matplotlib-users Mailing List for matplotlib

I deleted my /.matplotlib/fontManager.cache file and ran the script
again, and now everything is working fine.
Thank you for your help.
>It appears to be finding "wadalab-gothic" as the font, which is a=20
>Japanese font. Now, *why* it is doing that is the million dollar =
question.
>
>It should (by default) by loading the Bitstream Vera Sans font=20
>(Vera.ttf) from=20
>/usr/local/lib/python2.4/site-packages/matplotlib/mpl-data/fonts/ttf. I=
=20
>would verify that it is there and readable by the "user" that the CGI=20
>script runs under. You can try refreshing the font-finding cache by=20
>removing the file ~/.matplotlib/fontManager.cache.
>
>If that doesn't provide any clues, can you send me the fontManager.cache=
=20
>(probably best off-list), and I'll see what fonts it *is* finding, again=
=20
> hopefully providing more clues.
>
>One other thing to note about the output: it is loading the matplotlibrc=
=20
>from /home/www/www/cgi-bin/, (since it is present), and not from=20
>/home/private/mpl/.matplotlib/. Perhaps there is something incorrect in=
=20
>that matplotlibrc file.
>
>Cheers,
>Mike
>
>Tim Lewis wrote:
>>> Can you set "verbose.level" to "debug-annoying" in your matplotlibrc =
and=20
>>> send us the output? That may help provide an explanation as to why =
the=20
>>> text is not appearing. Also, for good measure, can you provide your=20
>>> matplotlibrc file, and information about the platform and versions of=
=20
>>> Python that you are using? =20
>>=20
>> See the attachments. Their platform is RedHat Linux and python 2.4.3
>>=20
>>> Do you get different results when you run at=20
>>> the commandline vs. from an http request? It could be that incorrect=
=20
>>> permissions (as user "apache", for instance) are causing the =
problems.
>>>
>>> Cheers,
>>> Mike
>>=20
>> I'd like to run it from the command line, but I haven't done it before
>> (and not sure how to do it); the web hosting server is in a land far
>> far away. :-) I am just running the script from a http request. I
>> can probably have them run it if need to.
>>=20
>> Thanks,
>>=20
>>> Tim Lewis wrote:
>>>> I'm using the code from=20
>>>> =
http://www.scipy.org/Cookbook/Matplotlib/Using_MatPlotLib_in_a_CGI_script=
=20
>>>> to generate plots from my web server. The plot shows up fine (w/o =
text)=20
>>>> but when I use xlabel("x-axis"), ylabel("y-axis"), or title("A =
Chart");=20
>>>> no text shows up on the plot. Everything seems fine with the =
install=20
>>>> and I don't get any errors when I run the script. It seems that =
that=20
>>>> matplotlib is unable to find the font's and just simply ignores them=
 --=20
>>>> I really dunno.
>>>>
>>>> Any suggestions?
>>>>
>>>>
>>>> =
------------------------------------------------------------------------
>>>>
>>>> =
-------------------------------------------------------------------------
>>>> SF.Net email is sponsored by:=20
>>>> Check out the new SourceForge.net Marketplace.
>>>> It's the best place to buy or sell services for
>>>> just about anything Open Source.
>>>> http://sourceforge.net/services/buy/index.php
>>>>
>>>>
>>>> =
------------------------------------------------------------------------
>>>>
>>>> _______________________________________________
>>>> Matplotlib-users mailing list
>>>> Mat...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

On Dec 10, 2007 11:53 AM, Venkat Ramanan <ve...@sr...> wrote:
> If anyone faces a similar issue, there is a solution here.
>
> http://scipy.org/Cookbook/Matplotlib/Interactive_Plotting
>
> Essentially, we should also check for "toolbar.mode"
You may also want to look at the widget lock variable, which the
toolbar manages and user code can acquire or view the lock, eg
examples/lasso_demo.py. This is somewhat more robust than using the
toolbar mode string because it will allow other code, not part of the
toolbar, to share and use the lock.
 def callback(self, verts):
 ind = nonzero(points_inside_poly(self.xys, verts))[0]
 for i in range(self.Nxy):
 if i in ind:
 self.facecolors[i] = Datum.colorin
 else:
 self.facecolors[i] = Datum.colorout
 self.canvas.draw_idle()
 self.canvas.widgetlock.release(self.lasso)
 del self.lasso
 def onpress(self, event):
 if self.canvas.widgetlock.locked(): return
 if event.inaxes is None: return
 self.lasso = Lasso(event.inaxes, (event.xdata, event.ydata),
self.callback)
 # acquire a lock on the widget drawing
 self.canvas.widgetlock(self.lasso)

If anyone faces a similar issue, there is a solution here.
http://scipy.org/Cookbook/Matplotlib/Interactive_Plotting
Essentially, we should also check for "toolbar.mode"
Thanks,
Venkat.
Venkat Ramanan wrote:
> Hi,
>
> I have written a simple image viewing tool with window/level controls 
> linked to the right mouse, which generally works okay.
>
> But when I use the pan/zoom button, clicking and dragging the right 
> mouse button changes the zoom as intended, but also affects the 
> window/level too which is undesirable.
>
> How to change the callback so that the pan/zoom mode doesn't affect 
> window/level?
>
> The code is attached.
>
> If there are better image viewing tools using matplotlib, I can 
> upgrade, but I couldn't find them on a quick search. The goal is to 
> add some plotting capability ( plot row, col on user-specified 
> coordinates) and some ROI drawing capability. ( See my other post for 
> those questions. )
>
> Matplotlib: 0.87.7, python: 2.5 ubuntu 7.04
>
> Thanks,
> Venkat.
>
> ------------------------------------------------------------------------
>
> #!/usr/bin/env python
> import scipy
> import pylab
> from pylab import cos, sqrt, arctan2, sqrt,pi,cm, clim, get_current_fig_manager
> import sys
> # Displaying an image with window/level controls
> # from matplotlib
>
> pylab.ion()
>
> xstart = 0;
> ystart = 0;
> win = 0;
> lev = 0;
> vmax_orig = 0;
> vmin_orig = 0;
>
> def on_click(event):
> #get the x and y coords, flip y from top to bottom
> global win,lev
> win = im.norm.vmax - im.norm.vmin;
> lev = (im.norm.vmax + im.norm.vmin)/2;
> x, y = event.x, event.y;
> if event.button==3:
> if event.inaxes is not None:
> global xstart,ystart
> xstart = event.xdata;
> ystart = event.ydata;
> #print 'click:data coords', event.xdata, event.ydata;
>
> def on_move(event):
> #get the x and y pixel coords
> x, y = event.x, event.y
> scale = 10;
> if event.button==3:
> if event.inaxes is not None:
> xdelta = event.xdata - xstart;
> ydelta = event.ydata - ystart;
> xratio = xdelta / (im.get_extent()[1]-im.get_extent()[0]);
> yratio = ydelta / (im.get_extent()[3]-im.get_extent()[2]);
>
> new_win = xratio*scale + win;
> new_lev = yratio*scale + lev;
> if new_win < 0: new_win = 0;
> 
> clim_high = new_lev + new_win/2;
> clim_low = new_lev - new_win/2;
> clim(clim_low,clim_high);
>
> #print 'move:deltas', xdelta, ydelta
> #print 'clim_low: ', clim_low, 'clim_high: ', clim_high
>
> def on_release(event):
> global win,lev
> x, y = event.x, event.y
> if event.button==2:
> if event.inaxes is not None:
> clim(vmin_orig,vmax_orig);
> print 'release: vmin: ',im.norm.vmin,'vmax: ',im.norm.vmax
>
> def viewimage(imdata):
> global im,vmax_orig,vmin_orig
> im=pylab.imshow(imdata,origin='lower',cmap=cm.gray);
> vmax_orig = im.norm.vmax;
> vmin_orig = im.norm.vmin;
> binding_id = pylab.connect('motion_notify_event', on_move)
> pylab.connect('button_press_event', on_click)
> pylab.connect('button_release_event', on_release)
> pylab.show();
>
> def main():
> # Creating the grid of coordinates x,y 
> x,y = scipy.ogrid[-1.:1.:.01, -1.:1.:.01]
> z = 3*y*(3*x**2-y**2)/4 + .5*cos(6*pi * sqrt(x**2 +y**2) + arctan2(x,y))
> viewimage(z);
>
> if __name__ == '__main__':
> main()
> 
> ------------------------------------------------------------------------
>
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> 

Thanks for the pointer. The matplotlib.widget.Cursor works much better 
for displaying crosshairs. ( due to blitting? )
I still haven't found a tool yet for drawing a polygon. The 
lasso_demo.py doesn't run on my system. Well, it runs, displays a 
scatter of points, but I'm not sure what is it supposed to do next.
Thanks,
Venkat.
PS: Sorry for personal post, I meant to post to the list but forgot to 
'reply all'
Darren Dale wrote:
> On Friday 07 December 2007 7:19:04 am José Gómez-Dans wrote:
> 
>> Hi,
>>
>> On Thursday 06 December 2007 19:39:59 Venkat Ramanan wrote:
>> 
>>> I'm looking for something analogous to Matlab's ginput() and roipoly().
>>> 
>> I'm no expert on this, but have a look at the lasso_demo.py example, which
>> shows something akin to roipoly(), and pick_event_demo.py and
>> pick_even_demo2.py, which show something like ginput() (although I think no
>> cross hairs :D).
>> 
>
> Check out cursor_demo.py and matplotlib.widgets.Cursor for cross hairs.
>
> -------------------------------------------------------------------------
> SF.Net email is sponsored by: 
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
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> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 
-- 
Venkat Ramanan,
Research Associate,
Imaging Research,
Sunnybrook Health Sciences Centre,
2075 Bayview Ave,
Toronto-M4N3M5
Ontario, Canada

You can use something like:
 subplots_adjust(left=0.3)
The value is in the range 0.0 - 1.0, and is spaced evenly across the 
whole figure.
Cheers,
Mike
Gerolf Ziegenhain wrote:
> Dear Mailinglist,
> 
> I want to create a horizontal historgram. The y-labels have more text, 
> than fits in the _normal_ layout. How could I increase the width of the 
> yticks legend?
> 
> Best regards:
> Gerolf
> 
> -- 
> Dipl. Phys. Gerolf Ziegenhain (ge...@zi... 
> <mailto:ge...@zi...>)
> Private: Klopstockstrasse 21 - 65187 Wiesbaden - Germany
> Office: Room 46-332 - Erwin-Schrödinger-Str.46 - TU Kaiserslautern - 
> Germany
> Web: gerolf.ziegenhain.com <http://gerolf.ziegenhain.com>
> 
> 
> ------------------------------------------------------------------------
> 
> -------------------------------------------------------------------------
> SF.Net email is sponsored by: 
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
> http://sourceforge.net/services/buy/index.php
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

On Monday 10 December 2007 8:21:03 am Michael Droettboom wrote:
> It appears to be finding "wadalab-gothic" as the font, which is a
> Japanese font. Now, *why* it is doing that is the million dollar question.
>
> It should (by default) by loading the Bitstream Vera Sans font
> (Vera.ttf) from
> /usr/local/lib/python2.4/site-packages/matplotlib/mpl-data/fonts/ttf. I
> would verify that it is there and readable by the "user" that the CGI
> script runs under. You can try refreshing the font-finding cache by
> removing the file ~/.matplotlib/fontManager.cache.
>
> If that doesn't provide any clues, can you send me the fontManager.cache
> (probably best off-list), and I'll see what fonts it *is* finding, again
> hopefully providing more clues.
>
> One other thing to note about the output: it is loading the matplotlibrc
> from /home/www/www/cgi-bin/, (since it is present), and not from
> /home/private/mpl/.matplotlib/. Perhaps there is something incorrect in
> that matplotlibrc file.
The matplotlibrc file was basically using all defaults. Have you tried 
deleting your site-packages/matplotlib* and the build/ directory from your 
mpl sources, and reinstalling?
Darren
> Tim Lewis wrote:
> >> Can you set "verbose.level" to "debug-annoying" in your matplotlibrc and
> >> send us the output? That may help provide an explanation as to why the
> >> text is not appearing. Also, for good measure, can you provide your
> >> matplotlibrc file, and information about the platform and versions of
> >> Python that you are using?
> >
> > See the attachments. Their platform is RedHat Linux and python 2.4.3
> >
> >> Do you get different results when you run at
> >> the commandline vs. from an http request? It could be that incorrect
> >> permissions (as user "apache", for instance) are causing the problems.
> >>
> >> Cheers,
> >> Mike
> >
> > I'd like to run it from the command line, but I haven't done it before
> > (and not sure how to do it); the web hosting server is in a land far
> > far away. :-) I am just running the script from a http request. I
> > can probably have them run it if need to.
> >
> > Thanks,
> >
> >> Tim Lewis wrote:
> >>> I'm using the code from
> >>> http://www.scipy.org/Cookbook/Matplotlib/Using_MatPlotLib_in_a_CGI_scri
> >>>pt to generate plots from my web server. The plot shows up fine (w/o
> >>> text) but when I use xlabel("x-axis"), ylabel("y-axis"), or title("A
> >>> Chart"); no text shows up on the plot. Everything seems fine with the
> >>> install and I don't get any errors when I run the script. It seems
> >>> that that matplotlib is unable to find the font's and just simply
> >>> ignores them -- I really dunno.
> >>>
> >>> Any suggestions?

It appears to be finding "wadalab-gothic" as the font, which is a 
Japanese font. Now, *why* it is doing that is the million dollar question.
It should (by default) by loading the Bitstream Vera Sans font 
(Vera.ttf) from 
/usr/local/lib/python2.4/site-packages/matplotlib/mpl-data/fonts/ttf. I 
would verify that it is there and readable by the "user" that the CGI 
script runs under. You can try refreshing the font-finding cache by 
removing the file ~/.matplotlib/fontManager.cache.
If that doesn't provide any clues, can you send me the fontManager.cache 
(probably best off-list), and I'll see what fonts it *is* finding, again 
 hopefully providing more clues.
One other thing to note about the output: it is loading the matplotlibrc 
from /home/www/www/cgi-bin/, (since it is present), and not from 
/home/private/mpl/.matplotlib/. Perhaps there is something incorrect in 
that matplotlibrc file.
Cheers,
Mike
Tim Lewis wrote:
>> Can you set "verbose.level" to "debug-annoying" in your matplotlibrc and 
>> send us the output? That may help provide an explanation as to why the 
>> text is not appearing. Also, for good measure, can you provide your 
>> matplotlibrc file, and information about the platform and versions of 
>> Python that you are using? 
> 
> See the attachments. Their platform is RedHat Linux and python 2.4.3
> 
>> Do you get different results when you run at 
>> the commandline vs. from an http request? It could be that incorrect 
>> permissions (as user "apache", for instance) are causing the problems.
>>
>> Cheers,
>> Mike
> 
> I'd like to run it from the command line, but I haven't done it before
> (and not sure how to do it); the web hosting server is in a land far
> far away. :-) I am just running the script from a http request. I
> can probably have them run it if need to.
> 
> Thanks,
> 
>> Tim Lewis wrote:
>>> I'm using the code from 
>>> http://www.scipy.org/Cookbook/Matplotlib/Using_MatPlotLib_in_a_CGI_script 
>>> to generate plots from my web server. The plot shows up fine (w/o text) 
>>> but when I use xlabel("x-axis"), ylabel("y-axis"), or title("A Chart"); 
>>> no text shows up on the plot. Everything seems fine with the install 
>>> and I don't get any errors when I run the script. It seems that that 
>>> matplotlib is unable to find the font's and just simply ignores them -- 
>>> I really dunno.
>>>
>>> Any suggestions?
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> -------------------------------------------------------------------------
>>> SF.Net email is sponsored by: 
>>> Check out the new SourceForge.net Marketplace.
>>> It's the best place to buy or sell services for
>>> just about anything Open Source.
>>> http://sourceforge.net/services/buy/index.php
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Matplotlib-users mailing list
>>> Mat...@li...
>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Hi,
I've a little problem with date conversion. I have a csv file which looks 
like :
"Data","Valor"
"15/01/2007"," 6,700012000"
"12/01/2007"," 6,659903000"
"11/01/2007"," 6,701586000"
I try to get date using function strpdate2num in load doing this :
from pylab import datestr2num, load
def comma_nb2float(A):
 return eval(A.replace(',','.'))
dates, valor = 
load("file.csv",delimiter=',',converters={0:strpdate2num('%d/%m/%Y'),1:comma_nb2float},skiprows=1, 
usecols=(0,1),unpack=True)
I got the following error message :
---------------------------------------------------------------------------
exceptions.ValueError Traceback (most recent 
call last)
/home/manu/Documents/Perso/....../<ipython console>
/usr/lib/python2.4/site-packages/matplotlib/mlab.py in load(fname, comments, 
delimiter, converters, skiprows, usecols, unpack)
 1353 if usecols is not None:
 1354 vals = line.split(delimiter)
-> 1355 row = [converterseq[j](vals[j]) for j in usecols]
 1356 else:
 1357 row = [converterseq[j](val) for j,val in 
enumerate(line.split(delimiter))]
/usr/lib/python2.4/site-packages/matplotlib/dates.py in __call__(self, s)
 182 return value: a date2num float
 183 """
--> 184 return date2num(datetime.datetime(*time.strptime(s, self.fmt)
[:6]))
 185
 186 def datestr2num(d):
/usr/lib/python2.4/_strptime.py in strptime(data_string, format)
 291 found = format_regex.match(data_string)
 292 if not found:
--> 293 raise ValueError("time data did not match format: data=%s 
fmt=%s" %
 294 (data_string, format))
 295 if len(data_string) != found.end():
ValueError: time data did not match format: data="15/01/2007" fmt=%d/%m/%Y
I didn't understood the problem, anyone can help me ?

On Dec 9, 2007 7:57 PM, Jordan Atlas <jc...@co...> wrote:
> Hello all,
>
> Does matplotlib allow the control of "fill" in data plots? For
> example, plotting data as 'empty' squares as opposed to 'filled'
> squares? I haven't been able to find anything in the documentation and
> I'm wondering if maybe I'm searching for the wrong keywords.
>
> Thank you,
>
> --Jordan
>
It does. Looking at everything listed under the axes class in matplotlib
is a good idea, there's lots there. There you find .plot() itself, and
under that
there is a description of all the aspects you can control in plotting
markers
(the circles, squares, etc. that you plot). Included there is mfc, or
marker
face color, which you can set to white or whatever the background of the
plot is so it appears unfilled. There's also edge color, edge width, marker
size, etc. See here:
http://matplotlib.sourceforge.net/matplotlib.axes.html

I am plotting multiple scatter plots to the same axis. For each
scatter plot, all points have the same shape and color. I would like
the legend to display the shape and color of the data points in each
collection (rather than displaying a rectangle for the color). The
result should be similar to the output from:
 plot(range(10), 'bo', label='1')
 legend()
The benefit with scatter is that I can have each data point being a
different size.

Hello all,
 Does matplotlib allow the control of "fill" in data plots? For 
example, plotting data as 'empty' squares as opposed to 'filled' 
squares? I haven't been able to find anything in the documentation and 
I'm wondering if maybe I'm searching for the wrong keywords.
Thank you,
--Jordan