matplotlib-users Mailing List for matplotlib (Page 3)

2014-03-22 20:23 GMT+01:00 Christopher Kuhlman <cku...@vb...>:
[...]
> For example, most recently, I am plotting 3 data sets; each data set has about 90,000 points.  If I plot all three sets in one PDF figure, the file size is over 2MB.
> This seems absurd to me.  I used R plotting for many years (again, my own homegrown code, for 6 years) and never had this issue, and I was making these kinds of plots/figures.
>
> I thought it may be a vector/raster issue, but the following web page says that PDF are generated as vector image, which, to my understanding (which could be wrong), is the more compact format.
> http://matplotlib.org/faq/usage_faq.html
[...]

Roughly speaking, size of vector files depend on the number of points
while size of raster files depends on the number of pixels. For your
use case (many points, small images) raster output should be more
compact.

Goyo

Hello:

I use matplotlib to generate x-y data plots; i.e., 2-D plots.  The problem is that the output files (the PDF files containing plots that are generated with matplotlib) are huge.  I can generate files that are 100's of KB or even MBs.  This seems absurd to me.  These file sizes cause programs that use them to come to a grinding halt.  My goal is to reduce the plot files that I produce with matplotlib.  Details follow.


----------

I use matplotlib from EPD.
Enthought Canopy Python 2.7.3 | 64-bit | (default, Aug  8 2013, 05:37:06) 

Matplotlib version:
>>> print matplotlib.__version__
1.3.0

OS:
I'm using Mac OS X Version 10.8.4.

----------

I use a home-grown code whose starting point was an example code on matplotlib website.

My relevant imports are:

import numpy
import scipy
import pylab
import matplotlib.pyplot as plt
import matplotlib

My plotting code lines are:


        ## PDF.
        outfile = "basefile" + ".pdf"
        ## pylab.savefig(outfile, bbox_inches=0)
        pylab.savefig(outfile,bbox_inches='tight')


----------

My PDF files contain simple plots which consist of (a) data points only, (b) lines between data points (data points not plotted), or (c) both data points and lines.

I have a consistent problem in that the files produced have sizes that seem way too big.
For example, most recently, I am plotting 3 data sets; each data set has about 90,000 points.  If I plot all three sets in one PDF figure, the file size is over 2MB.
This seems absurd to me.  I used R plotting for many years (again, my own homegrown code, for 6 years) and never had this issue, and I was making these kinds of plots/figures.

I thought it may be a vector/raster issue, but the following web page says that PDF are generated as vector image, which, to my understanding (which could be wrong), is the more compact format.
http://matplotlib.org/faq/usage_faq.html

Is there a command I can use to reduce the file size?  Since I am using these in reports and publications, the figures are almost always less than 3 inches by 3 inches in size; i.e., I do not have issues about taking a raster figure and trying to blow it up.  So I am not concerned about pixelation problems that occur when an image is increased in size.

Thank you very much.

c

Hi,

I am using an IPython notebook style that has a soft, yellow background
that I think is more appealing that white.  When I make a plot, I'd like
the background of the plot (ie, everything that is outside the x and y
axis) to be the same color.  I'm trying to change the figure.facecolor
parameter through rc params but I don't see any changes.  Is
figure.facecolor event he correct parameter?

Has anyone done this successfully?

Hi,

I am trying to plot a heat map using imshow. My data has 34 rows and 34
columns, so lower limit is 0 and upper is 33, but when I give these limits,
it partially removes some of the cells (see 33.png), when I give the limits
from 0 to 34, there is an extra white space inserted in the heat map which
isn't part of my data(see 34.png), my next try was to set limits from 0 to
33.5 which sort of solves this problem as the previously concealed colors
are now revealed(see 33.5.png), but now I see unqual grid cells on the
boundaries of the map (they are almost half the size of the grids cells
within the map).

My question is if my data has exactly 34 columns and 34 rows, why do I need
an extra 0.5 to do this. Secondly why is that one grid square encompasses
2-3 colors, shouldn't it just be one color per cell of the grid, which is
what I want to see in the map, how can I set the grid lines in such a
manner that one color appears per grid cell- is this because I use imshow?

Here is a snippet of my code:


fig = plt.figure(figsize=(25,25))
cmap.set_over('green')
cmap.set_under('grey')
gs=gridspec.GridSpec(1, 2,height_ratios=[1,1,-2,2]
,width_ratios=[1,1,-2,2],hspace=0,wspace=0)    phyl_ax=plt.subplot(gs[0])
ht_ax=plt.subplot(gs[1])
ht_ax.set_xlim(34,0) ## tried (33.5-0) and (33-0)
ht_ax.set_ylim(34,0) ## tried (33.5-0) and (33-0)
ht_ax.grid(True, which='both')
xticks=range(34)
ht_ax.xaxis.set_ticks(xticks)
ht_ax.yaxis.set_ticks(xticks)
for tick in ht_ax.xaxis.get_major_ticks():
        tick.label1.set_horizontalalignment('right')
img = ht_ax.imshow(data, cmap=cmap,
interpolation='nearest',vmax=threshold,aspect='auto')
phyl_ax.imshow(img,interpolation='bilinear',aspect='auto')

Note that ht_ax is what I use to draw the heat map

Does anyone see where I am going wrong?
Appreciate any help provided in advance!!

--Asma

Hi matplotlib users,

I am currently performing some experiments with plotting in matplotlib for
at web application. One thing I have noticed is that my image test sizes
are reduced by a factor 4.5 when not using antialiasing. And that for
pcolormesh the time it takes to produce a plot without antialiasing is
approximately half the time it takes to produce one with. And for my
application I do not really need antialiasing when the cost is so large.

I was therefore wondering whether it is possible to disable antialiasing
for pcolorfast? Otherwise I guess I will stick with pcolormesh and contourf.

Best regards,
Jesper

Dear Arnaldo,

sorry for the delay in reply. Thanks a lot. This solves my problem well.

Cheers,

Chao


On Sun, Mar 16, 2014 at 7:27 AM, Arnaldo Russo <arn...@gm...>wrote:

> Dear Chao,
>
> You could try this,
>
> import matplotlib
> import matplotlib.pyplot as plt
>
> # create a color bar with:
> sm = plt.cm.ScalarMappable(cmap=plt.get_cmap('Reds'))
> sm.set_array(range(10))
>
> # create an horizontal colorbar and put the ticks on the top.
> # in your case, you could plot colorbar on top, and tick at 'bottom'
> cb = plt.colorbar(sm, orientation='horizontal', location=1.0)
> cb.ax.xaxis.set_ticks_position('top')
> plt.show()
>
> Another way, you could find useful a function written by Ryan May [0]
>
> Hope that fits.
>
> Arnaldo.
>
> [0]
> https://www.mail-archive.com/mat...@li.../msg07447.html
>
>
> ---
> *Arnaldo D'Amaral Pereira Granja Russo*
> Lab. de Estudos dos Oceanos e Clima
> Instituto de Oceanografia - FURG
>
>
>
>
> 2014-03-10 14:39 GMT-03:00 Chao YUE <cha...@gm...>:
>
>> Dear all,
>>
>> I am using the matplotlib 1.2.0 version, is there some way to put the
>> label above the horizontal colorbar? like in the attached example, I would
>> like the labels to be shown above the colorbar?
>>
>> thanks a lot in advance,
>>
>> 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
>>
>> ************************************************************************************
>>
>>
>> ------------------------------------------------------------------------------
>> Learn Graph Databases - Download FREE O'Reilly Book
>> "Graph Databases" is the definitive new guide to graph databases and their
>> applications. Written by three acclaimed leaders in the field,
>> this first edition is now available. Download your free book today!
>> http://p.sf.net/sfu/13534_NeoTech
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>


-- 
***********************************************************************************
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
************************************************************************************

Hello.

Where do I look at so as to build my own patch ? Is it enough to look at,
for example, the class defining rectangles ?

Another question. Let suppose that I want to manage all the drawings, what
will I have to do ? Imagine for example that I want to produce a TiKz code
of a plot.

Best regards.
Christophe BAL

Stupid me! I overlooked parameter 'ax' of class Basemap. You can pass an
axis when creating a Basemap instance:

ax = fig.add_axes([0., 0., 1., 1.])
map = Basemap(...., ax=ax)

Best,
Remo


On 03/19/2014 04:41 PM, Remo Goetschi wrote:
> Dear matplotlib users,
> 
> I'm having trouble using Basemap through the object oriented interface
> of Matplotlib. All the examples on the website use pyplot. But that does
> not work if plots are generated in a parallel environment, i.e., in a
> web application, since pyplot is obviously not thread safe.
> 
> Does anyone have a working example of Basemap without pyplot?
> One of the issues I'm having is that
> 
> coastlines = map.drawcoastlines(linewidth=0.25)
> 
> does not show any coastlines. The underlying figure is created like this:
> 
> from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
> from matplotlib.figure import Figure, Axes
> 
> fig = Figure()
> canvas = FigureCanvas(fig)
> ax = Axes(fig, [0., 0., 1., 1.])
> fig.add_axes(ax)
> 
> I feel a bit lost here. Any help is appreciated.
> 
> Cheers,
> Remo
> 
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/13534_NeoTech
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 

Dear matplotlib users,

I'm having trouble using Basemap through the object oriented interface
of Matplotlib. All the examples on the website use pyplot. But that does
not work if plots are generated in a parallel environment, i.e., in a
web application, since pyplot is obviously not thread safe.

Does anyone have a working example of Basemap without pyplot?
One of the issues I'm having is that

coastlines = map.drawcoastlines(linewidth=0.25)

does not show any coastlines. The underlying figure is created like this:

from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
from matplotlib.figure import Figure, Axes

fig = Figure()
canvas = FigureCanvas(fig)
ax = Axes(fig, [0., 0., 1., 1.])
fig.add_axes(ax)

I feel a bit lost here. Any help is appreciated.

Cheers,
Remo

Hello everyone,

A couple of weeks, Euroscipy launched its call for proposal! This year, the
conference will take place in Cambridge (UK), from the 27th to 30th of
August.
Don't hesitate to submit an abstract!

For the second year in a row, participants will have the opportunity to
submit a paper to the proceedings.

Cheers,
N

---------- Forwarded message ----------
From: Ralf Gommers <ral...@gm...>
Date: 5 March 2014 20:37
Subject: [euroscipy-org] EuroSciPy 2014 Call for Abstracts
To: Organisation of EuroScipy <eur...@py...>,
con...@py..., num...@go..., Discussion of Numerical
Python <num...@sc...>, SciPy Users List <sci...@sc...>


Dear all,

EuroSciPy 2014, the Seventh Annual Conference on Python in Science, takes
place in Cambridge, UK on 27 - 30 August 2013. The conference features two
days of tutorials followed by two days of scientific talks. The day after
the main conference, developer sprints will be organized on projects of
interest to attendees.

The topics presented at EuroSciPy are very diverse, with a focus on
advanced software engineering and original uses of Python and its
scientific libraries, either in theoretical or experimental research, from
both academia and the industry. The program includes keynotes, contributed
talks and posters.

Submissions for talks and posters are welcome on our website (http://www.
euroscipy.org/2014/). In your abstract, please provide details on what
Python tools are being employed, and how. The deadline for submission is 14
April 2013.

Also until 14 April 2014, you can apply for a sprint session on 31 August
2014. See https://www.euroscipy.org/2014/calls/sprints/ for details.

Important dates:
April 14th: Presentation abstracts, poster, tutorial submission deadline.
Application for sponsorship deadline.
May 17th: Speakers selected
May 22nd: Sponsorship acceptance deadline
June 1st: Speaker schedule announced
June 6th, or 150 registrants: Early-bird registration ends
August 27-31st: 2 days of tutorials, 2 days of conference, 1 day of sprints

We look forward to an exciting conference and hope to see you in Cambridge
in August!

The EuroSciPy 2014 Team
http://www.euroscipy.org/2014/

Conference Chairs
--------------------------
Mark Hayes, Cambridge University, UK
Didrik Pinte, Enthought Europe, UK

Tutorial Chair
-------------------
David Cournapeau, Enthought Europe, UK

Program Chair
--------------------
Ralf Gommers, ASML, The Netherlands

Program Committee
-----------------------------
Tiziano Zito, Humboldt-Universität zu Berlin, Germany
Pierre de Buyl, Université libre de Bruxelles, Belgium
Emmanuelle Gouillart, Joint Unit CNRS/Saint-Gobain, France
Konrad Hinsen, Centre National de la Recherche Scientifique (CNRS), France
Raphael Ritz, Garching Computing Centre of the Max Planck Society, Germany
Stéfan van der Walt, Applied Mathematics, Stellenbosch University, South
Africa
Gaël Varoquaux, INRIA Parietal, Saclay, France
Nelle Varoquaux, Mines ParisTech, France
Pauli Virtanen, Aalto University, Finland
Evgeni Burovski, Lancaster University, UK
Robert Cimrman, New Technologies Research Centre, University of West
Bohemia, Czech Republic
Almar Klein, Cybermind, The Netherlands

Organizing Committee
------------------------------
Simon Jagoe, Enthought Europe, UK
Pierre de Buyl, Université libre de Bruxelles, Belgium


_______________________________________________
euroscipy-org mailing list
eur...@py...
https://mail.python.org/mailman/listinfo/euroscipy-org

Hello,
I've found how to do that.

   1. Donwload the binary ffmpeg from here <http://ffmpegmac.net/>.
   2. Copy this binary file into the folder anaconda/bin.

That's all !



2014-03-19 10:40 GMT+01:00 Christophe Bal <pro...@gm...>:

> Hello.
>
> In this page<http://matplotlib.org/1.3.1/examples/animation/moviewriter.html>,
> there is the example *moviewriter.py*. I can't use, and the error message
> is the following one.
>
> *File "//anaconda/lib/python2.7/site-packages/matplotlib/animation.py",
> line 64, in __getitem__    return self.avail[name]*
> *KeyError: 'ffmpeg'*
>
> Is there a way to use such kind of functionnality with Anaconda ?
>
> If not, is there a way to produce at least a folder containing each frame
> picture ?
>
> Christophe BAL
>

Hello.

In this page<http://matplotlib.org/1.3.1/examples/animation/moviewriter.html>,
there is the example *moviewriter.py*. I can't use, and the error message
is the following one.

*File "//anaconda/lib/python2.7/site-packages/matplotlib/animation.py",
line 64, in __getitem__    return self.avail[name]*
*KeyError: 'ffmpeg'*

Is there a way to use such kind of functionnality with Anaconda ?

If not, is there a way to produce at least a folder containing each frame
picture ?

Christophe BAL

Hello,

I have a good news for the Mac users who want to play with animations. I've
reinstalled Maverick OS on my Mac without any softwares, this is called a
clean installation, and then I've installed Anaconda, and XQuark (see
this<http://support.apple.com/kb/ht5293>
).

To make animations work, you just have to use the following two lines
before any other matplotlib imports.

import matplotlib
matplotlib.use('TkAgg')

I think this will work for any Mac OS supported by Anaconda. The use of
XQuark is only needed for Maverick.


2014-03-12 12:17 GMT+01:00 Christophe Bal <pro...@gm...>:

> I forgot to say that being under Mac O$, I can use with animate... So I do
> not know if i can build an infinite animation. Is it possible ?
>
>
> 2014-03-12 12:01 GMT+01:00 Christophe Bal <pro...@gm...>:
>
> Yes I've read it.
>>
>>
>>    1. It proposes to update infos about the figure, this is what I do in
>>    my update function which only change the color of one random rectangle
>>    every time that a timer asks to do it.
>>    2. Then it is said to use plt.draw(), which is what I do. If I use a
>>    timer, each draw takes merely 2 seconds for 64**2 fixed initial
>>    squares instead of being very quick for 16**2 fixed initial squares. It is
>>    certain that the draw is indeed a redraw.
>>
>>
>>
>> 2014-03-12 11:49 GMT+01:00 Derek <gam...@gm...>:
>>
>> Did you look at the link; the person updating the plots had the same
>>> issue - i.e. he did not know when the data would arrive or how long it
>>> would be active for.  That sounds like your situation?
>>>
>>>
>>> On 12 March 2014 11:59, Christophe Bal <pro...@gm...> wrote:
>>>
>>>> I forgot to say that here the use of animations is not good because, I
>>>> have no max playing time.
>>>>
>>>>
>>>> 2014-03-12 10:56 GMT+01:00 Christophe Bal <pro...@gm...>:
>>>>
>>>> Hello.
>>>>>
>>>>> First of all, I forgot the link to my post : here it is<http://stackoverflow.com/questions/22320407/matplotlib-update-only-some-parts-of-a-figure>
>>>>> .
>>>>>
>>>>> Yes, for pedagogical reason, I would like to use matplotlib for
>>>>> beginner programmers, like me :-), such as to do some 80 old school games.
>>>>>
>>>>> The problem I met using the draw method is that it takes 2 seconds for
>>>>> a figure of 64**2 squares. This is due to the fact that everythin is
>>>>> redraw. Here is my update method.
>>>>>
>>>>> *------------------------------------------------*
>>>>> *def update():*
>>>>> *    global colors, width, height*
>>>>>
>>>>> *    x = randint(0, width - 1)*
>>>>> *    y = randint(0, height - 1)*
>>>>>
>>>>> *    plotgrid[y][x].set_facecolor(choice(colors))*
>>>>>
>>>>> *    plt.draw()*
>>>>>
>>>>>
>>>>>
>>>>> 2014-03-12 10:44 GMT+01:00 Derek <gam...@gm...>:
>>>>>
>>>>> Its not really clear what you are trying to achieve (using Matplotlib
>>>>>> to play Tetris??); but this have some pointers:
>>>>>>
>>>>>>
>>>>>> http://stackoverflow.com/questions/10944621/dynamically-updating-plot-in-matplotlib
>>>>>>
>>>>>>
>>>>>> On 12 March 2014 11:33, Christophe Bal <pro...@gm...> wrote:
>>>>>>
>>>>>>> Hello.
>>>>>>>
>>>>>>> I've poste here a question but no one seems to have an hint to give
>>>>>>> so I repeat my question here.
>>>>>>>
>>>>>>> In the attached Python 3 code, I draw n**2 squares in black and then
>>>>>>> I dynamically change in a random way the colors of some squares.
>>>>>>>
>>>>>>> The problem I met is that at each new random choice, I redraw all
>>>>>>> the squares. I know that it is stupid for large number of squares.
>>>>>>>
>>>>>>> Is there a way to change some propriety of one square, and then to
>>>>>>> ask to matplotlib to redraw only what have changed ? I'm looking for
>>>>>>> something similar to `blint` for animations.
>>>>>>>
>>>>>>> Christophe BAL
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Learn Graph Databases - Download FREE O'Reilly Book
>>>>>>> "Graph Databases" is the definitive new guide to graph databases and
>>>>>>> their
>>>>>>> applications. Written by three acclaimed leaders in the field,
>>>>>>> this first edition is now available. Download your free book today!
>>>>>>> http://p.sf.net/sfu/13534_NeoTech
>>>>>>> _______________________________________________
>>>>>>> Matplotlib-users mailing list
>>>>>>> Mat...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

Thank you both a lot,

no idea why I've overseen this.

Am 17.03.2014 20:13, schrieb Eric Firing:
> On 2014/03/17 3:31 AM, Florian M. Wagner wrote:
>> Dear users,
>>
>> I would like label my subplots with a horizontally left-aligned letter
>> (wanted by the journal) and the normal, centered axes title, which
>> should both be vertically in line. The following example does not work:
>>
>>      from matplotlib import pyplot as plt
>>      import numpy as np
>>
>>      fig, ax1 = plt.subplots()
>>      x = np.linspace(1,10)
>>      y = (sin(x))
>>      ax1.plot(x,y)
>>
>>      def subplot_label(ax, letter, title):
>>           title = ax.set_title(title)
>>           pos = title.get_position()
>>           va = title.get_va()
>>           ax.text(0, pos[1], letter, transform=ax.transAxes,
>>      verticalalignment=va)
>>
>>      subplot_label(ax1, 'a)', 'This text is not aligned with the label')
>>
>>
>> Which property of the axes title am I missing?
> Is the following what you need?
>
> http://matplotlib.org/examples/pylab_examples/titles_demo.html
>
> Eric
>
>> Thank you for your help
>>
>
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/13534_NeoTech
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Hi,

I am very new to python, so sorry if the question is basic.

I am also very new to Django. I followed the instructions on
https://docs.djangoproject.com/en/1.6/intro/tutorial01/ through tutorial 4
to set up a sample webpage and play around with it.

I would like to generate plots via matplotlib and display the png files on
the webpage. However, I am not sure where to start. I looked at the
cookbook here:
http://wiki.scipy.org/Cookbook/Matplotlib/Django

but I was not sure which urls.py the recommended change needs to be made to
and where charts.py should go.

Does anyone know how to embed an image in a webpage. Is there a step by
step tutorial I could follow. I found some tutorials but they were dated
and do not work with the latest versions. I am using for python 2.7.5,
matplotlib u'1.4.x' and django 1.6.2.

Thanks,
Aarthi

On Mon, Mar 17, 2014 at 4:11 PM, Christophe Bal <pro...@gm...> wrote:

> Hello,
> does matplotlib can use a PySide backend ?
>
> I ask this question because PySide is installed with Anaconda.
>

The Qt4 backend can use either PySide or PyQt. It should use either if
they're installed.

Ryan

-- 
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma

Hello,
does matplotlib can use a PySide backend ?

I ask this question because PySide is installed with Anaconda.

Christophe BAL

Hi Oliver, thanks for the reply. I know about contourf and have tried it
before but couldn't get it working, I don't really understand the data
objects in python (I come from a PHP background) i.e what a numpy object is
and so on, so I was hoping someone with more experience in this could help
me out, hopefully take a quick look through my script and find a silly
mistake.

As far as my script is concerned you can just save it as a py file and run
it with the params I have specified if you wanted to see it working so its
not like I have done nothing and just asked for someone to write my entire
script, I have spent quite some time trying to work it out for myself :)

Thanks anyway



--
View this message in context: http://matplotlib.1069221.n5.nabble.com/matplolib-imshow-contour-heatmap-tp43078p43086.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

On 2014/03/17 3:31 AM, Florian M. Wagner wrote:
> Dear users,
>
> I would like label my subplots with a horizontally left-aligned letter
> (wanted by the journal) and the normal, centered axes title, which
> should both be vertically in line. The following example does not work:
>
>     from matplotlib import pyplot as plt
>     import numpy as np
>
>     fig, ax1 = plt.subplots()
>     x = np.linspace(1,10)
>     y = (sin(x))
>     ax1.plot(x,y)
>
>     def subplot_label(ax, letter, title):
>          title = ax.set_title(title)
>          pos = title.get_position()
>          va = title.get_va()
>          ax.text(0, pos[1], letter, transform=ax.transAxes,
>     verticalalignment=va)
>
>     subplot_label(ax1, 'a)', 'This text is not aligned with the label')
>
>
> Which property of the axes title am I missing?

Is the following what you need?

http://matplotlib.org/examples/pylab_examples/titles_demo.html

Eric

>
> Thank you for your help
>

Florian,

I think that you need to add the ax.titleOffsetTrans to the ax.transAxes transformation.

ax.text(0,pos[1],letter,transform=ax.transAxes+ax.titleOffsetTrans,va=va)

-Sterling

On Mar 17, 2014, at 6:31AM, Florian M. Wagner wrote:

> Dear users,
> 
> I would like label my subplots with a horizontally left-aligned letter (wanted by the journal) and the normal, centered axes title, which should both be vertically in line. The following example does not work: 
> 
> from matplotlib import pyplot as plt
> import numpy as np
> 
> fig, ax1 = plt.subplots()
> x = np.linspace(1,10)
> y = (sin(x))
> ax1.plot(x,y)
> 
> def subplot_label(ax, letter, title):
>     title = ax.set_title(title)
>     pos = title.get_position()
>     va = title.get_va()
>     ax.text(0, pos[1], letter, transform=ax.transAxes, verticalalignment=va)
>  
> subplot_label(ax1, 'a)', 'This text is not aligned with the label')
> 
> Which property of the axes title am I missing?
> 
> Thank you for your help
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/13534_NeoTech_______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Dear users,

I would like label my subplots with a horizontally left-aligned letter 
(wanted by the journal) and the normal, centered axes title, which 
should both be vertically in line. The following example does not work:

    from matplotlib import pyplot as plt
    import numpy as np

    fig, ax1 = plt.subplots()
    x = np.linspace(1,10)
    y = (sin(x))
    ax1.plot(x,y)

    def subplot_label(ax, letter, title):
         title = ax.set_title(title)
         pos = title.get_position()
         va = title.get_va()
         ax.text(0, pos[1], letter, transform=ax.transAxes,
    verticalalignment=va)

    subplot_label(ax1, 'a)', 'This text is not aligned with the label')


Which property of the axes title am I missing?

Thank you for your help

The matplotlib function contourf() should do what you want. Have a look at
this example:
http://matplotlib.org/examples/pylab_examples/contourf_demo.html

I apologize if it is not what you're looking for. I haven't read your whole
script, because it is not *a minimal working example* (http://www.sscce.org/)
and I'm not going to do your homework. If, after having tried contourf, you
find a bug or an explained feature, please do post again.


2014-03-15 19:06 GMT+01:00 sweep <rem...@gm...>:

> Hi, im trying to create a heatmap/colourmap/contour style plot similar to
> http://www.idlcoyote.com/cg_tips/outcontourbar.png but I cant seem to get
> it
> working correctly. The code takes a number of parameters on the command
> line
> because it is passed by an external PHP script. Essentially its a list of
> lat/lon/values which I want to interpolate and plot but I cant get anything
> like the image above, I cant get the vmin/vmax to work for the colorbar and
> I dont know why the whole plot is squared off rather than fading to white
> if
> you see what I mean
>
> import os
> import tempfile
> import math
> os.environ['MPLCONFIGDIR'] = tempfile.mkdtemp()
> import argparse
> import numpy as np
> import matplotlib
> matplotlib.use('Agg')
> import matplotlib.pyplot as plt
> import scipy.interpolate
>
> width = 800
> height = 600
>
> lat_min = []
> lon_min = []
> lat_max = []
> lon_max = []
>
> # assumes lat is y, lon is x, and image is 800x600
> def latToXY(lat):
>         global width, height, lat_min, lat_max
>         y = ((lat - lat_min) / (lat_max - lat_min)) * height
>         #print y
>         return y
>
> def lonToXY(lon):
>         global width, height, lon_min, lon_max
>         lon = math.fabs(lon)
>         x = ((lon - lon_min) / (lon_max - lon_min)) * width
>         #print x
>         return x
>
> def scipy_idw(x, y, z, xi, yi):
>     #interp = scipy.interpolate.Rbf(x, y, z, function='linear')
>     interp = scipy.interpolate.Rbf(x, y, z)
>     return interp(xi, yi)
>
> def plot(x,y,z,grid,legend_min,legend_max,filename):
>     plt.figure()
>     fig = plt.imshow(grid, vmin=legend_min, vmax=legend_max, extent=[0,
> 1024, 0, 768])
>     fig.axes.get_xaxis().set_visible(False) # hide axis labels
>     fig.axes.get_yaxis().set_visible(False)
>     #plt.hold(True)
>     plt.scatter(x,y,c=z)
>     plt.colorbar()
>     plt.savefig(filename)
>
> # grab all floats from command line
> parser = argparse.ArgumentParser()
> parser.add_argument('--l1', type=str)
> parser.add_argument('--l2', type=str)
> parser.add_argument('--l3', type=str)
> parser.add_argument('--min', type=str)
> parser.add_argument('--max', type=str)
> parser.add_argument('--filename', type=str)
> args = parser.parse_args()
>
> # create a list by splitting at the comma
> l1_list = args.l1.split(',') # ['1','2','3','4']
> l2_list = args.l2.split(',')
> l3_list = args.l3.split(',')
>
> legend_min = float(args.min)
> legend_max = float(args.max)
> filename = args.filename
>
> # convert string list to list of floats
> for i in range(len(l1_list)):
>         l1_list[i] = float(l1_list[i])
>         l2_list[i] = float(l2_list[i])
>         l3_list[i] = float(l3_list[i])
>
> lat_min = min( math.fabs(yy) for yy in l2_list )
> lat_max = max( math.fabs(yy) for yy in l2_list )
> lon_min = min( math.fabs(xx) for xx in l1_list )
> lon_max = max( math.fabs(xx) for xx in l1_list )
>
> # convert list of floats to x,y
> for i in range(len(l1_list)):
>         l1_list[i] = lonToXY(l1_list[i])
>         l2_list[i] = latToXY(l2_list[i])
>
> # convert list to numpy array
> x = np.array(l1_list)
> y = np.array(l2_list)
> z = np.array(l3_list)
>
> #print x
> #print y
> #print z
> nx, ny = 50, 50
> xi, yi = np.linspace(x.min(), x.max(), nx), np.linspace(y.min(), y.max(),
> ny)
> xi, yi = np.meshgrid(xi, yi)
> xi, yi = xi.flatten(), yi.flatten()
>
> grid2 = scipy_idw(x,y,z,xi,yi)
> grid2 = grid2.reshape((ny, nx))
>
> plot(x,y,z,grid2,legend_min,legend_max,filename)
>
> I call the script with the following parameters:
>
> plot.py --l1=-1.8791363,-1.8786206,-1.8796862,-1.878171
> --l2=57.458459,57.458153,57.458495,57.458036 --l3=42.3,37.8,43.5,47.7
> --min=0 --max=100 --filename=/tmp/plot.png
>
>
>
> Any help is greatly appreciated
>
> Thanks
>
>
>
> --
> View this message in context:
> http://matplotlib.1069221.n5.nabble.com/matplolib-imshow-contour-heatmap-tp43078.html
> Sent from the matplotlib - users mailing list archive at Nabble.com.
>
>
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/13534_NeoTech
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Dear Chao,

You could try this,

import matplotlib
import matplotlib.pyplot as plt

# create a color bar with:
sm = plt.cm.ScalarMappable(cmap=plt.get_cmap('Reds'))
sm.set_array(range(10))

# create an horizontal colorbar and put the ticks on the top.
# in your case, you could plot colorbar on top, and tick at 'bottom'
cb = plt.colorbar(sm, orientation='horizontal', location=1.0)
cb.ax.xaxis.set_ticks_position('top')
plt.show()

Another way, you could find useful a function written by Ryan May [0]

Hope that fits.

Arnaldo.

[0]
https://www.mail-archive.com/mat...@li.../msg07447.html


---
*Arnaldo D'Amaral Pereira Granja Russo*
Lab. de Estudos dos Oceanos e Clima
Instituto de Oceanografia - FURG




2014-03-10 14:39 GMT-03:00 Chao YUE <cha...@gm...>:

> Dear all,
>
> I am using the matplotlib 1.2.0 version, is there some way to put the
> label above the horizontal colorbar? like in the attached example, I would
> like the labels to be shown above the colorbar?
>
> thanks a lot in advance,
>
> 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
>
> ************************************************************************************
>
>
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/13534_NeoTech
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>

Hi, im trying to create a heatmap/colourmap/contour style plot similar to
http://www.idlcoyote.com/cg_tips/outcontourbar.png but I cant seem to get it
working correctly. The code takes a number of parameters on the command line
because it is passed by an external PHP script. Essentially its a list of
lat/lon/values which I want to interpolate and plot but I cant get anything
like the image above, I cant get the vmin/vmax to work for the colorbar and
I dont know why the whole plot is squared off rather than fading to white if
you see what I mean

import os    
import tempfile
import math
os.environ['MPLCONFIGDIR'] = tempfile.mkdtemp()
import argparse
import numpy as np
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import scipy.interpolate

width = 800
height = 600

lat_min = []
lon_min = []
lat_max = []
lon_max = []

# assumes lat is y, lon is x, and image is 800x600
def latToXY(lat):
	global width, height, lat_min, lat_max
	y = ((lat - lat_min) / (lat_max - lat_min)) * height
	#print y
	return y

def lonToXY(lon):
	global width, height, lon_min, lon_max
	lon = math.fabs(lon)	
	x = ((lon - lon_min) / (lon_max - lon_min)) * width
	#print x
	return x

def scipy_idw(x, y, z, xi, yi):
    #interp = scipy.interpolate.Rbf(x, y, z, function='linear')
    interp = scipy.interpolate.Rbf(x, y, z)
    return interp(xi, yi)

def plot(x,y,z,grid,legend_min,legend_max,filename):
    plt.figure()
    fig = plt.imshow(grid, vmin=legend_min, vmax=legend_max, extent=[0,
1024, 0, 768])
    fig.axes.get_xaxis().set_visible(False) # hide axis labels
    fig.axes.get_yaxis().set_visible(False)
    #plt.hold(True)
    plt.scatter(x,y,c=z)
    plt.colorbar()
    plt.savefig(filename)

# grab all floats from command line
parser = argparse.ArgumentParser()
parser.add_argument('--l1', type=str)
parser.add_argument('--l2', type=str)
parser.add_argument('--l3', type=str)
parser.add_argument('--min', type=str)
parser.add_argument('--max', type=str)
parser.add_argument('--filename', type=str)
args = parser.parse_args()

# create a list by splitting at the comma
l1_list = args.l1.split(',') # ['1','2','3','4']
l2_list = args.l2.split(',')
l3_list = args.l3.split(',')

legend_min = float(args.min)
legend_max = float(args.max)
filename = args.filename

# convert string list to list of floats
for i in range(len(l1_list)):
	l1_list[i] = float(l1_list[i]) 
	l2_list[i] = float(l2_list[i]) 
	l3_list[i] = float(l3_list[i])
	
lat_min = min( math.fabs(yy) for yy in l2_list )
lat_max = max( math.fabs(yy) for yy in l2_list )
lon_min = min( math.fabs(xx) for xx in l1_list )
lon_max = max( math.fabs(xx) for xx in l1_list )

# convert list of floats to x,y
for i in range(len(l1_list)):
	l1_list[i] = lonToXY(l1_list[i])
	l2_list[i] = latToXY(l2_list[i])

# convert list to numpy array
x = np.array(l1_list)
y = np.array(l2_list)
z = np.array(l3_list)

#print x
#print y
#print z
nx, ny = 50, 50
xi, yi = np.linspace(x.min(), x.max(), nx), np.linspace(y.min(), y.max(),
ny)
xi, yi = np.meshgrid(xi, yi)
xi, yi = xi.flatten(), yi.flatten()

grid2 = scipy_idw(x,y,z,xi,yi)
grid2 = grid2.reshape((ny, nx))

plot(x,y,z,grid2,legend_min,legend_max,filename)

I call the script with the following parameters:

plot.py --l1=-1.8791363,-1.8786206,-1.8796862,-1.878171
--l2=57.458459,57.458153,57.458495,57.458036 --l3=42.3,37.8,43.5,47.7
--min=0 --max=100 --filename=/tmp/plot.png



Any help is greatly appreciated

Thanks 



--
View this message in context: http://matplotlib.1069221.n5.nabble.com/matplolib-imshow-contour-heatmap-tp43078.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

I have used Anaconda with my students because it installs a standard 
environment on all platforms, it works very well and is easy to install.

I have also tried to Enthought Canopy but swicthed to Anaconda because 
Anaconda was as simple to use, came with hfewer restrictions and in my 
experience also fewer bugs and problems than Canopy.

Macorts also work very well, though. So that is a matter of taste, I 
guess. The upside to Anaconda is that I believe it runs the Qt4Agg 
backend by default for all platforms. Can anyone confirm this (I don't 
have access to a Mac at the moment)?

On Thu 13 Mar 2014 09:29:38 PM CET, Sterling Smith wrote:
> +1 for macports
> (I haven't used the others.)
>
> On Mar 13, 2014, at 10:12AM, Felix Patzelt wrote:
>
>> Are you sure that you want to use Python 3.3 on OSX 10.6??? Do you really still use 10.6? Do you want Python 3? I'm not sure on the current status, but many projects took quite a while to get ported over from Python 2. Furthermore, as often with free software, installation can be a bit tricky. It is certainly a very different experience than installing "normal" Mac applications.
>>
>> For a bit of context, most Linux distribution have some version of Python / Matplotlib in their respective package managers. These are easily installed if the particular package manager on your Linux offers the versions you want. Otherwise, you will have to do some work.
>>
>> OSX does not have an official package manager, but there are several inofficial options. I'm using http://www.macports.org which is slow because it installs its own private versions for everything, but it works very well. This is probably the easiest way to get all the open source stuff you want on your Mac and I use it a lot. Another popular and more lightweight package manager is homebrew, which relies more on the system libraries from Apple.
>>
>> The minimal installation instructions without a package manager seem to be these: https://github.com/rueckstiess/mtools/wiki/matplotlib-Installation-Guide If you're a real unix hacker, you can install everything from source. I did that before, and it takes a lot of time and in-depth knowledge.
>>
>> Finally, there are several pre-packaged distributions like https://www.enthought.com or  https://store.continuum.io/cshop/anaconda/ (see http://penandpants.com/install-python/). They might come with a normal OSX installer. Maybe https://code.google.com/p/spyderlib/ does the trick for you?
>>
>> Anyway, these are just some suggestions. Maybe you want to start a separate thread on the mailing list about the best way to install matplotlib on a mac. Please note that I cannot comment in detail on any of the installation methods that I didn't use myself.
>>
>>
>>
>>
>> Am 13.03.2014 um 17:36 schrieb Christophe Bal <pro...@gm...>:
>>
>>> I've tested a more simpler Python code.
>>>
>>> from pylab import *
>>> plot([1,2,3])
>>> show()
>>>
>>> This gives me a scary backend MacOSX version unknown. I've used the official DMG installer matplotlib-1.3.1-py3.3-python.org-macosx10.6.dmg.
>>>
>>> This seems to be a big problem. No ?
>>>
>>>
>>> $HOME=/Users/xxxx
>>> matplotlib data path /Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/matplotlib/mpl-data
>>> loaded rc file /Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/matplotlib/mpl-data/matplotlibrc
>>> matplotlib version 1.3.1
>>> verbose.level helpful
>>> interactive is False
>>> platform is darwin
>>> CACHEDIR=/Users/xxxx/.matplotlib
>>> Using fontManager instance from /Users/xxxx/.matplotlib/fontList.py3k.cache
>>> backend MacOSX version unknown
>>>
>>>
>>> 2014-03-13 17:31 GMT+01:00 Felix Patzelt <fe...@ne...>:
>>> Well, there is a list in ~/.matplotlib/matplotlibrc (see http://matplotlib.org/users/customizing.html)
>>>
>>>> #### CONFIGURATION BEGINS HERE
>>>>
>>>> # the default backend; one of GTK GTKAgg GTKCairo CocoaAgg FltkAgg
>>>> # MacOSX QtAgg Qt4Agg TkAgg WX WXAgg Agg Cairo GDK PS PDF SVG Template
>>>> # You can also deploy your own backend outside of matplotlib by
>>>> # referring to the module name (which must be in the PYTHONPATH) as
>>>> # 'module://my_backend'
>>>> backend      : Qt4Agg
>>>
>>> see also: http://stackoverflow.com/questions/5091993/list-of-all-available-matplotlib-backends
>>>
>>> I'm not sure about the dependencies, I guess you have to check out each one of them. If you don't use a package manager, resolving all dependency issues might be quite painful.
>>>
>>> Best,
>>> Felix Patzelt
>>>
>>> Am 13.03.2014 um 17:18 schrieb Christophe Bal <pro...@gm...>:
>>>
>>>> Thanks a lot for this big hint but neither TkAgg works nor Qt4Agg can work (because I do not have PyQt).
>>>>
>>>> Is there a complete list of all the backends ?
>>>>
>>>> Christophe BAL
>>>>
>>>
>>>
>>
>> ------------------------------------------------------------------------------
>> Learn Graph Databases - Download FREE O'Reilly Book
>> "Graph Databases" is the definitive new guide to graph databases and their
>> applications. Written by three acclaimed leaders in the field,
>> this first edition is now available. Download your free book today!
>> http://p.sf.net/sfu/13534_NeoTech_______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/13534_NeoTech
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users