matplotlib

On Saturday, June 30, 2012, Youbao Zhang wrote:

> Dear all,
>
> I successfully installed Python 3.2.3 + Numpy 1.6.2 + Matplotlib 1.2.x
> (Git version). I tried the following command sequence line by line:
>
> huskier@...$ python3.2
> Python 3.2.3 (default, Jun 30 2012, 07:14:35)
> [GCC 4.4.5] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> *>>> import matplotlib.pyplot as plt*
> *>>> plt.plot(range(10), range(10))*
> [<matplotlib.lines.Line2D object at 0x3c6f1d0>]
> *>>> plt.show()*
> >>>
>
> However, nothing happens when I typed plt.show(). There should be a figure
> window which I can get using python 2.6.
>
> I do not know what's wrong with my installation. OR matplotlib cannot be
> used with python 3? Any ideas?
>
> Best regards,
>
> Simon
>
> Most likely, you didn't have the Dec packages for any of the toolkits
available. Check your build log.

Ben Root

On 6/30/2012 11:45 AM, Youbao Zhang wrote:
> Dear all,
>
> I successfully installed Python 3.2.3 + Numpy 1.6.2 + Matplotlib 1.2.x
> (Git version). I tried the following command sequence line by line:
>
> huskier@...$ python3.2
> Python 3.2.3 (default, Jun 30 2012, 07:14:35)
> [GCC 4.4.5] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> *>>> import matplotlib.pyplot as plt*
> *>>> plt.plot(range(10), range(10))*
> [<matplotlib.lines.Line2D object at 0x3c6f1d0>]
> *>>> plt.show()*
>>>>
>
> However, nothing happens when I typed plt.show(). There should be a
> figure window which I can get using python 2.6.
>
> I do not know what's wrong with my installation. OR matplotlib cannot be
> used with python 3? Any ideas?
>
> Best regards,
>
> Simon
>

Did you create a `setup.cfg` file and enable `backend = TkAgg` before 
building matplotlib? Otherwise add a `import 
matplotlib;matplotlib.use("TkAgg")` statement at the top of the script.

Christoph

Thank you both of you.

The problem is that I did not have tk-dev packages before I compiled
Python3.2.3. After installing tk-dev and recompiled Python3.2.3 and
matplotlib 1.2.x with  a `setup.cfg` file and enable `backend = TkAgg`, I
can show the picture windows.

So exciting!

Best regards,

Simon

On Sun, Jul 1, 2012 at 3:39 AM, Christoph Gohlke <cgohlke@...> wrote:

> On 6/30/2012 11:45 AM, Youbao Zhang wrote:
> > Dear all,
> >
> > I successfully installed Python 3.2.3 + Numpy 1.6.2 + Matplotlib 1.2.x
> > (Git version). I tried the following command sequence line by line:
> >
> > huskier@...$ python3.2
> > Python 3.2.3 (default, Jun 30 2012, 07:14:35)
> > [GCC 4.4.5] on linux2
> > Type "help", "copyright", "credits" or "license" for more information.
> > *>>> import matplotlib.pyplot as plt*
> > *>>> plt.plot(range(10), range(10))*
> > [<matplotlib.lines.Line2D object at 0x3c6f1d0>]
> > *>>> plt.show()*
> >>>>
> >
> > However, nothing happens when I typed plt.show(). There should be a
> > figure window which I can get using python 2.6.
> >
> > I do not know what's wrong with my installation. OR matplotlib cannot be
> > used with python 3? Any ideas?
> >
> > Best regards,
> >
> > Simon
> >
>
> Did you create a `setup.cfg` file and enable `backend = TkAgg` before
> building matplotlib? Otherwise add a `import
> matplotlib;matplotlib.use("TkAgg")` statement at the top of the script.
>
> Christoph
>
>
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> Dear all,
>
> I have a CSV file with the first column with timestamps:
>
> 0:00:00 01/01/2007,       0.000,     10,       0.000,     10,
> 0.000,     10:
> 00:00:00 02/01/2007,       0.000,     10,       0.000,     10,
> 0.000,     10
> 00:00:00 03/01/2007,       0.000,     10,       0.000,     10,
> 0.000,     10
> ...
> 00:00:00 29/12/2009,       0.000,     10,       0.000,     10,
> 0.000,     10
> 00:00:00 30/12/2009,       0.000,     10,       0.000,     10,
> 0.000,     10
> 00:00:00 31/12/2009,       0.000,     10,       0.000,     10,
> 0.000,     10
>
> As you can see, the format is hour:minute:second (nor relevant, always
> 00) day/month/year.
>
> When loaded with mlab.csv2rec, it automatically detects them as dates
> and creates datetime objects, but it is not consistent with the
> interpretation of the dates. When the day is < 13, it interprets it as
> month/day/year. It's loaded correctly otherwise (as day/month/year). I
> could pre-process the files and change the dates format, but imho it's
> not very elegant. Any suggestion about how to address this issue?
>
> Regards,
> Sergi

You could use numpy.genfromtxt together with its `converters` parameter:

    converters : variable, optional
        The set of functions that convert the data of a column to a value.
        The converters can also be used to provide a default value
        for missing data: ``converters = {3: lambda s: float(s or 0)}``.

Cheers,
A.

On Fri, Jun 29, 2012 at 12:02 PM, Andreas Hilboll <lists@...> wrote:
>
> You could use numpy.genfromtxt together with its `converters` parameter:
>
>     converters : variable, optional
>         The set of functions that convert the data of a column to a value.
>         The converters can also be used to provide a default value
>         for missing data: ``converters = {3: lambda s: float(s or 0)}``.

I finally used:

def mkdate(text):
    return(dt.datetime.strptime(text.decode('utf8'),\
            '%H:%M:%S %d/%m/%Y'))

and

data = np.genfromtxt(\
            os.path.join(sys.argv[1],f),\
            delimiter=',',\
            skip_header=4,\
            usecols = (0, 1, 2),\
            dtype=(object, float, float),\
            converters={0: mkdate},\
            autostrip=True,\
            )

Thank you!

On Wed, Jun 27, 2012 at 5:02 PM, Daniel Platz
<mail.to.daniel.platz@...> wrote:
> Hello,
>
> I would like to plot a simple line using plt.plot(x, y, ‘w--’, lw=2)
> or with the corresponding axes instance ax.plot(x, y, ‘w--’, lw=2).
> However, I want the line to have a thin black edge like the edge of a
> marker. Is this possible? I tried to find a property of the Line2D
> object but I could not find anything. Has someone an idea?

Daniel,

Here's how civil-engineer-hack-fest that i'd use to do it:

import matplotlib.pyplot as plt
import numpy as np
x = np.arange(0,10,0.1)
y = -4 + 2*x - 1.5*x**2
fig, ax1 = plt.subplots()
ax1.plot(x, y, 'c-', lw=2.5, zorder=10)
ax1.plot(x, y, 'k-', lw=4.0, zorder=5)
plt.show()

Hope that helps.
-paul

On 06/26/2012 03:14 AM, Peter Würtz wrote:
> * Backends like svg or pdf are able to display the document upon show(). I
> don't know how this is achieved without creating a graphical user interface
> myself. The other backends don't implement it.

Not so--the non-interactive backends like svg and pdf do not do anything 
upon show(), so it sounds like nothing needs to be added to your pgf 
backend on this score.

Eric

efiring wrote:
> 
> Not so--the non-interactive backends like svg and pdf do not do anything 
> upon show(), so it sounds like nothing needs to be added to your pgf 
> backend on this score.
> 

Hmm right, when explicitly changing to non gui backends like "ps" or "pdf"
the show command is ignored too. I somehow thought that there must be an
implementation somewhere because I'll get a preview of a latex rendered
figure when using the text.usetex option.. but this option seems to trigger
a completely different rendering path anyways.

The funny thing is that when enabling text.usetex, which I'm not using in my
backend in any way, my PDF ends up with additional text elements I did not
create. I have no idea how matplotlib manages to tap into my PDF creation
process :D.

Anyway.. one less problem to worry about then :)
Thanks
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View this message in context: http://old.nabble.com/Pgf-Backend-with-Xelatex-support-tp34072290p34074505.html
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>
> Hi,
>
> When creating figures to be included in Latex documents I encountered a
> few
> problems. In the end the text rendering just doesn't blend in well, one
> way
> or another. I found that the problems can be fixed by using Xelatex, which
> provides full unicode support and is able to use the installed fonts of
> your
> operating system.
>
> I wrote a new backend that uses the "pgf" latex package for drawing
> matplotlib figures. It is compatible with pdflatex, xelatex and lualatex.
> The pgf pictures can be included in latex documents or can be directly
> compiled to PDF by the backend, utilizing the benefits of Xelatex.
>
> The code for the backend and a script creating a test figure is on github:
> https://github.com/pwuertz/matplotlib-backend-pgf/
>
> A document that demonstrates the benefits of using pgf/xelatex is also
> there:
> https://github.com/pwuertz/matplotlib-backend-pgf/raw/master/demo/demo.pdf
>
> Although I think the pgf backend is very useful already and produces
> figures
> in publication quality (an overused expression ;) ), there are still some
> loose ends. Basically, everything I need works but I don't have the time
> anymore to figure out all the rest. Maybe someone is interested in
> improving
> this backend, possibly making it a real option for the masses? I wrote
> down
> all open questions I had in TODO comments within the code. To summarize
> them:
>
> * The default font for the backend is the unicode variant of Computer
> Modern
> (CMU Serif), which might not be present on most users' systems. If you
> don't
> want to install/use it, you can just specify another (see test script). I
> could as well check for the fonts specified in the rc parameters but these
> just do fit in Latex documents.
>
> * When printing pgf commands, the actual font depends on the latex
> environment you are embedding the figure in. Matplotlib only needs a font
> for calculating the text positions and for direct PDF output.
>
> * I'm not sure how certain draw methods of the renderer should behave due
> to
> lack of documentation.
>
> * Some text properties like switching font families or making the text
> italic/bold are ignored since I did not need them.
>
> * Backends like svg or pdf are able to display the document upon show(). I
> don't know how this is achieved without creating a graphical user
> interface
> myself. The other backends don't implement it.
>
> * The method of obtaining the metrics of text elements is pretty cool I
> think (XelatexManager), but it breaks easily since there is no way of
> defining a timeout for reading the output of a subprocesses that keeps
> running during the figure creation process. Right now, if Latex doesn't
> understand a text-element the process stalls. An alternative is to run a
> new
> latex process for every single text element or start using threads.
>

Looks great! How do I use this with my currently installed matplotlib 1.1.0?

Cheers,
A.

Andreas Hilboll wrote:
> 
>> I wrote a new backend that uses the "pgf" latex package for drawing
>> matplotlib figures. It is compatible with pdflatex, xelatex and lualatex.
>> The pgf pictures can be included in latex documents or can be directly
>> compiled to PDF by the backend, utilizing the benefits of Xelatex.
>>
>> The code for the backend and a script creating a test figure is on
>> github:
>> https://github.com/pwuertz/matplotlib-backend-pgf/
> 
> Looks great! How do I use this with my currently installed matplotlib
> 1.1.0?
> 

The easiest way without touching your matplotlib installation is to fetch
"backend_pgf.py" from github and put it in the directory where you are
running your plotting script (or in any directory in python's search path).
Then have a look at "test_pgf_backend.py". It demonstrates how to select and
configure the pgf backend. Basically, you just call

matplotlib.use('module://backend_pgf')

to use it. With the backend selected, the show() command won't work anymore
since this is not a GUI backend, but you can now save the figure as ".pgf"
file (just the pgf commands for latex) or ".pdf" file (already compiled with
xelatex). Also make sure that you select a font that exists on your system

matplotlib.rcParams.update({"pgf.font": "CMU Serif"})

or you'll get an exception when saving the figure. As already said, you'll
get the best results when you install the Computer Modern Unicode Fonts
(Ubuntu Package: fonts-cmu, Manual Install:
http://sourceforge.net/projects/cm-unicode/). Be aware that if there is any
text element that produces an error in Latex the savefig call will stall
until I have found a better way to deal with such errors.


Incorporating the backend into matplotlib requires a little more work. You
have to copy the file to the folder where all the other modules reside (for
me it's /usr/lib/pymodules/python2.7/matplotlib/backends/) and then include
the "pgf" type in "backend_bases.py" one folder above. I'm not sure how to
handle the case when the user wants to create a pdf from backend_pgf instead
of backend_pdf since the only 'switch' is the extension of the file. But I'd
suggest to use the matplotlib.use method for now..

Good luck ;)
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On Mon, Jun 25, 2012 at 10:03 AM, julien tayon <julien@...> wrote:

> Hello,
>
> I made a crude sonogram https://gist.github.com/2983547 with the note
> names instead of the frequency. But, It really angers me not to be
> able to have a log scale for the frequency.
>
> Does any well known workaround exists?
> Is there an easy way to grosso modo do :
> x = time, y = frequency, z=amplitude of spectre with something like a
> specter of one croche at time = t according to the bpm and make an y
> scale logarithmic, then project the amplitude (z) with a colormap on
> x,y plane according to the amplitude, and and have 3D representation?
>
> Basically, I guess it boils down to know if combining those 2 is
> possible :
> http://matplotlib.sourceforge.net/examples/mplot3d/contourf3d_demo2.html
> + log scale for y. I guess I could improve the result by using
> logscale on Z and colormap
> (
> http://stackoverflow.com/questions/5748076/python-matplotlib-contour-plot-logarithmic-color-scale
> )
>
>
> Since it is only for fun, and I don't want to invest myself too much
> my question is really did I missed something while googling for an
> easy solution and if so, what are the good keywords?
>
> Cheers
> --
> Julien
>
>
Julien,

I am not entirely sure if I understood your question right, but I think I
can answer part of it.  With respect to using a log scale for 3d axes, it
*should* work, but unfortunately, I have never been able to get it to work
properly.  It is an outstanding bug for mplot3d.  The "work-around" is to
do the log transformation yourself for the input x/y/z data.

However, there is no reason why you can't use a LogNorm for your colormap.
Just so you understand, color scales in matplotlib are done in two parts.
We have the "Norm" objects which takes data and produce values between 0
and 1 (and handles bad, over, and under values accordingly).  And we have
"colormap" objects that take values from 0 to 1 and produce an RGB(A)
array.  By default, most functions in matplotlib will use the min/max of
the input data to automatically create a linear Norm object, and will use
the "prism" colormap.  However, you can create a LogNorm object and pass it
in as the 'norm' kwarg in most plotting functions.

I hope this helps!
Ben Root

On Mon, Jun 25, 2012 at 1:12 PM, mogliii <mogliii@...> wrote:

> Hi,
>
> In my script a variable number of graphs is generated. I want to place
> them in one column with arbitrary number of rows onto an A4 canvas (for
> pdf export).
>
> Unfortunately the figsize directive seems to have no effect. The figure
> is always 8x6 inch.
>
> Which code do I have to use in this case?
>
>
> My minimal code:
> #######################################
>
> import matplotlib.pyplot as plt
> from matplotlib.backends.backend_pdf import PdfPages
> import numpy as np
>
> x = np.arange(10)
> y = np.arange(10)
>
> fig_width_cm = 21                         # A4 page
> fig_height_cm = 29.7
> inches_per_cm = 1 / 2.58               # Convert cm to inches
> fig_width = fig_width_cm * inches_per_cm # width in inches
> fig_height = fig_height_cm * inches_per_cm       # height in inches
> fig_size = [fig_width, fig_height]
>
>
> pdf = PdfPages('outfile.pdf')
> fig = plt.figure(figsize = fig_size)
> allplots = 3  # This is the variable number of subplots
> f, axarr = plt.subplots(allplots, 1)
>
>
> for plot in range(allplots):
>    axarr[plot].plot(x+plot, y)
>
> pdf.savefig()
> pdf.close()
>
>
Your call to "plt.subplots" is creating a new figure object, which never
gets the figsize parameter (only the old figure object has that set).

Cheers!
Ben Root

On 25/06/12 18:30, Benjamin Root wrote:
>
>
>
> Your call to "plt.subplots" is creating a new figure object, which
> never gets the figsize parameter (only the old figure object has that
> set).
>
> Cheers!
> Ben Root
>

Hi,
indeed you are right. I added "f.set_size_inches(fig_size)" and it works
Also I had a wrong conversion of inch to cm (2.58 before).

Thank you for your help,
Mogliii



The final code:
#################

import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import numpy as np

x = np.arange(10)
y = np.arange(10)

fig_width_cm = 21                         # A4 page
fig_height_cm = 29.7
inches_per_cm = 1 / 2.54              # Convert cm to inches
fig_width = fig_width_cm * inches_per_cm # width in inches
fig_height = fig_height_cm * inches_per_cm       # height in inches
fig_size = [fig_width, fig_height]


pdf = PdfPages('outfile.pdf')
allplots = 3  # This is the variable number of subplots
f, axarr = plt.subplots(allplots, 1)
f.set_size_inches(fig_size)


for plot in range(allplots):
    axarr[plot].plot(x + plot, y)

pdf.savefig()
pdf.close()

Even better:

f, axarr = plt.subplots(allplots, 1, figsize = fig_size)

Its always difficult to predict which **kwargs could/would be valid...