:18)
>> > [GCC 4.3.3] on linux2
>> > Type "help", "copyright", "credits" or "license" for more information.
>> >
>> >>>> import pylab
>> >>>> pylab.plot([1, 3, 3])
>> >
>> > []
>> >
>> >>>> pylab.show()
>> >>>> pylab.show()
>> >
>> > the first pylab.show() shows the plot and stays hanging (this is ok)
>> > and then if I close it, to get back to the shell, the second call to
>> > show() does nothing.
>> >
>> > One fix is to use:
>> >
>> > ipython --pylab
>> >
>> > but if I just want to call regular python, or from my own script ---
>> > how do I plot for the second time?
>>
>> I still haven't figured out how to fix it, so any feedback would be
>> appreciated.
>>
>> Thanks,
>> Ondrej
>
>
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Re: [Matplotlib-users] calling show() twice in a row

2009-07-05 Thread Ondrej Certik
On Tue, Jun 30, 2009 at 12:09 PM, Ondrej Certik wrote:
> Hi,
>
> this must have been answered many times already, but I searched the
> archives, online docs, but couldn't find anything.
>
> If I do:
>
> $ python
> Python 2.6.2 (release26-maint, Apr 19 2009, 01:58:18)
> [GCC 4.3.3] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import pylab
>>>> pylab.plot([1, 3, 3])
> []
>>>> pylab.show()
>>>> pylab.show()
>>>>
>
> the first pylab.show() shows the plot and stays hanging (this is ok)
> and then if I close it, to get back to the shell, the second call to
> show() does nothing.
>
> One fix is to use:
>
> ipython --pylab
>
> but if I just want to call regular python, or from my own script ---
> how do I plot for the second time?

I still haven't figured out how to fix it, so any feedback would be appreciated.

Thanks,
Ondrej

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[Matplotlib-users] calling show() twice in a row

2009-06-30 Thread Ondrej Certik
Hi,

this must have been answered many times already, but I searched the
archives, online docs, but couldn't find anything.

If I do:

$ python
Python 2.6.2 (release26-maint, Apr 19 2009, 01:58:18)
[GCC 4.3.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pylab
>>> pylab.plot([1, 3, 3])
[]
>>> pylab.show()
>>> pylab.show()
>>>

the first pylab.show() shows the plot and stays hanging (this is ok)
and then if I close it, to get back to the shell, the second call to
show() does nothing.

One fix is to use:

ipython --pylab

but if I just want to call regular python, or from my own script ---
how do I plot for the second time?

Ondrej

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Re: [Matplotlib-users] plot a triangular mesh

2009-05-25 Thread Ondrej Certik
On Mon, May 25, 2009 at 1:03 AM, Robert Cimrman  wrote:
> Ondrej Certik wrote:
>>
>> On Fri, May 22, 2009 at 3:37 PM, Ondrej Certik  wrote:
>>>
>>> Thanks a lot John. I tried that and it does what I want. I just need
>>> to convert and probably average my 3 different values at the 3
>>> vertices of the triangle and color the triangle with that color. When
>>> I get it working, I'll send you a picture. :)
>>
>> Ok, I made a progress, it seems it's working. Script and picture
>> attached. You can compare to the mayavi plot above, it's almost
>> identical now. It took my some time playing with different parameters
>> of mpl to get here and I think it looks quite good. Still one can see
>> the artefacts though as John predicted, due to mpl not interpolating
>> the triangles.
>
> Nice!
>
> Just to prod you a bit: If you want to get rid of the hard mayavi dependence
> of femhub for 3D plots too, you could hack a (perspective/whatever)
> projection of 3D surface to 2D, remove invisible faces (normal points
> backwards) and plot the rest by the painter's algorithm (far faces first).

Well, I spent one afternoon playing with cairo, trying to implement
the triangle interpolation and the result was slower than matplotlib.
So gave up and I'll just use what can be done with mpl currently.

As to mayavi, I'd rather make it easier to install. The only tough
dependency is VTK, that takes lots of time to build, we already got
rid of all the others, so that's good.

Ondrej

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Re: [Matplotlib-users] plot a triangular mesh

2009-05-22 Thread Ondrej Certik
> Ok, I made a progress, it seems it's working. Script and picture

Forgot to attach the script.

Ondrej
from hermes2d import Mesh, H1Shapeset, PrecalcShapeset, H1Space, \
   WeakForm, Solution, ScalarView, LinSystem, DummySolver, Linearizer
from hermes2d.forms import set_forms
from hermes2d.examples import get_example_mesh
from numpy import array
import pylab
import matplotlib.cm as cm
import matplotlib.collections as collections
import matplotlib.pyplot as P

mesh = Mesh()
mesh.load(get_example_mesh())
mesh.refine_element(0)
shapeset = H1Shapeset()
pss = PrecalcShapeset(shapeset)

# create an H1 space
space = H1Space(mesh, shapeset)
space.set_uniform_order(5)
space.assign_dofs()

# initialize the discrete problem
wf = WeakForm(1)
set_forms(wf)
solver = DummySolver()
sys = LinSystem(wf, solver)
sys.set_spaces(space)
sys.set_pss(pss)

# assemble the stiffness matrix and solve the system
sys.assemble()
A = sys.get_matrix()
b = sys.get_rhs()
from scipy.linalg import cg
x, res = cg(A, b)
sln = Solution()
sln.set_fe_solution(space, pss, x)

l = Linearizer()
l.process_solution(sln)
v = l.get_vertices()
verts = []
vals = []
for t in l.get_triangles():
triangle = tuple([tuple(v[n][:2]) for n in t])
val = sum([v[n][2] for n in t])
vals.append(val/3.)
verts.append(triangle)

#vals = v[:, 2]
vals = array(vals)
print "Things converted to mpl format"

col = collections.PolyCollection(verts, linewidths=0, antialiaseds=0)
col.set_array(vals)
col.set_cmap(cm.jet)
fig = P.figure()
ax = fig.gca()
ax.add_collection(col)
ax.set_xlim(-1, 1)
ax.set_ylim(-1, 1)
ax.set_aspect("equal")
pylab.show()
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Re: [Matplotlib-users] plot a triangular mesh

2009-05-22 Thread Ondrej Certik
On Fri, May 22, 2009 at 7:06 AM, John Hunter  wrote:
> On Thu, May 21, 2009 at 9:31 PM, Ondrej Certik  wrote:
>> Hi,
>>
>> I have a set of vertices in 2D as triples (x, y, val), where the x, y
>> are 2D coordinates and "val" is the scalar value of the finite element
>> solution, here is an example:
>>
>> In [54]: l.get_vertices()
>> Out[54]:
>> array([[  0.e+00,  -1.e+00,  -2.22396971e-17],
>>       [  1.e+00,  -1.e+00,  -1.64798730e-17],
>>       [ -1.e+00,   0.e+00,   8.09899023e-17],
>>       ...,
>>       [  1.48437500e-01,  -1.5625e-02,   1.62359362e-01],
>>       [  1.32812500e-01,   0.e+00,   1.56012622e-01],
>>       [  1.32812500e-01,  -1.5625e-02,   1.50562411e-01]])
>>
>>
>> and I also have a set of triangles that connect those points, here is
>> an example:
>>
>> In [55]: l.get_triangles()
>> Out[55]:
>> array([[   3, 5448,   29],
>>       [  27, 5445,   28],
>>       [  29,   28,   26],
>>       ...,
>>       [5499, 5498, 5479],
>>       [5510, 5493, 5491],
>>       [5513, 5508, 5491]], dtype=int32)
>>
>>
>> The triangles define the 2D domain. What is the best way to get this
>> plotted with mpl? Should I write a loop using the "plot" command, or
>> is there a better alternative? So far, I am using the contour command
>> and I feed it just with the vertices, here is the code:
>
> The best way is to define your triangles as an n length list of
> triangle vertices
>
>  verts = [ ( (x00, y00), (x01, y01),  (x02, y02)),
>                 (x10, y10), (x11, y11),  (x12, y12)),
>                 ...
>    ]
>
> and have an equal length array of intensities for color mapping.
>
>  vals = np.array(N_color_intensities)
>
> Then create a PolyCollection:
>
>  import matplotlib.cm as cm
>  import matplotlib.collections as collections
>  col = collections.PolyCollection(verts)
>  col.set_array(val)
>  col.set_cmap(cm.hot)
>  ax.add_collection(col)
>
> add_collection doesn't get the autoscaling limits, if I recall
> correctly, so you will probably want to do
>
>  ax.set_xlim(xmin, xmax)
>  ax.set_ylim(ymin,. ymax)
>
> See also:
>
>  http://matplotlib.sourceforge.net/api/collections_api.html#matplotlib.collections.PolyCollection
>  http://matplotlib.sourceforge.net/search.html?q=codex+PolyCollection
>
>
> Unfortunately, we do not currently have support for interpolating
> between adjacent polys in a PolyCollection, so the result may not look
> as nice as mayavis.

Thanks a lot John. I tried that and it does what I want. I just need
to convert and probably average my 3 different values at the 3
vertices of the triangle and color the triangle with that color. When
I get it working, I'll send you a picture. :)



On Fri, May 22, 2009 at 7:32 AM, Eric Carlson  wrote:
> Here is an example using matplotlib.delaunay, which automatically
> returns the edges and triangules:

Thanks, that works too -- but it only plots the edges, right? I will
use that to plot the mesh, I need that as well.

For the FE solution, I'll use John's approach.

Ondrej

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Re: [Matplotlib-users] two scales in the same plot

2009-04-29 Thread Ondrej Certik
On Fri, Apr 24, 2009 at 1:10 PM, Sandro Tosi  wrote:
> Hi Ondrej,
> nice to see you here :)

Nice to see you too! :)

>
> On Fri, Apr 24, 2009 at 22:02, Ondrej Certik  wrote:
>> Hi,
>>
>> is there a way to have one plot with two functions, one using some
>> scale, the other one a different scale and show for example one scale
>> on the left, the other scale on the right?
>
> sure, twinx() is what you're looking for; here is a simple example:
>
> import matplotlib.pyplot as plt
> import numpy as np
> x = np.arange(0., np.e, 0.01)
> y1 = np.exp(-x)
> y2 = np.log(x)
> fig = plt.figure()
> ax1 = fig.add_subplot(111)
> ax1.plot(x, y1)
> ax1.set_ylabel('Y values for exp(-x)')
> ax2 = ax1.twinx()
> ax2.plot(x, y2, 'r')
> ax2.set_xlim([0,np.e])
> ax2.set_ylabel('Y values for ln(x)')
> ax2.set_xlabel('Same X for both exp(-x) and ln(x)')
>
> The values on X has to be of the same scale, tough, else the graph
> would look really weird.

Thanks a lot for the code. That worked. I was meeting some deadline,
so I forgot to reply that it worked.

Thanks Ryan and Jouni as well!

Ondrej

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[Matplotlib-users] two scales in the same plot

2009-04-24 Thread Ondrej Certik
Hi,

is there a way to have one plot with two functions, one using some
scale, the other one a different scale and show for example one scale
on the left, the other scale on the right?

I want to plot an atomic potential (one scale) and the corresponding
wave functions (different scale) in the same plot. I tried to look
through all examples and search this list, but didn't find anything.

Thanks a lot,
Ondrej

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Re: [Matplotlib-users] histogram(x, bin): x-axis range should be based on bin.min() and bin.max() when bin is a sequence

2008-12-19 Thread Ondrej Certik
On Fri, Dec 19, 2008 at 6:34 PM, Sandro Tosi  wrote:
> Hello Ondrej,
>
> On Fri, Dec 19, 2008 at 18:18, Ondrej Certik  wrote:
>> we got this Debian bug:
>>
>> http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=503148
> ...
>> I tested that this applies to 0.98.3.  Is this a bug?
>
> This is fixed in the latest release (0.98.4 or in 0.98.5); I'm working
> on uploading it Debian, together with John and Michael (and all dev
> team), to have a feasable release.

Ah, I didn't know you are on the mpl dev team as well. That's great.

Ondrej

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[Matplotlib-users] histogram(x, bin): x-axis range should be based on bin.min() and bin.max() when bin is a sequence

2008-12-19 Thread Ondrej Certik
Hi,

we got this Debian bug:

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=503148

Citing:

"
the following python code creates a histogram with an x-axis range of
0.1 min to 0.3 max (based on the mins and maxes of the x rather than bin).
the bins should be used to size the axis since the user specified that
he wanted to see those specific bins (even though they are empty).  note
that the 'range=' option would be a potential solution, but it is ignored
when bin is a sequence (presumably because the range would be chosen
based on bin's limits, but this isn't so).

  from pylab import *
  x = [0.18,0.22,0.19]
  bin = [0,0.1,0.2,0.3,0.4,0.5]
  hist(x,bin)
  show()

i believe that the x-axis ranges should instead be based on the mins and
maxes of bin when it is a sequence.

please forward this report upstream or let me know if you believe that it
belongs there.

thank you for your consideration
"

I tested that this applies to 0.98.3.  Is this a bug?

Thanks,
Ondrej

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Re: [Matplotlib-users] latest debian package

2008-10-08 Thread Ondrej Certik
On Wed, Oct 8, 2008 at 6:46 PM, Angus McMorland <[EMAIL PROTECTED]> wrote:
> Hi all,
>
> This is just a head's-up for those using debian and who upgrade
> regularly. There's a problem with the latest debian package to hit
> testing: 0.98.1-1, which is currently unusable, throwing up the error:
>
> ImportError: /usr/lib/python2.5/site-packages/matplotlib/nxutils.so:
> undefined symbol: __gxx_personality_v0
>
> It looks like someone has already decided what the appropriate fix is
> (http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=501578&sourceid=mozilla-search).
> Hopefully it'll make it through soon.

You can just install python-matlotlib from unstable, it works fine for me.

Ondrej

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Re: [Matplotlib-users] ./make.py html fails

2008-06-10 Thread Ondrej Certik
On Tue, Jun 10, 2008 at 3:35 AM, Ryan May <[EMAIL PROTECTED]> wrote:
> John Hunter wrote:
>>
>> I posted a snapshot of the docs at:
>>
>>   http://matplotlib.sourceforge.net/doc/html/index.html
>>
>
> WOW.  I love the way sphinx docs look.  But more importantly, great work
> you guys on improving the documentation.  As long as I've been using
> matplotlib (2 1/2 years now), it's been a very powerful and
> full-featured toolkit, but the problem was knowing where to find out how
> to make it do what you want (or more often even knowing that such a
> feature existed).  The examples were (and still are) a good place to
> look, but what you guys have put together here is asthetic and very
> useful, and it puts a nice public face on all the hard work you've done.

Indeed, that's the problem of many python projects (in my case sympy
...) that it's difficult to find out what it can do. But
once we switched to sphinx, I am much more motivated to write more
docs, as it looks good. :)

Ondrej

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Re: [Matplotlib-users] ./make.py html fails

2008-06-09 Thread Ondrej Certik
On Mon, Jun 9, 2008 at 5:41 PM, John Hunter <[EMAIL PROTECTED]> wrote:
> On Mon, Jun 9, 2008 at 10:23 AM, Ondrej Certik <[EMAIL PROTECTED]> wrote:
>
>> In the meantime, I am trying to package numpy 1.1 for Debian, but when
>> I installed it and did "import numpy", I got:
>>
>> ImportError: No module named ma
>
> Make sure you rm -rf the numpy* install dirs.  I think people have
> seen similar problems trying to install over old numpys (ditto for mpl
> 0.98)

The peculiar point is that it seems to work normally, but not when I
create the deb package, so it's probably Debian specific. I'll ask on
the numpy list if I won't figure it out myself.

>
> I posted a snapshot of the docs at:
>
>  http://matplotlib.sourceforge.net/doc/html/index.html

Thanks, looks good. Very nice docs.

Ondrej

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Re: [Matplotlib-users] ./make.py html fails

2008-06-09 Thread Ondrej Certik
On Mon, Jun 9, 2008 at 5:08 PM, John Hunter <[EMAIL PROTECTED]> wrote:
> On Mon, Jun 9, 2008 at 10:00 AM, Ondrej Certik <[EMAIL PROTECTED]> wrote:
>
>> My system wide matplotlib is 0.91.2-2. I tried to install the one from
>> svn, but it requires numpy 1.1, which is not yet in Debian. So if it
>> is not possible to generate the docs without numpy 1.1, I'll wait
>> until it gets into Debian.
>
> Yes, the docs project is specifically for the 0.98 svn trunk, which
> requires numpy 1.1
>
> I can post some build snapshots on the web ocassionally if people are
> interested.

Yes, I am very interested, especially I wanted to see Michael's CSS
styles. If you could post it on the web somewhere, it'd be awesome.

In the meantime, I am trying to package numpy 1.1 for Debian, but when
I installed it and did "import numpy", I got:

ImportError: No module named ma

So now I am going to figure out what's wrong. Anyway, that's why I
prefer proven software in Debian, so that I don't have to fix such
problems to see the docs. :) I need to fix the problem at some point
though anyway, so I'll do it now.

Ondrej

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[Matplotlib-users] ./make.py html fails

2008-06-09 Thread Ondrej Certik
Hi,

I did:


$ svn co 
https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/trunk/matplotlib
$ cd matplotlib/doc
$ ./make.py html
making figs
building pyplot_formatstr.py
building dollar_ticks.py
building pyplot_text.py
building pyplot_two_subplots.py
building fig_x.py
building pyplot_three.py
building fig_axes_customize_simple.py
building fig_axes_labels_simple.py
building pyplot_simple.py
building pyplot_mathtext.py
all figures made
/var/lib/python-support/python2.5/pygments/plugin.py:39: UserWarning:
Module pygments was already imported from
/var/lib/python-support/python2.5/pygments/__init__.py, but
/var/lib/python-support/python2.5 is being added to sys.path
  import pkg_resources
Sphinx v0.3, building html
trying to load pickled env... not found
building [html]: targets for 24 source files that are out of date
updating environment: 24 added, 0 changed, 0 removed
reading... api/artist_api api/index api/pyplot_api reST markup error:
/home/ondra/repos/matplotlib/doc/api/pyplot_api.rst:1100: (SEVERE/4)
Unexpected section title or transition.




My system wide matplotlib is 0.91.2-2. I tried to install the one from
svn, but it requires numpy 1.1, which is not yet in Debian. So if it
is not possible to generate the docs without numpy 1.1, I'll wait
until it gets into Debian.

Thanks,
Ondrej

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