matplotlib-users Mailing List for matplotlib (Page 4)

>>>>> "H=E9ctor" =3D=3D H=E9ctor Villafuerte D <hec...@te...=
m.gt> writes:
    H=E9ctor> savefig("c:\\tmp\\%s_%s" % (tel,table)) File
    H=E9ctor> "C:\Python23\Lib\site-packages\matplotlib\matlab.py", line
    H=E9ctor> 1115, in savefig manager.canvas.print_figure(*args,
    H=E9ctor> **kwargs) File
    H=E9ctor> "C:\Python23\Lib\site-packages\matplotlib\backends\backend_=
agg.py",
    H=E9ctor> line 419, in print_figure
    H=E9ctor> self.renderer._renderer.write_png(filename) IOError: could
    H=E9ctor> not open file

This is a new one; I think the file is not writable and it is not a
matplotlib problem per se.  Is it possible that C:\\tmp does not
exist?

You may want to try something along the lines of

import os

...snip...
dirname =3D 'c:\\tmp'
fname =3D os.path.join(dirname, '%s_%s' % (tel,table))
print 'dir exists', os.path.exists(dirname)
print 'filename', fname

file(fname, 'w').write('test\n')

and see if you can see what is going wrong.

JDH

>>>>> "H=E9ctor" =3D=3D H=E9ctor Villafuerte D <hec...@te...=
m.gt> writes:

    H=E9ctor> 720, in __init__ MultipleLocator.__init__(self,
    H=E9ctor> base*SEC_PER_MIN) NameError: global name 'SEC_PER_MIN' is
    H=E9ctor> not defined

This is a bug in ticker that will be fixed in the next bugfix
release.  If you want to fix it yourself now, edit
matplotlib/ticker.py and add SEC_PER_MIN to the list of things
imported from the dates module.  Ie,

from dates import EpochConverter, SEC_PER_HOUR, SEC_PER_DAY, SEC_PER_WEEK=
, \
     SEC_PER_MIN

The pcolor_demo.py and pcolor_demo2.py show somewhat different results:

------------
from matplotlib.matlab import *

def fun3(x,y):
    return (1- x/2 + x**5 + y**3)*exp(-x**2-y**2)

xi=arange(-3.0, 3.0, 0.05)
yi=arange(-3.0, 3.0, 0.05)
[Xi,Yi]=meshgrid(xi,yi);
Zi=fun3(Xi,Yi)    

if 1:
   cMap = ColormapJet(256)
   imshow(Zi, cMap)
   gca().set_image_extent(-3, 3, -3, 3)
else:
   pcolor(Xi, Yi, Zi, shading='flat')

show()


-------------


The y axis seem to be inverted on imshow when compared to pcolor. Was 
this intentional?

I changed the script and I got this error
Thanks for your help

########################################################################
NEW ERROR
########################################################################
C:\Documents and Settings\villaf>python e:\src\python\ttp\ttp_plot.py
1082763298.0 :  Fri Apr 23 15:34:58 2004 :      ttp_plot start
Traceback (most recent call last):
  File "e:\src\python\ttp\ttp_plot.py", line 60, in ?
    get_data('traffic', 'tmp_calls0', 3)
  File "e:\src\python\ttp\ttp_plot.py", line 37, in get_data
    plotting_date(tel[0], datum, vals)
  File "e:\src\python\ttp\ttp_plot.py", line 54, in plotting_date
    savefig("c:\\tmp\\%s_%s" % (tel,table))
  File "C:\Python23\Lib\site-packages\matplotlib\matlab.py", line 1115,=20
in savefig
    manager.canvas.print_figure(*args, **kwargs)
  File=20
"C:\Python23\Lib\site-packages\matplotlib\backends\backend_agg.py", line=20
419, in print_figure
    self.renderer._renderer.write_png(filename)
IOError: could not open file

########################################################################
SCRIPT
########################################################################
import time, ConfigParser, MySQLdb
import datetime
import matplotlib
matplotlib.use('Agg')
from matplotlib.matlab import *
from matplotlib.dates import PyDatetimeConverter, MONDAY
from matplotlib.ticker import WeekdayLocator, DayLocator, DateFormatter

config =3D ConfigParser.ConfigParser()
config.readfp(open('e:\\src\\python\\ttp\\ttp.conf', 'r'))
loc_host =3D config.get('DATABASE', 'loc_host')
loc_user =3D config.get('DATABASE', 'loc_user')
loc_passwd =3D config.get('DATABASE', 'loc_passwd')
loc_db =3D config.get('DATABASE', 'loc_db')

loc_db =3D MySQLdb.connect(host =3D loc_host, user =3D loc_user, passwd =3D=
=20
loc_passwd, db =3D loc_db)
cursor =3D loc_db.cursor()

def get_data(db, table, dig):

    cursor.execute("DROP TABLE IF EXISTS %s.tmp" % (db))
    cursor.execute("CREATE TABLE %s.tmp "
                   "SELECT fecha, mid(tel,1,%d) as tel, sum(minutos) as=20
min FROM %s.%s GROUP BY 1,2" % (db,dig,db,table))
    cursor.execute("SELECT DISTINCT tel FROM %s.tmp" % (db))
    tels =3D cursor.fetchall()
    for tel in tels:
        cursor.execute("SELECT fecha, min FROM %s.tmp WHERE tel =3D '%s'"=
=20
% (db,tel[0]))
        data  =3D cursor.fetchall()
        datum =3D [datetime.datetime(int(q[0][0:4]), int(q[0][4:6]),=20
int(q[0][6:8]), 0, 0) for q in data]
        vals  =3D [q[1] for q in data]
        plotting_date(tel[0], datum, vals)


def plotting_date(tel, datum, vals):

    ax =3D subplot(1,1,1)
    plot_date(datum, vals, PyDatetimeConverter())

    ax.xaxis.set_major_locator(WeekdayLocator(MONDAY))
    ax.xaxis.set_major_formatter(DateFormatter('%b %d'))
    ax.xaxis.set_minor_locator(DayLocator())
    ax.xaxis.autoscale_view()
    title('TEST')
    ylabel('test')
    labels =3D ax.get_xticklabels()
    set(labels, 'rotation', 'vertical')
    grid(True)
    savefig("c:\\tmp\\%s_%s" % (tel,table))


# --- main -- #
if __name__ =3D=3D '__main__':
    print time.mktime(time.localtime()), ': \t', time.asctime(), ': \t',=20
'ttp_plot start'
    get_data('traffic', 'tmp_calls0', 3)
    print time.mktime(time.localtime()), ': \t', time.asctime(), ': \t',=20
'ttp_plot end'



H=E9ctor Villafuerte D. wrote:

>
> hi all,
> i'm getting the following error when running this script.
> if the script doesn't iterate over "tels" it runs fine...
> it seems to do things right just once.
> thanks in advance,
> hector
>
>
> #######################################################################=
#########
> ERROR
> #######################################################################=
#########
>
> C:\Documents and Settings\villaf>python e:\src\python\ttp\ttp_plot.py
> 1082751605.0 :  Fri Apr 23 12:20:05 2004 :      ttp_plot start
> Traceback (most recent call last):
>   File "e:\src\python\ttp\ttp_plot.py", line 56, in ?
>     plotting_date('traffic', 'tmp_calls0', 3)
>   File "e:\src\python\ttp\ttp_plot.py", line 39, in plotting_date
>     plot_date(datum, vals, PyDatetimeConverter())
>   File "C:\Python23\Lib\site-packages\matplotlib\matlab.py", line=20
> 1011, in plot_date
>     try: lines =3D  gca().plot_date(*args, **kwargs)
>   File "C:\Python23\Lib\site-packages\matplotlib\axes.py", line 1198,=20
> in plot_date
>     locator =3D MinuteLocator(1)
>   File "C:\Python23\Lib\site-packages\matplotlib\ticker.py", line 720,=20
> in __init__
>     MultipleLocator.__init__(self, base*SEC_PER_MIN)
> NameError: global name 'SEC_PER_MIN' is not defined
>
>
> #######################################################################=
#########
> SCRIPT
> #######################################################################=
#########
>
> import time, ConfigParser, MySQLdb
> import datetime
> import matplotlib
> matplotlib.use('Agg')
> from matplotlib.matlab import *
> from matplotlib.dates import PyDatetimeConverter, MONDAY
> from matplotlib.ticker import WeekdayLocator, DayLocator, DateFormatter
>
> config =3D ConfigParser.ConfigParser()
> config.readfp(open('e:\\src\\python\\ttp\\ttp.conf', 'r'))
> loc_host =3D config.get('DATABASE', 'loc_host')
> loc_user =3D config.get('DATABASE', 'loc_user')
> loc_passwd =3D config.get('DATABASE', 'loc_passwd')
> loc_db =3D config.get('DATABASE', 'loc_db')
>
> loc_db =3D MySQLdb.connect(host =3D loc_host, user =3D loc_user, passwd=
 =3D=20
> loc_passwd, db =3D loc_db)
> cursor =3D loc_db.cursor()
>
> def plotting_date(db, table, dig):
>
>     cursor.execute("DROP TABLE IF EXISTS %s.tmp" % (db))
>     cursor.execute("CREATE TABLE %s.tmp "
>                    "SELECT fecha, mid(tel,1,%d) as tel, sum(minutos)=20
> as min FROM %s.%s GROUP BY 1,2" % (db,dig,db,table))
>     cursor.execute("SELECT DISTINCT tel FROM %s.tmp" % (db))
>     tels =3D cursor.fetchall()
>     for tel in tels:
>         cursor.execute("SELECT fecha, min FROM %s.tmp WHERE tel =3D=20
> '%s'" % (db,tel[0]))
>         data  =3D cursor.fetchall()
>         datum =3D [datetime.datetime(int(q[0][0:4]), int(q[0][4:6]),=20
> int(q[0][6:8]), 0, 0) for q in data]
>         vals  =3D [q[1] for q in data]
>
>         ax =3D subplot(1,1,1)
>         plot_date(datum, vals, PyDatetimeConverter())
>
>         ax.xaxis.set_major_locator(WeekdayLocator(MONDAY))
>         ax.xaxis.set_major_formatter(DateFormatter('%b %d'))
>         ax.xaxis.set_minor_locator(DayLocator())
>         ax.xaxis.autoscale_view()
>         title('TEST')
>         ylabel('test')
>         labels =3D ax.get_xticklabels()
>         set(labels, 'rotation', 'vertical')
>         grid(True)
>         savefig("c:\\tmp\\%s_%s_test" % (tel[0],table))
>
>
> # --- main -- #
> if __name__ =3D=3D '__main__':
>     print time.mktime(time.localtime()), ': \t', time.asctime(), ':=20
> \t', 'ttp_plot start'
>     plotting_date('traffic', 'tmp_calls0', 3)
>     print time.mktime(time.localtime()), ': \t', time.asctime(), ':=20
> \t', 'ttp_plot end'
>
>
>
>
>
>
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>

John Hunter wrote:

>>>>>> "Peter" == Peter Groszkowski <pgr...@ge...> writes:
>>>>>>           
>>>>>
>
>    Peter> Hi: I attach a pcolor plot. I would like to get rid of the
>    Peter> areas outside the larger circle and inside the smaller
>    Peter> circle. Ideally I would like them to be white. Currently I
>    Peter> create my plot using pcolor and then plot *lots* of white
>    Peter> circles (for the inside) and lines (for the outside) on
>    Peter> top, to get rid of the unwanted areas. This works but I
>    Peter> wonder whether there is a better/faster solution. I would
>    Peter> imagine I could set the values corresponding to the
>    Peter> unwanted areas to some particular color before I call
>    Peter> pcolor, but the issue is that I want those ares to be white
>    Peter> (or other color not included in the standard palette which
>    Peter> is used for plotting the area inside the annulus). Can this
>    Peter> be done?
>
> Inside the circle is easy - just set the facecolor of the circle to be
> white 'w', or whatever rgb tuple you want. How are you creating the
> circles, with plot, scatter, or instantiating your own Circle
> instances?
>  
>
I'm creating circles using the plot command, just transform my r and 
theta to x and y.
It turned out that this is trivial using the fill command - one liner. I 
haven't used fill before but it seems very handy for this sort of thing.

> Outside the circle requires implementing general clipping, which will
> be done but I can't say how soon right now.
>
Again did it with fill - two lines.

>  What backend are you
> using?  The circles don't look antialiased so I'm guessing not agg.
> agg and postscript are probably the best bets for getting general
> clipping support first.
>
>  
>
I have been using GD. You may remember a while ago, when I had some 
major performance issues (which turned out was because AA was on by 
default) you did a little analysis and concluded that GD is the fastest, 
even thought one needs to turn AA off. For most of my plotting, 
performance is crucial so I simply stuck with it. Another issue is the 
fact that Agg does not have a write-to-stream feature implemented.

> Another question: is there a reason you are using pcolor rather than
> imshow?  imshow will give you the same result with interpolation and
> dramatic performance benefits.  Since you aren't using faceted shading
> or otherwise tweaking the pcolor rectangles, you don't gain anything
> by using pcolor unless you need a backend that doesn't support imshow
> yet (gd?)
>  
>
Yes. Was using GD. Did some testing with Agg, and in the imshow plots do 
look quite nice. When write-to-stream feature gets added (or get around 
to adding it myself) will use imshow() instead of pcolor().

>    Peter> Another question is in regards to showing tics in pcolor
>    Peter> plots. In my "legend" on the right, I would like them to be
>    Peter> visible, but they get overwritten. I suppose I could plot
>    Peter> each manually after I do pcolor; is it how this is meant to
>    Peter> be done?
>
> This is an easy fix.  Basically you just need to move the axis drawing
> to the end of the axes drawing code.  Currently it is done before any
> before any lines or patches are drawn.  Try replacing
> matplotlib.Axes._draw with the code below.
>
>  
>
Yeah, this worked nice.

> I'll make a deal: if you contribute some code to produce the nice
> color legend you made, I'll try and implement general clipping!
>  
>
Well...  to be honest, with your **magic** fill command I don't really 
need 'general clipping' and would prefer write-to-stream for Agg.. so I 
propose you implement whichever more people would find useful.

The code is rather trivial, and works great in my case (specific fig 
dimensions and layout), but one would probably have to think about the 
details of having it as a part of the core library and work for general 
cases; some of the numbers when calling axes() might have to be adjusted.


So an example might be:

#!/usr/bin/python

import sys, os
from matplotlib.matlab import *
from matplotlib.ticker import NullLocator

figure(1, figsize=(6,5), facecolor='w', edgecolor='w', dpi=150)   #This 
size woks best for me.

mainAxes=axes([0.125, 0.05, 0.655, 0.83], frameon=0)

xi=linspace(-4,4,200);
yi=linspace(-4,4,200);
[Xi,Yi]=meshgrid(xi,yi);
Zi=fromfunction(lambda i,j: (i+j)%40, (200,200))     #Some dummy data

pcolor(Xi, Yi, Zi, shading='flat')   #Could use imshow()

#Remove the x and y ticks. Is this how it's done in 0.53?
mainAxes.xaxis.set_major_locator(NullLocator())
mainAxes.yaxis.set_major_locator(NullLocator()) 

legendAxes=axes([0.85, 0.05, 0.05, 0.83])

#Essentially want to make sure that the smallest/largest values on the 
legend correspond to the smallest/largest values in Zi
yy=ravel(Zi)
ymin,ymax=floor(min(yy)), ceil(max(yy))
dy=float(abs((ymax)-(ymin)))/256.0
x=arange(0,50)    #When this is smaller, imshow() does not display the 
legend properly, but for pcolor could just do arange(0,2)
y=arange(ymin,ymax,dy)

Xi,Yi=meshgrid(x,y)

pcolor(Xi, Yi, Yi, shading='flat')        #Again could use imshow()

legendAxes.xaxis.set_major_locator(NullLocator())
legendAxes.set_ylim([ymin,ymax])

show()



-- 
Peter Groszkowski         Gemini Observatory
Tel: +1 808 974-2509      670 N. A'ohoku Place
Fax: +1 808 935-9235      Hilo, Hawai'i 96720, USA

hi all,
i'm getting the following error when running this script.
if the script doesn't iterate over "tels" it runs fine...
it seems to do things right just once.
thanks in advance,
hector


################################################################################
ERROR
################################################################################

C:\Documents and Settings\villaf>python e:\src\python\ttp\ttp_plot.py
1082751605.0 :  Fri Apr 23 12:20:05 2004 :      ttp_plot start
Traceback (most recent call last):
   File "e:\src\python\ttp\ttp_plot.py", line 56, in ?
     plotting_date('traffic', 'tmp_calls0', 3)
   File "e:\src\python\ttp\ttp_plot.py", line 39, in plotting_date
     plot_date(datum, vals, PyDatetimeConverter())
   File "C:\Python23\Lib\site-packages\matplotlib\matlab.py", line 1011, 
in plot_date
     try: lines =  gca().plot_date(*args, **kwargs)
   File "C:\Python23\Lib\site-packages\matplotlib\axes.py", line 1198, 
in plot_date
     locator = MinuteLocator(1)
   File "C:\Python23\Lib\site-packages\matplotlib\ticker.py", line 720, 
in __init__
     MultipleLocator.__init__(self, base*SEC_PER_MIN)
NameError: global name 'SEC_PER_MIN' is not defined


################################################################################
SCRIPT
################################################################################

import time, ConfigParser, MySQLdb
import datetime
import matplotlib
matplotlib.use('Agg')
from matplotlib.matlab import *
from matplotlib.dates import PyDatetimeConverter, MONDAY
from matplotlib.ticker import WeekdayLocator, DayLocator, DateFormatter

config = ConfigParser.ConfigParser()
config.readfp(open('e:\\src\\python\\ttp\\ttp.conf', 'r'))
loc_host = config.get('DATABASE', 'loc_host')
loc_user = config.get('DATABASE', 'loc_user')
loc_passwd = config.get('DATABASE', 'loc_passwd')
loc_db = config.get('DATABASE', 'loc_db')

loc_db = MySQLdb.connect(host = loc_host, user = loc_user, passwd = 
loc_passwd, db = loc_db)
cursor = loc_db.cursor()

def plotting_date(db, table, dig):

     cursor.execute("DROP TABLE IF EXISTS %s.tmp" % (db))
     cursor.execute("CREATE TABLE %s.tmp "
                    "SELECT fecha, mid(tel,1,%d) as tel, sum(minutos) as 
min FROM %s.%s GROUP BY 1,2" % (db,dig,db,table))
     cursor.execute("SELECT DISTINCT tel FROM %s.tmp" % (db))
     tels = cursor.fetchall()
     for tel in tels:
         cursor.execute("SELECT fecha, min FROM %s.tmp WHERE tel = '%s'" 
% (db,tel[0]))
         data  = cursor.fetchall()
         datum = [datetime.datetime(int(q[0][0:4]), int(q[0][4:6]), 
int(q[0][6:8]), 0, 0) for q in data]
         vals  = [q[1] for q in data]

         ax = subplot(1,1,1)
         plot_date(datum, vals, PyDatetimeConverter())

         ax.xaxis.set_major_locator(WeekdayLocator(MONDAY))
         ax.xaxis.set_major_formatter(DateFormatter('%b %d'))
         ax.xaxis.set_minor_locator(DayLocator())
         ax.xaxis.autoscale_view()
         title('TEST')
         ylabel('test')
         labels = ax.get_xticklabels()
         set(labels, 'rotation', 'vertical')
         grid(True)
         savefig("c:\\tmp\\%s_%s_test" % (tel[0],table))


# --- main -- #
if __name__ == '__main__':
     print time.mktime(time.localtime()), ': \t', time.asctime(), ': 
\t', 'ttp_plot start'
     plotting_date('traffic', 'tmp_calls0', 3)
     print time.mktime(time.localtime()), ': \t', time.asctime(), ': 
\t', 'ttp_plot end'

> >>>>> "Kenneth" == Kenneth McDonald <kmm...@wi...> writes:
>
>     Kenneth> 1) (Simple) Is there a defined behavior for matplotlib
>     Kenneth> when it attempts to graph data containing NaN values?
>     Kenneth> (OK, I admit-- it's really, really late, and I have tried
>     Kenneth> it to see what happens.  But even that wouldn't tell me
>     Kenneth> if that was the _defined_ behavior :-))
>
I guess the question I have is what would you expect to happen?
My impression is that different people want to treat "missing"
data different ways. I'd say it should be a mistake to try to
plot NaNs. But taking the concept further, and generalizing
these to missing values, I'd be open to plotting functions
that accept masks if there was a common consensus as to what
those functions should do with those masks.

> No, it's not defined.  I don't know that NaN is defined across
> platforms in python.  See my recent question on comp.lang.python
>
> http://groups.google.com/groups?hl=en&lr=&ie=UTF-8&oe=UTF-8&thread
m=mailman.141.1080681106.20120.python-list%40python.org&rnum=3&prev=/groups%
> 3Fq%3Dtest%2Bnan%2Bgroup%253A*python*%26ie%3DUTF-8%26oe%3DUTF-8%26
> hl%3Den%26btnG%3DGoogle%2BSearch
>
> Perhaps Todd or Perry can comment on what the status of NaN vis-a-vis
> Numeric and numarray.  This has come up a number of times before, and
> would be nice to be able to handle it.  As always, these ease of use
> features imply a performance cost that the typical user may not want
> to pay....
>
Todd has already explained that numarray can easily generate masks
from NaNs or other ieee special values.
>

Hello -

 

I''ve got a wxDialog where, among other controls, I have a wxList and a
FigureCanvasWx. Depending on what single item is selected in the wxList, the
FigureCanvasWx should show the appropriate graph. It's important that the
matplotlib-generated graph stay in the dialog along with the other controls
(I don't want to generate a separate frame for the graph).

 

I don't want to have to recompute the graph using matplotlib to refresh the
FigureCanvasWx if the user selects a different item in the List. Is there a
way to generate the graphs, temporarily store the figures (without having to
write them to the hard drive using savefig),  and show the appropriate graph
based upon the List selection?

 

I thought about generating and saving the graphs to disk and then loading
them in and using them as bitmaps in the wxDialog when needed - however,
that doesn't seem very efficient as the program would have to access the
disk and load the bitmap every time the list selection changed.

 

If it helps, here's part of the code used in creating the FigureCanvasWx:

 

def __init__(self, parent):

        self._init_ctrls(parent) # Create all other dialog controls

        

        self.fig = Figure((4.7,4), 75)

        self.canvas = FigureCanvasWx(self, -1, self.fig)

        self.canvas.SetPosition(wxPoint(480,400))

 

 

Thanks in advance,

 

Dave Engelsma

Lacks Wheel Trim Systems

 

On Thu, 2004-04-22 at 06:11, Gary Ruben wrote:
> I've installed 0.53 on my Win98 and Win2000 PCs and both suffer a problem which seems specific to the default Agg backend. It's an interoperability problem with trying to use TkAgg from the SciTE editor IDE or from an IDLE module window.

As JDH suggested, TkAgg works (as far as I've tested anyway) with IDLE
by using the -n flag when starting IDLE;  I build -n into the shortcut
for IDLE on my desktop.

In general, TkAgg is known to work with:

python
idle -n
IPython

TkAgg is known not work with:

SciTE 
pythonw
Pythonwin
idle

Both of the latter shells fail with a RuntimeError "abnormal program
termination".

I checked on www.python.org about Tkinter and Pythonwin and they're
known not to work together so that explains TkAgg on Pythonwin.
http://www.python.org/topics/tkinter/trouble.html

I also looked into SciTE a little and discovered that it is related to
Scintilla which in turn was derived from Pythonwin.
http://www.scintilla.org/
This indicates to me that the same problem with Tkinter may be affecting
both (SciTE and Pythonwin)... but I am out on a limb.

Regards,
Todd
-- 
Todd Miller <jm...@st...>

On Thu, 2004-04-22 at 08:48, John Hunter wrote:
> >>>>> "Kenneth" == Kenneth McDonald <kmm...@wi...> writes:
> 
>     Kenneth> 1) (Simple) Is there a defined behavior for matplotlib
>     Kenneth> when it attempts to graph data containing NaN values?
>     Kenneth> (OK, I admit-- it's really, really late, and I have tried
>     Kenneth> it to see what happens.  But even that wouldn't tell me
>     Kenneth> if that was the _defined_ behavior :-))
> 
> No, it's not defined.  I don't know that NaN is defined across
> platforms in python.  See my recent question on comp.lang.python
> 
> http://groups.google.com/groups?hl=en&lr=&ie=UTF-8&oe=UTF-8&threadm=mailman.141.1080681106.20120.python-list%40python.org&rnum=3&prev=/groups%3Fq%3Dtest%2Bnan%2Bgroup%253A*python*%26ie%3DUTF-8%26oe%3DUTF-8%26hl%3Den%26btnG%3DGoogle%2BSearch
> 
> Perhaps Todd or Perry can comment on what the status of NaN vis-a-vis
> Numeric and numarray.  

I'm not aware of any functionality in Numeric for dealing with IEEE
special values.  (Looking in the Numeric manual suggests that problems
with these values lead to the development of the Masked Array capability
as an alternative.)  Lack of support for IEEE special values in Numeric
makes it difficult to provide a unified approach in matplotlib.

numarray has a module (ieeespecial) for dealing with different IEEE
special values, including NaN.  In numarray.ieeespecial are functions
for identifying the locations of and setting IEEE special values to some
other value.  My thought was that you could use these functions in your
own code to define whatever behavior you want.  This is perhaps more
work than is convenient but has the advantage that you can do it now
yourself.  

Regards,
Todd

-- 
Todd Miller <jm...@st...>

>>>>> "Yann" == Yann Le Du <yan...@no...> writes:

    Yann> So it looks as though you check for change in content, but
    Yann> not for change in size.

Yep, you're right.  mathtext does cache for efficiency and the
fontsize key was not being used in the cache.  This does not affect
normal text, which does the caching properly.  The good news it's a
one-line-fix.  In matplotlib.mathtext.math_parse_s, change the
cacheKey to

    cacheKey = (s, dpi, fontsize)

Thanks for the detailed report.

JDH

>>>>> "Flavio" == Flavio Codeco Coelho <fcc...@fi...> writes:

    Flavio> it worked in 0.5.2

    Flavio> What is the problem?

I implemented new tick locator in 0.53 which should provide nicer
default tick locations as well as better user customization.  I failed
to test for the equal data limits case, which several people have
already reported.  This is fixed in CVS.  

Early next week, probably Monday, I will accumulate all the reported
bugs and fixes into a 0.53.1 release, so please continue to let me
know as you find them.

Note if you actually want to see the result of your plot, you'll need
to add a marker

  from matplotlib.matlab import *
  plot ([1], 'o')

since otherwise you have a zero length line.


JDH

On Wed, 21 Apr 2004, John Hunter wrote:

> >>>>> "Yann" == Yann Le Du <yan...@no...> writes:
> 
>     Yann> puts the text horizontally instead of vertically. 
> 
> See http://matplotlib.sourceforge.net/matplotlib.mathtext.html for a
> list of known issues with mathtext.  Short answer, it's on the list of
> things to do.

Ok, thanks


>     Yann> don't get any effect using fontsize :
> 
> Fixed in matplotlib-0.53.  What, you mean you haven't upgraded yet?
> :-)

I have indeed ! Always keen to upgrade fine software !

And here's what I found out (with probable solution at the end). I run 
python shell, then I do :

from matplotlib.matlab import *
plot([1,2,3,4])
xlabel(r'$\alpha > \beta$',fontsize=5)
show()

and then this figure pops up, and it works fine. Now I close the window
and I do :

xlabel(r'$\alpha > \beta$',fontsize=20)
show()

but nothing changes in the size of the x label.

Now if I change the size AND the content, then it works fine :

xlabel(r'$\alpha$',fontsize=20)
show()

This gives me a size 20 alpha.

So it looks as though you check for change in content, but not for change
in size.

YLD

I'm trying to run the first tutorial example in matplotlib-0.53 and am 
running into an ImportError. Here's the python script I'm trying to run:

import matplotlib
matplotlib.use('TkAgg')
from matplotlib.matlab import *
plot([1,2,3,4])
show()

Here's the output I'm getting:


light:gerry> python matplotlibtest.py
Traceback (most recent call last):
  File "matplotlibtest.py", line 15, in ?
    from matplotlib.matlab import *
  File 
"/d2/gerry/local/ActivePython-2.3/lib/python2.3/site-packages/matplotlib/matlab.py", 
line 129, in ?
    from backends import new_figure_manager, error_msg, \
  File 
"/d2/gerry/local/ActivePython-2.3/lib/python2.3/site-packages/matplotlib/backends/__init__.py", 
line 29, in ?
    from backend_tkagg import error_msg, draw_if_interactive, show, 
new_figure_manager
  File 
"/d2/gerry/local/ActivePython-2.3/lib/python2.3/site-packages/matplotlib/backends/backend_tkagg.py", 
line 8, in ?
    import tkagg                 # Paint image to Tk photo blitter extension
  File 
"/d2/gerry/local/ActivePython-2.3/lib/python2.3/site-packages/matplotlib/backends/tkagg.py", 
line 1, in ?
    import _tkagg
ImportError: 
/d2/gerry/local/ActivePython-2.3/lib/python2.3/site-packages/matplotlib/backends/_tkagg.so: 
undefined symbol: XFreePixmap


Thanks for any help.

--Gerry Wiener

I had been using multi-line ticklabels in my plots. They worked fine in
in 0.52 (except for postscript output).  Much to my dismay, I find that
in 0.53 multi-line ticklabels do not work at all. The embedded '\n'
shows up as a small box, and the lines run together.

I hope that this will be fixed soon.

Thanks.

	-Al Schapira

Thanks for all the great features in matplotlib 0.53.

date_demo2.py with 0.53 looks normal initially. However, if you compress
the scale by clicking the (-) Horizontal magnifier, the new date
ticklabels that shift in from the right are horizontal, not vertical.

I found that if you expand and then compress, the original ticklabels
remain vertical, but the new ones (those not present in the original
plot) shift in horizontal. Looks like the 'rotation' attribute of the
additional ticklabels should have been copied from the original ones.

	-Al Schapira

I shouldn't have jumped to conclusions. Agg seems OK. GTKAgg works from SciTE and IDLE just using show().
If I substitute this:

manager = get_current_fig_manager()
manager.window.show()
raw_input('paused')

then a window is opened but nothing is painted onto the canvas area from either IDLE or SciTE.
It looks like GTKAgg might be the backend of choice for these environments.

Gary

----- Original Message -----
From: John Hunter <jdh...@ac...>
Date: Thu, 22 Apr 2004 08:09:52 -0500
To: "Gary Ruben" <ga...@em...>
Subject: Re: [Matplotlib-users] Agg backend problem with 0.53

> >>>>> "Gary" == Gary Ruben <ga...@em...> writes:
> 
>     Gary> It's evidently something to do with threads and is probably
>     Gary> an inherent problem with Agg. I'm just bringing this to the
>     Gary> attention of others here who may be having similar
>     Gary> problems. Perhaps John knows what's going on and whether
>     Gary> anything can be done about it. The convenience of working in
>     Gary> SciTE For the moment,
> 
> I would be very surprised if it's agg - I think it's a GUI conflict on
> the Tk side.  Todd is this related to the idle -n thingie?  If so,
> perhaps a FAQ and status report are warranted.
> 
> Gary, since you say GTK is working, you may also want to check GTKAgg
> which will help up narrow it down to Tk, and would rule out agg
> problems.  But since SciTE is GTK based, you probably need make sure
> that matplotlib is not firing up it's own gtk mainloop, by not calling
> 'show'.  You can show your GTK figures manually if necessary by doing
> 
>    manager = get_current_fig_manager()
>    manager.window.show()
> 
> This is a GTK specific call applicable only if the GTK mainloop is
> already running (as I suspect it is in SciTE, which I haven't used),
> It is probably a good idea to standardize the API here across GUIs to
> handle exactly this case.
> 
> The larger question is why would there be a GTK/Tk conflict?  In any
> case, let us know if you learn anything else.
> 
> JDH
> 

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When compiling matplotlib on debian with :
python setup.py install --home=/home/jonas/python

I get an error message about not being able to find tk.h (appended
below). This is with (I believe) all necessary tk libraries installed.
When I set CPATH=/usr/include/tcl8.4 and then try, it compiles just
fine. Is there any way we could make the tk-finding code a bit smarter
so it would work out of the box on debian? 

Thanks for such an amazing plotting package -- at last, I might be able
to ditch matlab!
		...Eric

[full error below]

running install
running build
running build_py
running build_ext
building 'matplotlib.backends._tkagg' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall
-Wstrict-prototypes -fPI
C -I/usr/lib/tcl8.4/../../include -I/usr/include -Isrc -Iagg2/include
-I/usr/inc
lude -I/usr/lib/tcl8.4/../../include/freetype2 -I/usr/include/freetype2
-Isrc/fr
eetype2 -Iagg2/include/freetype2 -I/usr/include/freetype2
-I/usr/include/python2
.3 -c src/_tkagg.cpp -o build/temp.linux-i686-2.3/src/_tkagg.o
src/_tkagg.cpp:20:19: tk.h: No such file or directory
src/_tkagg.cpp:28: error: syntax error before `*' token
src/_tkagg.cpp:32: error: `ClientData' was not declared in this scope
src/_tkagg.cpp:32: error: parse error before `,' token
src/_tkagg.cpp: In function `int PyAggImagePhoto(...)':
src/_tkagg.cpp:35: error: `Tk_PhotoHandle' undeclared (first use this
function)
src/_tkagg.cpp:35: error: (Each undeclared identifier is reported only
once for 
   each function it appears in.)
src/_tkagg.cpp:35: error: parse error before `;' token
src/_tkagg.cpp:36: error: `Tk_PhotoImageBlock' undeclared (first use
this 
   function)
src/_tkagg.cpp:40: error: `argc' undeclared (first use this function)
src/_tkagg.cpp:41: error: `interp' undeclared (first use this function)
src/_tkagg.cpp:41: error: `argv' undeclared (first use this function)
src/_tkagg.cpp:42: error: `Tcl_AppendResult' undeclared (first use this 
   function)
src/_tkagg.cpp:43: error: `TCL_ERROR' undeclared (first use this
function)
src/_tkagg.cpp:47: error: `photo' undeclared (first use this function)
src/_tkagg.cpp:47: error: `Tk_FindPhoto' undeclared (first use this
function)
src/_tkagg.cpp:65: error: `block' undeclared (first use this function)
src/_tkagg.cpp:88: error: `Tk_PhotoBlank' undeclared (first use this
function)
src/_tkagg.cpp:90: error: `Tk_PhotoPutBlock' undeclared (first use this 
   function)
src/_tkagg.cpp:92: error: `TCL_OK' undeclared (first use this function)
src/_tkagg.cpp: In function `PyObject* _tkinit(PyObject*, PyObject*)':
src/_tkagg.cpp:108: error: `Tcl_Interp' undeclared (first use this
function)
src/_tkagg.cpp:117: error: parse error before `)' token
src/_tkagg.cpp:122: error: 'struct TkappObject' has no member named
'interp'
src/_tkagg.cpp:128: error: `Tcl_CmdProc' undeclared (first use this
function)
src/_tkagg.cpp:128: error: parse error before `)' token
error: command 'gcc' failed with exit status 1

>>>>> "Gary" == Gary Ruben <ga...@em...> writes:

    Gary> It's evidently something to do with threads and is probably
    Gary> an inherent problem with Agg. I'm just bringing this to the
    Gary> attention of others here who may be having similar
    Gary> problems. Perhaps John knows what's going on and whether
    Gary> anything can be done about it. The convenience of working in
    Gary> SciTE For the moment,

I would be very surprised if it's agg - I think it's a GUI conflict on
the Tk side.  Todd is this related to the idle -n thingie?  If so,
perhaps a FAQ and status report are warranted.

Gary, since you say GTK is working, you may also want to check GTKAgg
which will help up narrow it down to Tk, and would rule out agg
problems.  But since SciTE is GTK based, you probably need make sure
that matplotlib is not firing up it's own gtk mainloop, by not calling
'show'.  You can show your GTK figures manually if necessary by doing

   manager = get_current_fig_manager()
   manager.window.show()

This is a GTK specific call applicable only if the GTK mainloop is
already running (as I suspect it is in SciTE, which I haven't used),
It is probably a good idea to standardize the API here across GUIs to
handle exactly this case.

The larger question is why would there be a GTK/Tk conflict?  In any
case, let us know if you learn anything else.

JDH

>>>>> "Kenneth" == Kenneth McDonald <kmm...@wi...> writes:

    Kenneth> 1) (Simple) Is there a defined behavior for matplotlib
    Kenneth> when it attempts to graph data containing NaN values?
    Kenneth> (OK, I admit-- it's really, really late, and I have tried
    Kenneth> it to see what happens.  But even that wouldn't tell me
    Kenneth> if that was the _defined_ behavior :-))

No, it's not defined.  I don't know that NaN is defined across
platforms in python.  See my recent question on comp.lang.python

http://groups.google.com/groups?hl=en&lr=&ie=UTF-8&oe=UTF-8&threadm=mailman.141.1080681106.20120.python-list%40python.org&rnum=3&prev=/groups%3Fq%3Dtest%2Bnan%2Bgroup%253A*python*%26ie%3DUTF-8%26oe%3DUTF-8%26hl%3Den%26btnG%3DGoogle%2BSearch

Perhaps Todd or Perry can comment on what the status of NaN vis-a-vis
Numeric and numarray.  This has come up a number of times before, and
would be nice to be able to handle it.  As always, these ease of use
features imply a performance cost that the typical user may not want
to pay....

    Kenneth> 2) I expect to be using matplotlib quite a bit in the
    Kenneth> future, and will likely be using it in a more
    Kenneth> object-oriented mode (i.e. not through the matlab-style
    Kenneth> interface), since that's what I like better. I haven't
    Kenneth> seen any "howto" documents for using the OO API. Do any
    Kenneth> exist? I'd be happy to make notes and write a tutorial as
    Kenneth> I learn, but don't want to duplicate work that already
    Kenneth> exists.

I wrote a little example which I'll include below.  The pure OO API is
not really designed to be too user friendly.  Eg to instantiate a
line, you do

        vline = Line2D(
            dpi, bbox,
            xdata=x, ydata=y,
            color=color,
            antialiased=False,   # no need to antialias vert lines
            transx = ax.xaxis.transData,
            transy = ax.yaxis.transData)

It's useful if you want to have total control of the lines
transformations, bounding boxes and so on, but is overkill for making
most plots.  Likewise, instantiating your own Axes and Figures
requires a extra overhead.  This is addressed more in the example
below, which recommends a hybrid approach.

If you want to take some of this and extend it into a guide of sorts,
that would be great.  If what you are looking for is a developer's
guide which describes the process of Figure, Axes, Line2D, Text, etc,
creation and how to use them together, that doesn't exist yet.

However, matplotlib is undergoing rapid development and changes.  One
nice thing about having people use the matlab interface is that it
frees me to refactor the OO API.  There have been several major
refactorings to date.  If a lot of people are using this API, and it's
documented, it is more difficult to change.  I am not totally happy
with the current design (eg it us cumbersome to have to pass all those
objects just to create a line) so for now I prefer not to have too
many people creating lots of code with the OO API.  I think the
overall design is stable (Figures contain Axes which contain Text,
Axis and Lines, etc) but some of the constructor signatures may
change.

The hybrid approach I recommend below keeps you safely at the
interface level and insulated from any API changes, which can be
painful for application developers.  It does, however, enable you to
write more pythonic code.

Here is the new examples/pythonic_matplotlib.py:

"""
Some people prefer to use the python object oriented face rather than
the matlab interface to matplotlib.  This example show you how.

Unless you are an application developer, I recommend using part of the
matlab interface, particularly the figure, close, subplot, axes, and
show commands.  These hide a lot of complexity from you that you don't
need to see in normal figure creation, like instantiating DPI
instances, managing the bounding boxes of the figure elements,
creating and reaslizing GUI windows and embedding figures in them.

If you are an application developer and want to embed matplotlib in
your application, follow the lead of examples/embedding_in_wx.py,
examples/embedding_in_gtk.py or examples/embedding_in_tk.py.  In this
case you will want to control the creation of all your figures,
embedding them in application windows, etc.

If you seen an example in the examples dir written in matlab
interface, and you want to emulate that using the true python method
calls, there is an easy mapping.  Many of those examples use 'set' to
control figure properties.  Here's how to map those commands onto
instance methods

The syntax of set is

  set(object or sequence, somestring, attribute)

if called with an object, set calls

  object.set_somestring(attribute)

if called with a sequence, set does

  for object in sequence:
       object.set_somestring(attribute)

So for your example, if a is your axes object, you can do

  a.set_xticklabels([])
  a.set_yticklabels([])
  a.set_xticks([])
  a.set_yticks([])
"""


from matplotlib.matlab import figure, close, axes, subplot, show
from matplotlib.numerix import arange, sin, pi

t = arange(0.0, 1.0, 0.01)

fig = figure(1)

ax1 = subplot(211)
ax1.plot(t, sin(2*pi*t))
ax1.grid(True)
ax1.set_ylim( (-2,2) )
ax1.set_ylabel('1 Hz')
ax1.set_title('A sine wave or two')

for label in ax1.get_xticklabels():
    label.set_color('r')


ax2 = subplot(212)
ax2.plot(t, sin(2*2*pi*t))
ax2.grid(True)
ax2.set_ylim( (-2,2) )
l = ax2.set_xlabel('Hi mom')
l.set_color('g')
l.set_fontsize(15)

show()        

Just a little follow-up point. The normal axis autoscaling, with "plot(t, s, 'b-')" commented out, doesn't take account of the errorbar extrema. That is, the errorbars extend beyond the autoscaled window, whereas the window should be scaled to fully contain the errorbars.

----- Original Message -----
From: "Gary Ruben" <ga...@em...>
Date: Thu, 22 Apr 2004 20:19:10 +1000
To: mat...@li...
Subject: [Matplotlib-users] axis scaling anomaly

> Here's an example of my attempt to plot errorbar data with a series line of a different colour. This example reveals an anomaly with the axis scaling which may the sign of an underlying bug. If you comment out the "plot(t, s, 'b-')" line and run the example, the axes autoscale. If you run the example as is, the scaling changes for some reason.
> Gary Ruben
> :
> 
> 
> from matplotlib.matlab import *
> 
> t = arange(0.1, 4, 0.1)
> s = exp(-t)
> e = 0.1*randn(len(s))
> f = 0.1*randn(len(s))
> 
> grid(1)
> lines = errorbar(t, s, e, f, '.', capsize=4)
> set(lines, 'color', 'g')
> plot(t, s, 'b-')
> xlabel('Distance (m)')
> ylabel('Height (m)')
> title('Mean and standard error as a function of distance')
> show()



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Here's an example of my attempt to plot errorbar data with a series line of a different colour. This example reveals an anomaly with the axis scaling which may the sign of an underlying bug. If you comment out the "plot(t, s, 'b-')" line and run the example, the axes autoscale. If you run the example as is, the scaling changes for some reason.
Gary Ruben
:


from matplotlib.matlab import *

t = arange(0.1, 4, 0.1)
s = exp(-t)
e = 0.1*randn(len(s))
f = 0.1*randn(len(s))

grid(1)
lines = errorbar(t, s, e, f, '.', capsize=4)
set(lines, 'color', 'g')
plot(t, s, 'b-')
xlabel('Distance (m)')
ylabel('Height (m)')
title('Mean and standard error as a function of distance')
show()
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I've installed 0.53 on my Win98 and Win2000 PCs and both suffer a problem which seems specific to the default Agg backend. It's an interoperability problem with trying to use TkAgg from the SciTE editor IDE or from an IDLE module window. If I use the TkAgg backend from a DOS window, it works OK. Also, if I change the backend to GTK, all is well from all environments.

Here is the output if I run an example from SciTE under Win98. Win2000 fails similarly.

>pythonw -u errorbar_demo.pyw
Fatal Python error: PyEval_RestoreThread: NULL tstate

>Process failed to respond; forcing abrupt termination...>Exit code: 0

It's evidently something to do with threads and is probably an inherent problem with Agg. I'm just bringing this to the attention of others here who may be having similar problems. Perhaps John knows what's going on and whether anything can be done about it. The convenience of working in SciTE For the moment, 

Gary Ruben
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1) (Simple) Is there a defined behavior for matplotlib when
it attempts to graph data containing NaN values? (OK, I admit--
it's really, really late, and I have tried it to see what happens.
But even that wouldn't tell me if that was the _defined_
behavior :-))

2) I expect to be using matplotlib quite a bit in the future,
and will likely be using it in a more object-oriented mode
(i.e. not through the matlab-style interface), since that's
what I like better. I haven't seen any "howto" documents
for using the OO API. Do any exist? I'd be happy to make
notes and write a tutorial as I learn, but don't want to
duplicate work that already exists.

Thanks,
Ken

>>>>> "Yann" == Yann Le Du <yan...@no...> writes:

    Yann> puts the text horizontally instead of vertically. 

See http://matplotlib.sourceforge.net/matplotlib.mathtext.html for a
list of known issues with mathtext.  Short answer, it's on the list of
things to do.

    Yann> don't get any effect using fontsize :

Fixed in matplotlib-0.53.  What, you mean you haven't upgraded yet?
:-)

JDH