matplotlib-users Mailing List for matplotlib

I need to compute coherence between a bunch of different signals, for a
bunch of different trials, and it seems like cohere_pairs() is exactly what
I should use. However, I'm a little confused about the output. If I use
cohere() to produce the coherence values for two signals, I get an array of
coherence values, one for each frequency in the frequency array. However,
if I use cohere_pairs() with just that pair specified, I get the same
frequency array but a single value for that pair. See the example output
below:
>>> X = np.random.rand(1024,2)
>>> c, f = mpl.mlab.cohere(X[:,0], X[:,1])
>>> c.shape, f.shape
((129,), (129,))
>>> c, p, f = mpl.mlab.cohere_pairs(X, [(0,1)])
>>> f.shape
(129,)
>>> c
0.67176286373547267
>From reading the doc strings I was under the impression that the value
'c[(i,j)]' (output from cohere_pairs) should be the same output you would
get from running 'cohere(X[:,i], X[:,j])'. Is this a bug, or am I missing
something?
Thanks,
-Barrett
-- 
Barrett Heyneman
PhD Student
Stanford University
Mechanical Engineering, Design Division

Hi Ben,
I search for keyword 'format' and don't find relevant issue. So I add one.
cheers,
Chao
2012年5月4日 Benjamin Root <ben...@ou...>
>
>
> On Fri, May 4, 2012 at 9:11 AM, Chao YUE <cha...@gm...> wrote:
>
>> Dear all,
>>
>> I use the default GTKAgg backend. When I explore the figure in
>> interactive mode, I find a list of formats to select for the figure format.
>> But the default one is .png, so how can I change to .jpg?
>>
>> In [7]: mat.get_backend()
>> Out[7]: 'GTKAgg'
>>
>> thanks et cheers,
>>
>> Chao
>>
>
> Chao,
>
> It is currently not possible, but I think it has been made into a feature
> request already. If you don't see it in the github issues list, could you
> please add one?
>
> Cheers!
> Ben Root
>
>
-- 
***********************************************************************************
Chao YUE
Laboratoire des Sciences du Climat et de l'Environnement (LSCE-IPSL)
UMR 1572 CEA-CNRS-UVSQ
Batiment 712 - Pe 119
91191 GIF Sur YVETTE Cedex
Tel: (33) 01 69 08 29 02; Fax:01.69.08.77.16
************************************************************************************

Dear all,
Is it possible to have a customized linestyle for line plots?
such as I want '--.--.--.' or '-*-*-*' or others.
I read the documentation part of set_drawstyle and a post here:
http://old.nabble.com/Changing-the-Dash-Spacing--td33381003.html#a33381003
but still not clear. Could anyone give a very small example?
thanks et cheers,
Chao
-- 
***********************************************************************************
Chao YUE
Laboratoire des Sciences du Climat et de l'Environnement (LSCE-IPSL)
UMR 1572 CEA-CNRS-UVSQ
Batiment 712 - Pe 119
91191 GIF Sur YVETTE Cedex
Tel: (33) 01 69 08 29 02; Fax:01.69.08.77.16
************************************************************************************

On Fri, May 4, 2012 at 9:11 AM, Chao YUE <cha...@gm...> wrote:
> Dear all,
>
> I use the default GTKAgg backend. When I explore the figure in interactive
> mode, I find a list of formats to select for the figure format.
> But the default one is .png, so how can I change to .jpg?
>
> In [7]: mat.get_backend()
> Out[7]: 'GTKAgg'
>
> thanks et cheers,
>
> Chao
>
Chao,
It is currently not possible, but I think it has been made into a feature
request already. If you don't see it in the github issues list, could you
please add one?
Cheers!
Ben Root

Dear all,
I use the default GTKAgg backend. When I explore the figure in interactive
mode, I find a list of formats to select for the figure format.
But the default one is .png, so how can I change to .jpg?
In [7]: mat.get_backend()
Out[7]: 'GTKAgg'
thanks et cheers,
Chao
-- 
***********************************************************************************
Chao YUE
Laboratoire des Sciences du Climat et de l'Environnement (LSCE-IPSL)
UMR 1572 CEA-CNRS-UVSQ
Batiment 712 - Pe 119
91191 GIF Sur YVETTE Cedex
Tel: (33) 01 69 08 29 02; Fax:01.69.08.77.16
************************************************************************************

On Fri, May 4, 2012 at 5:44 AM, Cumberland, Burly <
Bur...@co...> wrote:
> Hi,****
>
> Just recently upgraded to Matplotlib 1.1.0 from 1.0.1. I make significant
> use of the pixel marker in plot. For instance:****
>
> plt.plot(self.dat.duration, self.dat.fmpwr, 'b,', label="Power",
> markevery= self.skip)****
>
> ****
>
> I've found that since upgrading all my plots appear to be black now if
> they us the pixel marker ',' option. Upon closer inspection it looks like
> there may be some colour (but not the standard shade of blue or red) to the
> pixels but as they layer up they appear black. This is a bit frustrating as
> my plots were bright blue, bright red etc.****
>
> ****
>
> Does anyone know if the default behaviour has changed in the most recent
> release, any ideas how I get the colour back?****
>
>
Adding markeredgecolor='b' to the plot() call restores the full color. (I
don't know when or why the behavior changed.)
Warren

Hi,
Just recently upgraded to Matplotlib 1.1.0 from 1.0.1. I make significant use of the pixel marker in plot. For instance:
plt.plot(self.dat.duration, self.dat.fmpwr, 'b,', label="Power", markevery= self.skip)
I've found that since upgrading all my plots appear to be black now if they us the pixel marker ',' option. Upon closer inspection it looks like there may be some colour (but not the standard shade of blue or red) to the pixels but as they layer up they appear black. This is a bit frustrating as my plots were bright blue, bright red etc.
Does anyone know if the default behaviour has changed in the most recent release, any ideas how I get the colour back?
Thanks in advance.
Burly.

Hi John,
Have you tried pupynere module?
http://pypi.python.org/pypi/pupynere/
https://bitbucket.org/robertodealmeida/pupynere/
[ ]
---
*Arnaldo D'Amaral Pereira Granja Russo*
Lab. de Estudos dos Oceanos e Clima
Instituto de Oceanografia - FURG
2012年5月4日 John <was...@gm...>
> Hello,
>
> I'm working with the latest netcdf4-python (svn updated recently). It
> has been built with the Netcdf 4.1.1 and HDF 4.2.5 and HDF5 1.8.5
> patch libraries. The installation is on Ubuntu 64bit 10.04 LTS.
>
> I get some very strange behavior when trying to read a file, which
> actually causes Ipython to close:
> In [3]: from netCDF4 import DataSet as NetCDFFile
> In [4]: nci = NetCDFFile('100730_tawo_TAWO-var.nc')
> python: v1hpg.c:190: v1h_get_nc_type: Assertion `type == NC_BYTE ||
> type == NC_CHAR || type == NC_SHORT || type == NC_INT || type ==
> NC_FLOAT || type == NC_DOUBLE' failed.
> Aborted
> $
>
> Does anyone have a suggestion where to look for the root cause of
> this? From the searches I've done it seems it is likely related to the
> dynamic linking of the libraries at build time.
>
> Thank you,
> john
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
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> _______________________________________________
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>

Thanks for spotting this. Done.
On 05/03/2012 07:28 PM, Pengkui Luo wrote:
> It may be a minor one, but can the web manager delete the last 
> sentence on this page? It is the same as the previous sentence...
>
> http://matplotlib.sourceforge.net/devel/coding_guide.html
>
> ~Pengkui
>
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Hello,
I'm working with the latest netcdf4-python (svn updated recently). It
has been built with the Netcdf 4.1.1 and HDF 4.2.5 and HDF5 1.8.5
patch libraries. The installation is on Ubuntu 64bit 10.04 LTS.
I get some very strange behavior when trying to read a file, which
actually causes Ipython to close:
In [3]: from netCDF4 import DataSet as NetCDFFile
In [4]: nci = NetCDFFile('100730_tawo_TAWO-var.nc')
python: v1hpg.c:190: v1h_get_nc_type: Assertion `type == NC_BYTE ||
type == NC_CHAR || type == NC_SHORT || type == NC_INT || type ==
NC_FLOAT || type == NC_DOUBLE' failed.
Aborted
$
Does anyone have a suggestion where to look for the root cause of
this? From the searches I've done it seems it is likely related to the
dynamic linking of the libraries at build time.
Thank you,
john

On 05/03/2012 04:31 PM, Ignas Anikevicius wrote:
> Dear Michael,
>
> Sorry for such a lengthy email, but I wanted to ask about dependencies
> as well. I am trying to get python and py3k versions of matplotlib
> working. In addition to this I am trying to do this with git/master
> version. I can build Python2 version, but I could not do it with Python3.
>
> Could you tell me which packages are indeed needed to build python
> git/master? What are differences between Python2 and Python3
> dependencies? I could later provide a patch for the git/master INSTALL
> file.
I'm not familiar with the package naming scheme used below. What OS is 
this on?
>
> So, the compile dependencies are as follows?
> media-libs/libpng # Needed?
Yes.
> dev-python/imaging # Only for docs?
No longer needed by git master.
> dev-python/xlwt # What about this package?
Only needed if using the optional exceltools package.
>
> Runtime dependencies?
> virtual/ttf-fonts # I guess theese are needed for selecting
> media-fonts/stix-fonts # different fonts, or is it the case that
> media-fonts/texcm-ttf # mpl uses LaTeX fonts already?
These are shipped in the matplotlib git repository, so aren't strictly 
necessary.
> dev-python/pyparsing # Necessary?
Likewise.
> cairo? ( dev-python/pycairo ) # What about pango?
This is required if you want to use the GtkCairo backend. Pango is a 
dependency of cairo, but not a direct dependency of matplotlib. If your 
platform does package dependency resolution, that should be taken care 
of automatically.
> excel? ( dev-python/xlwt )
See above.
> latex? ( # Needed only for latex'ing
> virtual/latex-base
Needed to build the docs or for "true" LaTeX font support (when the 
option text.usetex is True)
> app-text/ghostscript-gpl
Needed for testing.
> app-text/poppler[utils] # Needed?
Not needed.
> dev-texlive/texlive-fontsrecommended
> )"
Possibly needed, depending how things are packaged on your system.
In addition to above, you'll need the numpy development packages. 
Optionally, you'll want PyQt4 or PySide, wxPython, pygtk (pygobject on 
Python 3) or tkinter. But you only need one GUI framework of your 
preference. If using pygtk or tkinter, you'll also need to install the 
development headers.
>
> I started to follow the development of MPL a bit and IIRC it is
> now possible to install a python3 version along with the Python2. What
> is more one can use Pyside instead of pyqt4 for qt. But what about gtk?
> What libs are needed if I want to use gtk and python3? I remember, that
> there were some issues, but do not know whether they were resolved.
The issues is that you can't use Gtk with Agg, only with Cairo under 
Python 3. I've put a mailing list message into the pygobject developers 
about adding the necessary functionality to make this work, but have 
received no response for months.
>
> Maybe it would be a good idea to reflect the Python3 status/dependencies
> in the documentation?
Yes -- those are probably static enough now to do that.
>
> Either way, thanks very much for working on the project!
You're welcome.
Mike
>
> All best,
> Ignas A.

On 5/3/2012 7:01 AM, Michael Droettboom wrote:
> On 05/03/2012 09:48 AM, Benjamin Root wrote:
>>
>>
>> On Wed, May 2, 2012 at 3:59 PM, David Erickson <der...@st... 
>> <mailto:der...@st...>> wrote:
>>
>> On 5/1/2012 5:41 AM, Benjamin Root wrote:
>>>
>>>
>>> On Tue, May 1, 2012 at 6:42 AM, David Erickson
>>> <der...@st... <mailto:der...@st...>> wrote:
>>>
>>> Hi I need to use the symlog yscale in my graph, I have a lot
>>> of data
>>> that needs to be displayed linearly, with a small fraction
>>> at the upper
>>> end of the range that needs to be displayed in log scale due
>>> to its
>>> distance from the main data. The symlog scale works great,
>>> however I'd
>>> like to adjust the actual vertical graph position where it
>>> crosses from
>>> linear to log (not the threshold), because right now only
>>> ~25% of the y
>>> space is being given to linear, and I'd like it to be more
>>> like 80%. Is
>>> this possible?
>>>
>>> Thanks!
>>> David
>>>
>>>
>>> Isn't linthreshy what you are looking for? It denotes the range
>>> where the scale is linear. So, if it is 25, then from -25 to 25
>>> the scale will be linear. After 25, it will be log.
>>>
>>> Maybe I am missing something in your description?
>>>
>>> Cheers!
>>> Ben Root
>>>
>>
>> Hi Ben,
>> No unfortunately linthreshy only controls the crossover point
>> from linear to log scale, it does not give you control over where
>> this occurs on the figure's y coordinates. I've attached a
>> picture to explain, currently the linear part of the graph is
>> only being given around 25% of the vertical space, I'd like to
>> reverse that and give linear ~75% and log at the top only the
>> remaining 25%. Is this possible? I've been digging around in
>> the SymmetricalLogScale and SymmetricalLogLocator classes and
>> can't even tell how this range is allocated.
>>
>> Thanks in advance!!
>> -David
>>
>>
>> David,
>>
>> Thanks, that is much clearer what you are looking for. You are 
>> right, I can't seem to find any sort of obvious way to get what you 
>> want. Reading the docs for the SymLog scale indicates to me that the 
>> author intended for the logrithmic portion to be most interesting and 
>> the linear portion was only supposed to be a work-around the whole 
>> log(0) issue. Could you file an issue on the github page so that we 
>> can mark it as a feature request?
>
> Just getting to this after some unexpected absences. Yes -- that is 
> how symlog was originally intended, so there isn't currently any way 
> to configure it. Please file the issue and assign it to me. I'll 
> have a look at what needs to be added to support this.
>
> Mike
Perfect, thanks Mike!
-David