matplotlib-users — Discussion related to using matplotlib

[Matplotlib-users] matplotlib interactive windows hang

[Daniele V. <dva...@vi...>]

I am testing matplotlib for the first time, but it continuously hang after a
really short time.

I read all the troubles about running it from an ide, so i'm using plain
cmd.

Microsoft Windows 2000 [Versione 5.00.2195]
(C) Copyright 1985-2000 Microsoft Corp.

C:\Documents and Settings\daniele>python
Python 2.3.4 (#53, May 25 2004, 21:17:02) [MSC v.1200 32 bit (Intel)] on
win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from matplotlib.matlab import *
>>> t = arange(0.0, 5.2, 0.2)
>>> plot(t, t, 'r--', t, t**2, 'bs', t, t**3, 'g^')
[<matplotlib.lines.Line2D instance at 0x0100F6E8>, <matplotlib.lines.Line2D
inst
ance at 0x0100F788>, <matplotlib.lines.Line2D instance at 0x0100F7B0>]

The window pops up as expected. Now i switch to an ie window to watch online
docs looking for axis command syntax...
When i'm back to the prompt, the plot window is frozen. If visualized it
doesn't redraw itself and clicking on the close button in the menu bar pops
it up the not-responding-app dialog.

The Python prompt is still functional. When i try to exit i get (WXAgg
backend):

>>> ^Z

Fatal Python error: PyEval_RestoreThread: NULL tstate

abnormal program termination

C:\Documents and Settings\daniele>

The problem doesn't depend from the backend used: i tried, TkAgg, WX, WXAgg.
Sontimes i can add a title to a graph but it will always hang within a
minute.

I have a pretty fresh installation of Python 2.3.4 with numpy 0.9. I used
matplotlib-0.54.2-numarray0.9.win32-py2.3.exe. I also tried to use
matplotlib 0.54.1 but it looks like it need numpy to work (i think it's
wrong, i installed the numarray version) and i don't want to install it. No
tries with other releases. I currently don't have any problem in running
neither wxwindows nor tk apps.

Does anybody experienced the same problem?

Regards

--
Daniele Varrazzo
Dipartimento di Biologia Molecolare
Universita' di Siena
Via Fiorentina, 1   53100 SIENA  (Italy)

RE : [Matplotlib-users] crash on matplotlib.matlab import on win32

[Gregory L. <gre...@ff...>]

I checked on another WinXP computer, and it works on this one - seems
that I have to play the windows re-install game, or hunt down what the
exact differences between these 2 WinXP computers are :-/... 
The fact that only matplotlib exhibit this behavior is strange though, I
checked in the code (hence cc to the devel list) and the problem is
linked to an assert in the destructor of PythonExtensionBase, checking
that the ref counting of this object is 0 and exiting Python interpreter
if it is not the case...Hum, obviously I do not know the code at all,
but could the problem be linked to a destruction sequence beeing
somewhat different on my computer (for whatever reasons :-/)? 
This worry me (in addition to bother me not beeing able to run
matplotlib on my laptop for the moment ;-) ), cause it may be the sign
of "difficult to solve and reproduce" installation problems for a
package we may use in a distributed software package in the future...
I will keep investigating, but if there is a developer have any idea
about this (like, a hint about why there is this assert there and what
can cause it to fail),  it would be great!

Thanks a lot, and congratulation for matplotlib, it looks the most
promising python plotting packages I have found yet! :-)

RE : [Matplotlib-users] crash on matplotlib.matlab import on win32

[Gregory L. <gre...@ff...>]

Thanks for helping with this problem!

I just tried on a win2000 Pro computer, and indeed, no problem...
Then, on my WinXP laptop, I removed python, reinstalled it (2.3.4), next
numarray (0.9), then matplotlib (0.54.2), the exact same windows
installers that were used on the Win2000 computer, and same problem as
before, crash on matplotlib.matlab import...Weird!

I will try to perform the same installation on another WinXP computer,
to be sure the problem is not related to incompatibilities with other
softwares installed on my laptop, or some registery entries, and keep
the list informed of the results of this test.

Best regards,

Greg.

Re: [stsci] Re: [Matplotlib-users] crash on matplotlib.matlab import on win32

[Philippe B. <pb...@pa...>]

Todd Miller <jm...@st...> =E9crit :

> > I just tried to install matplotlib on a WinXP computer, after a
> > successfull install on Linux.
> > The problem I encounter is the following (transcript of an
> > interractive session):=20
> > Python 2.3.4 (#53, May 25 2004, 21:17:02) [MSC v.1200 32 bit (Intel)]
> > on win32
> > Type "help", "copyright", "credits" or "license" for more information.
> > >>> import matplotlib
> > >>> matplotlib.use("TkAgg")
> > >>> from matplotlib.matlab import *
> > Assertion failed: ob_refcnt =3D=3D 0, file CXX/cxx_extensions.cxx, li=
ne
> > 1031

> I tried this configuration on Windows 2000 Pro and it worked fine.
> I haven't tried this configuration on Windows XP yet...  I'll try later
> to see if I can reproduce the problem.

I tried this code with WinXP version 5.1 and python 2.3.2, and I
have not problem it's Ok :-)

                      Philippe Bouige

Re: [Matplotlib-users] crash on matplotlib.matlab import on win32

[Todd M. <jm...@st...>]

On Wed, 2004-06-23 at 12:42, Gregory Lielens wrote:
> Hello All,
> I just tried to install matplotlib on a WinXP computer, after a
> successfull install on Linux.
> The problem I encounter is the following (transcript of an
> interractive session): 
>  
> ---
> C:\Python23>python
> Python 2.3.4 (#53, May 25 2004, 21:17:02) [MSC v.1200 32 bit (Intel)]
> on win32
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import matplotlib
> >>> matplotlib.use("TkAgg")
> >>> from matplotlib.matlab import *
> Assertion failed: ob_refcnt == 0, file CXX/cxx_extensions.cxx, line
> 1031
>  
> This application has requested the Runtime to terminate it in an
> unusual way.
> Please contact the application's support team for more information.
>  
> C:\Python23>
>  
> ---
>  
> This work on Linux, and I can not find any hint in the doc to a
> backend/python interpreter incompatibility explaining this error.
>  
> I use  numarray version 0.9 (win installer), python 2.3.4 (as shown in
> the session transcript), and matplotlib 0.54.2, last windows installer
> (the 2004/06/08 21:54:42 build which I think correct some problems
> with numarray)
>  
> Now I am wondering if I do something I shouldn't, if my system or
> installation is responsible, or if it is a bug in this particular
> matplotlib distribution...Any idea? 

I tried this configuration on Windows 2000 Pro and it worked fine.

I haven't tried this configuration on Windows XP yet...  I'll try later
to see if I can reproduce the problem.

Regards,
Todd

[Matplotlib-users] crash on matplotlib.matlab import on win32

[Gregory L. <gre...@ff...>]

Hello All,
I just tried to install matplotlib on a WinXP computer, after a
successfull install on Linux.
The problem I encounter is the following (transcript of an interractive
session): 
 
---

C:\Python23>python
Python 2.3.4 (#53, May 25 2004, 21:17:02) [MSC v.1200 32 bit (Intel)] on
win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import matplotlib
>>> matplotlib.use("TkAgg")
>>> from matplotlib.matlab import *
Assertion failed: ob_refcnt == 0, file CXX/cxx_extensions.cxx, line 1031
 
This application has requested the Runtime to terminate it in an unusual
way.
Please contact the application's support team for more information.
 
C:\Python23>
 
---
 
This work on Linux, and I can not find any hint in the doc to a
backend/python interpreter incompatibility explaining this error.
 
I use  numarray version 0.9 (win installer), python 2.3.4 (as shown in
the session transcript), and matplotlib 0.54.2, last windows installer
(the 2004/06/08 21:54:42 build which I think correct some problems with
numarray)
 
Now I am wondering if I do something I shouldn't, if my system or
installation is responsible, or if it is a bug in this particular
matplotlib distribution...Any idea? 
 
Best regards,
 
Greg.

RE: [Matplotlib-users] Problem with vlines ... and tcl !!!

[Perry G. <pe...@st...>]

John Hunter wrote:
> 
> Now on to your problem.  This is caused by a difference in how Numeric
> and numarray treak rank 0 arrays
> 
>     >>> from Numeric import asarray
>     >>> len(asarray(0))
>     1
>     >>> from numarray import asarray
>     >>> len(asarray(0))
>     Traceback (most recent call last):
>       File "<stdin>", line 1, in ?
>     ValueError: Rank-0 array has no length.
> 
> I don't know why there is this difference but I'm sure Todd or Perry
> can comment at length :-).
> 
Boy can we (and we have on the numpy list in the past). 
But I risk boring those who really don't care. The issue relates
to consistency. If rank-0 arrays have a shape of () (and they
do), then they:

1) should not be indexable.
2) they have no length.

Currently Numeric gives len=1 and allows indexing with [0]

It's seemed to me that we need some sort of construct similar to
array() that will turn scalars into rank-1 len-1 arrays which
can be used like scalars for broadcasting purposes (albeit with
different coercion rules; that's a different topic though), and
where len() and indexing will work.

Another proposal is to treat all arrays (including rank-0) as 
allowing indexing with any number of 0 indices beyond the defined shape:
I.e., if 

x = arange(10)
x[3,0] # same as x[3]

So it's a known issue and we are thinking about how best to solve it.

> To solve your vline problem, you need to make the vmin and vmax args
> of vlines (or hlines) iterable.  Ie
> 
> old
> 
>   vlines(t, 0, s, color='k')
> 
> new
> 
>   vlines(t, [0], s, color='k')
>   
> Should work!  Thanks for letting us know.
> 
> 

Re: [Matplotlib-users] Problem with vlines ... and tcl !!!

[John H. <jdh...@ac...>]

>>>>> "Philippe" == Philippe Bouige <pb...@pa...> writes:

    Philippe> Hello,

    Philippe>     I try 'vline_demo' in directory 'example' and I have
    Philippe> problem with vlines ... error : "rank-O array has no
    Philippe> length". I try also with hlines and I have the same
    Philippe> problem ...

    Philippe>     I also this error with all the demo : error reading
    Philippe> package index file C:/Python23/tcl/tix8.1/pkgIndex.tcl:
    Philippe> invalid command name "lt}]}"

    Philippe>     Have you a explanation ?

This turns out to be numarray specific - most of my tests use Numeric
which is why I didn't catch that.  I'll try and make sure I do a
numarray specific test in the future.  Todd, perhaps you should also
make a note to run backend_driver on your numarray build, at least for
Agg.  That wouldn't have helped this time, because vline_demo.py was
not in the regression suite, but I've added it.

Now on to your problem.  This is caused by a difference in how Numeric
and numarray treak rank 0 arrays

    >>> from Numeric import asarray
    >>> len(asarray(0))
    1
    >>> from numarray import asarray
    >>> len(asarray(0))
    Traceback (most recent call last):
      File "<stdin>", line 1, in ?
    ValueError: Rank-0 array has no length.

I don't know why there is this difference but I'm sure Todd or Perry
can comment at length :-).

To solve your vline problem, you need to make the vmin and vmax args
of vlines (or hlines) iterable.  Ie

old

  vlines(t, 0, s, color='k')

new

  vlines(t, [0], s, color='k')
  
Should work!  Thanks for letting us know.

John Hunter

[Matplotlib-users] Problem with vlines ... and tcl !!!

[Philippe B. <pb...@pa...>]

Hello,

    I try 'vline_demo' in directory 'example' and I have problem
    with vlines ... error : "rank-O array has no length". I try
    also with hlines and I have the same problem ...

    I also this error with all the demo :
    error reading package index file
    C:/Python23/tcl/tix8.1/pkgIndex.tcl: invalid command name "lt}]}"

    Have you a explanation ?
         
         Thank you very for your help
         (I work with python 2.3 / windowXP)
                Philippe

Re: [Matplotlib-users] Problem with ganged candlestick plots

[John H. <jdh...@ac...>]

>>>>> "Thomas" == Thomas Barket <tho...@ya...> writes:

    Thomas> Hello, When I run the following script, the ganged
    Thomas> candlestick plots appear as expected.  However, there is a
    Thomas> second plot behind but sticking out (with different x and
    Thomas> y axes) that shouldn't be there.  Am I not doing this
    Thomas> correctly?  I can't see where in the code below I am
    Thomas> mistakenly creating two plots that overlap, or is there a
    Thomas> bug with ganged candlesticks?

Hi Thomas,

Delete the line that reads

  sub = subplot(1, 1, 1)

you are creating a subplot that you never use.  subplot and axes are
both Axes creations commands.  Since you manually create your axes
with axes, you don't need the subplot.

There is a problem with ganged plots in that the ytick labels tend to
overlap at the borders.  You can fix this using a custom tick
formatter - I can help you with this if you need.

JDH

[Matplotlib-users] Problem with ganged candlestick plots

[Thomas B. <tho...@ya...>]

Hello,

When I run the following script, the ganged candlestick plots appear as
expected.  However, there is a second plot behind but sticking out (with
different x and y axes) that shouldn't be there.  Am I not doing this
correctly?  I can't see where in the code below I am mistakenly creating two
plots that overlap, or is there a bug with ganged candlesticks?

Tks vm,

Tom

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

from matplotlib.matlab import *
from matplotlib.dates import MONDAY
from matplotlib.finance import candlestick
from matplotlib.ticker import WeekdayLocator, DayLocator, DateFormatter

series1 = []
series1.append((1041379200, 100.0, 100.5, 99.0, 102.0))
series1.append((1041465600, 101.0, 101.5, 98.0, 103.0))
series1.append((1041552000, 103.0, 104.0, 103.0, 106.0))
series1.append((1041638400, 105.0, 102.5, 102.0, 108.0))
series2 = []
series2.append((1041379200, 1000.0, 1000.5, 999.0, 1002.0))
series2.append((1041465600, 1001.0, 1001.5, 998.0, 1003.0))
series2.append((1041552000, 1003.0, 1004.0, 1003.0, 1006.0))
series2.append((1041638400, 1005.0, 1002.5, 1002.0, 1008.0))
series3 = []
series3.append((1041379200, 10000.0, 10000.5, 9999.0, 10002.0))
series3.append((1041465600, 10001.0, 10001.5, 9998.0, 10003.0))
series3.append((1041552000, 10003.0, 10004.0, 10003.0, 10006.0))
series3.append((1041638400, 10005.0, 10002.5, 10002.0, 10008.0))

sub = subplot(1, 1, 1)

ax1 = axes([0.1, 0.1,  0.8, 0.25])  # lower
ax2 = axes([0.1, 0.35, 0.8, 0.25])  # middle
ax2.set_xticklabels([])
ax3 = axes([0.1, 0.6,  0.8, 0.25])  # upper
ax3.set_xticklabels([])

candlestick(ax1, series1, width=0.6)
candlestick(ax2, series2, width=0.6)
candlestick(ax3, series3, width=0.6)

mondays = WeekdayLocator(MONDAY)
days = DayLocator()
fmt = DateFormatter('%b %d')

ax1.xaxis.set_major_locator(mondays)
ax1.xaxis.set_major_formatter(fmt)
ax1.xaxis.set_minor_locator(days)
ax1.autoscale_view()

show()

Re: [Matplotlib-users] Unable add_axis in FigureCanvasWx

[John H. <jdh...@ac...>]

>>>>> "Stephen" == Stephen Roderick <snr...@ya...> writes:

    Stephen> I'm using matplotlib 0.54.2 (failed in 0.53.1 also) on
    Stephen> Mac OS X with Python 2.3 and wxPython 2.5.1.5, and get
    Stephen> the following traceback from this code. Looking at the
    Stephen> backend_wx.py, I can find no other mention of
    Stephen> "FigureBase" anywhere else. What should this line
    Stephen> actually be? (I tried a few thoughts, but none worked)

    Stephen> I'm basically trying to create a class that encapsulates
    Stephen> a multi-value temperature bar graph, using the Observer
    Stephen> pattern, and have inherited from the FigureCanvasWx
    Stephen> class. If this is incorrect, I'm all ears to alternative
    Stephen> suggestions.

Try replacing line 888 in backend_wx with 

        FigureCanvasBase.add_axis(self, a)

Sorry for the trouble....

Re: [Matplotlib-users] specgram ?

[John H. <jdh...@ac...>]

>>>>> "MWallis" == MWallis  <mw...@sw...> writes:

    MWallis> I am having some problems using the specgram function
    MWallis> with gtk and was wondering if anyone had an example they
    MWallis> were willing to share.

See http://matplotlib.sf.net/examples for the current examples.
Normally, you can always get the examples directory in the src
distribution (*.tar.gz or *.zip) but on the last release I failed to
upload a zip file.

The example you are looking for is called specgram_demo.py.  

  http://matplotlib.sf.net/examples/specgram_demo.py

Hope this helps,
JDH

Re: [Matplotlib-users] semilog error plots

[John H. <jdh...@ac...>]

    from matplotlib.matlab import *
    m = array([0.1, 0.2, 0.3, 0.6, 0.8, 1,  3])
    r = array([18, 180, 1800, 1.8, 0.18, 250, 2.8])
    plot(m, r)
    set(gca(), "yscale", "log")
    show()

This is a known issue I've been meaning to work on.  Here's what is
happening.  On the plot command the tick locator is autoranging the
axes and ymin becomes 0.  Since the log transformation applies to the
tick locations as well as the data, it is log transforming the tick
location of zero.  To fix this, I need to check the axes range when
the call to set yscale is made and fix it.  In the meantime, you can
explicity set the ylim after the call to plot and before the call to
yscale.

    from matplotlib.matlab import *
    m = array([0.1, 0.2, 0.3, 0.6, 0.8, 1,  3])
    r = array([18, 180, 1800, 1.8, 0.18, 250, 2.8])
    plot(m, r)
    set(gca(), 'ylim', (0.1, 2000))
    set(gca(), "yscale", "log")
    show()


JDH

Re: [Matplotlib-users] problem reading data file in stock_demo.py

[John H. <jdh...@ac...>]

>>>>> "Thomas" == Thomas Barket <tho...@ya...> writes:

    Thomas> C:\Matplotlib\matplotlib src\examples>python stock_demo.py
    Thomas> Traceback (most recent call last): File "stock_demo.py",
    Thomas> line 4, in ?  from matplotlib.matlab import * File
    Thomas> "C:\Python23\lib\site-packages\matplotlib\matlab.py", line
    Thomas> 134, in ?  from axes import Axes File
    Thomas> "C:\Python23\lib\site-packages\matplotlib\axes.py", line
    Thomas> 9, in ?  from artist import Artist File
    Thomas> "C:\Python23\lib\site-packages\matplotlib\artist.py", line
    Thomas> 4, in ?  from transforms import identity_transform File
    Thomas> "C:\Python23\lib\site-packages\matplotlib\transforms.py",
    Thomas> line 181, in ?  from _transforms import IDENTITY, LOG10,
    Thomas> Func, FuncXY, PolarXY ImportError: cannot import name
    Thomas> IDENTITY

    Thomas> C:\Matplotlib\matplotlib src\examples>

Something is wrong with your installation.  My transforms.py line 181
is something different.  _transforms should be providing IDENTITY.

    Thomas> Is version 0.54.2 not the correct starting point for doing
    Thomas> this unzip?  If solving this is a hassle, I don't mind
    Thomas> going back to the old 0.54.2 and waiting for the bug fixes
    Thomas> that come with the next proper release.

We're planning on doing a release in the near future, so if you can
wait for the new installer, that would be easiest.

JDH

[Matplotlib-users] Unable add_axis in FigureCanvasWx

[Stephen R. <snr...@ya...>]

I'm using matplotlib 0.54.2 (failed in 0.53.1 also) on Mac OS X with  
Python 2.3 and wxPython 2.5.1.5, and get the following traceback from  
this code. Looking at the backend_wx.py, I can find no other mention of  
"FigureBase" anywhere else. What should this line actually be? (I tried  
a few thoughts, but none worked)

I'm basically trying to create a class that encapsulates a multi-value  
temperature bar graph, using the Observer pattern, and have inherited  
from the FigureCanvasWx class. If this is incorrect, I'm all ears to  
alternative suggestions.

TIA


Code:

class ociTemperatureGraph(FigureCanvasWx, Observer):
     def __init__(self, parent):
         wxPanel.__init__(self, parent, -1)
         self.fig = Figure((3,3), 75)
         self.subplot = Subplot(self.fig, 111)
<snip>
         self.add_axis(self.subplot)    <<-- blows up here


Traceback (most recent call last):
   File "./ociTemperatureGraph.py", line 86, in ?
     main()
   File "./ociTemperatureGraph.py", line 74, in main
     frame = PlotFigure()
   File "./ociTemperatureGraph.py", line 60, in __init__
     self.fig = ociTemperatureGraph(self)
   File "./ociTemperatureGraph.py", line 42, in __init__
     self.add_axis(self.subplot)
   File  
"/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
python2.3/site-packages/matplotlib/backends/backend_wx.py", line 888,  
in add_axis
     FigureBase.add_axis(self, a)
NameError: global name 'FigureBase' is not defined

Re: [Matplotlib-users] semilog error plots

[Gary R. <ga...@em...>]

As a followup to my reply to this (the suggestion found by searching the list archives and due to John Hunter), I tried an example errorbar plot and got a traceback. I think this is highlighting a bug as demonstrated by the following example. It's not an errorbar plot, but errorbar generates a traceback too. Danny, if you get a traceback, it'd be worth letting the list know:

from matplotlib.matlab import *
m = array([0.1, 0.2, 0.3, 0.6, 0.8, 1,  3])
r = array([18, 180, 1800, 1.8, 0.18, 250, 2.8])
semilogy(m, r)
set(gca(), "yscale", "linear")
show()

works fine


whereas


from matplotlib.matlab import *
m = array([0.1, 0.2, 0.3, 0.6, 0.8, 1,  3])
r = array([18, 180, 1800, 1.8, 0.18, 250, 2.8])
plot(m, r)
set(gca(), "yscale", "log")
show()

generates a traceback:

Traceback (most recent call last):
  File "C:\APPS\PYTHON23\Lib\site-packages\matplotlib\backends\backend_gtkagg.py", line 75, in callback
    self.draw()
  File "C:\APPS\PYTHON23\Lib\site-packages\matplotlib\backends\backend_gtkagg.py", line 42, in draw
    agg.draw()
  File "C:\APPS\PYTHON23\Lib\site-packages\matplotlib\backends\backend_agg.py", line 296, in draw
    self.figure.draw(self.renderer)
  File "C:\APPS\PYTHON23\Lib\site-packages\matplotlib\figure.py", line 130, in draw
    for a in self.axes: a.draw(renderer)
  File "C:\APPS\PYTHON23\Lib\site-packages\matplotlib\axes.py", line 597, in draw
    self.transData.freeze()  # eval the lazy objects
ValueError: Cannot take log of nonpositive value


I think both should work.
John, is this a bug?

Gary Ruben
-- 
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Re: [Matplotlib-users] semilog error plots

[Gary R. <ga...@em...>]

Hi Danny,

Have you tried adding

set(gca(), "yscale", "log")

after your errorbar line?
I think this does what you want.

Gary Ruben

----- Original Message -----
> Is there any way to do semi-log y errorbar plots? I know there is the
> errorbar plot, and the semi-log plot. If I use an errorbar plot and
> take the logarithm of the y data, then the y axis ticking won't look
> right. Is there a way to fake this that I don't know about.
> 
> thanks,
> Danny

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RE: [Matplotlib-users] problem reading data file in stock_demo.py

[Thomas B. <tho...@ya...>]

John,

Tks vm for your reply.  I was able to get the script
to run with your "examples" directory.  Much
appreciated.  

However, when I unzipped the py.60a.zip files over my
site-packages directory and re-ran the script, I got
the following error:

C:\Matplotlib\matplotlib src\examples>python
stock_demo.py Traceback (most recent call last):
  File "stock_demo.py", line 4, in ?
    from matplotlib.matlab import *
  File
"C:\Python23\lib\site-packages\matplotlib\matlab.py",
line 134, in ?
    from axes import Axes
  File
"C:\Python23\lib\site-packages\matplotlib\axes.py",
line 9, in ?
    from artist import Artist
  File
"C:\Python23\lib\site-packages\matplotlib\artist.py",
line 4, in ?
    from transforms import identity_transform
  File
"C:\Python23\lib\site-packages\matplotlib\transforms.py",
line 181, in ?
    from _transforms import IDENTITY, LOG10, Func,
FuncXY, PolarXY
ImportError: cannot import name IDENTITY

C:\Matplotlib\matplotlib src\examples>

Is version 0.54.2 not the correct starting point for
doing this unzip?  If solving this is a hassle, I
don’t mind going back to the old 0.54.2 and waiting
for the bug fixes that come with the next proper
release.

Tks again,

Tom

-----Original Message-----
From: John Hunter
[mailto:jdh...@ac...]
Sent: Monday, June 21, 2004 2:26 PM
To: Thomas Barket
Cc: mat...@li...
Subject: Re: [Matplotlib-users] problem reading data
file in stock_demo.py

>>>>> "Thomas" == Thomas Barket
<tho...@ya...> writes:

    Thomas> Hello, i cant get stock_demo.py to run
correctly.  it
    Thomas> seems there is a problem reading the data
files,
    Thomas> specifically using numarray/Numeric's
"fromstring" on the
    Thomas> example data files.  the first result
below is with
    Thomas> numarray and the second is with Numeric. 
im using python
    Thomas> 2.3.4 and matplotlib 0.54.2 win32 for
python 2.3.

Where are you getting the examples dir from?  I notice
that I failed to upload a zip file that includes the
examples directory with the
0.54.2 release.  Are you using one from a previous
release?

It looks like you make have a corrupt stock data file.
 I was able to load the stock_demo example using both
the numeric and numarray win32 builds, with either
numerix setting in my rc file.

I did, however, discover a bug in the navigation code
in that example related to data clipping.

The zip file below fixes the latter problem.  Unzip it
in your site-packages dir (do not remove the old
matplotlib code, just unzip this over it)

 
http://nitace.bsd.uchicago.edu:8080/files/share/matplotlib-py.60a.zip

And get a fresh examples dir from 

 
http://nitace.bsd.uchicago.edu:8080/files/share/matplotlib-examples.60a.zip

Hope this helps,
JDH

RE: [Matplotlib-users] problem reading data file in stock_demo.py

[Thomas B. <tho...@ya...>]

John,

Tks vm for your reply.  I was able to get the script to run with your
"examples" directory.  Much appreciated.  

However, when I unzipped the py.60a.zip files over my site-packages
directory and re-ran the script, I got the following error:

C:\Matplotlib\matplotlib src\examples>python stock_demo.py
Traceback (most recent call last):
  File "stock_demo.py", line 4, in ?
    from matplotlib.matlab import *
  File "C:\Python23\lib\site-packages\matplotlib\matlab.py", line 134, in ?
    from axes import Axes
  File "C:\Python23\lib\site-packages\matplotlib\axes.py", line 9, in ?
    from artist import Artist
  File "C:\Python23\lib\site-packages\matplotlib\artist.py", line 4, in ?
    from transforms import identity_transform
  File "C:\Python23\lib\site-packages\matplotlib\transforms.py", line 181,
in ?
    from _transforms import IDENTITY, LOG10, Func, FuncXY, PolarXY
ImportError: cannot import name IDENTITY

C:\Matplotlib\matplotlib src\examples>

Is version 0.54.2 not the correct starting point for doing this unzip?  If
solving this is a hassle, I don't mind going back to the old 0.54.2 and
waiting for the bug fixes that come with the next proper release.

Tks again,

Tom

-----Original Message-----
From: John Hunter [mailto:jdh...@ac...] 
Sent: Monday, June 21, 2004 2:26 PM
To: Thomas Barket
Cc: mat...@li...
Subject: Re: [Matplotlib-users] problem reading data file in stock_demo.py

>>>>> "Thomas" == Thomas Barket <tho...@ya...> writes:

    Thomas> Hello, i cant get stock_demo.py to run correctly.  it
    Thomas> seems there is a problem reading the data files,
    Thomas> specifically using numarray/Numeric's "fromstring" on the
    Thomas> example data files.  the first result below is with
    Thomas> numarray and the second is with Numeric.  im using python
    Thomas> 2.3.4 and matplotlib 0.54.2 win32 for python 2.3.

Where are you getting the examples dir from?  I notice that I failed to
upload a zip file that includes the examples directory with the
0.54.2 release.  Are you using one from a previous release?

It looks like you make have a corrupt stock data file.  I was able to load
the stock_demo example using both the numeric and numarray win32 builds,
with either numerix setting in my rc file.

I did, however, discover a bug in the navigation code in that example
related to data clipping.

The zip file below fixes the latter problem.  Unzip it in your site-packages
dir (do not remove the old matplotlib code, just unzip this over it)

  http://nitace.bsd.uchicago.edu:8080/files/share/matplotlib-py.60a.zip

And get a fresh examples dir from 

 
http://nitace.bsd.uchicago.edu:8080/files/share/matplotlib-examples.60a.zip

Hope this helps,
JDH

[Matplotlib-users] semilog error plots

[danny s. <dan...@ya...>]

Is there any way to do semi-log y errorbar plots? I know there is the
errorbar plot, and the semi-log plot. If I use an errorbar plot and
take the logarithm of the y data, then the y axis ticking won't look
right. Is there a way to fake this that I don't know about.

thanks,
Danny


		
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Take Yahoo! Mail with you! Get it on your mobile phone.
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Re: [Matplotlib-users] problem reading data file in stock_demo.py

[John H. <jdh...@ac...>]

>>>>> "Thomas" == Thomas Barket <tho...@ya...> writes:

    Thomas> Hello, i cant get stock_demo.py to run correctly.  it
    Thomas> seems there is a problem reading the data files,
    Thomas> specifically using numarray/Numeric's "fromstring" on the
    Thomas> example data files.  the first result below is with
    Thomas> numarray and the second is with Numeric.  im using python
    Thomas> 2.3.4 and matplotlib 0.54.2 win32 for python 2.3.

Where are you getting the examples dir from?  I notice that I failed
to upload a zip file that includes the examples directory with the
0.54.2 release.  Are you using one from a previous release?

It looks like you make have a corrupt stock data file.  I was able to
load the stock_demo example using both the numeric and numarray win32
builds, with either numerix setting in my rc file.

I did, however, discover a bug in the navigation code in that example
related to data clipping.

The zip file below fixes the latter problem.  Unzip it in your
site-packages dir (do not remove the old matplotlib code, just unzip
this over it)

  http://nitace.bsd.uchicago.edu:8080/files/share/matplotlib-py.60a.zip

And get a fresh examples dir from 

  http://nitace.bsd.uchicago.edu:8080/files/share/matplotlib-examples.60a.zip

Hope this helps,
JDH

[Matplotlib-users] problem reading data file in stock_demo.py

[Thomas B. <tho...@ya...>]

Hello,

i cant get stock_demo.py to run correctly.  it seems
there is a problem reading the data files,
specifically using numarray/Numeric's "fromstring" on
the example data files.  the first result below is
with numarray and the second is with Numeric.  im
using python 2.3.4 and matplotlib 0.54.2 win32 for
python 2.3.

C:\Matplotlib\matplotlib src\examples>python
stock_demo.py
Traceback (most recent call last):
  File "stock_demo.py", line 7, in ?
    (d1, p1, d2, p2 ) = get_two_stock_data()
  File "C:\Matplotlib\matplotlib
src\examples\data_helper.py", line 12, in
get_two_stock_data
    M1 = fromstring( file('data/%s.dat' % ticker1,
'rb').read(), 'd')
  File
"C:\Python23\Lib\site-packages\numarray\numarraycore.py",
line 358, in fromstring
    raise ValueError("Type size inconsistent with
string length")
ValueError: Type size inconsistent with string length


C:\Matplotlib\matplotlib src\examples>python
stock_demo.py
Traceback (most recent call last):
  File "stock_demo.py", line 7, in ?
    (d1, p1, d2, p2 ) = get_two_stock_data()
  File "C:\Matplotlib\matplotlib
src\examples\data_helper.py", line 12, in
get_two_stock_data
    M1 = fromstring( file('data/%s.dat' % ticker1,
'rb').read(), 'd')
ValueError: string size must be a multiple of element
size

since the example data files are binary, i cant figure
out how to investigate what may be happening with
them.

Is there something else i should be doing?

Tks vm,

Tom

Re: [Matplotlib-users] plot_date problem

[John H. <jdh...@ac...>]

>>>>> "Peter" == Peter Groszkowski <pgr...@ge...> writes:

    Peter> self.nonsingular(self.dataInterval.get_bounds()) TypeError:
    Peter> nonsingular() takes exactly 3 arguments (2 given)
    Peter> -------------

Should be 

  self.nonsingular(*self.dataInterval.get_bounds())

    Peter> 2) The auto-scaling in plot_date() does not scale properly
    Peter> in some special cases. Consider this:

The example seems to work now with the above change and the changes
you suggested in below.

    Peter> ticks.Base when int() gives zero. Also, to finalize this,
    Peter> one would have to write a DayMultiLocator type class for

I added DayMultiLocator to matplotlib.ticker

    Peter> the Weeks, otherwise when the number of weeks is close, but
    Peter> less then the number of weeks in numticks*months it will
    Peter> get crowded. This will probably be a little more involved
    Peter> than dealing with days, but perhaps one could use your
    Peter> existent WeekdayLocator class to simplify the problem.

A WeekMultiLocator would be useful, but it's not a priority for me.
If you come up with one, send it my way.

    Peter> Also note that there was an error in defining months in
    Peter> your code; I changed the line to:

    Peter> months = span/(SEC_PER_DAY*31) # approx

Thanks for the fix.


    Peter> Let me know what you think.

Looks good; thanks!

JDH

Re: [Matplotlib-users] plot_date problem

[Peter G. <pgr...@ge...>]

Thanks for the prompt response and the detailed explanation.

The scaling is working now, and I have not encountered those old problems. There are a couple of things I should mention however:

1) The axes.auto_scale() seems to be broken. I get a following error:

------------
Traceback (most recent call last):
 File "./e3.py", line 97, in ?
   ax.autoscale_view()
 File "/usr/lib/python2.2/site-packages/matplotlib/axes.py", line 436, in autoscale_view
   tup = locator.autoscale()
 File "/usr/lib/python2.2/site-packages/matplotlib/ticker.py", line 327, in autoscale
   return  self.nonsingular(self.dataInterval.get_bounds())
TypeError: nonsingular() takes exactly 3 arguments (2 given)
-------------


When I run this:

--------
#!/usr/bin/env python

import time
from matplotlib.dates import EpochConverter
from matplotlib.matlab import *
from matplotlib.ticker import FuncFormatter, NullLocator,  MinuteLocator, DayLocator, HourLocator, MultipleLocator, DateFormatter

wantLegend=1

time1=[1087192789.89]
data1=[-65.54]

time2=[
1087161589.89 ,
1087192289.0,
1087192389.0,
1087192489.0,
1087192589.0,
1087192689.0,
1087192789.89 ,
1087192889.0,
1087192989.0,
1087193089.0,
1087193189.0,
1087193289.0,
1087238100.0 ,
]
data2=[
-55.44
-64.54 ,
-66.54 ,
-61.54 ,
-69.54 ,
-45.66,
-55.54 ,
-77.54,
-65.54 ,
-49.54 ,
-57.54 ,
-68.54 ,
-55.54 ,
-23.44
]

ax = subplot(111)

p1Size=len(time1)
p2Size=len(time2)

p1=plot_date(time1, data1, None, '-', color='r')
p2=plot_date(time2, data2, None, '-', color='b')

p1=plot(time1, data1,'-', color='r')
p2=plot(time2, data2,'-', color='b')

now=time2[-1]
then=time2[0]

deltaSec=now-then
deltaTickSec=deltaSec/7.0

tickList=[item for item in list(arange(then, now, deltaTickSec))]

def tickString(x, pos):
   return time.strftime("%H:%M:%S", time.localtime(x))

formatter = FuncFormatter(tickString)

ax.set_xticks(tickList)

ax.xaxis.set_major_formatter(formatter)
ax.xaxis.set_minor_locator(NullLocator())

#This line does not work.
ax.autoscale_view()

if wantLegend:
   legend((p1, p2), ('small data set (%d)' % p1Size, 'large data set  (%d)' % p2Size))

xlabel('time')
grid(True)

show()
#savefig('./blah.png')

------

Things work when I comment out the line:

ax.autoscale_view()


2) The auto-scaling in plot_date() does not scale properly in some special cases. Consider this:

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

time2= [
1087321489.89,   1087321500.0,
1087321789.89,   1087321800.0,   1087322089.89,   1087322100.0,   1087322389.89,   1087322700.0,   1087322989.89,   
1087323000.0,   1087323289.89,   1087323300.0,   1087323589.89,   1087323600.0,   1087323889.89,   1087323900.0,   
1087324189.89,   1087324200.0,   1087324489.89,   1087324500.0,   ]
  data2=[    3.02,
       3.02,
       3.14,
       3.14,
       3.21,
       3.21,
       3.26,
       3.26,
       3.39,
       3.39,
       3.51,
       3.51,
       3.58,
       3.58,
       3.75,
       3.75,
       4.0,
       4.0,
       4.22,
       4.22,]

plot_date(time2, data2, None, '-', color='b')
xlabel('time')
grid(True)

show()
---------------

The same thing happens over differnt ranges when the amount of ticks is large. Perhaps you may use something similar to the code below 
(from axes.py) to deal with these things. Note the ceilings get rid of the AssertErrors in ticks.Base when int() gives zero. Also, to finalize this, 
one would have to write a DayMultiLocator type class for the Weeks, otherwise when the number of weeks is close, but less then the number 
of weeks in numticks*months it will get crowded. This will probably be a little more involved than dealing with days, but perhaps one could use 
your existent WeekdayLocator class to simplify the problem.

Also note that there was an error in defining months in your code; I changed the line to:

months = span/(SEC_PER_DAY*31)  # approx  

-----------
   def plot_date(self, d, y, converter, fmt='bo', **kwargs):
       """
       plot_date(d, y, converter, fmt='bo', **kwargs)

       d is a sequence of dates; converter is a dates.DateConverter
       instance that converts your dates to seconds since the epoch for
       plotting.  y are the y values at those dates.  fmt is a plot
       format string.  kwargs are passed on to plot.  See plot for more
       information.

       pass converter = None if your dates are already in epoch format
       """

       if not self._hold: self.cla()

       if converter is not None:
           e = array([converter.epoch(thisd) for thisd in d])
       else:
           e = d
                 assert(len(e))
       ret = self.plot(e, y, fmt, **kwargs)

       span  = self.dataLim.intervalx().span()

       if span==0: span = SEC_PER_MIN
       minutes = span/SEC_PER_MIN
       hours  = span/SEC_PER_HOUR
       days   = span/SEC_PER_DAY
       weeks  = span/SEC_PER_WEEK
       months = span/(SEC_PER_DAY*31)  # approx              years  = span/(SEC_PER_WEEK*52)   # approx

       #These should go to the top module.
       from math import ceil
       from ticker import DayMultiLocator
             numticks = 5
       if years>numticks:
           locator = YearLocator(ceil(years/numticks))  # define
           fmt = '%Y'
       elif months>numticks:
           locator = MonthLocator(ceil(months/numticks))  # define
           fmt = '%b %Y'
                    elif weeks>numticks:
           locator = WeekdayLocator(0)
           fmt = '%b %d'

       #Hack - need a DayLocator which operates like HourLocator
       #ie. Have a tick every so many days other than every day at a
       #particular hour.
       #This is a class I added to ticker.py:
##         class DayMultiLocator(MultipleLocator):
##             """
##             Make ticks on day which are multiples of base
##             """
##             def __init__(self, base):
##                 MultipleLocator.__init__(self, base*SEC_PER_DAY)

       elif days>numticks:
           locator = DayMultiLocator(ceil(days/numticks))
           fmt = '%b %d'
       elif hours>numticks:
           locator = HourLocator(ceil(hours/numticks))
           fmt = '%H:%M\n%b %d'
       elif minutes>numticks:
           locator = MinuteLocator(ceil(minutes/numticks))
           fmt = '%H:%M:%S'
       else:
           locator = MinuteLocator(1)
           fmt = '%H:%M:%S'

       formatter = DateFormatter(fmt)
       self.xaxis.set_major_locator(locator)
       self.xaxis.set_major_formatter(formatter)
       self.autoscale_view()
       return ret

Let me know what you think.

Peter


John Hunter wrote:

>>>>>> "Peter" == Peter Groszkowski <pgr...@ge...> writes:
>>>>>>           
>
>
>    Peter> It does?! Do you mean that this is done automatically? Can
>    Peter> you show me an example of this using only the time module
>    Peter> (since I use python2.2, dont have datetime)? I thought that
>    Peter> I had to manually set things up and tell matplotlib whether
>
> No, it's designed to work automagically.  If you take a look at
> axes.Axes.plot_date you'll see how it works.  It looks at the max/min
> span of your data and chooses a locator and formatter accordingly.
> All the examples use custom locators and formatters ( I was busy
> showing off how you could customize), but you don't need to
>
> from matplotlib.matlab import *
>
> time2= [ 1087161589.89 , 1087192289.0, 1087192389.0, 1087192489.0,
>         1087192589.0, 1087192689.0, 1087192789.89 , 1087192889.0,
>         1087192989.0, 1087193089.0, 1087193189.0, 1087193289.0, 1087238100.0,
>         ]
>    data2=[ -55.44 -64.54 , -66.54 , -61.54 , -69.54 , -45.66, -55.54,
>        -77.54, -65.54 , -49.54 , -57.54 , -68.54 , -55.54 , -23.44 ]
>
> plot_date(time2, data2, None, '-', color='b')
> xlabel('time')
> grid(True)
>
> show()
>
> In general you should try not to set the limits or ticks explicitly
> since this is the job of the autolocator.  I realize you were
> encountering troubles and this is what led you to do it.  Hopefully
> the discussion below will save you from having to do this.
>
>    Peter> On the other note, regarding the weird scaling that I
>    Peter> talked about (and showed pretty pics for) in my last mail,
>    Peter> I finally put together a small script that exposes the
>    Peter> problem. It is a bit rough because I ripped bits and pieces
>    Peter> from here and there, but shows the issue. Use the
>    Peter> 'wantBadPlot' and 'wantStandardDateTics' to see how things
>    Peter> go wrong.
>
> I looked at this and figured out the root cause of the problem.  Your
> "bad data" is a singleton plot
>
>  time1=[1087192789.89]
>  data1=[-65.54]
>  p1=plot_date(time1, data1, None, '-', color='r')
>
> These are difficult to deal with - I'll explain why.  The default
> linear transformation maps data limits to display limits, and needs to
> divide by the data span to do so.  In this case min=max so the span is
> zero and the transformation is undefined.  To handle this case, I
> detect the span=0 case and reset the data limits, lowering the min a
> bit and raising the max a bit. 
> In earlier versions of maptlotlib, I did
>
>            minx, maxx = min(xdata), max(xdata)
>            if minx==maxx:
>                minx -= 1
>                maxx += 1
>
> A problem arose if a person issued multiple calls to plot, first with
> a singleton and then with a range of data, all really small
>
> >>> plot([1e-9], [10])  # x limits are now approx -1, 1 due to above
> >>> plot([1e-9,2e-9,3e-9], [10,20,30])
> after the second call the data limits are still -1,1 because the limit
> code only changes the data limits if the new lines are outside the
> range of the existing limits.  In this case they are not.  The effect
> is the plot is badly scaled since the data limits are wide compared to
> all the xdata.
>
> Thinking myself clever (first mistake!), I rewrote the above code as
>
>            minx, maxx = min(xdata), max(xdata)
>            if minx==maxx:
>                minx -= 0.001*abs(minx)
>                maxx += 0.001*abs(maxx)
>
> So the scaling would be proportionate to the data size.  This helps in
> some cases, but is failing for you.  Again, in your example code, you
> do the dreaded singleton plot followed by more plot commands
>
>    p1=plot_date([1087192789.89], [-65.54], None, '-', color='r')
>    p2=plot_date(times, values, None, '-', color='r')
>
> Since minx==maxx in the first plot, the xlimits become 1086105597.1,
> 1088279982.67.  This is very wide compared to the subsequent range of
> data you put in in the second plot_date call.  This explains the bad
> scaling you are seeing.
>
> Upon writing this, I realized that the fundamental problem is that I
> am manipulating data limits to deal with a singular range, when the
> data limits should *always* accurately reflect the true data limits
> (doh!).  It's the view limits that need to be mucked with to handle
> this case.  I had to make a number of changes throughout the code to
> get everybody playing nicely with this new insight, but now everything
> is working.  Even your wantBadPlot example!
>
> Give it a try:
>
>  http://nitace.bsd.uchicago.edu:8080/files/share/matplotlib-0.54.3a.tar.gz
>
> and let me know if it passes your tests.
>
> JDH
>  
>






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