matplotlib-users Mailing List for matplotlib

Hi all,

   I am really enjoying working with matplotlib and hats off to an 
excellent effort.

   I have done a cursory search of the mailing list archives but didn't 
find the answer to a practical question that I ran into in MATLAB all 
the time (which is where I'm coming from in terms of familiarity).

   Suppose I have an array to plot, and I want to exclude certain points 
from being plotted.  In MATLAB, I would set the y vector points I wanted 
excluded to "NaN" and then the plot routine would draw connected lines 
up to the point before the excluded one, skip the bad/not wanted point, 
and then continue drawing lines beginning at the next point.

   How does one accomplish that using matplotlib?  This actually comes 
up quite often in our radar work here, in cases where we are making log 
plots of vectors which may contain zeros.

cheers,
-- 
----
Phil Erickson                   email:  pj...@ha...
Atmospheric Sciences Group      WWW:    http://www.haystack.mit.edu
MIT Haystack Observatory        voice:  781 981 5769
Westford, MA  01886  USA        fax:    781 981 5766

Public key: http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x54878872

>>>>> "Dominique" == Dominique Orban <do...@da...> writes:

    Dominique> Allright thanks. In Linux, i can compile the new
    Dominique> matplotlib with gcc 3.3.  I notice the same problem
    Dominique> with fontTools. This time i do have a FontTools.pth in
    Dominique> my source directory, but it isn't copied to
    Dominique> /whatever/python2.3/site-packages when i run python
    Dominique> setup.py install.

Just copy the file to site-packages.  This problem is fixed in CVS but
with Paul's new font finder hopefully it will soon be a non-issue.

    Dominique> Now it doesn't find _backend_agg. Sorry to be bugging
    Dominique> you with all these minor annoyances.

No problem - I want to fix these problems as soon as possible so keep
them coming.  

Did you edit setup.py?  You need to set the flags BUILD_AGG and
BUILD_FONTTOOLS.  If this doesn't do it for you, please post compile
errors or tracebacks.

    Dominique> Also i notice the 'afm' problem i reported earlier with
    Dominique> the PS backend hasn't been fixed. Did you receive my
    Dominique> little fix?

Thanks for the reminder - it had slipped too low in the pile and I
forgot about it.  It's in now.

JDH

John Hunter wrote:
> 
> ttfquery and FontTools are packages to enable cross platform
> font-finding.  I am very interested in factoring out this dependency
> since it complicates installation (as you are seeing).  [ Perry, if
> anyone in your group is still interested in this, there is a
> reasonably well documented example in cvs examples/ftface_props.py
> that shows how to access all the relevant freetype attributes (family
> name, is italics, etc) using the matplotlib.ft2face module ]

Hi John,

I'm currently working on a replacment for FontTools. I hope to have something 
out in the next day or so.

  -- Paul

-- 
Paul Barrett, PhD      Space Telescope Science Institute
Phone: 410-338-4475    ESS/Science Software Branch
FAX:   410-338-4767    Baltimore, MD 21218

* On Tue, 02 Mar 2004, John Hunter wrote:
>
> >>>>> "Dominique" == Dominique Orban <do...@da...> writes:
> 
>     Dominique> I don't have it actually. It is on neither of my
>     Dominique> Windows installs.  Can i just create it?
> 
> OK, this is a bug in the windows installer - fixed for next release.
> Yes, just create it.

Allright thanks. In Linux, i can compile the new matplotlib with gcc 3.3.
I notice the same problem with fontTools. This time i do have a
FontTools.pth in my source directory, but it isn't copied to
/whatever/python2.3/site-packages when i run
python setup.py install.

Now it doesn't find _backend_agg. Sorry to be bugging you with all
these minor annoyances.

Also i notice the 'afm' problem i reported earlier with the PS
backend hasn't been fixed. Did you receive my little fix?

Dominique

>>>>> "Dominique" == Dominique Orban <do...@da...> writes:

    Dominique> I don't have it actually. It is on neither of my
    Dominique> Windows installs.  Can i just create it?

OK, this is a bug in the windows installer - fixed for next release.
Yes, just create it.

    Dominique> I haven't seen any other user complain about
    Dominique> this. Could this come from an upgrade of matplotlib?
    Dominique> During the upgrade, it seems to be backing up stuff but
    Dominique> who knows what it is doing exactly.

Well, you would only notice it if 1) you haven't installed FontTools
before 2) you are using windows 3) you are trying to use on of the
FontTools dependent backends (Agg, GD) and 4) you are kind enough to
report the problem.  

    Dominique> The font.cache is in site-packages/ttfquery, i presume
    Dominique> this is correct?

After you fix the FontTools.pth problem erase this file and it will be
automagically recreated by ttfquery.

JDH

* On Tue, 02 Mar 2004, John Hunter wrote:

> Critically, you should also have
> c:\Python23\Lib\site-packages\FontTools.pth.  I am pretty certain it
> is in the windows installer.  This file should contain one line, which
> reads simply 
> 
> FontTools
> 
> If you don't have it I would like to know!  

I don't have it actually. It is on neither of my Windows installs.
Can i just create it?

I haven't seen any other user complain about this. Could this come from
an upgrade of matplotlib? During the upgrade, it seems to be backing up
stuff but who knows what it is doing exactly.
 
> All of this is consistent with a missing FontTools.pth.  ttfquery will
> try and load each windows font, but catches all exceptions and
> continues.  So you'll get an exception *for each font* the first time
> you load ttfquery if something is wrong with your install.  After you
> have fixed fontools, be sure to remove site-packages/font.cache so
> ttfquery can regenerate the font cache.

The font.cache is in site-packages/ttfquery, i presume this is correct?
 
> Agg is a pure image backend - ie, it only produces image output.  In
> the next release of matplotlib (this week) there will are 2 GUI
> backends that use agg for rendering GtkAgg and TkAgg, both of which
> are compiled into the windows installer.

Great!
 
Thanks much,
Dominique

* On Tue, 02 Mar 2004, John Hunter wrote:
>
> >>>>> "Dominique" == Dominique Orban <do...@da...> writes:
> 
>     Dominique> I am in Windows 2000 and XP. I am using 0.50e in Linux,
>     Dominique> because i am upgrading my gcc. The newer 0.50 won't
>     Dominique> compile with the gcc i have now.  I only get the 'None
>     Dominique> Active' in Linux though. I suspect it comes from my
>     Dominique> GTK. I am using KDE and installing Gnome libraries when
>     Dominique> i need them.  There might be a glitch somewhere.
> 
> Note, you can just set all the BUILD_* flags at the top of setup.py
> and matplotlib won't try and compile anything.  It will install all of
> the pre 0.50 modules (GTK, WX, PS, etc) but you won't have access to
> Agg.

Yes i will try that to start with. In the end, i'll want to use Agg
though, given the apparent quality of the plots.
 
> For the record, what gcc were you using and what error message did you
> get?  

gcc version 2.95.3 20010315 (SuSE)

I wanted to try the Intel c++ compiler for Linux, but am not sure how
to tell setup.py which compiler i want to use and with which options.

'python setup.py build' eventually gives

gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -Isrc -Iagg2/include -I/usr/include/freetype1 -I/usr/local/include/python2.3 -c src/_backend_agg.cpp -o build/temp.linux-i686-2.3/src/_backend_agg.o
In file included from /usr/local/include/python2.3/Python.h:8,
   from src/_backend_agg.h:40,
   from src/_backend_agg.cpp:8:
  /usr/local/include/python2.3/pyconfig.h:847: warning: `_POSIX_C_SOURCE' redefined
  /usr/include/features.h:171: warning: this is the location of the previous definition
  src/_backend_agg.cpp:286: multiple storage classes in declaration of `RendererAgg_Type'
error: command 'gcc' failed with exit status 1

Many thanks for the help.
Dominique

>>>>> "Dominique" == Dominique Orban <do...@da...> writes:

    Dominique> I am in Windows 2000 and XP. I am using 0.50e in Linux,
    Dominique> because i am upgrading my gcc. The newer 0.50 won't
    Dominique> compile with the gcc i have now.  I only get the 'None
    Dominique> Active' in Linux though. I suspect it comes from my
    Dominique> GTK. I am using KDE and installing Gnome libraries when
    Dominique> i need them.  There might be a glitch somewhere.

Note, you can just set all the BUILD_* flags at the top of setup.py
and matplotlib won't try and compile anything.  It will install all of
the pre 0.50 modules (GTK, WX, PS, etc) but you won't have access to
Agg.

For the record, what gcc were you using and what error message did you
get?  

Thanks,
JDH

>>>>> "Dominique" == Dominique Orban <do...@da...> writes:

    Dominique> Just wanted to signal some path issues with the current
    Dominique> Windows installer. I have looked in the mailing list,
    Dominique> but haven't seen anyone having the same problem.

    Dominique> In both Windows 2000 and XP, installation of Matplotlib
    Dominique> 0.50 results in the following directory hierarchy in my
    Dominique> main Python directory c:\Python23\Lib\site-packages
    Dominique> (Enthought Edition):

    Dominique>   FontTools/ fontTools/ sstruct.py ttLib/

Critically, you should also have
c:\Python23\Lib\site-packages\FontTools.pth.  I am pretty certain it
is in the windows installer.  This file should contain one line, which
reads simply 

FontTools

If you don't have it I would like to know!  

ttfquery and FontTools are packages to enable cross platform
font-finding.  I am very interested in factoring out this dependency
since it complicates installation (as you are seeing).  [ Perry, if
anyone in your group is still interested in this, there is a
reasonably well documented example in cvs examples/ftface_props.py
that shows how to access all the relevant freetype attributes (family
name, is italics, etc) using the matplotlib.ft2face module ]

    Dominique> it says it cannot import 'fontTools' (lowercase f,
    Dominique> uppercase T).  Changing the name of the top directory
    Dominique> (FontTools) to 'fontTools' doesn't solve it of course,
    Dominique> since what it is looking for is the innermost
    Dominique> one. Hence i must move the 'fontTools' directory one
    Dominique> level up. Next, it can import ttLib, scans my TTFPATH,
    Dominique> but breaks down (after litterally one zillion messages)
    Dominique> saying that 'module' has no attribute 'SFNTReader'. It
    Dominique> is in fact trying to import sfnt and is stuck in the
    Dominique> __init__() of Class TTFont. Drastically reducing my
    Dominique> TTFPATH, i see that the error is in fact coming from
    Dominique> the fact that it cannot import module 'sstruct' in
    Dominique> sfnt.py.

All of this is consistent with a missing FontTools.pth.  ttfquery will
try and load each windows font, but catches all exceptions and
continues.  So you'll get an exception *for each font* the first time
you load ttfquery if something is wrong with your install.  After you
have fixed fontools, be sure to remove site-packages/font.cache so
ttfquery can regenerate the font cache.

    Dominique> That stuns me. A 'from fontTools import sstruct' would
    Dominique> do. How comes Python isn't looking recursively into
    Dominique> directories? I guess moving everything to the top level
    Dominique> isn't a good idea. Also, still in sfnt.py, the 'import
    Dominique> struct' works, but i have no clue where it finds this
    Dominique> one; a search was unsuccessful. Anyhow, including
    Dominique> 'c:\Python23\fontTools' into the PYTHONPATH solves it
    Dominique> but i thought directories would be parsed recursively.

    Dominique> Also, can you only use savefig() with the Agg backend?
    Dominique> show() isn't popping any window.

Agg is a pure image backend - ie, it only produces image output.  In
the next release of matplotlib (this week) there will are 2 GUI
backends that use agg for rendering GtkAgg and TkAgg, both of which
are compiled into the windows installer.

    Dominique> As they told me to at SuSE, i'm having a lot of fun.

You mean battling the hairy windows beast?

JDH

S=E6l=20

Thanks for the detailed answerS I will try to go one step further for the u=
nclear question.
I hope this will help other users too :)

>   - I want to systematically disable the vertical zoom/move on the
>     second subplot, but not the first. How can I do that ?
>=20
> Well, when the menu is working properly that is how you do it.  By
> "systematically", do you mean by default so it's disabled when the
> plot comes up?
>=20
> If so, this depends on how you are building your GUI window.
> Basically you need to get your hands on the gtk.Toolbar instance,
> which contains an omenu (gtk.OptionMenu) attribute (wait until the
> next release, a couple of days, where I've cleaned this up a bit).
> Eg, if you are using the matlab interface
>=20
>   manager =3D get_current_fig_manager()
>   items =3D manager.toolbar.omenuItems
>   items[-1].set_active(False)
>=20
> Turns off navigation for the last subplot.  items[0] would turn off
> navigation for the first subplot, and so on.

Indeed I meant 'by default' and you answered partially my question.
I would like to disable only the veritcal zoom, not the horizontal one.
Is it possible ?


>   - How can I activate a tooltip on top of my plots ?
>=20
> You'll have to read up on gtk tooltips.  Depends on what elements you
> want to add tips to.  Give me a little more info.  DO you want to add
> tips to the navigation buttons or lines on your plot or text elements
> or what?

I am aware of tooltips in pygtk, and I would liek to use them on the axes o=
nly.
As I understood those axes are included in a figure which is a DrwaingArea.=
 But DrawingArea do not accept tooltip easily.
Did you implement a workaround to have a tooltip on the axes



>   - How could I add a button to directly print out the picture in the too=
lbar ?
>=20
> Print as in to a printer?  No support for that yet and am not sure I
> want to go there right now (cross platform printing would might take
> lot of work).  Best I can offer you currently is the savefig button.
> I think gnome-print has made a fair amount of progress since I first
> wrote matplotlib so if you want to be on the vanguard and explore this
> option I would be happy.


I used the NavigationToolbar as a GTKToolbar and added a button with the fu=
nction I wanted.
This solved my problem




>   - Is there any density plot available ?
>=20
> Do you mean hist?
The histogram provide a similar plot to what I want.
I am currently using it, but when i zoom horizontally I can get very few an=
d large bars.
Therefore I would be interested in a simple curve fitted to pass through al=
l the tops of histograms.
This would make the picture more consistent throughout the zooming

If the curve was filled it would be even better :)


> - I have MANY small plots on my graph. Is there a cost effective way
>   to filter which plots to show ?
>=20
> I don't know what this means.  Wouldn't you want to show all the plots
> on your figure?  Why else would you put them there?  Please elaborate.

Within one Sublot I have thousands of small "lines" plotted. This takes tim=
e to draw and show on the screen
Within my software I would like to be able to filter interactively that inf=
ormation according to various criteria to show only few of them
In order to do that cost effectively I was wondering if matplotlib provides=
 an option to show/hide specific "lines" that I could turn on/off
That woudl avoid me to redraw the whole picture after 1 single change



Takk

Kve=F0ja



Jean-Baptiste

--=20
-----------------------------
Jea...@de...

Department of Statistics
deCODE genetics     Sturlugata,8
570 2993          101 Reykjav=EDk

Just wanted to signal some path issues with the current
Windows installer. I have looked in the mailing list, but
haven't seen anyone having the same problem.

In both Windows 2000 and XP, installation of Matplotlib 0.50
results in the following directory hierarchy in my main Python
directory c:\Python23\Lib\site-packages (Enthought Edition):

  FontTools/
     fontTools/
        sstruct.py
        ttLib/

When i try to import the Agg backend:

    import matplotlib
    matplotlib.use( 'Agg' )
    from matplotlib.matlab import *

it says it cannot import 'fontTools' (lowercase f, uppercase T).
Changing the name of the top directory (FontTools) to 'fontTools'
doesn't solve it of course, since what it is looking for is the
innermost one. Hence i must move the 'fontTools' directory one
level up. Next, it can import ttLib, scans my TTFPATH, but breaks
down (after litterally one zillion messages) saying that 'module'
has no attribute 'SFNTReader'. It is in fact trying to import
sfnt and is stuck in the __init__() of Class TTFont. Drastically
reducing my TTFPATH, i see that the error is in fact coming from
the fact that it cannot import module 'sstruct' in sfnt.py.

That stuns me. A 'from fontTools import sstruct' would do. How
comes Python isn't looking recursively into directories? I guess
moving everything to the top level isn't a good idea. Also,
still in sfnt.py, the 'import struct' works, but i have no clue
where it finds this one; a search was unsuccessful. Anyhow,
including 'c:\Python23\fontTools' into the PYTHONPATH solves it
but i thought directories would be parsed recursively.

Also, can you only use savefig() with the Agg backend? show()
isn't popping any window.

As they told me to at SuSE, i'm having a lot of fun.

Dominique

* On Mon, 01 Mar 2004, John Hunter wrote:

> It looks like there is a "print" statement somewhere in your code.
> It's possible that this was from a vestigial debug command I left in.
> I don't get get it on my system.  Are you using matplotlib-0.50?  I
> also don't get the "None Active" line.

I am in Windows 2000 and XP. I am using 0.50e in Linux, because i am
upgrading my gcc. The newer 0.50 won't compile with the gcc i have now.
I only get the 'None Active' in Linux though. I suspect it comes from
my GTK. I am using KDE and installing Gnome libraries when i need them.
There might be a glitch somewhere.
 
> I'm using this as a test script  
> 
>     from matplotlib.matlab import *
> 
>     x = 100*rand(100000)
>     y = 100*rand(100000)
>     s = rand(100000)
> 
>     scatter(x,y,s)
>     #plot(x,y,'o')
>     show()
> 
> Takes about 30s on my system.  Note that plot with circles can be must
> faster that scatter if you don't need to vary the size or color of the
> symbols.

I see that plot is usually faster than scatter. The script works fine
with smaller data sets, and takes a pretty long time with larger sets.
 
> There are several areas where matplotlib performance is subpar -
> mostly for large numbers of patches (circles for scatter, rectangles
> for pcolor).  Fixing this is a fairly high priority and I have a good
> idea how to go about it - see
> http://sourceforge.net/mailarchive/message.php?msg_id=7142332 for a
> recent discussion.  I think in the next 3-4 weeks I can get this
> fixed.  Basically, the plan is to set up an additional backend method
> or two that the various backends may optionally implement in extension
> code for performance.

That would be wonderful. I have never looked into the Gnuplot code but
they have a fairly efficient algorithm. Plotting data sets like that i
described takes less than a second on my laptop (from the Python
interface). It would be great if matplotlib could do it too.
 
> Are you using the default GTK that comes with SuSE or did you upgrade?
> I have gotten myself into a world of pain before trying to upgraded
> GTK libs on a linux box.  It does look like you are getting some
> unusual behavior.  Make sure you are using the latest matplotlib and
> try running the test script I posted above.  If you still get the same
> errors, something is whacked with your install or paths.  Otherwise,
> stay tuned for performance enhancements coming soon to theaters
> everywhere.

You can be sure i'm staying tuned.

Dominique