matplotlib-users Mailing List for matplotlib

Me and my team are almost to the finishing point. Our final problem is
getting the graph to update. 
When we run the graph the get the following issue: "
Traceback (most recent call last):
 File "/home/gnelson/scc08whole/branch/realistic2d/gtkgui.py", line 100, in
update
 self.ax.draw_artist(plt.contourf)
 File "/usr/lib/python2.5/site-packages/matplotlib/axes.py", line 1535, in
draw_artist
 a.draw(self._cachedRenderer)
AttributeError: 'function' object has no attribute 'draw'"
Our Code is at: " http://code.google.com/p/scc08/ " 
and we are using the gtkgui.py
import time
import gtk, gobject
import matplotlib
matplotlib.use('GTKAgg')
import matplotlib.pyplot as plt
from driver import Driver
import numpy as np
class Gui:
 def updateData(self):
 self.updateTemps()
 self.getMats()
 self.addTimeSteps()
 self.getAirPts()
 self.getGroundPts()
 self.getBridgePts()
 def updateTemps(self):
 self.temps = []
 temp = self.dr.myGrid.fields
 for i in range(len(temp)):
 self.temps.append([])
 for j in range(len(temp[i])):
 self.temps[i].append(temp[i][j].temperature)
 def getMats(self):
 self.mats = []
 temp = self.dr.myGrid.fields
 for i in range(len(temp)):
 self.mats.append([])
 for j in range(len(temp[i])):
 self.mats[i].append(temp[i][j].density)
 self.mats
 def setUserInput(self):
 str = raw_input("What do you want: Ground or Air? (The default is
air) \n")
 if(str == "Ground" or str == "ground"):
 self.type = 1
 else:
 self.type = 2
 def getAirPts(self):
 temp = self.dr.myGrid.fields
 for i in range(len(temp)):
 for j in range(len(temp[i])):
 if(temp[i][j].material == 'air'):
 self.airData.append(temp[i][j].temperature)
 return
 def getBridgePts(self):
 temp = self.dr.myGrid.fields
 for i in range(len(temp)):
 for j in range(len(temp[i])):
 if(temp[i][j].material == 'concrete'):
 self.bridgeData.append(temp[i][j].temperature)
 return
 def getGroundPts(self):
 if (type == 1):
 return None
 else:
 temp = self.dr.myGrid.fields
 for i in range(len(temp)):
 for j in range(len(temp[i])):
 if(temp[i][j].material == 'soil'):
 self.groundData.append(temp[i][j].temperature)
 return
 def addTimeSteps(self):
 self.time.append(self.step)
 def update(self, *args):
 print "WTF Delta?!?"
 self.step = 0
 if self.background is None:
 self.background = self.canvas.copy_from_bbox(self.ax.bbox)
 self.updateData()
 # restore the clean slate background
 self.canvas.restore_region(self.background)
 # update the data
 print "GROUND DATA:"
 print len(self.groundData)
 print "TIME DATA"
 print len(self.time)
 if(self.type != 2):
 self.groundLine = self.ax.plot(self.groundData , self.time,
'g-+')
 self.bridgeLine = self.ax.plot(self.bridgeData , self.time,
'r-o')
 self.airLine = self.ax.plot(self.airData, self.time, 'b-s')
 self.contour = self.ax2.contourf(self.temps)
 self.colorbar = self.fig.colorbar(self.contour)
 # just draw the animated artist
 self.ax.draw_artist(self.groundLine)
 self.ax.draw_artist(self.airLine)
 self.ax.draw_artist(self.bridgeLine)
 self.ax.draw_artist(plt.contourf)
# self.ax.draw_artist(colorbar)
 # just redraw the axes rectangle
 self.canvas.blit(self.ax.bbox)
 self.cnt += 1
 self.step += .004
 self.dr.run(10)
 self.time.append(self.step*10)
 return True
 update.cnt = 0
 update.background = None
 def setup(self):
 self.fig = plt.figure()
 self.ax = self.fig.add_subplot(211)
 self.ax2 = self.fig.add_subplot(212)
 self.canvas = self.fig.canvas
 self.ax.grid() # to ensure proper background restore
 self.canvas.draw()
 # create some globals
 self.airData = []
 self.groundData = []
 self.bridgeData = []
 self.time = []
 self.step = 0
 self.setUserInput()
 self.temps = []
 self.mats = []
 self.dr = Driver(.5, .5, 0.0004, type, (7,7,9,9), (16,16))
 self.cnt = 0
 self.background = None
 # don't use time steps over 4 * 10 ** -4
 self.updateTemps()
 self.gmats = self.getMats()
 # create the initial graphs
 self.contour = self.ax2.contourf(self.temps)
 self.colorbar = self.fig.colorbar(self.contour)
 self.groundLine, = self.ax.plot(self.groundData , self.time, 'g-+')
 self.bridgeLine, = self.ax.plot(self.bridgeData , self.time, 'r-o')
 self.airLine, = self.ax.plot(self.airData , self.time, 'b-s')
 
if __name__ == "__main__":
 mygui = Gui()
 def start_anim(event):
 gobject.idle_add(mygui.update)
 mygui.canvas.mpl_disconnect(start_anim.cid)
 
 mygui.setup()
 start_anim.cid = mygui.canvas.mpl_connect('draw_event', start_anim)
 plt.show()
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Dear Matplotlib Folks,
When I run pylab.plot, I get a weird warning:
** (python:20754): WARNING **: Couldn't connect to system bus
** (python:20754): WARNING **: Couldn't connect to system bus
<matplotlib.lines.Line2D object at 0x1225850>
(Note that this was copied by hand because the system on which I run
Matplotlib is currently unable to connect to the global internet.)
The first line really is repeated.
The number after "python:" changes from one instance of the warning to
another.
I am running:
Red Hat Enterprise Linux ES release 4 (Nahant Update 3)
At least, that is what is in /etc/redhat-release.
The warning is not fatal and I can display what I attempted to plot with
pylab.show. However, the warning has a significant impact on the
interactive usability of Python and matplotlib as a replacement for Matlab.
Anyone have any suggestions or observations?
Yours,
David Sigeti
-- 
View this message in context: http://www.nabble.com/Warning-from-pylab.plot-on-Linux-tp22793709p22793709.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

Jeff - Copying the rest of the files solved the problem. Thanks!
--Mike
Jeff Whitaker wrote:
> Michael Hearne wrote:
>> I am experimenting with the Enthought Python Distribution (EPD) on 
>> MacOS 10.5, which includes BaseMap version 0.99.1. I have existing 
>> modules that use the 'full' resolution data. These modules are 
>> currently failing with the error message below.
>>
>> I have tried copying what looked like the full resolution data sets 
>> (gshhs_f.dat and gshhsmeta_f.dat) from my 0.99.2 source installation 
>> into the EPD basemap data directory, and rerun my scripts, with no 
>> success.
>>
>> I looked at my most recent copy of the basemap README and cannot find 
>> any reference to the boundary datasets.
>>
>> So, a question for Jeff, and a request for Enthought:
>> 1) How do I update the EPD with the full resolution data
>> 2) Can the EPD be updated to include the full resolution boundary data?
>>
>> Thanks,
>>
>> Mike
>>
>> ***************************
>> IOError: Unable to open boundary dataset file. Only the 'crude', 'low',
>> 'intermediate' and 'high' resolution datasets are installed by default.
>> If you are requesting a 'full' resolution dataset, you may need to
>> download and install those files separately
>> (see the basemap README for details).
>> Exception caught: Unable to open boundary dataset file. Only the 
>> 'crude', 'low',
>> 'intermediate' and 'high' resolution datasets are installed by default.
>> If you are requesting a 'full' resolution dataset, you may need to
>> download and install those files separately
>> (see the basemap README for details).
>> ***************************
>>
>> ------------------------------------------------------------------------------ 
>>
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>> 
> Mike: To save space, the EPD folks took out the full resolution 
> datasets. Manually copying the files should work - are you sure you 
> got them in the right place (the mpl_toolkits/basemap/data 
> directory)? You probably have to copy more than the gshhs file (the 
> states, rivers and countries too).
>
> -Jeff
>

Michael Hearne wrote:
> I am experimenting with the Enthought Python Distribution (EPD) on MacOS 
> 10.5, which includes BaseMap version 0.99.1. I have existing modules 
> that use the 'full' resolution data. These modules are currently 
> failing with the error message below.
>
> I have tried copying what looked like the full resolution data sets 
> (gshhs_f.dat and gshhsmeta_f.dat) from my 0.99.2 source installation 
> into the EPD basemap data directory, and rerun my scripts, with no success.
>
> I looked at my most recent copy of the basemap README and cannot find 
> any reference to the boundary datasets.
>
> So, a question for Jeff, and a request for Enthought:
> 1) How do I update the EPD with the full resolution data
> 2) Can the EPD be updated to include the full resolution boundary data?
>
> Thanks,
>
> Mike
>
> ***************************
> IOError: Unable to open boundary dataset file. Only the 'crude', 'low',
> 'intermediate' and 'high' resolution datasets are installed by default.
> If you are requesting a 'full' resolution dataset, you may need to
> download and install those files separately
> (see the basemap README for details).
> Exception caught: Unable to open boundary dataset file. Only the 
> 'crude', 'low',
> 'intermediate' and 'high' resolution datasets are installed by default.
> If you are requesting a 'full' resolution dataset, you may need to
> download and install those files separately
> (see the basemap README for details).
> ***************************
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 
Mike: To save space, the EPD folks took out the full resolution 
datasets. Manually copying the files should work - are you sure you got 
them in the right place (the mpl_toolkits/basemap/data directory)? You 
probably have to copy more than the gshhs file (the states, rivers and 
countries too).
-Jeff
-- 
Jeffrey S. Whitaker Phone : (303)497-6313
Meteorologist FAX : (303)497-6449
NOAA/OAR/PSD R/PSD1 Email : Jef...@no...
325 Broadway Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg

I am experimenting with the Enthought Python Distribution (EPD) on MacOS 
10.5, which includes BaseMap version 0.99.1. I have existing modules 
that use the 'full' resolution data. These modules are currently 
failing with the error message below.
I have tried copying what looked like the full resolution data sets 
(gshhs_f.dat and gshhsmeta_f.dat) from my 0.99.2 source installation 
into the EPD basemap data directory, and rerun my scripts, with no success.
I looked at my most recent copy of the basemap README and cannot find 
any reference to the boundary datasets.
So, a question for Jeff, and a request for Enthought:
1) How do I update the EPD with the full resolution data
2) Can the EPD be updated to include the full resolution boundary data?
Thanks,
Mike
***************************
IOError: Unable to open boundary dataset file. Only the 'crude', 'low',
'intermediate' and 'high' resolution datasets are installed by default.
If you are requesting a 'full' resolution dataset, you may need to
download and install those files separately
(see the basemap README for details).
Exception caught: Unable to open boundary dataset file. Only the 
'crude', 'low',
'intermediate' and 'high' resolution datasets are installed by default.
If you are requesting a 'full' resolution dataset, you may need to
download and install those files separately
(see the basemap README for details).
***************************

I've got the NavigationToolbar2 going nicely on my app
(OO, embedded in wx, mpl 0.98.5), and was wondering
how difficult it might be to change how the pan works,
in the following way...
Right now, when I show a plot, I am grabbing a subset
of data from the database. Panning within that plot
allows exploration of *just that data*. E.g., if I have
values between x = 100 and x = 200, I can pan past
either of these values, but there are no more data points
beyond that, because I didn't fetch those points when I
created the plot.
What would be nice is if, on panning, I could fetch
new points, namely those that are found in that part of
the x axis. This would be just like Google Maps' ability
to allow one to pan the map over and see new land area,
because it fetches those land patches of the map.
I could of course just fetch all the data I have first
and set the x limits to show the requested subset
of data initially, but I thought maybe it would
be more efficient to only get what is requested and
then grab more data on pans. I thought I'd ask if
anyone had done something like this already.
Thanks,
Che

As Darren said, normed=1 means that the integral of the histogram is
normalized to one, not the height. In other words, the total area under the
histogram curve is set to one.
Imagine a histogram with a single bin. If the width of the bin is less than
one, the height must be greater than one in order for the area to equal one.
Therefore the y-axis scale can be greater than one even when normed=1.
-Roban
On Mon, Mar 30, 2009 at 12:11 PM, Bala subramanian <
bal...@gm...> wrote:
> There was a typo in my previous mail.
> y axis goes scale is more than one when i use normed=1. I am not getting
> why this happens.
>
>
> On Mon, Mar 30, 2009 at 6:10 PM, Bala subramanian <
> bal...@gm...> wrote:
>
>>
>>
>>
>> Darren,
>>> But y axis goes scale is than one when i use normed=1. I am not getting
>>> why this happens.
>>>
>>>
>>> On Mon, Mar 30, 2009 at 5:39 PM, Darren Dale <dsd...@gm...> wrote:
>>>
>>>> On Mon, Mar 30, 2009 at 11:25 AM, Bala subramanian <
>>>> bal...@gm...> wrote:
>>>>
>>>>> Friends,
>>>>>
>>>>> I tried to plot a histogram and pdf of my data (data file attached
>>>>> 1.dat). When i see the figure (attached file test.png) , i see y axis more
>>>>> than 1 (although it should not when i use normed=1. I am not getting why
>>>>> this happens.
>>>>>
>>>>> Somebody kindly write me i) Why the y-axis scales more than 1 ii) after
>>>>> plotting histogram and pdf, how to delete the histogram and show only the
>>>>> normal curve.
>>>>>
>>>>> The following are the commands i used.
>>>>> data=load('1.dat')
>>>>> x=[:,1]
>>>>> mu=mean(x);st=std(x)
>>>>> n,bins,patch=hist(x,50,normed=1,histtype='stepfilled')
>>>>> y = normpdf( bins, mu, st)
>>>>> plot(bins, y, 'k--', linewidth=1.5)
>>>>>
>>>>
>>>> hist plots a distribution whose integral is 1.
>>>>
>>>
>>>
>>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>

There was a typo in my previous mail.
y axis goes scale is more than one when i use normed=1. I am not getting why
this happens.
On Mon, Mar 30, 2009 at 6:10 PM, Bala subramanian <bal...@gm...
> wrote:
>
>
>
> Darren,
>> But y axis goes scale is than one when i use normed=1. I am not getting
>> why this happens.
>>
>>
>> On Mon, Mar 30, 2009 at 5:39 PM, Darren Dale <dsd...@gm...> wrote:
>>
>>> On Mon, Mar 30, 2009 at 11:25 AM, Bala subramanian <
>>> bal...@gm...> wrote:
>>>
>>>> Friends,
>>>>
>>>> I tried to plot a histogram and pdf of my data (data file attached
>>>> 1.dat). When i see the figure (attached file test.png) , i see y axis more
>>>> than 1 (although it should not when i use normed=1. I am not getting why
>>>> this happens.
>>>>
>>>> Somebody kindly write me i) Why the y-axis scales more than 1 ii) after
>>>> plotting histogram and pdf, how to delete the histogram and show only the
>>>> normal curve.
>>>>
>>>> The following are the commands i used.
>>>> data=load('1.dat')
>>>> x=[:,1]
>>>> mu=mean(x);st=std(x)
>>>> n,bins,patch=hist(x,50,normed=1,histtype='stepfilled')
>>>> y = normpdf( bins, mu, st)
>>>> plot(bins, y, 'k--', linewidth=1.5)
>>>>
>>>
>>> hist plots a distribution whose integral is 1.
>>>
>>
>>
>

Darren,
> But y axis goes scale is than one when i use normed=1. I am not getting why
> this happens.
>
>
> On Mon, Mar 30, 2009 at 5:39 PM, Darren Dale <dsd...@gm...> wrote:
>
>> On Mon, Mar 30, 2009 at 11:25 AM, Bala subramanian <
>> bal...@gm...> wrote:
>>
>>> Friends,
>>>
>>> I tried to plot a histogram and pdf of my data (data file attached
>>> 1.dat). When i see the figure (attached file test.png) , i see y axis more
>>> than 1 (although it should not when i use normed=1. I am not getting why
>>> this happens.
>>>
>>> Somebody kindly write me i) Why the y-axis scales more than 1 ii) after
>>> plotting histogram and pdf, how to delete the histogram and show only the
>>> normal curve.
>>>
>>> The following are the commands i used.
>>> data=load('1.dat')
>>> x=[:,1]
>>> mu=mean(x);st=std(x)
>>> n,bins,patch=hist(x,50,normed=1,histtype='stepfilled')
>>> y = normpdf( bins, mu, st)
>>> plot(bins, y, 'k--', linewidth=1.5)
>>>
>>
>> hist plots a distribution whose integral is 1.
>>
>
>

that fixed it.. thanks!
On Mon, Mar 30, 2009 at 11:02 AM, John Hunter <jd...@gm...> wrote:
>
>
> On Mon, Mar 30, 2009 at 8:22 AM, Tyler B <bo...@gm...> wrote:
>
>> My graph, which had been working just fine, randomly decided to stop
>> filling the width of the x-axis: http://screencast.com/t/vr3AaXIq
>>
>> Here's the code I'm using (nothing fancy.. I took out all unnecessary
>> formatting and it didn't help):
>>
>> fig = plt.figure(facecolor ='w', frameon=False)
>> ax = plt.subplot(111)
>> lines = ax.plot(r_dates, r_inbox, 'w-')
>>
>> I'm out of ideas.. what could be causing this?
>
>
>
> Sorry, I'm not sure what "filling the width of the x-axis" means or what
> you are expecting to see. If you want to the x and y limits to be collapsed
> to your data limits, you need to do
>
> ax.axis('tight')
>
> JDH
>
>

On Mon, Mar 30, 2009 at 11:25 AM, Bala subramanian <
bal...@gm...> wrote:
> Friends,
>
> I tried to plot a histogram and pdf of my data (data file attached 1.dat).
> When i see the figure (attached file test.png) , i see y axis more than 1
> (although it should not when i use normed=1. I am not getting why this
> happens.
>
> Somebody kindly write me i) Why the y-axis scales more than 1 ii) after
> plotting histogram and pdf, how to delete the histogram and show only the
> normal curve.
>
> The following are the commands i used.
> data=load('1.dat')
> x=[:,1]
> mu=mean(x);st=std(x)
> n,bins,patch=hist(x,50,normed=1,histtype='stepfilled')
> y = normpdf( bins, mu, st)
> plot(bins, y, 'k--', linewidth=1.5)
>
hist plots a distribution whose integral is 1.

On Mon, Mar 30, 2009 at 8:22 AM, Tyler B <bo...@gm...> wrote:
> My graph, which had been working just fine, randomly decided to stop
> filling the width of the x-axis: http://screencast.com/t/vr3AaXIq
>
> Here's the code I'm using (nothing fancy.. I took out all unnecessary
> formatting and it didn't help):
>
> fig = plt.figure(facecolor ='w', frameon=False)
> ax = plt.subplot(111)
> lines = ax.plot(r_dates, r_inbox, 'w-')
>
> I'm out of ideas.. what could be causing this?
Sorry, I'm not sure what "filling the width of the x-axis" means or what you
are expecting to see. If you want to the x and y limits to be collapsed to
your data limits, you need to do
 ax.axis('tight')
JDH

My graph, which had been working just fine, randomly decided to stop filling
the width of the x-axis: http://screencast.com/t/vr3AaXIq
Here's the code I'm using (nothing fancy.. I took out all unnecessary
formatting and it didn't help):
fig = plt.figure(facecolor ='w', frameon=False)
ax = plt.subplot(111)
lines = ax.plot(r_dates, r_inbox, 'w-')
I'm out of ideas.. what could be causing this?
Thanks!
Tyler