matplotlib-users Mailing List for matplotlib (Page 7)

On 19/05/2010 20:45, David wrote:
> Werner F. Bruhin<werner.bruhin@...>  writes:
>
>    
>>
>> On 19/05/2010 19:55, David Grudoski wrote:
>>
>>    I'm trying to build an executable using
>> PY2EXE; running Python 2.5.2 and wxPython 2.8.10.1 and MatplotLib 0.99.0
>>    I tried using the setup.py from the
>> PY2EXE.org Matplotlib page and although everything compiles correctly
>> and generates an executable.
>>    When I launch the executable I get the
>> following error:
>>    ================================================
>>    "The application requires a version of
>> wxPython greater than or equal to 2.8, but a matching version was not
>> found."
>>    You currently have these version(s)
>> installed.
>>
>>    ================================================
>>
>>
>>    I can compile an executable with PY2EXE and
>> wxPython that works fine, but apparantly somethins in the setup for
>> matplotlib is causing a problem.
>>
>>    Has anyone else seen this problem or know of
>> a solution?
>>
>> You need to patch matplotlib (backend_wx.py), see the bottom of this
>> page:http://www.py2exe.org/index.cgi/MatPlotLib
>> Werner
>>
>>
>> ------------------------------------------------------------------------------
>>
>>
>>
>> _______________________________________________
>> Matplotlib-users mailing list
>> Matplotlib-users@...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>      
> Thanks for the reply Werner,
> I decided to try and construct the executable from the site using the
> "embedding_in_wx2.py" example. Again making sure the patch was in place on the
> backend_wx.py I again ran the python setup.py py2exe and everything compiled.
> Now when I run the exe it generate the following log file errors:
> Traceback (most recent call last):
>    File "embedding_in_wx2.py", line 21, in<module>
>    File "zipextimporter.pyo", line 82, in load_module
>    File "matplotlib\backends\backend_wxagg.pyo", line 20, in<module>
>    File "zipextimporter.pyo", line 82, in load_module
>    File "matplotlib\figure.pyo", line 19, in<module>
>    File "zipextimporter.pyo", line 82, in load_module
>    File "matplotlib\axes.pyo", line 14, in<module>
>    File "zipextimporter.pyo", line 82, in load_module
>    File "matplotlib\collections.pyo", line 21, in<module>
>    File "zipextimporter.pyo", line 82, in load_module
>    File "matplotlib\backend_bases.pyo", line 32, in<module>
>    File "zipextimporter.pyo", line 82, in load_module
>    File "matplotlib\widgets.pyo", line 12, in<module>
>    File "zipextimporter.pyo", line 82, in load_module
>    File "matplotlib\mlab.pyo", line 376, in<module>
> TypeError: unsupported operand type(s) for %: 'NoneType' and 'dict'
>    
This is due to using "optimize 1 or 2" in py2exe, the work around is to 
fix four lines in mpl.mlab.py as shown on the wiki page mentioned in the 
last thread.

Werner

Yes, it's true that uncommenting path.simplify : False line inside the
matplotlibrc file fixes the artifacts.  However, it also produces HUGE
PDF/EPS file sizes.  Perhaps, it's better to change path.simplify parameter
as needed inside the code via:

import matplotlib.pyplot as plt
plt.rcParams['path.simplify'] = False
# Plotting Code Block goes here
plt.rcdefaults()

Does anyone have another fix for this problem that DOES NOT produce HUGE
PDF/EPS files?


efiring wrote:
> 
> Jouni K. Seppänen wrote:
>> Jordan Dawe <jd...@eo...> writes:
>> 
>>> Contourf plots that I output in vector format files have little
>>> triangular glitches at the contour boundaries if the contoured array
>>> is larger than about 200x200. The same files in png format are
>>> perfect, even at very high dpi values.
>> 
>> The current svn trunk doesn't have the really jarring little triangles
>> (at least in the pdf output), but there are still several very obtuse
>> white triangles between the regions. Rasterization at a high dpi makes
>> the output somewhat better at the cost of larger output files:
>> 
>> c=contourf(X, Y, Z, 10)
>> axis((-3, 3, -3, 3))
>> savefig('unrasterized.pdf')
>> for d in c.collections:
>>     d.set_rasterized(True)
>> savefig('rasterized.pdf',dpi=200)
> 
> 
> At least in the trunk--and maybe in 0.99.0--the problem is caused by 
> path simplification.  In the trunk, for the eps file, it goes away 
> completely if I use a matplotlibrc with
> 
> path.simplify : False
> 
> In the trunk, what seems to be happening is that when a contour boundary 
> is almost straight, but has an inflection point, the curves for the 
> adjacent patch boundaries are simplified slightly differently.  This is 
> not surprising; if nothing else, the path will be traveled in a 
> different direction when it is an outer boundary than when it is an 
> inner boundary (for a set of concentric boundaries).
> 
> Jordan, try using a local matplotlibrc with the above.  Unless you are 
> already customizing via a local matplotlibrc, that line is all you need.
> 
> One reason the trunk behavior differs from 0.99.0 is that contour patch 
> boundaries are now being turned into compound boundaries instead of 
> using a branch cut to connect the outside path to the inside path.  I 
> suspect simplification is causing the artifacts in both cases, though.
> 
> Eric
> 
> 
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Hello, 
I came across  problem of label rotation with autofmt_xdate() in subplothost
too. Is there a new version with the bug fixed or a workaround to doing the
label rotation in subplothost? 
Thanks,
Solomon

Jae-Joon Lee wrote:
> 
> The workarounds suggested in this thread does not work?
> To me, the ordinal thing is not actually a bug,  but you need some
> extra caution to avoid this error happening.
> 
> The issue with the label roration is a different matter though.
> 
> Regards,
> 
> -JJ
> 
> 
> On Wed, Jan 13, 2010 at 8:16 AM, Rodribat <rod...@gm...> wrote:
>>
>>
>> Hi matplotlib users!
>>
>> Did someone solve the problem of use fig.autofmt_xdate() function with
>> SubplotHost object?
>> I googled for it and I found this question only here, without solution.
>> Is
>> there a bug? Anyone knows
>> someway to solve this?
>>
>> Thank you,
>>
>> []'s
>>
>> Rodrigo Batista
>>
>>
>> David GUERINEAU wrote:
>>>
>>> Hi matplotlib_users !
>>>
>>> I'm David from Berlin, and believe I'm experiencing some problem with
>>> the
>>> SubplotHost module:
>>>
>>> I'm generating graphs from hudge databases of cpu and ethernet
>>> statistics,
>>> and I wanted to mix several graphs concerning ethernet statistics in the
>>> same figure,
>>> with time as x axis, and bytes-in, bytes-out, packets-in, packets-out
>>> and
>>> number of
>>> collisions as three different y axes, with three different scale.
>>>
>>> I took the inspiration from
>>>
>>> for the x axes and from
>>>
>>> http://matplotlib.sourceforge.net/examples/axes_grid/demo_parasite_axes2.html
>>> for the y axes
>>>
>>> The following code is a synthetic reproduction of the problem I'm
>>> experiencing (it is also attached):
>>>
>>> from matplotlib.dates import date2num
>>> from matplotlib import pyplot
>>> from matplotlib import pylab
>>> from mpl_toolkits.axes_grid.parasite_axes import SubplotHost
>>> from datetime import datetime
>>>
>>> dates = [ 733581.20833333337, 733581.20837962965, 733581.20842592593,
>>> 733581.20847222221, 733581.20851851848,
>>>       733581.20855324075, 733581.20858796302, 733581.2086342593,
>>> 733581.20866898145, 733581.20871527772]
>>> rxB = [054L, 130L, 144L, 54L, 36L, 9L, 35L, 43L, 85L, 43L]
>>> txB = [4L, 9L, 9L, 5L, 4L, 4L, 4L, 5L, 6L, 5L]
>>> rxP = [77, 228, 251, 112, 77, 42, 75, 97, 147, 91]
>>> txP = [61, 177, 188, 90, 61, 40, 64, 76, 113, 77]
>>> col = [1, 0, 0, 0, 0, 0, 0, 0, 0, 0]
>>>
>>> ethPlot = pyplot
>>> fig = ethPlot.figure()
>>> host = SubplotHost(fig, 111)
>>>
>>> host.set_ylabel("kB/s")
>>> host.set_xlabel("Time")
>>>
>>> par1 = host.twinx()
>>> par2 = host.twinx()
>>>
>>> par1.set_ylabel("Packets/s")
>>>
>>> par2.axis["right"].set_visible(False)
>>>
>>> offset = 60, 0
>>> new_axisline = par2.get_grid_helper().new_fixed_axis
>>> par2.axis["right2"] = new_axisline(loc="right",
>>>                     axes=par2,
>>>                     offset=offset)
>>>
>>> par2.axis["right2"].label.set_visible(True)
>>> par2.axis["right2"].set_label("Collisions")
>>>
>>> par1.set_ylim(0, 6000)
>>> par2.set_ylim(0, 7000)
>>>
>>> host.axis([ dates[0], ( dates[0] + 0.041  ), -7000, 7000])
>>> par1.axis([ dates[0], ( dates[0] + 0.041  ), -10000, 10000])
>>> par2.axis([ dates[0], ( dates[0] + 0.041  ), -700, 700])
>>>
>>> fig.add_axes(host)
>>> ethPlot.subplots_adjust(right=0.75)
>>>
>>> drawRxByt, = host.plot_date(dates, rxB, 'g', tz=None, xdate=True,
>>> ydate=False, label="kB/s in")
>>> drawTxByt, = host.plot_date(dates, txB, 'b', tz=None, xdate=True,
>>> ydate=False, label="kB/s out")
>>> drawRxPaq, = par1.plot_date(dates, rxP, 'm', tz=None, xdate=True,
>>> ydate=False, label="packets/s in")
>>> drawTxPaq, = par1.plot_date(dates, txP, 'y', tz=None, xdate=True,
>>> ydate=False, label="packets/s out")
>>> drawColls, = par2.plot_date(dates, col, 'r', tz=None, xdate=True,
>>> ydate=False, label="collisions")
>>>
>>> fig.autofmt_xdate()
>>>
>>> host.set_xlabel("Time")
>>> host.set_ylabel("kB/s")
>>> par1.set_ylabel("Packets/s")
>>>
>>> host.legend()
>>>
>>> host.axis["left"].label.set_color(drawRxByt.get_color())
>>> host.axis["left"].label.set_color(drawTxByt.get_color())
>>> par1.axis["right"].label.set_color(drawRxPaq.get_color())
>>> par1.axis["right"].label.set_color(drawtxPaq.get_color())
>>> par2.axis["right2"].label.set_color(drawColls.get_color())
>>>
>>> ethPlot.draw()
>>> pylab.savefig( './test.png', dpi=(640/8))
>>>
>>>
>>>
>>>
>>> Maybe I do something wrong somewhere here, but other scripts that do the
>>> same for a single graphwork like a charm. So it's not a question of
>>> dataType
>>> or something. To compare with a working code, here is the first version
>>> of
>>> the fuction that does the job on single graphs without any problem :
>>>
>>> def drawEthGraph(filename, hdates, rxP, txP, rxB, txB, col):
>>>   ethPlot = pyplot
>>>   fig = ethPlot.figure()
>>>   ax = fig.add_subplot(111)
>>>   ax.plot_date(hdates, rxP, 'g', None, True, False)
>>>   ax.plot_date(hdates, txP, 'b', None, True, False)
>>>   ax.plot_date(hdates, rxB, 'g', None, True, False)
>>>   ax.plot_date(hdates, txB, 'b', None, True, False)
>>>   ax.plot_date(hdates, col, 'r', None, True, False)
>>>   ax.axis([ hdates[0], ( hdates[0] + 0.042  ), -7000, 7000])
>>>   ax.grid(True)
>>>   fig.autofmt_xdate()
>>>   pylab.savefig( filename, dpi=(640/8))
>>>
>>>
>>> I don't think I understand the whole process of generation, but I
>>> thought
>>> at
>>> least at the beginnig I was having a good feeling with this API.
>>> Now I wonder how to go around this. Maybe you'll have an idea :-o
>>>
>>> Best regards
>>>
>>> DvD
>>>
>>> from matplotlib.dates import date2num
>>> from matplotlib import pyplot
>>> from matplotlib import pylab
>>> from mpl_toolkits.axes_grid.parasite_axes import SubplotHost
>>> from datetime import datetime
>>>
>>> dates = [ 733581.20833333337, 733581.20837962965, 733581.20842592593,
>>> 733581.20847222221, 733581.20851851848,
>>>         733581.20855324075, 733581.20858796302, 733581.2086342593,
>>> 733581.20866898145, 733581.20871527772]
>>> rxB = [054L, 130L, 144L, 54L, 36L, 9L, 35L, 43L, 85L, 43L]
>>> txB = [4L, 9L, 9L, 5L, 4L, 4L, 4L, 5L, 6L, 5L]
>>> rxP = [77, 228, 251, 112, 77, 42, 75, 97, 147, 91]
>>> txP = [61, 177, 188, 90, 61, 40, 64, 76, 113, 77]
>>> col = [1, 0, 0, 0, 0, 0, 0, 0, 0, 0]
>>>
>>> ethPlot = pyplot
>>> fig = ethPlot.figure()
>>> host = SubplotHost(fig, 111)
>>>
>>> host.set_ylabel("kB/s")
>>> host.set_xlabel("Time")
>>>
>>> par1 = host.twinx()
>>> par2 = host.twinx()
>>>
>>> par1.set_ylabel("Packets/s")
>>>
>>> par2.axis["right"].set_visible(False)
>>>
>>> offset = 60, 0
>>> new_axisline = par2.get_grid_helper().new_fixed_axis
>>> par2.axis["right2"] = new_axisline(loc="right",
>>>                                   axes=par2,
>>>                                   offset=offset)
>>>
>>> par2.axis["right2"].label.set_visible(True)
>>> par2.axis["right2"].set_label("Collisions")
>>>
>>> par1.set_ylim(0, 6000)
>>> par2.set_ylim(0, 7000)
>>>
>>> host.axis([ dates[0], ( dates[0] + 0.041  ), -7000, 7000])
>>> par1.axis([ dates[0], ( dates[0] + 0.041  ), -10000, 10000])
>>> par2.axis([ dates[0], ( dates[0] + 0.041  ), -700, 700])
>>>
>>> fig.add_axes(host)
>>> ethPlot.subplots_adjust(right=0.75)
>>>
>>> drawRxByt, = host.plot_date(dates, rxB, 'g', tz=None, xdate=True,
>>> ydate=False, label="kB/s in")
>>> drawTxByt, = host.plot_date(dates, txB, 'b', tz=None, xdate=True,
>>> ydate=False, label="kB/s out")
>>> drawRxPaq, = par1.plot_date(dates, rxP, 'm', tz=None, xdate=True,
>>> ydate=False, label="packets/s in")
>>> drawTxPaq, = par1.plot_date(dates, txP, 'y', tz=None, xdate=True,
>>> ydate=False, label="packets/s out")
>>> drawColls, = par2.plot_date(dates, col, 'r', tz=None, xdate=True,
>>> ydate=False, label="collisions")
>>>
>>> fig.autofmt_xdate()
>>>
>>> host.set_xlabel("Time")
>>> host.set_ylabel("kB/s")
>>> par1.set_ylabel("Packets/s")
>>>
>>> host.legend()
>>>
>>> host.axis["left"].label.set_color(drawRxByt.get_color())
>>> host.axis["left"].label.set_color(drawTxByt.get_color())
>>> par1.axis["right"].label.set_color(drawRxPaq.get_color())
>>> par1.axis["right"].label.set_color(drawtxPaq.get_color())
>>> par2.axis["right2"].label.set_color(drawColls.get_color())
>>>
>>> ethPlot.draw()
>>> pylab.savefig( './test.png', dpi=(640/8))
>>>
>>>
>>>
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>>>
>>>
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On 5/19/10 3:24 PM, Mike Bauer wrote:
> Hello,
>
> I am hoping that there is a way to use matplotlib to process a sea 
> level pressure field and extract the closed contours therein so that I 
> have a collection of lists with the (lon,lat) pairs that define the 
> perimeter of each closed contour. At the very least I would like a 
> perimeter list of each contour closed or not.
>
> I'm guessing the answer might be something like this
> http://www.mail-archive.com/mat...@li.../msg07915.html
>
> Thank you for any ideas.
>
> Mike

Mike:  Yep, that's a good place to start.

-Jeff

-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Hello,

I am hoping that there is a way to use matplotlib to process a sea level
pressure field and extract the closed contours therein so that I have a
collection of lists with the (lon,lat) pairs that define the perimeter of
each closed contour. At the very least I would like a perimeter list of each
contour closed or not.

I'm guessing the answer might be something like this
http://www.mail-archive.com/mat...@li.../msg07915.html

Thank you for any ideas.

Mike

Well I was able to compile the "embedding_in_wx5.py" example
 ( I'm not sure why or how) but it works.

"embedding_in_wx2.py" still won't compile but I was able to compile my program 
and get it to run as expected.

I'll leave this as another unresolved mystery of programming...

My thanks to the Werner for being there and helping me work this out.

On 05/19/2010 10:28 AM, Benjamin Root wrote:
> Maybe I am misunderstanding your problem, but you can select 'semilog'
> for the x/yscale parameter.

You mean "symlog".

See 
http://matplotlib.sourceforge.net/examples/pylab_examples/symlog_demo.html

Although the example doesn't show it, the axis limits don't have to be 
symmetric.  For example, on the top plot, you can use

gca().set_xlim([0, 100])

to show only the right-hand side.

Eric


>
> Ben Root
>
> On Wed, May 19, 2010 at 7:03 AM, Christer Malmberg
> <Chr...@st...
> <mailto:Chr...@st...>> wrote:
>
>     Hi,
>
>     my problem is that I need a graph with a discontinous y-axis. Let me
>     explain the problem: in my field (microbiology) the data generated
>     from for example growth assays have a huge range (10^0-10^9), which
>     has to be plotted on a semilogy style plot (cell concentration vs.
>     time). The problem is that 0 cells is a useful number to plot
>     (indicates cell concentration lower than detection limit), but of
>     course not possible to show in a log diagram. This is easily solved on
>     old-style logarithmic graph paper; since the data will be either 0, or
>      >1 it is customary just to draw a zero x-axis at 10^-1 on the paper
>     and that's that. On the computer, this is extremely hard. Most people
>     I know resort to various tricks in Excel, such as entering a small
>     number (0.001 etc) and starting the y-axis range from 10^1 to hide the
>     problem. This makes excel draw a line, instead of leaving out the dot
>     and line entirely. The part of the curve below the x-axis is then
>     manually cut off in a suitable image editor. Needless to say, this is
>     extremely kludgy. Even professional graphing packages like Graphpad
>     Prism resort to similar kludges (re-define 0 values to 0.1, change the
>     y-axis tick label to "0" etc.) This problem of course exists in other
>     fields, while investigating a solution I found a guy who worked with
>     aerosol contamination in clean rooms, and he needed to plot values
>     logarithmically, at the same time as showing detector noise around
>     1-10 particles. He solved it by the same trick I would like to do in
>     Matplotlib, namely plotting a standard semilogy plot but with the
>     10^-1 to 10^0 decade being replaced by a 0-1 linear axis on the same
>     side.
>
>     The guy in this post has the same problem and a useful example:
>     http://ubuntuforums.org/showthread.php?t=394851
>
>     His partial solution is quite bad though, and I just got stuck while
>     trying to improve it. I looked around the gallery for useful examples,
>     and the closest I could find is the twinx/twiny function, but I didn't
>     manage a plot that put one data curve across both axes.
>
>     This code gives an image that maybe explains what I'm trying to do:
>
>     =======================================
>     t = array([0,1,2,4,6,9,12,24])
>     y = array([1000000, 500000, 100000, 100, 5, 1, 0, 0])
>     subplot(111, xscale="linear", yscale="log")
>     errorbar(x, y, yerr=0.4*y)
>     linbit = axes([0.125, 0.1, 0.775, 0.1],frameon=False)
>     linbit.xaxis.set_visible(False)
>     for tl in linbit.get_yticklabels():
>          tl.set_color('r')
>     show()
>     =======================================
>
>     (the y=0 points should be plotted and connected to the line in the
>     log part)
>
>     Is this possible to do in matplotlib? Could someone give me a pointer
>     on how to go on?
>
>     Sorry for the long mail,
>
>     /C
>
>
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Colleagues,

I am trying to follow the http://matplotlib.sourceforge.net/users/pyplot_tutorial.html tutorial with little success. The very first import fails with either 64 or 32-bit python. Any hints I have missed?

$ python
Python 2.6.1 (r261:67515, Feb 11 2010, 00:51:29)
[GCC 4.2.1 (Apple Inc. build 5646)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

>>> import matplotlib.pyplot as plt
Traceback (most recent call last):
 File "<stdin>", line 1, in <module>
 File "/Library/Python/2.6/site-packages/matplotlib-0.99.1.1-py2.6-macosx-10.3-fat.egg/matplotlib/pyplot.py", line 6, in <module>
   from matplotlib.figure import Figure, figaspect
 File "/Library/Python/2.6/site-packages/matplotlib-0.99.1.1-py2.6-macosx-10.3-fat.egg/matplotlib/figure.py", line 16, in <module>
   import artist
 File "/Library/Python/2.6/site-packages/matplotlib-0.99.1.1-py2.6-macosx-10.3-fat.egg/matplotlib/artist.py", line 5, in <module>
   from transforms import Bbox, IdentityTransform, TransformedBbox, TransformedPath
 File "/Library/Python/2.6/site-packages/matplotlib-0.99.1.1-py2.6-macosx-10.3-fat.egg/matplotlib/transforms.py", line 34, in <module>
   from matplotlib._path import affine_transform
ImportError: /Library/Python/2.6/site-packages/matplotlib-0.99.1.1-py2.6-macosx-10.3-fat.egg/matplotlib/_path.so: no appropriate 64-bit architecture (see "man python" for running in 32-bit mode)

>>> exit()

$ defaults write com.apple.versioner.python Prefer-32-Bit -bool yes

$ python
Python 2.6.1 (r261:67515, Feb 11 2010, 00:51:29)
[GCC 4.2.1 (Apple Inc. build 5646)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

>>> import matplotlib.pyplot as plt
Bus error

$

Sincerely,
Vlad

This e-mail and its attachments are intended only for the individual or entity to whom it is addressed and may contain information that is confidential, privileged, inside information, or subject to other restrictions on use or disclosure. Any unauthorized use, dissemination or copying of this transmission or the information in it is prohibited and may be unlawful. If you have received this transmission in error, please notify the sender immediately by return e-mail, and permanently delete or destroy this e-mail, any attachments, and all copies (digital or paper). Unless expressly stated in this e-mail, nothing in this message should be construed as a digital or electronic signature.

Maybe I am misunderstanding your problem, but you can select 'semilog' for
the x/yscale parameter.

Ben Root

On Wed, May 19, 2010 at 7:03 AM, Christer Malmberg <
Chr...@st...> wrote:

> Hi,
>
> my problem is that I need a graph with a discontinous y-axis. Let me
> explain the problem: in my field (microbiology) the data generated
> from for example growth assays have a huge range (10^0-10^9), which
> has to be plotted on a semilogy style plot (cell concentration vs.
> time). The problem is that 0 cells is a useful number to plot
> (indicates cell concentration lower than detection limit), but of
> course not possible to show in a log diagram. This is easily solved on
> old-style logarithmic graph paper; since the data will be either 0, or
>  >1 it is customary just to draw a zero x-axis at 10^-1 on the paper
> and that's that. On the computer, this is extremely hard. Most people
> I know resort to various tricks in Excel, such as entering a small
> number (0.001 etc) and starting the y-axis range from 10^1 to hide the
> problem. This makes excel draw a line, instead of leaving out the dot
> and line entirely. The part of the curve below the x-axis is then
> manually cut off in a suitable image editor. Needless to say, this is
> extremely kludgy. Even professional graphing packages like Graphpad
> Prism resort to similar kludges (re-define 0 values to 0.1, change the
> y-axis tick label to "0" etc.) This problem of course exists in other
> fields, while investigating a solution I found a guy who worked with
> aerosol contamination in clean rooms, and he needed to plot values
> logarithmically, at the same time as showing detector noise around
> 1-10 particles. He solved it by the same trick I would like to do in
> Matplotlib, namely plotting a standard semilogy plot but with the
> 10^-1 to 10^0 decade being replaced by a 0-1 linear axis on the same
> side.
>
> The guy in this post has the same problem and a useful example:
> http://ubuntuforums.org/showthread.php?t=394851
>
> His partial solution is quite bad though, and I just got stuck while
> trying to improve it. I looked around the gallery for useful examples,
> and the closest I could find is the twinx/twiny function, but I didn't
> manage a plot that put one data curve across both axes.
>
> This code gives an image that maybe explains what I'm trying to do:
>
> =======================================
> t = array([0,1,2,4,6,9,12,24])
> y = array([1000000, 500000, 100000, 100, 5, 1, 0, 0])
> subplot(111, xscale="linear", yscale="log")
> errorbar(x, y, yerr=0.4*y)
> linbit = axes([0.125, 0.1, 0.775, 0.1],frameon=False)
> linbit.xaxis.set_visible(False)
> for tl in linbit.get_yticklabels():
>     tl.set_color('r')
> show()
> =======================================
>
> (the y=0 points should be plotted and connected to the line in the log
> part)
>
> Is this possible to do in matplotlib? Could someone give me a pointer
> on how to go on?
>
> Sorry for the long mail,
>
> /C
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Werner F. Bruhin <werner.bruhin@...> writes:

> 
> 
> On 19/05/2010 19:55, David Grudoski wrote:
> 
>   I'm trying to build an executable using
> PY2EXE; running Python 2.5.2 and wxPython 2.8.10.1 and MatplotLib 0.99.0
>   I tried using the setup.py from the
> PY2EXE.org Matplotlib page and although everything compiles correctly
> and generates an executable.
>   When I launch the executable I get the
> following error:
>   ================================================
>   "The application requires a version of
> wxPython greater than or equal to 2.8, but a matching version was not
> found."
>   You currently have these version(s)
> installed.
>   
>   ================================================
>   
>   
>   I can compile an executable with PY2EXE and
> wxPython that works fine, but apparantly somethins in the setup for
> matplotlib is causing a problem.
>   
>   Has anyone else seen this problem or know of
> a solution?
> 
> You need to patch matplotlib (backend_wx.py), see the bottom of this
> page:http://www.py2exe.org/index.cgi/MatPlotLib
> Werner
> 
> 
> ------------------------------------------------------------------------------
> 
> 
> 
> _______________________________________________
> Matplotlib-users mailing list
> Matplotlib-users@...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 

Thanks for the reply Werner,
I decided to try and construct the executable from the site using the
"embedding_in_wx2.py" example. Again making sure the patch was in place on the
backend_wx.py I again ran the python setup.py py2exe and everything compiled.
Now when I run the exe it generate the following log file errors:
Traceback (most recent call last):
  File "embedding_in_wx2.py", line 21, in <module>
  File "zipextimporter.pyo", line 82, in load_module
  File "matplotlib\backends\backend_wxagg.pyo", line 20, in <module>
  File "zipextimporter.pyo", line 82, in load_module
  File "matplotlib\figure.pyo", line 19, in <module>
  File "zipextimporter.pyo", line 82, in load_module
  File "matplotlib\axes.pyo", line 14, in <module>
  File "zipextimporter.pyo", line 82, in load_module
  File "matplotlib\collections.pyo", line 21, in <module>
  File "zipextimporter.pyo", line 82, in load_module
  File "matplotlib\backend_bases.pyo", line 32, in <module>
  File "zipextimporter.pyo", line 82, in load_module
  File "matplotlib\widgets.pyo", line 12, in <module>
  File "zipextimporter.pyo", line 82, in load_module
  File "matplotlib\mlab.pyo", line 376, in <module>
TypeError: unsupported operand type(s) for %: 'NoneType' and 'dict'

On 19/05/2010 19:55, David Grudoski wrote:
> I'm trying to build an executable using PY2EXE; running Python 2.5.2 
> and wxPython 2.8.10.1 and MatplotLib 0.99.0
> I tried using the setup.py from the PY2EXE.org Matplotlib page and 
> although everything compiles correctly and generates an executable.
> When I launch the executable I get the following error:
> ================================================
> "The application requires a version of wxPython greater than or equal 
> to 2.8, but a matching version was not found."
> You currently have these version(s) installed.
> ================================================
>
> I can compile an executable with PY2EXE and wxPython that works fine, 
> but apparantly somethins in the setup for matplotlib is causing a problem.
>
> Has anyone else seen this problem or know of a solution?
You need to patch matplotlib (backend_wx.py), see the bottom of this page:
http://www.py2exe.org/index.cgi/MatPlotLib

Werner

I'm trying to build an executable using PY2EXE; running Python 2.5.2  
and wxPython 2.8.10.1 and MatplotLib 0.99.0
I tried using the setup.py from the PY2EXE.org Matplotlib page and  
although everything compiles correctly and generates an executable.
When I launch the executable I get the following error:
================================================
"The application requires a version of wxPython greater than or equal  
to 2.8, but a matching version was not found."
You currently have these version(s) installed.
================================================

I can compile an executable with PY2EXE and wxPython that works fine,  
but apparantly somethins in the setup for matplotlib is causing a  
problem.

Has anyone else seen this problem or know of a solution?
Thanks
David
(setup.py is attached)


Hi,

I am a wondering if it's possible to have few line distinguishing marks on
the data lines on a chart such as circle, start, square. When I use some
thing like this for the color of the graph (i.e. rs, k^), it uses the shape
for each data point and the lines becomes very thick. All I want is to put
4-5 shaper markers on each line with line (the data line will have few
hundred data points).

Many thanks,
Omer

The functionality of the gridspec is now merged into the matplotlib.
The updated documentation can be found in

http://matplotlib.sourceforge.net/trunk-docs/users/gridspec.html

Regards,

-JJ


On Tue, May 11, 2010 at 11:57 AM, Jae-Joon Lee <lee...@gm...> wrote:
> Hi,
>
>  gridspec is a module that implements matplotlib’s Subplot slightly
> differently. Current matplotlib’s Subplot only allows a Subplot to
> occupy a single cell of the n x m grid. gridspec enables a Subplot to
> occupy multiple cells.
>
>  http://leejjoon.github.com/mpl_toolkits-gridspec/
>
> The code is hosted in the github repo
>
>  http://github.com/leejjoon/mpl_toolkits-gridspec
>
> and the source can be downloaded from
>
>  http://github.com/leejjoon/mpl_toolkits-gridspec/downloads
>
> This is motivated from the discussion in the mailing list a while ago.
>
> http://sourceforge.net/mailarchive/message.php?msg_id=4A0DA94E.1040500%40american.edu
>
> I originally prepared this as a patch for matplotlib
> (http://article.gmane.org/gmane.comp.python.matplotlib.general/19097),
> but never committed. Instead, it is packaged as a mpl_tookit module.
>
> Regards,
>
> -JJ
>

Thanks for the suggestions, 'annotate' is what I need, I think.
I get errors though, also when I run the example scripts 
from here: 
http://matplotlib.sourceforge.net/trunk-docs/users/annotations_guide.html#using-complex-coordinate-with-annotation .

I get the error 'NoneType' object is not iterable when I try plt.show()
or try to save to eps.

So I am not sure if I have the correct version of matplotlib installed.
I checked out the newest matplotlib from the svn repository, removed my
current installed version and installed the version in the 'trunk/'
directory. 'annotate' did not work.
Later, I installed matplotlib from the '/branches/v0_99_maint'
directory. 
In both cases there were no errors in the installation, but still
'annotate' did not work.

Could it be that I have the wrong library from the svn repository
installed? Does r8319 mean release #8319? 

Kind Regards

Hannes

On Tue, 2010-05-18 at 13:34 -0400, Jae-Joon Lee wrote:
> This can be done relatively easily with the current svn version of
> matplotlib (r8319).
> Below is the modified version of your code.
> 
> See
> 
>
http://matplotlib.sourceforge.net/trunk-docs/users/annotations_guide.html#using-complex-coordinate-with-annotation
> 
> for how the annotation works.
> 
> While this is certainly possible with the released version, but it
> will require you to write a few tens of lines of code. Basically, you
> need create a custom Text class that update its position during the
> drawing time.
> 
> Regards,
> 
> -JJ
> 
> ###Code
> import scipy
> import matplotlib.pyplot as plt
> 
> fig = plt.figure()
> ax = fig.add_subplot(121)
> plt.plot(scipy.sin(scipy.arange(1,100, 0.001)))
> plt.xlabel('xlabel')
> yl = plt.ylabel("ylabel")
> 
> plt.annotate("A", (0,1.), xycoords=(yl, "axes fraction"),
>              xytext=(0, 14), textcoords="offset points",
>              fontsize=14)
> 
> ax = fig.add_subplot(122)
> plt.plot(scipy.cos(scipy.arange(1,100, 0.001)))
> plt.xlabel('xlabel')
> 
> my_ticklabel = ax.get_yticklabels()[-2]
> # Note that there is no guarantee that all ticklabels are drawn.
> plt.annotate("B", (0,1.), xycoords=(my_ticklabel, "axes fraction"),
>              xytext=(0, 14), textcoords="offset points",
>              fontsize=14)
> 
> ###End Code
> 
> 
> On Mon, May 17, 2010 at 11:08 AM, hettling <het...@fe...> wrote:
> > Dear all,
> >
> > I'm struggling with the following problem plotting my data:
> >
> > I have a figure with two panels next to each other, which I want to
> > label 'A' and 'B'. I want to left-justify my panel labels, but not
to
> > the box that contains the plot, but to the y-axis label. I played
around
> > with 'text()' and 'title()', but did not find a good solution except
for
> > giving the coordinates manually to 'text()'. This would be very
> > inconvenient though, because I have many different plots on
different
> > scales.
> > Here is what I tried:
> >
> > ###Code
> > import scipy
> > import matplotlib.pyplot as plt
> >
> > fig = plt.figure()
> > ax = fig.add_subplot(121)
> > plt.plot(scipy.sin(scipy.arange(1,100, 0.001)))
> > plt.xlabel('xlabel')
> > plt.ylabel("ylabel")
> > plt.text(0,1,"A", fontsize=14, transform=ax.transAxes)
> >
> > ax = fig.add_subplot(122)
> > plt.plot(scipy.cos(scipy.arange(1,100, 0.001)))
> > plt.text(0,1,"B", fontsize=14, transform=ax.transAxes)
> > plt.xlabel('xlabel')
> > ###End Code
> >
> > So the texts 'A' and 'B' should be a little bit higher and more to
the
> > left. The 'A' I want to align with the y-axis label of the left
plot,
> > the 'B' with the values of the y-axis of the right plot.
> >
> > I hope my question is clear, I will appreciate any help!
> >
> > Thanks in advance,
> >
> > Hannes
> >
> >
> >
------------------------------------------------------------------------------
> >
> > _______________________________________________
> > Matplotlib-users mailing list
> > Mat...@li...
> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> >

Hi,

my problem is that I need a graph with a discontinous y-axis. Let me  
explain the problem: in my field (microbiology) the data generated  
from for example growth assays have a huge range (10^0-10^9), which  
has to be plotted on a semilogy style plot (cell concentration vs.  
time). The problem is that 0 cells is a useful number to plot  
(indicates cell concentration lower than detection limit), but of  
course not possible to show in a log diagram. This is easily solved on  
old-style logarithmic graph paper; since the data will be either 0, or  
 >1 it is customary just to draw a zero x-axis at 10^-1 on the paper  
and that's that. On the computer, this is extremely hard. Most people  
I know resort to various tricks in Excel, such as entering a small  
number (0.001 etc) and starting the y-axis range from 10^1 to hide the  
problem. This makes excel draw a line, instead of leaving out the dot  
and line entirely. The part of the curve below the x-axis is then  
manually cut off in a suitable image editor. Needless to say, this is  
extremely kludgy. Even professional graphing packages like Graphpad  
Prism resort to similar kludges (re-define 0 values to 0.1, change the  
y-axis tick label to "0" etc.) This problem of course exists in other  
fields, while investigating a solution I found a guy who worked with  
aerosol contamination in clean rooms, and he needed to plot values  
logarithmically, at the same time as showing detector noise around  
1-10 particles. He solved it by the same trick I would like to do in  
Matplotlib, namely plotting a standard semilogy plot but with the  
10^-1 to 10^0 decade being replaced by a 0-1 linear axis on the same  
side.

The guy in this post has the same problem and a useful example:
http://ubuntuforums.org/showthread.php?t=394851

His partial solution is quite bad though, and I just got stuck while  
trying to improve it. I looked around the gallery for useful examples,  
and the closest I could find is the twinx/twiny function, but I didn't  
manage a plot that put one data curve across both axes.

This code gives an image that maybe explains what I'm trying to do:

=======================================
t = array([0,1,2,4,6,9,12,24])
y = array([1000000, 500000, 100000, 100, 5, 1, 0, 0])
subplot(111, xscale="linear", yscale="log")
errorbar(x, y, yerr=0.4*y)
linbit = axes([0.125, 0.1, 0.775, 0.1],frameon=False)
linbit.xaxis.set_visible(False)
for tl in linbit.get_yticklabels():
     tl.set_color('r')
show()
=======================================

(the y=0 points should be plotted and connected to the line in the log part)

Is this possible to do in matplotlib? Could someone give me a pointer  
on how to go on?

Sorry for the long mail,

/C

On 19/05/2010 01:17, New2Python wrote:
> Thanks, I changed the matplotlibrc file to use the WXAgg backend and then had
> to copy the file into the mpl.get_configdir() and in my local working dir
> for it to work.
>
> The file runs however a python error screen pops up and then closes without
> giving me the chance to read it, anybody know how to stop the window from
> closing so quickly
>    
You have probably set "wx.App(redirect=True)", change to "False" and 
then you should see the exception in your IDE.

Werner

Thanks, I changed the matplotlibrc file to use the WXAgg backend and then had
to copy the file into the mpl.get_configdir() and in my local working dir
for it to work.

The file runs however a python error screen pops up and then closes without
giving me the chance to read it, anybody know how to stop the window from
closing so quickly

Thanks

Marco



Michael Droettboom-3 wrote:
> 
> It should only try to import that backend when configured to do so.  You 
> may need to change your matplotlibrc to point to your desired backend.
> 
> Mike
> 
> New2Python wrote:
>> Thanks, must have skipped over that one - I added the statements and it
>> has
>> fixed it :) however now there is an issue elsewhere. I get the message
>>
>>   File "matplotlib\backends\__init__.pyo", line 25, in pylab_setup
>> ImportError: No module named backend_tkagg
>>
>> and the traceback call this
>>
>> from pylab import *
>>
>> I have _tkagg as an exclude
>>
>> looks like somebody else had this problem but nobody solved it
>> http://mail.scipy.org/pipermail/scipy-user/2005-July/004777.html
>>
>> any one know how to solve this?
>>
>> I tried to include matplotlib.backends.backend_tkagg, then this popped up
>> with a tkinter import error.
>>
>> Regards
>>
>> Marco
>>
>>
>>
>>
>>
>>
>> New2Python wrote:
>>   
>>> Hi All,
>>>
>>> I hope someone can help, I have run into a few problems when trying to
>>> execute an exe file created when I use py2exe with matplotlib.
>>> I have python2.5, matplotlib v0.99.1 and py2exe from GUI2Exe v0.5.0
>>> optimisation is python -OO
>>> the files compile correctly however when I execute the exe I get an
>>> error
>>> as shown below
>>> this is an extract
>>>
>>>   File "matplotlib\mlab.pyo", line 380, in <module>
>>> TypeError: unsupported operand type(s) for %: 'NoneType' and 'dict'
>>>
>>> the traceback points to this line of my code
>>>
>>> from matplotlib.backends.backend_wxagg import NavigationToolbar2WxAgg
>>>
>>> does anyone know how to solve this, i have seen references made to numpy
>>> but not matplotlib
>>>
>>> Regards
>>>
>>> Marco
>>>
>>>
>>>
>>>
>>>     
>>
>>   
> 
> -- 
> Michael Droettboom
> Science Software Branch
> Operations and Engineering Division
> Space Telescope Science Institute
> Operated by AURA for NASA
> 
> 
> ------------------------------------------------------------------------------
> 
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 
> 

-- 
View this message in context: http://old.nabble.com/py2exe-and-matplotlib-errors-when-executing-exe-tp28589875p28602527.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

> http://matplotlib.sourceforge.net/faq/howto_faq.html#use-show


Here is some more detail, that I actually think
should be added to the above link.
http://stackoverflow.com/questions/458209/is-there-a-way-to-detach-matplotlib-plots-so-that-the-computation-can-continue

hth,
Alan Isaac

Nick,

Check out this demo on the MPL website:
http://matplotlib.sourceforge.net/examples/api/histogram_demo.html

This line in particular:
n, bins, patches = ax.hist(x, 50, normed=...)

The variables 'n' and 'bins' can be fed into ax.bar() later on. I could swear that this was clear from the docstring, but that's definitely not the case anymore. I'll submit a patch to the list tomorrow if I can remember to work on it some tonight. 

Do see the docstring for an explanation of what can be done with the 'patches' variable.

Hope this helps,
-paul

> -----Original Message-----
> From: Nick Schurch [mailto:N.S...@du...]
> Sent: Tuesday, May 18, 2010 6:56 AM
> To: mat...@li...
> Subject: [Matplotlib-users] hist question...
> 
> Hi all,
> 
> Is there anyway of re-ploting the distribution generated by hist at a
> later point? I want to call it in a subroutine and have the resulting
> distributions returned so I can plot them without having to
> recalculate them each time. I couldn't find anything int he online
> documentation but I figured it'd be something like:
> 
> import matplotlib.pyplot as plt
> hplot=plt.hist(data, bins=1000)
> 
> plt.hist(hplot)
> or
> plt.hist(hplot[0],bins=hplot[1])
> or
> plt.plot(hist)
> 
> 
> etc, but nothing works.
> 
> --
> Cheers,
> 
> Nick Schurch
> 
> Data Analysis Group (The Barton Group),
> School of Life Sciences,
> University of Dundee,
> Dow St,
> Dundee,
> DD1 5EH,
> Scotland,
> UK
> 
> Tel: +44 1382 388707
> Fax: +44 1382 345 893
> 
> -------------------------------------------------------------------------
> -----
> 
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

First of all, what are you trying to do?
What does "figure is created" mean.
Do you need it to be drawn on the monitor?
Why not save your figure(s) to file(s)?

Cheers,
Alan

Thanks.

On Tuesday 18 May 2010 12:13:27 pm John Hunter wrote:
> On Tue, May 18, 2010 at 12:58 PM, Jae-Joon Lee <lee...@gm...> wrote:
> > All the artists that are drawn are kept in the figure instance, so you
> > can inspect the figure instance.
> > And you may use findobj for that if you want.
> > On the other hand, Axes.texts keeps a list of text instances in the
> > axes (e.g., gca().texts).
>
> For more detail see the artist tutorial which describes the various
> containers and how to remove objects from them
>
>
> http://matplotlib.sourceforge.net/users/artists.html#axes-container
>
> JDH

On Tue, May 18, 2010 at 12:58 PM, Jae-Joon Lee <lee...@gm...> wrote:

> All the artists that are drawn are kept in the figure instance, so you
> can inspect the figure instance.
> And you may use findobj for that if you want.
> On the other hand, Axes.texts keeps a list of text instances in the
> axes (e.g., gca().texts).
>

For more detail see the artist tutorial which describes the various
containers and how to remove objects from them


http://matplotlib.sourceforge.net/users/artists.html#axes-container

JDH

On Sun, May 16, 2010 at 3:19 PM, Philipp K. Janert
<py...@be...> wrote:
> Is this the best way to do this, or is there another way
> (or one that does not require an explicit draw()?). Also,

Any change in your figure is realized when you "draw()" the figure. So
there is no way that does not require an explicit draw.

An alternative is to make the artist invisible (use set_visible method).

> what if I have failed to save the text instance - do I have
> to walk the object tree using findobj()?
>

All the artists that are drawn are kept in the figure instance, so you
can inspect the figure instance.
And you may use findobj for that if you want.
On the other hand, Axes.texts keeps a list of text instances in the
axes (e.g., gca().texts).

Regards,

-JJ

This can be done relatively easily with the current svn version of
matplotlib (r8319).
Below is the modified version of your code.

See

http://matplotlib.sourceforge.net/trunk-docs/users/annotations_guide.html#using-complex-coordinate-with-annotation

for how the annotation works.

While this is certainly possible with the released version, but it
will require you to write a few tens of lines of code. Basically, you
need create a custom Text class that update its position during the
drawing time.

Regards,

-JJ

###Code
import scipy
import matplotlib.pyplot as plt

fig = plt.figure()
ax = fig.add_subplot(121)
plt.plot(scipy.sin(scipy.arange(1,100, 0.001)))
plt.xlabel('xlabel')
yl = plt.ylabel("ylabel")

plt.annotate("A", (0,1.), xycoords=(yl, "axes fraction"),
             xytext=(0, 14), textcoords="offset points",
             fontsize=14)

ax = fig.add_subplot(122)
plt.plot(scipy.cos(scipy.arange(1,100, 0.001)))
plt.xlabel('xlabel')

my_ticklabel = ax.get_yticklabels()[-2]
# Note that there is no guarantee that all ticklabels are drawn.
plt.annotate("B", (0,1.), xycoords=(my_ticklabel, "axes fraction"),
             xytext=(0, 14), textcoords="offset points",
             fontsize=14)

###End Code


On Mon, May 17, 2010 at 11:08 AM, hettling <het...@fe...> wrote:
> Dear all,
>
> I'm struggling with the following problem plotting my data:
>
> I have a figure with two panels next to each other, which I want to
> label 'A' and 'B'. I want to left-justify my panel labels, but not to
> the box that contains the plot, but to the y-axis label. I played around
> with 'text()' and 'title()', but did not find a good solution except for
> giving the coordinates manually to 'text()'. This would be very
> inconvenient though, because I have many different plots on different
> scales.
> Here is what I tried:
>
> ###Code
> import scipy
> import matplotlib.pyplot as plt
>
> fig = plt.figure()
> ax = fig.add_subplot(121)
> plt.plot(scipy.sin(scipy.arange(1,100, 0.001)))
> plt.xlabel('xlabel')
> plt.ylabel("ylabel")
> plt.text(0,1,"A", fontsize=14, transform=ax.transAxes)
>
> ax = fig.add_subplot(122)
> plt.plot(scipy.cos(scipy.arange(1,100, 0.001)))
> plt.text(0,1,"B", fontsize=14, transform=ax.transAxes)
> plt.xlabel('xlabel')
> ###End Code
>
> So the texts 'A' and 'B' should be a little bit higher and more to the
> left. The 'A' I want to align with the y-axis label of the left plot,
> the 'B' with the values of the y-axis of the right plot.
>
> I hope my question is clear, I will appreciate any help!
>
> Thanks in advance,
>
> Hannes
>
>
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